Paperbase

American Gut: an Open Platform for Citizen Science Microbiome Research

McDonald, Daniel Hyde, Embriette Debelius, Justine W. Morton, James T. Gonzalez, Antonio Ackermann, Gail Aksenov, Alexander A. Behsaz, Bahar Brennan, Caitriona Chen, Yingfeng Goldasich, Lindsay DeRight Dorrestein, Pieter C. Dunn, Robert R. Fahimipour, Ashkaan K. Gaffney, James Gilbert, Jack A. Gogu, Grant Green, Jessica L. Hugenholtz, Philip Humphrey, Greg Huttenhower, Curtis Jackson, Matthew A. Janssen, Stefan Jeste, Dilip V. Jiang, Lingjing Kelley, Scott T. Knights, Dan Kosciolek, Tomasz Ladau, Joshua Leach, Jeff Marotz, Clarisse Meleshko, Dmitry Melnik, Alexey V. Metcalf, Jessica L. Mohimani, Hosein Montassier, Emmanuel Navas-Molina, Jose Nguyen, Tanya T. Peddada, Shyamal Pevzner, Pavel Pollard, Katherine S. Rahnavard, Gholamali Robbins-Pianka, Adam Sangwan, Naseer Shorenstein, Joshua Smarr, Larry Song, Se Jin Spector, Timothy Swafford, Austin D. Thackray, Varykina G. Thompson, Luke R. Tripathi, Anupriya Vazquez-Baeza, Yoshiki Vrbanac, Alison Wischmeyer, Paul Wolfe, Elaine Zhu, Qiyun Knight, Rob Amer Gut Consortium

Msystems, 2018

https://doi.org/10.1128/mSystems.00031-18

Rob Knight

Knight Rob

ORCID: 0000-0002-0975-9019

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. 10.1038/nbt.3893

Current understanding of the human microbiome. 10.1038/nm.4517

Early life gut microbiota is associated with rapid infant growth in Hispanics from Southern California. 10.1080/19490976.2021.1961203

Insight into the function and evolution of the Wood-Ljungdahl pathway in Actinobacteria. 10.1038/s41396-021-00935-9

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. 10.1101/2020.11.13.370387

Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity. 10.1101/2020.08.17.238444

Methods for phylogenetic analysis of microbiome data. 10.1038/s41564-018-0156-0

Publisher Correction: Enterotypes in the landscape of gut microbial community composition. 10.1038/s41564-018-0114-x

Enterotypes in the landscape of gut microbial community composition. 10.1038/s41564-017-0072-8

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. 10.1371/journal.pcbi.1009056

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes. 10.1101/gr.275777.121

Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence. 10.1101/2021.07.16.452756

Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers. 10.1038/s41396-021-01016-7

Structure-based protein function prediction using graph convolutional networks. 10.1038/s41467-021-23303-9

Challenges in benchmarking metagenomic profilers. 10.1038/s41592-021-01141-3

Taxonomic signatures of cause-specific mortality risk in human gut microbiome. 10.1038/s41467-021-22962-y

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data. 10.1111/biom.13481

Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition. 10.1128/msystems.01329-20

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications 10.1038/nbt.1823

The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010. 10.4056/aigs.1443528

Origins of the genetic code: The escaped triplet theory 10.1146/annurev.biochem.74.082803.133119

Defining the human microbiome 10.1111/j.1753-4887.2012.00493.x

Dietary prebiotics and bioactive milk fractions improve NREM sleep, enhance REM sleep rebound and attenuate the stress-induced decrease in diurnal temperature and gut microbial alpha diversity 10.3389/fnbeh.2016.00240

Meta-analyses of human gut microbes associated with obesity and IBD 10.1016/j.febslet.2014.09.039

Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations 10.1128/mBio.01526-14

Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment 10.1145/1646468.1646481

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill 10.1038/ismej.2013.254

Meeting report for the 1st skin microbiota workshop, boulder, co October 15-16 2012 10.1186/1944-3277-9-13

Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk 10.1017/S0007114516004165

Host remodeling of the gut microbiome and metabolic changes during pregnancy 10.1016/j.cell.2012.07.008

A distinct immunogenic region of glutamic acid decarboxylase 65 is naturally processed and presented by human islet cells to cytotoxic CD8 T cells 10.1111/cei.12436

Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities 10.1128/AEM.01996-06

Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation 10.1073/pnas.0902366106

A population of Pax7-expressing muscle progenitor cells show differential responses to muscle injury dependent on developmental stage and injury extent 10.3389/fnagi.2015.00161

Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch 10.1016/j.jmb.2013.02.023

Authors' reply to Mawer and Wilcox and Mullish and Williams 10.1136/bmj.h6132

The bacterial microbiota in the oral mucosa of rural Amerindians 10.1099/mic.0.043174-0

Selection, history and chemistry: The three faces of the genetic code 10.1016/S0968-0004(99)01392-4

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species 10.1007/s00442-015-3507-z

Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems 10.1890/10-0426.1

Specification of sensory neurons occurs through diverse developmental programs functioning in the brain and spinal cord 10.1002/dvdy.24184

Ghost-tree: Creating hybrid-gene phylogenetic trees for diversity analyses 10.1186/s40168-016-0153-6

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges 10.1101/gr.085464.108

Tfap2 transcription factors in zebrafish neural crest development and ectodermal evolution 10.1002/jez.b.21189

Direct sequencing of the human microbiome readily reveals community differences 10.1186/gb-2010-11-5-210

Human gut microbiome viewed across age and geography 10.1038/nature11053

Sources of bacteria in outdoor air across cities in the midwestern United States 10.1128/AEM.05498-11

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity 10.3389/fmicb.2014.00298

Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice 10.1053/j.gastro.2013.01.047

Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment 10.1111/1462-2920.12539

How delivery mode and feeding can shape the bacterial community in the infant gut 10.1503/cmaj.130147

Moving pictures of the human microbiome 10.1186/gb-2011-12-5-r50

Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010 10.4056/sigs.1333437

The impact of the gut microbiota on human health: An integrative view 10.1016/j.cell.2012.01.035

Forensic identification using skin bacterial communities 10.1073/pnas.1000162107

Which is more important for classifying microbial communities: Who's there or what they can do? 10.1038/ismej.2014.157

Comparison of fecal collection methods for microbiota studies in Bangladesh 10.1128/AEM.00361-17

Using the gut microbiota as a novel tool for examining colobine primate GI health 10.1016/j.gecco.2016.06.004

Lifestyle chemistries from phones for individual profiling 10.1073/pnas.1610019113

The ecology of the phyllosphere: Geographic and phylogenetic variability in the distribution of bacteria on tree leaves 10.1111/j.1462-2920.2010.02258.x

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins 10.1073/pnas.1000071108

Metabolie syndrome and altered gut microbiota in mice lacking toll-like receptor 5 10.1126/science.1179721

A Microbiome Foundation for the Study of Crohn's Disease 10.1016/j.chom.2017.02.012

Comparison of collection methods for fecal samples for discovery metabolomics in epidemiologic studies 10.1158/1055-9965.EPI-16-0409

Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories 10.1261/rna.2183806

Bacterial phylogeny structures soil resistomes across habitats 10.1038/nature13377

Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences 10.1038/ismej.2011.208

Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes 10.1111/1462-2920.13684

Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice 10.1016/j.chom.2012.07.004

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers 10.1093/nar/gkn491

Evolution of mammals and their gut microbes 10.1126/science.1155725

Vertebrate genome evolution: A slow shuffle or a big bang? 10.1002/(SICI)1521-1878(199908)21:8<697::AID-BIES9>3.0.CO;2-X

Biogeography and habitat modelling of high-alpine bacteria 10.1038/ncomms1055

Vertebrate hosts as Islands: Dynamics of selection, immigration, loss, persistence, and potential function of bacteria on salamander skin 10.3389/fmicb.2016.00333

MIxS-BE: A MIxS extension defining a minimum information standard for sequence data from the built environment 10.1038/ismej.2013.176

Finding specific RNA motifs: Function in a zeptomole world? 10.1261/rna.2138803

Skin bacteria provide early protection for newly metamorphosed southern leopard frogs (Rana sphenocephala) against the frog-killing fungus, Batrachochytrium dendrobatidis 10.1016/j.biocon.2015.04.007

Convergence of gut microbiomes in myrmecophagous mammals 10.1111/mec.12501

Changes through time: Integrating microorganisms into the study of succession 10.1016/j.resmic.2010.06.002

Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples 10.1128/AEM.04137-13

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns 10.1038/nmeth.1499

The molecular basis of nuclear genetic code change in ciliates 10.1016/S0960-9822(01)00028-8

Using QIIME to analyze 16s rRNA gene sequences from microbial communities 10.1002/9780471729259.mc01e05s27

Culturing: Looking it up in our gut 10.1038/nmicrobiol.2016.169

Human oral, gut, and plaque microbiota in patients with atherosclerosis 10.1073/pnas.1011383107

Microbial eukaryotes in the human microbiome: Ecology, evolution, and future directions 10.3389/fmicb.2011.00153

Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks 10.1038/nmicrobiol.2016.177

Xenobiotics and the human gut microbiome: Metatranscriptomics reveal the active players 10.1016/j.cmet.2013.02.013

Experimental and analytical tools for studying the human microbiome 10.1038/nrg3129

Cohabiting family members share microbiota with one another and with their dogs 10.7554/eLife.00458

The gut microbiota in human energy homeostasis and obesity 10.1016/j.tem.2015.07.002

EMPeror: A tool for visualizing high-throughput microbial community data 10.1186/2047-217X-2-16

Is the genetic code really a frozen accident? New evidence from in vitro selection 10.1111/j.1749-6632.1999.tb08915.x

PyCogent: A toolkit for making sense from sequence 10.1186/gb-2007-8-8-r171

Microbes do not follow the elevational diversity patterns of plants and animals 10.1890/10-1170.1

QIIME allows analysis of high-throughput community sequencing data 10.1038/nmeth.f.303

UniFrac: A new phylogenetic method for comparing microbial communities 10.1128/AEM.71.12.8228-8235.2005

Soil bacterial and fungal communities across a pH gradient in an arable soil 10.1038/ismej.2010.58

Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity 10.1111/mec.12846

Subsistence strategies in traditional societies distinguish gut microbiomes 10.1038/ncomms7505

Faecal transplants 10.1136/bmj.h5149

TopiaryExplorer: Visualizing large phylogenetic trees with environmental metadata 10.1093/bioinformatics/btr517

From molecules to dynamic biological communities 10.1007/s10539-013-9364-4

Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species 10.1007/s00248-017-1041-8

Intestinal adaptation in proximal and distal segments: Two epithelial responses diverge after intestinal separation 10.1016/j.surg.2016.10.033

Commensal Bacteria and MAMPs Are Necessary for Stress-Induced Increases in IL-1β and IL-18 but Not IL-6, IL-10 or MCP-1 10.1371/journal.pone.0050636

The human microbiome: Eliminating the biomedical/environmental dichotomy in microbial ecology 10.1111/j.1462-2920.2006.01222_3.x

Gut microbes and the brain: Paradigm shift in neuroscience 10.1523/JNEUROSCI.3299-14.2014

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat 10.1016/j.chom.2009.08.003

Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish 10.1016/j.chom.2012.08.003

A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins 10.1074/mcp.M800384-MCP200

Context and the human microbiome 10.1186/s40168-015-0117-2

Seasonal variation of postmortem microbial communities 10.1007/s12024-015-9667-7

Diversity of rickettsiales in the microbiome of the lone star tick, amblyomma americanum 10.1128/AEM.02987-13

The under-recognized dominance of Verrucomicrobia in soil bacterial communities 10.1016/j.soilbio.2011.03.012

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains 10.1371/journal.pbio.1001920

Diversity, distribution and sources of bacteria in residential kitchens 10.1111/1462-2920.12036

Gut microbiomes of Malawian twin pairs discordant for kwashiorkor 10.1126/science.1229000

Composition of human skin microbiota affects attractiveness to malaria mosquitoes 10.1371/journal.pone.0028991

Finding the Missing Links among Metabolites, Microbes, and the Host 10.1016/j.immuni.2014.05.015

Do proteins predate DNA? 10.1126/science.286.5440.690

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing 10.1038/nmeth.2276

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex 10.1038/nmeth.1184

PyNAST: A flexible tool for aligning sequences to a template alignment 10.1093/bioinformatics/btp636

Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits 10.1021/acssynbio.5b00133

Bacterial colonization and succession in a newly opened hospital 10.1126/scitranslmed.aah6500

High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity 10.1053/j.gastro.2009.08.042

The pediatric intestinal mucosal microbiome remains altered after clinical resolution of inflammatory and ischemic disease 10.1016/j.surg.2016.05.005

Development of the human gastrointestinal microbiota and insights from high-throughput sequencing 10.1053/j.gastro.2011.02.011

Alterations in the gut microbiota associated with HIV-1 infection 10.1016/j.chom.2013.08.006

Role of the microbiome, probiotics, and 'dysbiosis therapy' in critical illness 10.1097/MCC.0000000000000321

Diversity, structure and convergent evolution of the global sponge microbiome 10.1038/ncomms11870

New insight into the diversity of life's building blocks: Evenness, not variance 10.1089/ast.2011.2280

Bacteria from diverse habitats colonize and compete in the mouse gut 10.1016/j.cell.2014.09.008

Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs) 10.1371/journal.pone.0054703

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives 10.1093/nar/gkq066

Mosquito microbiome dynamics, a background for prevalence and seasonality of West Nile virus 10.3389/fmicb.2017.00526

Evolutionary rates vary among rRNA structural elements 10.1093/nar/gkm101

Simple, recurring RNA binding sites for L-arginine 10.1261/rna.1979410

Rewiring the keyboard: Evolvability of the genetic code 10.1038/35047500

Widespread colonization of the lung by Tropheryma whipplei in HIV infection 10.1164/rccm.201211-2145OC

Artificial Selection: Finding Function amongst Randomized Sequences 10.1002/9783527619504.ch47

Effects of field conditions on fecal microbiota 10.1016/j.mimet.2016.09.017

Dietary effects on human gut microbiome diversity 10.1017/S0007114514004127

An Elegan(t) Screen for Drug-Microbe Interactions 10.1016/j.chom.2017.04.014

The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome 10.1186/2047-217X-1-7

Variation in the microbiota of Ixodes ticks with regard to geography, species, and sex 10.1128/AEM.01562-15

Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas) 10.1038/ismej.2015.168

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection 10.1186/s40168-015-0070-0

Using QIIME to analyze 16S rrna gene sequences from microbial communities 10.1002/0471250953.bi1007s36

Sharing and archiving nucleic acid structure mapping data 10.1261/rna.2753211

Advancing analytical algorithms and pipelines for billions of microbial sequences 10.1016/j.copbio.2011.11.028

Obesity alters gut microbial ecology 10.1073/pnas.0504978102

Why microbiome treatments could pay off soon 10.1038/scientificamerican0315-S5

Pathological rate matrices: From primates to pathogens 10.1186/1471-2105-9-550

Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats 10.1371/journal.pone.0125889

Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes 10.1111/j.1462-2920.2010.02277.x

Advancing the microbiome research community 10.1016/j.cell.2014.09.022

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences 10.7717/peerj.545

Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States 10.1126/science.1243768

Interleukin-1β (IL-1β) promotes susceptibility of toll-like receptor 5 (TLR5) deficient mice to colitis 10.1136/gut.2011.240556

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis 10.1093/bib/bbr009

Characterizing microbial communities through space and time 10.1016/j.copbio.2011.11.017

Collecting fecal samples for microbiome analyses in epidemiology studies 10.1158/1055-9965.EPI-15-0951

Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle 10.1152/ajpregu.00387.2012

DNA extraction for streamlined metagenomics of diverse environmental samples 10.2144/000114559

Fecal microbiome in epidemiologic studies-response 10.1158/1055-9965.EPI-16-0161

Bacterial communities of disease vectors sampled across time, space, and species 10.1038/ismej.2009.111

The hospital microbiome project: Meeting report for the 1st hospital microbiome project workshop on sampling design and building science measurements, chicago, usa, june 7th-8th 2012 10.4056/sigs.3717348

Short-term temporal variability in airborne bacterial and fungal populations 10.1128/AEM.01467-07

Linking long-term dietary patterns with gut microbial enterotypes 10.1126/science.1208344

Evidence for a persistent microbial seed bank throughout the global ocean 10.1073/pnas.1217767110

Metagenomic covariation along densely sampled environmental gradients in the Red Sea 10.1038/ismej.2016.99

How biologists conceptualize genes: An empirical study 10.1016/j.shpsc.2004.09.005

Worlds within worlds: Evolution of the vertebrate gut microbiota 10.1038/nrmicro1978

Ribosomal RNA, the lens into life 10.1261/rna.050799.115

Sequencing our way towards understanding global eukaryotic biodiversity 10.1016/j.tree.2011.11.010

Stress response, gut microbial diversity and sexual signals correlate with social interactions 10.1098/rsbl.2016.0352

Size, constant sequences, and optimal selection 10.1261/rna.2161305

Rethinking enterotypes 10.1016/j.chom.2014.09.013

tRNA creation by hairpin duplication 10.1007/s00239-004-0315-1

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease 10.1016/j.cell.2016.11.018

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample 10.1073/pnas.1000080107

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision 10.1038/ismej.2015.235

Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (plethodon cinereus) 10.1038/ismej.2013.200

Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water 10.1016/j.watres.2014.11.003

RNA-amino acid binding: A stereochemical era for the genetic code 10.1007/s00239-009-9270-1

Short pyrosequencing reads suffice for accurate microbial community analysis 10.1093/nar/gkm541

Heritable components of the human fecal microbiome are associated with visceral fat 10.1186/s13059-016-1052-7

Genetic Determinants of the Gut Microbiome in UK Twins 10.1016/j.chom.2016.04.017

Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato) 10.1186/1471-2180-13-114

Succession of microbial consortia in the developing infant gut microbiome 10.1073/pnas.1000081107

Dynamics of the human gut microbiome in inflammatory bowel disease 10.1038/nmicrobiol.2017.4

The founding charter of the Genomic Observatories Network 10.1186/2047-217X-3-2

A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses 10.1038/ismej.2008.127

Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans 10.1126/science.1198719

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples 10.1111/j.1574-6968.2010.01965.x

RNA structure prediction from evolutionary patterns of nucleotide composition 10.1093/nar/gkn987

Genetic and environmental control of host-gut microbiota interactions 10.1101/gr.194118.115

Analysis of membrane proteins from human chronic myelogenous leukemia cells: Comparison of extraction methods for multidimensional LC-MS/MS 10.1021/pr050313z

Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code 10.1007/s00239-004-0314-2

Comparison of methods for estimating the nucleotide substitution matrix 10.1186/1471-2105-9-511

From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal 10.1261/rna.881308

Tools for the microbiome: Nano and beyond 10.1021/acsnano.5b07826

Database-Driven Grid Computing and Distributed Web Applications: A Comparison 10.1002/9780470191637.ch11

Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data 10.1016/J.ENG.2017.01.020

Estimate of the abundance of cardiomyopathic mutations in the β-myosin gene 10.1016/j.ijcard.2008.12.199

Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA 10.1261/rna.2220210

Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples 10.1021/acs.analchem.7b01381

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation 10.1016/j.tim.2011.07.006

Environmental and ecological factors that shape the gut bacterial communities of fish: A meta-analysis 10.1111/j.1365-294X.2012.05552.x

Keemei: Cloud-based validation of tabular bioinformatics file formats in Google Sheets 10.1186/s13742-016-0133-6

Vertebrate decomposition is accelerated by soil microbes 10.1128/AEM.00957-14

Satellite remote sensing data can be used to model marine microbial metabolite turnover 10.1038/ismej.2014.107

Diversity, stability and resilience of the human gut microbiota 10.1038/nature11550

Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau 10.1111/j.1462-2920.2012.02799.x

Bacterial communities associated with the lichen symbiosis 10.1128/AEM.02257-10

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood 10.1101/gr.140608.112

Guilt by association: The arginine case revisited 10.1017/S1355838200000145

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest 10.1038/ismej.2014.36

Global patterns in bacterial diversity 10.1073/pnas.0611525104

Fast find: A novel computational approach to analyzing combinatorial motifs 10.1186/1471-2105-7-1

Predictive modeling of gingivitis severity and susceptibility via oral microbiota 10.1038/ismej.2014.32

Conceptualizing a Genomics Software Institute (GSI) 10.4056/sigs.2485911

Tracking down the sources of experimental contamination in microbiome studies 10.1186/s13059-014-0564-2

Replenishing our defensive microbes 10.1002/bies.201300018

Insights from Characterizing Extinct Human Gut Microbiomes 10.1371/journal.pone.0051146

The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome 10.1371/journal.pbio.1001377

Unlocking the potential of metagenomics through replicated experimental design 10.1038/nbt.2235

Tiny microbes, enormous impacts: What matters in gut microbiome studies? 10.1186/s13059-016-1086-x

ConStrains identifies microbial strains in metagenomic datasets 10.1038/nbt.3319

Microbial community assembly and metabolic function during mammalian corpse decomposition 10.1126/science.aad2646

Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome 10.1002/mds.26942

PH is a good predictor of the distribution of anoxygenic purple phototrophic bacteria in Arctic soils 10.1016/j.soilbio.2014.03.014

Fat and vitamin intakes during pregnancy have stronger relations with a proinflammatory maternal microbiota than does carbohydrate intake 10.1186/s40168-016-0200-3

Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents 10.1038/ismej.2012.81

Microbiology of death 10.1016/j.cub.2016.03.042

A meta-analysis of changes in bacterial and archaeal communities with time 10.1038/ismej.2013.54

PrimerProspector: De novo design and taxonomic analysis of barcoded polymerase chain reaction primers 10.1093/bioinformatics/btr087

SnapShot: The Human Microbiome 10.1016/j.cell.2014.07.019

Microbial Skin Inhabitants: Friends Forever 10.1016/j.cell.2016.04.035

The microbiome explored: Recent insights and future challenges 10.1038/nrmicro2973

Supervised classification of microbiota mitigates mislabeling errors 10.1038/ismej.2010.148

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics 10.1021/ac035229m

Using machine learning to identify major shifts in human gut microbiome protein family abundance in disease 10.1109/BigData.2016.7840731

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms 10.1038/ismej.2012.8

Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate 10.1007/s00248-017-0938-6

Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei 10.1128/AEM.00447-09

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study 10.1097/PSY.0000000000000512

Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys 10.1038/ismej.2011.186

Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences 10.1038/ismej.2011.187

The Earth Microbiome project: Successes and aspirations 10.1186/s12915-014-0069-1

Microbial biogeography of public restroom surfaces 10.1371/journal.pone.0028132

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer 10.1038/nm.4039

Mathematical approaches for describing microbial populations: Practice and theory for extrapolation of rich environments 10.1002/9781118409855.ch4

Meeting report of the RNA ontology consortium January 8-9, 2011 10.4056/sigs.1724282

Associations between human milk oligosaccharides and infant body composition in the first 6 mo of life 10.3945/ajcn.115.115451

Prevalence and genetic diversity of Blastocystis in family units living in the United States 10.1016/j.meegid.2016.08.018

Ancient human oral plaque preserves a wealth of biological data 10.1038/ng.2930

Examining the global distribution of dominant archaeal populations in soil 10.1038/ismej.2010.171

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Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue 10.1111/1556-4029.13949

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Expanding the scope and scale of microbiome research 10.1186/s13059-019-1804-2

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Molecular and microbial microenvironments in chronically diseased lungs associated with cystic fibrosis 10.1128/mSystems.00375-19

Suppression of the gut microbiome ameliorates age-related arterial dysfunction and oxidative stress in mice 10.1113/JP277336

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Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India 10.1128/mSphere.00731-20

Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes 10.1038/s41396-018-0175-0

Major shifts in gut microbiota during development and its relationship to growth in ostriches 10.1111/mec.15087

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Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces 10.1186/s40168-019-0666-x

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A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria 10.3390/md19010020

The microbiome and its potential for pharmacology 10.1007/164_2019_317

Age- And sex-dependent patterns of gut microbial diversity in human adults 10.1128/mSystems.00261-19

Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice 10.1016/j.cell.2019.05.004

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Effects of the microalgae Chlamydomonas on gastrointestinal health 10.1016/j.jff.2019.103738

Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media 10.1093/gigascience/giaa156

Association of Loneliness and Wisdom With Gut Microbial Diversity and Composition: An Exploratory Study 10.3389/fpsyt.2021.648475

Context-aware dimensionality reduction deconvolutes gut microbial community dynamics 10.1038/s41587-020-0660-7

Comparison of oral collection methods for studies of microbiota 10.1158/1055-9965.EPI-18-0312

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Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome 10.1371/journal.pone.0229001

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Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort 10.1128/mBio.01751-18

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks 10.1371/journal.pcbi.1007007

Reply to Moossavi and Azad, “quantifying and interpreting the association between early-life gut microbiota composition and childhood obesity” 10.1128/MBIO.00047-19

Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus 10.1038/s41396-018-0214-x

Quantifying and understanding well-to-well contamination in microbiome research 10.1128/mSystems.00186-19

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GABA-modulating bacteria of the human gut microbiota 10.1038/s41564-018-0307-3

Porting and optimizing UniFrac for GPUs: Reducing microbiome analysis runtimes by orders of magnitude 10.1145/3311790.3399614

Exploring the Composition and Functions of Plastic Microbiome Using Whole-Genome Sequencing 10.1021/acs.est.0c07952

Paroxetine Administration Affects Microbiota and Bile Acid Levels in Mice 10.3389/fpsyt.2020.00518

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Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis 10.1016/j.eurpsy.2018.05.011

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Best practices for analysing microbiomes 10.1038/s41579-018-0029-9

Consent insufficient for data release−Response 10.1126/science.aax7509

Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans 10.1016/j.cell.2020.09.009

Microbial biogeography and ecology of the mouth and implications for periodontal diseases 10.1111/prd.12268

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Erratum to: The sponge microbiome project. 10.1093/gigascience/giy145

Guiding longitudinal sampling in IBD cohorts 10.1136/gutjnl-2017-315352

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Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome 10.1186/s40168-019-0636-3

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree 10.1038/s41589-020-00677-3

High-throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego county 10.1128/MSYSTEMS.00045-21

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians 10.1016/j.cgh.2018.09.017

Coordinating and assisting research at the SARS-CoV-2/ microbiome nexus 10.1128/MSYSTEMS.00999-20

Expanding magnetic organelle biogenesis in the domain Bacteria 10.1186/s40168-020-00931-9

Toward unrestricted use of public genomic data 10.1126/science.aaw1280

Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection 10.1186/s40168-021-01026-9

Single-cell transcriptomics reveal a correlation between genome architecture and gene family evolution in ciliates 10.1128/mBio.02524-19

Triclosan leads to dysregulation of the metabolic regulator FGF21 exacerbating high fat diet-induced nonalcoholic fatty liver disease 10.1073/pnas.2017129117

Ground beef microbiome changes with antimicrobial decontamination interventions and product storage 10.1371/journal.pone.0217947

Effects of Immunization With the Soil-Derived Bacterium Mycobacterium vaccae on Stress Coping Behaviors and Cognitive Performance in a “Two Hit” Stressor Model 10.3389/fphys.2020.524833

Subgingival Microbiota and Longitudinal Glucose Change: The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS) 10.1177/0022034519881978

SARS-CoV-2 Screening among Symptom-Free Healthcare Workers 10.1017/ice.2021.81

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Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity 10.1093/ibd/izaa262

Home chemical and microbial transitions across urbanization 10.1038/s41564-019-0593-4

Benchmarking urine storage and collection conditions for evaluating the female urinary microbiome 10.1038/s41598-019-49823-5

Evaluating metagenomic prediction of the metaproteome in a 4.5-year study of a patient with Crohn’s disease 10.1128/MSYSTEMS.00337-18

SHOGUN: A modular, accurate and scalable framework for microbiome quantification 10.1093/bioinformatics/btaa277

CD8 T cells drive anorexia, dysbiosis, and blooms of a commensal with immunosuppressive potential after viral infection 10.1073/pnas.2003656117

Empress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets 10.1128/MSYSTEMS.01216-20

Enhanced Characterization of Drug Metabolism and the Influence of the Intestinal Microbiome: A Pharmacokinetic, Microbiome, and Untargeted Metabolomics Study 10.1111/cts.12785

Trait-like vulnerability of higher-order cognition and ability to maintain wakefulness during combined sleep restriction and circadian misalignment 10.1093/sleep/zsz113

IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis 10.1016/j.jid.2019.05.024

Reduced independence in daily living is associated with the gut microbiome in people with HIV and HCV 10.1128/mSystems.00528-20

Host variables confound gut microbiota studies of human disease 10.1038/s41586-020-2881-9

High-Resolution longitudinal dynamics of the cystic fibrosis sputum microbiome and metabolome through antibiotic therapy 10.1128/mSystems.00292-20

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing 10.1038/s41592-020-01041-y

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus) 10.1002/mbo3.716

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes 10.1186/s40168-020-00857-2

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities 10.1016/j.cels.2019.09.004

Multiple sclerosis-associated changes in the composition and immune functions of spore-forming bacteria 10.1128/mSystems.00083-18

The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/s12915-019-0660-6

Disease-modifying therapies alter gut microbial composition in MS 10.1212/NXI.0000000000000517

Current Concepts, Opportunities, and Challenges of Gut Microbiome-Based Personalized Medicine in Nonalcoholic Fatty Liver Disease 10.1016/j.cmet.2020.11.010

Gut microbiota in wild and captive Guizhou snub-nosed monkeys, Rhinopithecus brelichi 10.1002/ajp.22989

Large-scale replicated field study of maize rhizosphere identifies heritable microbes 10.1073/pnas.1800918115

Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data 10.1038/s41587-020-0700-3

Author Correction: Regional variation limits applications of healthy gut microbiome reference ranges and disease models. 10.1038/s41591-018-0219-z

Three-dimensional culture of oral progenitor cells: Effects on small extracellular vesicles production and proliferative function 10.1111/jop.12981

Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16-17, 2017 10.1186/s40168-018-0596-z

Human skin, oral, and gut microbiomes predict chronological age 10.1128/mSystems.00630-19

Identifying and predicting novelty in microbiome studies 10.1128/mBio.02099-18

Fecal Microbiota Transplantation Is Highly Effective in Real-World Practice: Initial Results From the FMT National Registry 10.1053/j.gastro.2020.09.038

Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media 10.1038/s41597-019-0331-z

High-throughput miniaturized 16S rRNA amplicon library preparation reduces costs while preserving microbiome integrity 10.1128/mSystems.00166-18

Species-level functional profiling of metagenomes and metatranscriptomes 10.1038/s41592-018-0176-y

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases 10.1038/s41586-019-1237-9

Effects of Diet versus Gastric Bypass on Metabolic Function in Diabetes 10.1056/NEJMoa2003697

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 10.1038/s41467-020-16366-7

Is there convergence of gut microbes in blood-feeding vertebrates? 10.1098/rstb.2018.0249

The genetic basis for adaptation of modeldesigned syntrophic co-cultures 10.1371/journal.pcbi.1006213

Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information 10.1101/gr.260380.119

Red Sea SAR11 and Prochlorococcus single-cell genomes reflect globally distributed pangenomes 10.1128/AEM.00369-19

Niche partitioning of a pathogenic microbiome driven by chemical gradients 10.1126/sciadv.aau1908

ReDU: a framework to find and reanalyze public mass spectrometry data 10.1038/s41592-020-0916-7

Reply to: Examining microbe–metabolite correlations by linear methods 10.1038/s41592-020-01007-0

Associations of fecal microbial profiles with breast cancer and nonmalignant breast disease in the Ghana Breast Health Study 10.1002/ijc.33473

Microbe-metabolite associations linked to the rebounding murine gut microbiome postcolonization with vancomycin-resistant enterococcus faecium 10.1128/mSystems.00452-20

A microbiome-based index for assessing skin health and treatment effects for atopic dermatitis in children 10.1128/mSystems.00293-19

Absence of CCR2 reduces spontaneous intestinal tumorigenesis in the Apc^Min^/+ mouse model 10.1002/ijc.33477

QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data 10.1002/cpbi.100

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads 10.1186/s13059-019-1834-9

Striped UniFrac: enabling microbiome analysis at unprecedented scale 10.1038/s41592-018-0187-8

Role of the microbiome in human development 10.1136/gutjnl-2018-317503

Qiita: rapid, web-enabled microbiome meta-analysis 10.1038/s41592-018-0141-9

The gut microbiome, aging, and longevity: A systematic review 10.3390/nu12123759

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media 10.1038/s41597-019-0051-4

Influence of Intermittent Hypoxia/Hypercapnia on Atherosclerosis, Gut Microbiome, and Metabolome 10.3389/fphys.2021.663950

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations 10.1016/j.tim.2018.11.003

A distinct microbiome signature in posttreatment lyme disease patients 10.1128/mBio.02310-20

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment 10.1186/s40168-020-00960-4

Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults 10.1016/j.bbi.2020.02.004

Household paired design reduces variance and increases power in multi-city gut microbiome study in multiple sclerosis 10.1177/1352458520924594

Exposure to toxic metals triggers unique responses from the rat gut microbiota 10.1038/s41598-018-24931-w

Global chemical effects of the microbiome include new bile-acid conjugations 10.1038/s41586-020-2047-9

Farm-like indoor microbiota in non-farm homes protects children from asthma development 10.1038/s41591-019-0469-4

Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules 10.1101/gr.265645.120

Creating a 3D microbial and chemical snapshot of a human habitat. 10.1038/s41598-018-21541-4

Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome. 10.1371/journal.pntd.0006344

Microbiome and metagenome analyses of a closed habitat during human occupation 10.1128/mSystems.00367-20

Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations 10.1371/journal.pone.0224757

Temporal, environmental, and biological drivers of the mucosal microbiome in a Wild Marine Fish, Scomber japonicus 10.1128/MSPHERE.00401-20

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month 10.1186/s40168-019-0645-2

Altered Gut Microbiota and Host Metabolite Profiles in Women with Human Immunodeficiency Virus 10.1093/cid/ciz1117

Multiple-disease detection and classification across cohorts via microbiome search 10.1128/mSystems.00150-20

Author Correction: Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity. 10.1186/s13059-020-01970-z

Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection 10.1084/jem.20192276

Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk 10.1016/j.bbi.2020.10.003

Triplicate PCR reactions for 16S rRNA gene amplicon sequencing are unnecessary 10.2144/btn-2018-0192

Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States 10.1016/j.cell.2021.03.052

Regional variation limits applications of healthy gut microbiome reference ranges and disease models 10.1038/s41591-018-0164-x

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus 10.1186/s12866-018-1341-2

Learning representations of microbe–metabolite interactions 10.1038/s41592-019-0616-3

Establishing microbial composition measurement standards with reference frames 10.1038/s41467-019-10656-5

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny 10.1186/s13059-019-1807-z

American Gut: An open platform for citizen science microbiome research 10.1128/MSYSTEMS.00031-18

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities 10.2144/BTN-2020-0153

Author Correction: Inflammation-induced IgA⁺ cells dismantle anti-liver cancer immunity. 10.1038/s41586-018-0304-y

Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing 10.1016/j.envint.2020.105604

Microbial Diversity in Clinical Microbiome Studies: Sample Size and Statistical Power Considerations 10.1053/j.gastro.2019.11.305

Calour: an Interactive, Microbe-Centric Analysis Tool 10.1128/MSYSTEMS.00269-18

Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects 10.1016/j.schres.2018.09.014

Challenges in the construction of knowledge bases for human microbiome-disease associations 10.1186/s40168-019-0742-2

Evaluating organism-wide changes in the metabolome and microbiome following a single dose of antibiotic 10.1128/MSYSTEMS.00340-20

Links between environment, diet, and the hunter-gatherer microbiome 10.1080/19490976.2018.1494103

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism 10.1038/s41467-018-05336-9

The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment 10.3389/fmicb.2020.02015

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea 10.1038/s41467-019-13443-4

Microbiome analyses of blood and tissues suggest cancer diagnostic approach 10.1038/s41586-020-2095-1

A novel sparse compositional technique reveals microbial perturbations 10.1128/MSYSTEMS.00016-19

Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study 10.1038/s41598-020-59016-0

Quantifying live microbial load in human saliva samples over time reveals stable composition and dynamic load 10.1128/MSYSTEMS.01182-20

Associations of the fecal microbial proteome composition and proneness to diet-induced obesity 10.1074/mcp.RA119.001623

Vitamin D metabolites and the gut microbiome in older men 10.1038/s41467-020-19793-8

Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'Omics 10.1093/gbe/evy133

Early-life gut dysbiosis linked to juvenile mortality in ostriches 10.1186/s40168-020-00925-7

Mortality Risk Profiling of Staphylococcus aureus Bacteremia by Multi-omic Serum Analysis Reveals Early Predictive and Pathogenic Signatures 10.1016/j.cell.2020.07.040

Species abundance information improves sequence taxonomy classification accuracy 10.1038/s41467-019-12669-6

Organ-level protein networks as a reference for the host effects of the microbiome 10.1101/gr.256875.119

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893) 10.1038/nbt0718-660d

Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota 10.1038/s41597-020-00656-2

Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs 10.1128/mSystems.00635-19

Animal Models for Microbiome Research and Drug Discovery 10.1016/j.ddmod.2019.09.001

FXR Regulates Intestinal Cancer Stem Cell Proliferation 10.1016/j.cell.2019.01.036

The effect of legume supplementation on the gut microbiota in rural Malawian infants aged 6 to 12 months 10.1093/ajcn/nqaa011

Intermittent hypoxia and hypercapnia reproducibly change the gut microbiome and metabolome across rodent model systems 10.1128/mSystems.00058-19

Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020 10.1186/s40168-020-00951-5

Association between the gut microbiota and blood pressure in a population cohort of 6953 individuals 10.1161/JAHA.120.016641

Longitudinal survey of microbiome associated with particulate matter in a megacity 10.1186/s13059-020-01964-x

Early-career scientists shaping the world 10.1128/mSystems.00196-19

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm 10.1038/s41467-018-04409-z

The gut-liver axis and the intersection with the microbiome 10.1038/s41575-018-0011-z

A gut bacterial amyloid promotes a-synuclein aggregation and motor impairment in mice 10.7554/eLife.53111

Leveling up citizen science 10.1038/s41587-020-0694-x

Evaluating the information content of shallow shotgun metagenomics 10.1128/mSystems.00069-18

Effects of processed meat and drinking water nitrate on oral and fecal microbial populations in a controlled feeding study 10.1016/j.envres.2021.111084

Depression in individuals coinfected with HIV and HCV is associated with systematic differences in the gut microbiome and metabolome 10.1128/mSystems.00465-20

Coinfection and infection duration shape how pathogens affect the African buffalo gut microbiota 10.1038/s41396-020-00855-0

Microbial ecology of atlantic salmon (Salmo salar) hatcheries: Impacts of the built environment on fish mucosal microbiota 10.1128/AEM.00411-20

Handwashing and detergent treatment greatly reduce SARS-CoV-2 viral load on halloween candy handled by COVID-19 patients 10.1128/mSystems.01074-20

Author Correction: Farm-like indoor microbiota in non-farm homes protects children from asthma development. 10.1038/s41591-019-0546-8

The Effects of Captivity on the Mammalian Gut Microbiome. 10.1093/icb/icx090

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. 10.1038/nbt0218-196a

Leukotriene B₄-receptor-1 mediated host response shapes gut microbiota and controls colon tumor progression. 10.1080/2162402x.2017.1361593

Genetic influences on the human oral microbiome. 10.1186/s12864-017-4008-8

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. 10.1126/science.aan4834

Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models. 10.1073/pnas.1711235114

Mass Spectrometry-Based Chemical Cartography of a Cardiac Parasitic Infection. 10.1021/acs.analchem.7b02423

The sponge microbiome project. 10.1093/gigascience/gix077

Dramatic Differences in Gut Bacterial Densities Correlate with Diet and Habitat in Rainforest Ants. 10.1093/icb/icx088

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. 10.1038/nbt.3981

Impacts of the Human Gut Microbiome on Therapeutics. 10.1146/annurev-pharmtox-042017-031849

Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites. 10.1128/msystems.00093-17

Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project. 10.1038/nature24485

Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome. 10.1128/mbio.01343-17

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus. 10.1371/journal.pone.0184336

A communal catalogue reveals Earth's multiscale microbial diversity. 10.1038/nature24621

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. 10.1016/j.chom.2017.10.001

Evaluating the impact of domestication and captivity on the horse gut microbiome. 10.1038/s41598-017-15375-9

Erratum: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. 10.1038/nature25028

Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes. 10.1128/msystems.00092-17

Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality. 10.1111/1365-2656.12781

Exploration of the Germline Genome of the Ciliate Chilodonella uncinata through Single-Cell Omics (Transcriptomics and Genomics). 10.1128/mbio.01836-17

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction. 10.1128/msystems.00188-17

Expanding our Understanding of the Role of the Microbiome in Health and Disease. 10.1016/j.arcmed.2018.02.002

Bacterial density rather than diversity correlates with hatching success across different avian species. 10.1093/femsec/fiy022

Coprolites reveal ecological interactions lost with the extinction of New Zealand birds. 10.1073/pnas.1712337115

Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models. 10.3390/genes9020104

Improving saliva shotgun metagenomics by chemical host DNA depletion. 10.1186/s40168-018-0426-3

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. 10.1128/msystems.00218-17

Bacterial community changes in an industrial algae production system. 10.1016/j.algal.2017.09.010

Earth Microbiome Project and Global Systems Biology. 10.1128/msystems.00217-17

Hopanoid-producing bacteria in the Red Sea include the major marine nitrite oxidizers. 10.1093/femsec/fiy063

Integrated Approaches to Analyze Big Data in the Perinatal/Neonatal Space. 10.1089/bfm.2018.29072.rjk

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information. 10.1128/msystems.00021-18

Gut microbiota utilize immunoglobulin A for mucosal colonization. 10.1126/science.aaq0926

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. 10.1186/s40168-018-0470-z

Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas. 10.1016/j.cels.2018.04.010

Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome. 10.1128/msystems.00020-18

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. 10.3389/fmicb.2018.02559

Microbiota as in farm homes protect children from asthma 10.1183/13993003.congress-2018.oa337

Diet and the Gut Microbiome in 10–18-Month-Old Children Living in Urban Slums of Mumbai, India (OR01-08-19) 10.1093/cdn/nzz040.or01-08-19

Neighborhoods to Nucleotides—Advances and Gaps for an Obesity Disparities Systems Epidemiology Model 10.1007/s40471-019-00221-5

Global chemical analysis of biology by mass spectrometry 10.1038/s41570-017-0054

Visualizing 'omic feature rankings and log-ratios using Qurro. 10.1093/nargab/lqaa023

A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis. 10.1016/j.cmet.2020.06.005

Association of Body Mass Index with Fecal Microbial Diversity and Metabolites in the Northern Finland Birth Cohort. 10.1158/1055-9965.epi-20-0824

Dietary factors, gut microbiota, and serum trimethylamine-N-oxide associated with cardiovascular disease in the Hispanic Community Health Study/Study of Latinos. 10.1093/ajcn/nqab001

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. 10.21203/rs.3.rs-56028/v1

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. 10.1101/2021.02.06.21251159

The early evolution of the genetic code. 10.1016/s0092-8674(00)80866-1

Measuring adaptation within the genetic code. 10.1016/s0968-0004(99)01531-5

Early fixation of an optimal genetic code. 10.1093/oxfordjournals.molbev.a026331

An amphioxus Krox gene: insights into vertebrate hindbrain evolution. 10.1007/s004270000092

Identification of conserved C2H2 zinc-finger gene families in the Bilateria. 10.1186/gb-2001-2-5-research0016

A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. 10.1186/gb-2001-2-4-research0010

Analyzing partially randomized nucleic acid pools: straight dope on doping. 10.1093/nar/gng030

Do universal codon-usage patterns minimize the effects of mutation and translation error? 10.1186/gb-2005-6-11-r91

Information, probability, and the abundance of the simplest RNA active sites. 10.2741/3137

Systems biology: Understanding function from genes to networks 10.2174/157016409788680974

The mind-body-microbial continuum. 10.31887/dcns.2011.13.1/agonzalez

Analytic Strategies for Understanding Host-Associated Microbial Communities: Faster and cheaper DNA sequencing technologies combined with open-access analytic software packages are opening new vistas 10.1128/microbe.6.389.1

Human microbiome science: Vision for the future, Bethesda, MD, July 24 to 26, 2013 10.1186/2049-2618-2-16

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. 10.1038/nbt0718-660a

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. 10.7554/elife.01104

Ret function in muscle stem cells points to tyrosine kinase inhibitor therapy for facioscapulohumeral muscular dystrophy. 10.7554/elife.11405

Chris Callewaert

Callewaert Chris

ORCID: 0000-0001-7697-9188

http://www.drarmpit.com

American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/mSystems.00031-18

Best practices for analysing microbiomes 10.1038/s41579-018-0029-9

Dupilumab-mediated IL-4R alpha blockade decreases Staphylococcus aureus colonization and increases microbial diversity in patients with Atopic Dermatitis (AD) 10.1016/j.jid.2018.06.036

Impacts of the Human Gut Microbiome on Therapeutics 10.1146/annurev-pharmtox-042017-031849

The Microbiome and Human Biology 10.1146/annurev-genom-083115-022438

Towards a bacterial treatment for armpit malodour 10.1111/exd.13259

The effect of feed water dissolved organic carbon concentration and composition on organic micropollutant removal and microbial diversity in soil columns simulating river bank filtration 10.1016/j.chemosphere.2015.09.017

A laboratory-scale column study comparing organic micropollutant removal and microbial diversity for two soil types 10.1016/j.scitotenv.2015.07.056

Bacterial Exchange in Household Washing Machines 10.3389/fmicb.2015.01381

Novel biocompatible nanocapsules for slow release of fragrances on the human skin 10.1016/j.nbt.2014.09.001

Artificial sweat composition to grow and sustain a mixed human axillary microbiome 10.1016/j.mimet.2014.05.005

Deodorants and antiperspirants affect the axillary bacterial community 10.1007/s00403-014-1487-1

Microbial Odor Profile of Polyester and Cotton Clothes after a Fitness Session 10.1128/AEM.01422-14

Characterization of Staphylococcus and Corynebacterium Clusters in the Human Axillary Region 10.1371/journal.pone.0070538

The resource footprint of biobased products: a key issue in the sustainable development of biorefineries 10.1002/bbb.304

FRT – FONDATION RENE TOURAINE 10.1111/exd.13160

IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis 10.1016/j.jid.2019.05.024

Biological and Chemical Processes that Lead to Textile Malodour Development 10.3390/microorganisms8111709

The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/s12915-019-0660-6

A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children 10.1128/msystems.00293-19

Home chemical and microbial transitions across urbanization 10.1038/s41564-019-0593-4

Algorithmic Learning for Auto-deconvolution of GC-MS Data to Enable Molecular Networking within GNPS 10.1101/2020.01.13.905091

Zeb2 drives invasive and microbiota-dependent colon carcinoma 10.1038/s43018-020-0070-2

Publisher Correction: Zeb2 drives invasive and microbiota-dependent colon carcinoma 10.1038/s43018-020-0097-4

Dietary Emulsifiers Alter Composition and Activity of the Human Gut Microbiota in vitro, Irrespective of Chemical or Natural Emulsifier Origin 10.3389/fmicb.2020.577474

Dietary emulsifiers alter composition and activity of the human gut microbiota in vitro, irrespective of chemical or natural emulsifier origin 10.1101/2020.06.28.174946

Skin Microbiome and its Interplay with the Environment 10.1007/s40257-020-00551-x

102 Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Patients With Atopic Dermatitis 10.1016/j.jid.2019.07.106

Gut–Skin Axis: Current Knowledge of the Interrelationship between Microbial Dysbiosis and Skin Conditions 10.3390/microorganisms9020353

The Future of Functional Clothing for an Improved Skin and Textile Microbiome Relationship 10.3390/microorganisms9061192

Jonathan A. Eisen

Eisen Jonathan A.

ORCID: 0000-0002-0159-2197

https://phylogenomics.wordpress.com/about/disclosures/

http://microBE.net

http://phylogenomics.blogspot.com

http://phylogenomics.wordpress.com

http://twitter.com/phylogenomics

Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh 10.1111/1462-2920.12388

MIxS-BE: A MIxS extension defining a minimum information standard for sequence data from the built environment 10.1038/ismej.2013.176

Open science and reporting animal studies: who's accountable? 10.1371/journal.pbio.1001757

PhyloSift: Phylogenetic analysis of genomes and metagenomes 10.7717/peerj.243

Draft Genome Sequences of Extended-Spectrum β-Lactamase-Producing Escherchia coli Strains Isolated from Patients in Lebanon. 10.1128/genomeA.00123-14

Draft Genome Sequence of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Isolated from a Patient in Lebanon. 10.1128/genomeA.00121-14

Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12. 10.1128/genomeA.00109-14

Expert Failure: Re-evaluating Research Assessment 10.1371/journal.pbio.1001677

Genome sequence of the moderately thermophilic sulfur-reducing bacterium Thermanaerovibrio velox type strain (Z-9701(T)) and emended description of the genus Thermanaerovibrio. 10.4056/sigs.4237901

Genome sequence of Frateuria aurantia type strain (Kondo 67(T)), a xanthomonade isolated from Lilium auratium Lindl. 10.4056/sigs.4338002

Insights into the phylogeny and coding potential of microbial dark matter 10.1038/nature12352

High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)). 10.4056/sigs.3537045

Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGA(T)). 10.4056/sigs.3547050

Complete genome sequence of Coriobacterium glomerans type strain (PW2(T)) from the midgut of Pyrrhocoris apterus L. (red soldier bug). 10.4056/sigs.3507020

Complete genome sequence of the bile-resistant pigment-producing anaerobe alistipes finegoldii type strain (ahn2437T) 10.4056/sigs.3527032

Genome sequence of the thermophilic fresh-water bacterium spirochaeta caldaria type strain (h1t), reclassification of spirochaeta caldaria, spirochaeta stenostrepta, and spirochaeta zuelzerae in the genus treponema as treponema caldaria comb. nov., treponema stenostrepta comb. nov., and treponema zuelzerae comb. nov., and emendation of the genus treponema 10.4056/sigs.3096473

Gene conservation among endospore-forming bacteria reveals additional sporulation genes in Bacillus subtilis 10.1128/JB.01778-12

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing 10.1073/pnas.1217107110

Draft genome sequence of Leucobacter sp. strain UCD-THU (phylum Actinobacteria) 10.1128/genomeA.00325-13

Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment 10.1038/ncomms3120

Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift. 10.4056/sigs.3607108

Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)). 10.4056/sigs.3637201

Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva. 10.4056/sigs.3617113

Systematic Identification of Gene Families for Use as "Markers" for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups 10.1371/journal.pone.0077033

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices 10.1371/journal.pone.0062510

The Impact of Helicobacter pylori Infection on the Gastric Microbiota of the Rhesus Macaque 10.1371/journal.pone.0076375

Draft genome sequence of Microbacterium sp. strain UCD-TDU (phylum Actinobacteria) 10.1128/genomeA.00120-13

Draft genome sequence of an actinobacterium, Brachybacterium muris strain UCD-AY4 10.1128/genomeA.00086-13

Draft genome sequence of Curtobacterium flaccumfaciens strain UCD-AKU (phylum Actinobacteria) 10.1128/genomeA.00244-13

Draft genome sequence of Kocuria sp. strain UCD-OTCP (phylum Actinobacteria) 10.1128/genomeA.00172-13

Draft genome sequence of Dietzia sp. strain UCD-THP (phylum Actinobacteria) 10.1128/genomeA.00197-13

Draft genome sequence of the arsenate-respiring bacterium Chrysiogenes arsenatis strain DSM 11915 10.1128/genomeA.00953-13

Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence 10.1186/1471-2164-14-95

Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)). 10.4056/sigs.3117229

Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)). 10.4056/sigs.3296896

Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)). 10.4056/sigs.3216895

Yeast communities of diverse Drosophila species: Comparison of two symbiont groups in the same hosts 10.1128/AEM.01741-12

Genome-scale analysis of programmed DNA elimination sites in tetrahymena thermophila 10.1534/g3.111.000927

Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR). 10.4056/sigs.2004684

Complete genome sequence of Cellulophaga lytica type strain (LIM-21). 10.4056/sigs.1774329

Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845). 10.4056/sigs.1553862

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. 10.4056/sigs.1433550

Erratum to: Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). 10.4056/sigs.881234

The complete genome sequence of Haloferax volcanii DS2, a model archaeon 10.1371/journal.pone.0009605

Complete genome sequence of Halogeometricum borinquense type strain (PR3). 10.4056/sigs.23264

Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255). 10.4056/sigs.33592

Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment 10.1038/nature03170

Comparative studies of resistin expression and phylogenomics in human and mouse 10.1016/j.bbrc.2003.09.093

TIGRFAMs: a protein family resource for the functional identification of proteins. 10.1093/nar/29.1.41

DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae 10.1038/35020000

Complete genome sequence of Neisseria meningitidis serogroup B strain MC58 10.1126/science.287.5459.1809

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana 10.1038/45471

The phylogenetic relationships of Chlorobium tepidum and Chloroflexus aurantiacus based upon their RecA sequences. 10.1111/j.1574-6968.1998.tb12978.x

Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis 10.1101/gr.8.3.163

The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species 10.1007/BF00173192

Evolution of the SNF2 family of proteins: Subfamilies with distinct sequences and functions 10.1093/nar/23.14.2715

Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences 10.1093/nar/22.13.2634

PhyloMETAGenomics 10.4016/30804.01

A genomic encyclopedia of bacteria and archaea 10.4016/30805.01

Jonathan Eisen discusses GEBA project at DOE JGI 10.4016/15184.01

"A genomic encyclopedia of bacteria and archaea" talk by Jonathan Eisen 10.4016/7258.01

A personal perspective on open access publishing 10.4016/20784.01

Jonathan Eisen and the GEBA project - video linked to news release re Dec. 2009 Nature paper 10.4016/15185.01

"Genomic Encyclopedia of Bacteria and Archaea (GEBA)"- Jonathan Eisen @ '09 DOE JGI User Meeting 10.4016/10750.01

11+ things everyone needs to know about microbes 10.15200/winn.142971.15784

Methylisothiazolinone in household items - a growing (or well, killing) problem #germophobia 10.15200/winn.142971.16225

The Genetic Data Environment 10.1385/0-89603-358-9:13

Sequenced strains must be saved from extinction 10.1038/35102737

What does the term microbiome mean? And where did it come from? A bit of a surprise .. 10.15200/winn.142971.16196

Faculty of 1000 evaluation for Evolutionary origins of genomic repertoires in bacteria. 10.3410/f.1025510.304719

Faculty of 1000 evaluation for The 1.2-megabase genome sequence of Mimivirus. 10.3410/f.1021840.247738

Draft genome sequence of Planomicrobium glaciei UCD-HAM (phylum Firmicutes) 10.1128/genomeA.01209-15

The United States Culture Collection Network (USCCN): Enhancing microbial genomics research through living microbe culture collections 10.1128/AEM.01176-15

Genomic encyclopedia of bacterial and archaeal type strains, phase III: The genomes of soil and plant-associated and newly described type strains 10.1186/s40793-015-0017-x

Swabs to genomes: A comprehensive workflow 10.7717/peerj.960

Forensic analysis of the microbiome of phones and shoes. 10.1186/s40168-015-0082-9

Draft genome sequences of 26 Porphyromonas strains isolated from the canine oral microbiome 10.1128/genomeA.00187-15

Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species 10.1073/pnas.1503928112

Whole genome sequencing of extended-spectrum β-lactamase producing Klebsiella pneumoniae isolated from a patient in Lebanon 10.3389/fcimb.2015.00032

Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178T (Phylum Thermodesulfobacteria). 10.1128/genomeA.01490-14

Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347T (Phylum Nitrospirae). 10.1128/genomeA.01489-14

Draft genome sequence of Enterobacter sp. strain UCD-UG_FMILLET (phylum Proteobacteria) 10.1128/genomeA.01461-14

Draft genome sequence of Burkholderia gladioli strain UCD-UG_CHAPALOTE (phylum Proteobacteria) 10.1128/genomeA.01462-14

Structure, variation, and assembly of the root-associated microbiomes of rice 10.1073/pnas.1414592112

Draft genome sequences of Escherichia coli strains isolated from septic patients 10.1128/genomeA.01278-14

The microbes we eat: Abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types 10.7717/peerj.659

Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae. 10.1186/1944-3277-9-10

Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response 10.1371/journal.pgen.1004784

The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: A blueprint for thriving in and out of symbiosis 10.1186/1471-2164-15-924

Draft genome sequence of the pyridinediol-fermenting bacterium Synergistes jonesii 78-1 10.1128/genomeA.00833-14

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains 10.1371/journal.pbio.1001920

Draft genome sequence of the endosymbiont "Candidatus Ruthia magnifica" UCD-CM (phylum Proteobacteria) 10.1128/genomeA.00717-14

microBEnet: Lessons Learned from Building an Interdisciplinary Scientific Community in the Online Sphere 10.1371/journal.pbio.1001884

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products 10.7717/peerj.415

Complete genome sequence of Coprothermobacter proteolyticus DSM 5265 10.1128/genomeA.00470-14

Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring 10.4056/sigs.3016383

Draft genome sequence of Tatumella sp. strain UCD-D_suzukii (phylum Proteobacteria) isolated from Drosophila suzukii larvae 10.1128/genomeA.00349-14

Draft genome sequences of Streptococcus pyogenes strains associated with throat and skin infections in Lebanon 10.1128/genomeA.00358-14

Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. 10.4056/sigs.5138968

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project 10.4056/sigs.5068949

Prokaryotic super program advisory committee DOE joint genome institute, Walnut Creek, CA, March 27, 2012 10.4056/sigs.4638348

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance 10.1371/journal.pcbi.1002743

Badomics words and the power and peril of the ome-meme 10.1186/2047-217x-1-6

Faculty of 1000 evaluation for Effects of size and temperature on metabolic rate. 10.3410/f.1000605.22656

Faculty of 1000 evaluation for A phylogenomic approach to microbial evolution. 10.3410/f.1002748.29817

Faculty of 1000 evaluation for Mechanisms of evolution in Rickettsia conorii and R. prowazekii. 10.3410/f.1001869.12356

Faculty of 1000 evaluation for Meiotic arrest and aneuploidy in MLH3-deficient mice. 10.3410/f.1007473.126658

Faculty of 1000 evaluation for Identification of a DNA nonhomologous end-joining complex in bacteria. 10.3410/f.1009303.126013

Faculty of 1000 evaluation for The methionine salvage pathway in Bacillus subtilis. 10.3410/f.1006835.87156

Faculty of 1000 evaluation for Preserving genome integrity: the DdrA protein of Deinococcus radiodurans R1. 10.3410/f.1019802.241540

Faculty of 1000 evaluation for Symbiosis insights through metagenomic analysis of a microbial consortium. 10.3410/f.1044103.494012

Faculty of 1000 evaluation for Biochemical and molecular characterisation of Tetrahymena thermophila extracellular cysteine proteases. 10.3410/f.1031536.368723

Faculty of 1000 evaluation for Metagenomic DNA fragments that affect Escherichia coli mutational pathways. 10.3410/f.1013506.387929

Faculty of 1000 evaluation for Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. 10.3410/f.1032609.374723

Faculty of 1000 evaluation for Automated protein subfamily identification and classification. 10.3410/f.1091125.550038

Towards Automated Phylogenomic Inference 10.1002/9781118010518.ch25

Microbial resistance to disinfectants in animal shelters 10.15363/thinklab.3

Evolution. By Nicholas H. Barton, Derek E. G. Briggs, Jonathan A. Eisen, David Goldstein, and Nipam H. Patel .:Evolution 10.1086/590583

Genetic and physical mapping of DNA replication origins in Haloferax volcanii 10.1371/journal.pgen.0030077.eor

Faculty of 1000 evaluation for Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer. 10.3410/f.1033431.388937

Faculty of 1000 evaluation for Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. 10.3410/f.1021654.247673

Faculty of 1000 evaluation for The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. 10.3410/f.1122941.580852

Growth of 48 built environment bacterial isolates on board the International Space Station (ISS) 10.7717/peerj.1842

Draft genome sequences of two Pseudoalteromonas porphyrae strains isolated from seagrass sediment 10.1128/genomeA.00092-16

Draft genome sequence of Cobetia sp. UCD-24C, isolated from roots and leaves of the seagrass Zostera marina 10.1128/genomeA.00116-16

Draft genome sequences of two Pseudoalteromonas strains isolated from roots and leaf blades of the seagrass Zostera marina 10.1128/genomeA.00010-16

Draft genome sequences of two Vibrio splendidus strains, isolated from seagrass sediment 10.1128/genomeA.01769-15

Draft Genome Sequence of Klebsiella pneumoniae KGM-IMP216 Harboring blaCTX-M-15, blaDHA-1, blaTEM-1B, blaNDM-1, blaSHV-28, and blaOXA-1, Isolated from a Patient in Lebanon. 10.1128/genomeA.01632-15

Draft genome sequences of Acinetobacter baumannii strains harboring the blaNDM-1 gene isolated in Lebanon from civilians wounded during the Syrian civil war 10.1128/genomeA.01678-15

Additional draft genome sequences of Escherichia coli strains isolated from septic patients 10.1128/genomeA.01614-15

Transcriptomes of post-mitotic neurons identify the usage of alternative pathways during adult and embryonic neuronal differentiation. 10.1186/s12864-015-2215-8

Draft genome sequence of Bacillus vietnamensis strain UCD-SED5 (Phylum Firmicutes) 10.1128/genomeA.01376-15

Draft genome sequence of Bacillus safensis JPL-MERTA-8-2, isolated from a Mars-Bound Spacecraft 10.1128/genomeA.01360-15

Draft genome sequence of Porphyrobacter mercurialis (sp. nov.) strain Coronado 10.1128/genomeA.00856-15

Microbial mat communities along an oxygen gradient in a perennially ice-covered Antarctic lake 10.1128/AEM.02699-15

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes 10.1371/journal.pcbi.1004573

Comparative genomics of the genus porphyromonas identifies adaptations for heme synthesis within the prevalent canine oral species porphyromonas cangingivalis 10.1093/gbe/evv220

Porphyrobacter mercurialis sp. nov., isolated froma stadium seat and emended description of the genus Porphyrobacter 10.7717/peerj.1400

Draft genome sequence of Pseudoalteromonas tetraodonis strain UCD-SED8 (Phylum Gammaproteobacteria) 10.1128/genomeA.01276-15

Accounting for alignment uncertainty in phylogenomics 10.1371/journal.pone.0030288

Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA(T)) from a deep-sea hydrothermal vent. 10.4056/sigs.2465574

Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T)). 10.4056/sigs.2344929

Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21). 10.4056/sigs.2114901

Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262). 10.4056/sigs.2124912

Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. 10.4056/sigs.2144922

Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10). 10.4056/sigs.2235024

Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113). 10.4056/sigs.2154937

Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20). 10.4056/sigs.2164949

Bacterial communities of diverse Drosophila species: Ecological context of a host-microbe model system 10.1371/journal.pgen.1002272

Phosphate transporters in marine phytoplankton and their viruses: Cross-domain commonalities in viral-host gene exchanges 10.1111/j.1462-2920.2011.02576.x

The phylogenetic diversity of metagenomes 10.1371/journal.pone.0023214

Mauve assembly metrics 10.1093/bioinformatics/btr451

Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1). 10.4056/sigs.1844518

Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A). 10.4056/sigs.2014648

Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL). 10.4056/sigs.1824509

Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2). 10.4056/sigs.2064705

Complete genome sequence of Tsukamurella paurometabola type strain (no. 33). 10.4056/sigs.1894556

Complete genome sequence of Mahella australiensis type strain (50-1 BON). 10.4056/sigs.1864526

Complete genome sequence of Treponema succinifaciens type strain (6091). 10.4056/sigs.1984594

Complete genome sequence of Haliscomenobacter hydrossis type strain (O). 10.4056/sigs.1964579

Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)). 10.4056/sigs.1814460

Complete genome sequence of Deinococcus maricopensis type strain (LB-34). 10.4056/sigs.1633949

Drivers of bacterial β-diversity depend on spatial scale 10.1073/pnas.1016308108

Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6). 10.4056/sigs.1463589

Complete genome sequence of Bacteroides salanitronis type strain (BL78). 10.4056/sigs.1704212

Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139). 10.4056/sigs.1784330

Complete genome sequence of Odoribacter splanchnicus type strain (1651/6). 10.4056/sigs.1714269

Complete genome sequence of Oceanithermus profundus type strain (506). 10.4056/sigs.1734292

Complete genome sequence of Marivirga tractuosa type strain (H-43). 10.4056/sigs.1623941

Complete genome sequence of Desulfurococcus mucosus type strain (O7/1). 10.4056/sigs.1644004

Stalking the fourth domain in metagenomic data: Searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees 10.1371/journal.pone.0018011

Complete genome sequence of Leadbetterella byssophila type strain (4M15). 10.4056/sigs.1413518

Complete genome sequence of Truepera radiovictrix type strain (RQ-24). 10.4056/sigs.1563919

Complete genome sequence of Weeksella virosa type strain (9751). 10.4056/sigs.1603927

Complete genome sequence of Cellulophaga algicola type strain (IC166). 10.4056/sigs.1543845

Complete genome sequence of Bacteroides helcogenes type strain (P 36-108). 10.4056/sigs.1513795

Complete genome sequence of Isosphaera pallida type strain (IS1B). 10.4056/sigs.1533840

Complete genome sequence of Paludibacter propionicigenes type strain (WB4). 10.4056/sigs.1503846

Complete genome sequence of Thermomonospora curvata type strain (B9). 10.4056/sigs.1453580

Complete genome sequence of Desulfobulbus propionicus type strain (1pr3). 10.4056/sigs.1613929

Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1). 10.4056/sigs.1523807

PhyLOTU: A high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data 10.1371/journal.pcbi.1001061

The genome sequence of methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the methanosarcinaceae inhabiting freshwater and saline environments 10.1155/2010/690737

Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1). 10.4056/sigs.1273360

Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1). 10.4056/sigs.1233249

Complete genome sequence of Thermaerobacter marianensis type strain (7p75a). 10.4056/sigs.1373474

Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509). 10.4056/sigs.1363462

Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3). 10.4056/sigs.1253298

Complete genome sequence of Methanothermus fervidus type strain (V24S). 10.4056/sigs.1283367

Complete genome sequence of Desulfarculus baarsii type strain (2st14). 10.4056/sigs.1243258

Complete genome sequence of Intrasporangium calvum type strain (7 KIP). 10.4056/sigs.1263355

Complete genome sequence of Ferrimonas balearica type strain (PAT). 10.4056/sigs.1161239

Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1). 10.4056/sigs.1153107

Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847). 10.4056/sigs.1183143

Complete genome sequence of Sulfurimonas autotrophica type strain (OK10). 10.4056/sigs.1173118

Complete genome sequence of Candidatus Ruthia magnifica 10.4056/sigs.1103048

Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228). 10.4056/sigs.1143106

Complete genome sequence of Arcanobacterium haemolyticum type strain (11018). 10.4056/sigs.1123072

Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P). 10.4056/sigs.1133078

Complete genome sequence of Vulcanisaeta distributa type strain (IC-017). 10.4056/sigs.1113067

Complete genome sequence of Olsenella uli type strain (VPI D76D-27C). 10.4056/sigs.1082860

Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288). 10.4056/sigs.1062906

Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1). 10.4056/sigs.1072907

Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207). 10.4056/sigs.1092865

Complete genome sequence of Meiothermus ruber type strain (21). 10.4056/sigs.1032748

Complete genome sequence of Planctomyces limnophilus type strain (Mu 290). 10.4056/sigs.1052813

Complete genome sequence of Cellulomonas flavigena type strain (134). 10.4056/sigs.1012662

Complete genome sequence of Acidaminococcus fermentans type strain (VR4). 10.4056/sigs.1002553

Complete genome sequence of Meiothermus silvanus type strain (VI-R2). 10.4056/sigs.1042812

Erratum to: Complete genome sequence of Atopobium parvulum type strain (IPP 1246). 10.4056/sigs.992408

Complete genome sequence of Arcobacter nitrofigilis type strain (CI). 10.4056/sigs.912121

Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24). 10.4056/sigs.952166

Complete genome sequence of Brachyspira murdochii type strain (56-150). 10.4056/sigs.831993

Complete genome sequence of Aminobacterium colombiense type strain (ALA-1). 10.4056/sigs.902116

Complete genome sequence of Thermosphaera aggregans type strain (M11TL). 10.4056/sigs.821804

Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460). 10.4056/sigs.892105

Complete genome sequence of Archaeoglobus profundus type strain (AV18). 10.4056/sigs.942153

Complete genome sequence of Thermobispora bispora type strain (R51). 10.4056/sigs.962171

Introducing W.A.T.E.R.S.: A Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences 10.1186/1471-2105-11-317

Metagenomic sequencing of an in vitro-simulated microbial community 10.1371/journal.pone.0010209

Biotorrents: A file sharing service for scientific data 10.1371/journal.pone.0010071

Complete genome sequence of Segniliparus rotundus type strain (CDC 1076). 10.4056/sigs.791633

Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300). 10.4056/sigs.811799

Complete genome sequence of Conexibacter woesei type strain (ID131577). 10.4056/sigs.751339

Complete genome sequence of Kribbella flavida type strain (IFO 14399). 10.4056/sigs.731321

Complete genome sequence of Thermocrinis albus type strain (HI 11/12). 10.4056/sigs.761490

Complete genome sequence of Spirosoma linguale type strain (1). 10.4056/sigs.741334

Complete genome sequence of Nakamurella multipartita type strain (Y-104). 10.4056/sigs.721316

Complete genome sequence of Geodermatophilus obscurus type strain (G-20). 10.4056/sigs.711311

Complete genome sequence of Sulfurospirillum deleyianum type strain (5175). 10.4056/sigs.671209

Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034). 10.4056/sigs.661199

Complete genome sequence of Haloterrigena turkmenica type strain (4k). 10.4056/sigs.681272

Complete genome sequence of Veillonella parvula type strain (Te3). 10.4056/sigs.521107

Complete genome sequence of Gordonia bronchialis type strain (3410). 10.4056/sigs.611106

Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)). 10.4056/sigs.581048

Complete genome sequence of Streptosporangium roseum type strain (NI 9100). 10.4056/sigs.631049

Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA). 10.4056/sigs.591104

Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07). 10.4056/sigs.571102

Complete genome sequence of Haliangium ochraceum type strain (SMP-2). 10.4056/sigs.69.1277

Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). 10.4056/sigs.601105

Complete genome sequence of Pirellula staleyi type strain (ATCC 27377). 10.4056/sigs.51657

Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21). 10.4056/sigs.47643

Complete genome sequence of Streptobacillus moniliformis type strain (9901). 10.4056/sigs.48727

Complete genome sequence of Rhodothermus marinus type strain (R-10). 10.4056/sigs.46736

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea 10.1038/nature08656

Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883). 10.4056/sigs.40645

Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134). 10.4056/sigs.41646

Complete genome sequence of Kangiella koreensis type strain (SW-125). 10.4056/sigs.36635

Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1). 10.4056/sigs.37633

Complete genome sequence of Halomicrobium mukohataei type strain (arg-2). 10.4056/sigs.42644

Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575). 10.4056/sigs.39508

Complete genome sequence of Halorhabdus utahensis type strain (AX-2). 10.4056/sigs.31864

Genomics of emerging infectious disease: A PLoS collection 10.1371/journal.pbio.1000224

Complete genome sequence of Sanguibacter keddieii type strain (ST-74). 10.4056/sigs.16197

Complete genome sequence of Dyadobacter fermentans type strain (NS114). 10.4056/sigs.19262

Complete genome sequence of Saccharomonospora viridis type strain (P101). 10.4056/sigs.20263

Complete genome sequence of Catenulispora acidiphila type strain (ID 139908). 10.4056/sigs.17259

Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b). 10.4056/sigs.1854

Complete genome sequence of Anaerococcus prevotii type strain (PC1). 10.4056/sigs.24194

Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845). 10.4056/sigs.15195

Complete genome sequence of Cryptobacterium curtum type strain (12-3). 10.4056/sigs.12260

Complete genome sequence of Atopobium parvulum type strain (IPP 1246). 10.4056/sigs.29547

Human gut microbiome adopts an alternative state following small bowel transplantation 10.1073/pnas.0904847106

Complete genome sequence of Desulfomicrobium baculatum type strain (X). 10.4056/sigs.13134

Complete genome sequence of Kytococcus sedentarius type strain (541). 10.4056/sigs.761

Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10). 10.4056/sigs.492

Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122). 10.4056/sigs.1162

Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICP). 10.4056/sigs.1463

Complete genome sequence of Actinosynnema mirum type strain (101). 10.4056/sigs.21137

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3). 10.4056/sigs.22138

The complete genome of Teredinibacter turnerae T7901: An intracellular endosymbiont of marine wood-boring bivalves (shipworms) 10.1371/journal.pone.0006085

Assembling the marine metagenome, one cell at a time 10.1371/journal.pone.0005299

Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola 10.1371/journal.pgen.1000362

Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum 10.1371/journal.pone.0004207

Acidithiobacillus ferrooxidans metabolism: From genome sequence to industrial applications 10.1186/1471-2164-9-597

Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure 10.1186/1471-2164-9-562

A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans 10.1186/gb-2008-9-11-r158

A simple, fast, and accurate method of phylogenomic inference 10.1186/gb-2008-9-10-r151

An automated phylogenetic tree-based Small subunit rRNA Taxonomy and Alignment Pipeline (STAP) 10.1371/journal.pone.0002566

Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. 10.1128/AEM.01577-07

On the taxonomic status of the intracellular bacterium Wolbachia pipientis: should this species name include the intracellular bacteria of filarial nematodes? 10.1099/ijs.0.65248-0

Identification of a fourth family of lycopene cyclases in photosynthetic bacteria 10.1073/pnas.0702984104

Genetic and physical mapping of DNA replication origins in Haloferax volcanii 10.1371/journal.pgen.0030077

Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes 10.1371/journal.pbio.0050082

The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific 10.1371/journal.pbio.0050077

The Sorcerer II global ocean sampling expedition: Expanding the universe of protein families 10.1371/journal.pbio.0050016

The Calyptogena magnifica chemoautotrophic symbiont genome 10.1126/science.1138438

Evolution of sensory complexity recorded in a myxobacterial genome 10.1073/pnas.0607335103

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote 10.1371/journal.pbio.0040286

Use of HAPPY mapping for the higher order assembly of the Tetrahymena genome 10.1016/j.ygeno.2006.05.002

Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. 10.1371/journal.pbio.0040188

Comparative genomics of emerging human ehrlichiosis agents 10.1371/journal.pgen.0020021

Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts 10.1128/AEM.72.2.1680-1683.2006

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information about a Phylogenetic Analysis (MIAPA) 10.1089/omi.2006.10.231

Life in hot carbon monoxide: The complete genome sequence of carboxydothermus hydrogenoformans Z-2901 10.1371/journal.pgen.0010065

Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella 10.1073/pnas.0501424102

Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: Implications for the taxonomy of the orders 'Rhodobacterales' and Caulobacterales 10.1099/ijs.0.63510-0

Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes 10.1126/science.1102226

Genomic insights into methanotrophy: The complete genome sequence of Methylococcus capsulatus (Bath) 10.1371/journal.pbio.0020303

Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance 10.1534/genetics.104.029249

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough 10.1038/nbt959

Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes 10.1073/pnas.0307639101

Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: A streamlined genome overrun by mobile genetic elements 10.1371/journal.pbio.0020069

Environmental Genome Shotgun Sequencing of the Sargasso Sea 10.1126/science.1093857

Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments 10.1126/science.1088727

Complete genome sequence of the oral pathogenic bacterium Porphyromonas gingivalis strain W83 10.1128/JB.185.18.5591-5601.2003

Complete genome sequence of the broad-host-range vibriophage KVP40: Comparative genomics of a T4-related bacteriophage 10.1128/JB.185.17.5220-5233.2003

Modeling bacterial evolution with comparative-genome-based marker systems: Application to Mycobacterium tuberculosis evolution and pathogenesis 10.1128/JB.185.11.3392-3399.2003

Phylogenomics: Intersection of evolution and genomics 10.1126/science.1086292

The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria 10.1038/nature01586

Complete genome sequence of the Q-fever pathogen Coxiella burnetii 10.1073/pnas.0931379100

Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis 10.1126/science.1080613

The value of complete microbial genome sequencing (you get what you pay for) 10.1128/JB.184.23.6403-6405.2002

Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 10.1046/j.1462-2920.2002.00366.x

Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis 10.1038/nbt749

Genome sequence of the human malaria parasite Plasmodium falciparum 10.1038/nature01097

Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains 10.1128/JB.184.19.5479-5490.2002

The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts 10.1073/pnas.192319099

Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae 10.1073/pnas.182380799

The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium 10.1073/pnas.132181499

Phylogenetic Analysis and Gene Functional Predictions: Phylogenomics in Action 10.1006/tpbi.2002.1594

A cut above: Discovery of an alternative excision repair pathway in bacteria 10.1073/pnas.062062599

Unsuspected diversity among marine aerobic anoxygenic phototrophs 10.1038/415630a

The genome of the natural genetic engineer Agrobacterium tumefaciens C58 10.1126/science.1066804

Complete genome sequence of a virulent isolate of Streptococcus pneumoniae 10.1126/science.1061217

Microbial genes in the human genome: lateral transfer or gene loss? 10.1126/science.1061036

Sequence and analysis of the Arabidopsis genome 10.1016/S1369-5266(00)00144-8

Complete genome sequence of Caulobacter crescentus 10.1073/pnas.061029298

Gastrogenomics 10.1038/35054158

Genome of Thermotoga maritima MSB8 10.1016/S0076-6879(01)30374-9

Genomic perspective on the photobiology of Halobacterium species NRC-1, a phototrophic, phototactic, and UV-tolerant haloarchaeon 10.1023/A:1013879706863

Horizontal gene transfer among microbial genomes: New insights from complete genome analysis 10.1016/S0959-437X(00)00143-X

Assessing evolutionary relationships among microbes from whole-genome analysis 10.1016/S1369-5274(00)00125-9

Genome data: what do we learn? 10.1016/S0959-440X(00)00094-4

Microbial genome sequencing 2000: New insights into physiology, evolution and expression analysis 10.1016/S0923-2508(00)00125-X

A phylogenomic study of DNA repair genes, proteins, and processes 10.1016/S0921-8777(99)00050-6

Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1 10.1126/science.286.5444.1571

Going to extremes 10.1016/S0168-9525(99)01739-4

Erratum: Comparative genomics of emerging human ehrlichiosis agents (Plos Genetics 2,2 DOI: 10.1371/journal.pgen.0020021) 10.1371/journal.pgen.0020213

Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima 10.1038/20601

In silico-initiated cloning and molecular characterization of a novel human member of the L1 gene family of neural cell adhesion molecules 10.1007/s004390050829

A phylogenomic study of the MutS family of proteins 10.1093/nar/26.18.4291

Second gene for gonadotropin-releasing hormone in humans 10.1073/pnas.95.1.305

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource 10.1186/1471-2105-13-264

Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization 10.1371/journal.pone.0043866

An Integrated Pipeline for de Novo Assembly of Microbial Genomes 10.1371/journal.pone.0042304

Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux 10.1371/journal.pone.0041389

Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)). 10.4056/sigs.2736042

Microbedb: A locally maintainable database of microbial genomic sequences 10.1093/bioinformatics/bts273

Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)). 10.4056/sigs.2726028

Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)). 10.4056/sigs.2475579

Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T)). 10.4056/sigs.2665915

Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)). 10.4056/sigs.2786069

Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1(T)), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. 10.4056/sigs.2796069

Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1) 10.4056/sigs.2816096

Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)). 10.4056/sigs.2746047

Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T)). 10.4056/sigs.2756060

Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T)). 10.4056/sigs.2456004

Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney. 10.4056/sigs.2435521

Aggregating, tagging and integrating biodiversity research 10.1371/journal.pone.0019491

Gene synteny and evolution of genome architecture in trypanosomatids 10.1016/j.molbiopara.2003.11.012

Sequencing and analysis of a 63 kb bacterial artificial chromosome insert from the Wolbachia endosymbiont of the human filarial parasite Brugia malayi 10.1016/S0020-7519(01)00367-8

Comparative genomics and understanding of microbial biology 10.3201/eid0605.000510

Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. 10.1093/nar/28.6.1397

Play up your lab’s leadership in open science! 10.15363/thinklab.d3

Jonathan Eisen and the GEBA project - video linked to news release re Dec. 2009 Nature paper 10.4016/15185.03

ThinkLab as a vetting system for traditional grants 10.15363/thinklab.d58

Faculty of 1000 evaluation for An RNA ligase from Deinococcus radiodurans. 10.3410/f.1020920.239539

Faculty of 1000 evaluation for Microbial ecology of four coral atolls in the Northern Line Islands. 10.3410/f.1102259.580849

Faculty of 1000 evaluation for Microbial diversity in the deep sea and the underexplored "rare biosphere". 10.3410/f.1033627.388857

Microbial resistance to disinfectants in animal shelters 10.15363/thinklab.a4

CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads 10.1007/978-3-540-78839-3_3

Faculty of 1000 evaluation for Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. 10.3410/f.1095049.550037

Automated and accurate estimation of gene family abundance from shotgun metagenomes 10.1101/022335

Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes 10.1002/9781118010518.ch20

Faculty of 1000 evaluation for The bacterial catalase from filarial DNA preparations derives from common pseudomonad contaminants and not from Wolbachia endosymbionts. 10.3410/f.1020939.239546

Faculty of 1000 evaluation for Genetic manipulation of carotenoid biosynthesis in the green sulfur bacterium Chlorobium tepidum. 10.3410/f.1020534.235456

Faculty of 1000 evaluation for Convergent evolution of MutS and topoisomerase II for clamping DNA crossovers and stacked Holliday junctions. 10.3410/f.1002683.29819

Faculty of 1000 evaluation for Trends between gene content and genome size in prokaryotic species with larger genomes. 10.3410/f.1017565.204289

Faculty of 1000 evaluation for A simple algorithm to infer gene duplication and speciation events on a gene tree. 10.3410/f.1001991.22655

Faculty of 1000 evaluation for Nine mutants of Chlorobium tepidum each unable to synthesize a different chlorosome protein still assemble functional chlorosomes. 10.3410/f.1017166.202315

Faculty of 1000 evaluation for Textpresso: an ontology-based information retrieval and extraction system for biological literature. 10.3410/f.1022775.262636

Faculty of 1000 evaluation for Convergent evolution of chromosomal sex-determining regions in the animal and fungal kingdoms. 10.3410/f.1022776.261681

Faculty of 1000 evaluation for Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. 10.3410/f.1009412.126011

Faculty of 1000 evaluation for Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. 10.3410/f.1009441.126659

Faculty of 1000 evaluation for Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. 10.3410/f.1009411.126010

Faculty of 1000 evaluation for The role of endosymbiotic Wolbachia bacteria in the pathogenesis of river blindness. 10.3410/f.1004975.70505

Faculty of 1000 evaluation for Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. 10.3410/f.1006834.87155

Faculty of 1000 evaluation for Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. 10.3410/f.1029248.375054

Faculty of 1000 evaluation for Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchers. 10.3410/f.1024493.289717

Faculty of 1000 evaluation for The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. 10.3410/f.1025440.298961

Faculty of 1000 evaluation for Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere. 10.3410/f.1027749.334927

Faculty of 1000 evaluation for Distribution, expression, and motif variability of ankyrin domain genes in Wolbachia pipientis. 10.3410/f.1027992.335903

Faculty of 1000 evaluation for A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. 10.3410/f.1033630.387855

Faculty of 1000 evaluation for The uvrA, uvrB and uvrC genes are required for repair of ultraviolet light induced DNA photoproducts in Halobacterium sp. NRC-1. 10.3410/f.1044118.494030

Faculty of 1000 evaluation for UniFrac--an online tool for comparing microbial community diversity in a phylogenetic context. 10.3410/f.1046138.496053

Correction: An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP) 10.1371/annotation/c1aa88dd-4360-4902-8599-4d7edca79817

Erratum to “Comparative studies of resistin expression and phylogenomics in human and mouse” [Biochem. Biophys. Res. Commun. 310 (2003) 927–935] 10.1016/j.bbrc.2003.11.001

A science renga 10.1038/31091

Faculty of 1000 evaluation for High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae. 10.3410/f.1044120.494032

Microbiology of the Built Environment (via microBEnet) 10.6084/M9.FIGSHARE.C.2861203.V2

Microbiology of the Built Environment (via microBEnet) 10.6084/M9.FIGSHARE.C.2861203

Rhesus Gastric Microbiome 10.6084/M9.FIGSHARE.153835.V2

Rhesus Gastric Microbiome 10.6084/M9.FIGSHARE.153835.V3

Rhesus Gastric Microbiome 10.6084/M9.FIGSHARE.153835.V1

Compost Bin 10.6084/M9.FIGSHARE.97425.V1

Evolution of DNA repair genes, proteins and processes 10.6084/M9.FIGSHARE.91470.V1

Shotgun sequencing and assembly of the genome of Geospiza magnirostris – one of the Darwin’s finches 10.6084/M9.FIGSHARE.94516.V1

Phylogenomic based functional prediction 10.6084/M9.FIGSHARE.95620.V1

Phylogenomics (prediction of function using phylogenetic trees) 10.6084/M9.FIGSHARE.94061.V1

Eisen et al. 2000 X-files 10.6084/M9.FIGSHARE.94047.V1

Raw reads from genome sequencing of Leucobacter sp. str. UCD-THU 10.6084/M9.FIGSHARE.201772.V1

Compost Bin 10.6084/M9.FIGSHARE.97425

Shotgun sequencing and assembly of the genome of Geospiza magnirostris – one of the Darwin’s finches 10.6084/M9.FIGSHARE.94516

Phylogenomic based functional prediction 10.6084/M9.FIGSHARE.95620

24 Single Gene Alignments for Bacteria and Archaea 10.6084/M9.FIGSHARE.156111

Concatenated alignment of 24 genes for bacteria and archaea 10.6084/M9.FIGSHARE.156059

24 Single Gene Alignments for Bacteria 10.6084/M9.FIGSHARE.156085

Raw Illumina reads from genomic sequencing of Microbacterium sp. str. UCD-TDU 10.6084/M9.FIGSHARE.157179

Evolution of DNA repair genes, proteins and processes 10.6084/M9.FIGSHARE.91470

Eisen et al. 1995. SNF2 Evolution datasets 10.6084/M9.FIGSHARE.157190

Raw reads from Kocuria sp. str. UCD-OTCP genome sequencing project 10.6084/M9.FIGSHARE.157191

Phylogenomics (prediction of function using phylogenetic trees) 10.6084/M9.FIGSHARE.94061

Eisen et al. 2000 X-files 10.6084/M9.FIGSHARE.94047

24 Single Gene Alignments for Bacteria 10.6084/M9.FIGSHARE.156085.V1

Raw Illumina reads from genomic sequencing of Microbacterium sp. str. UCD-TDU 10.6084/M9.FIGSHARE.157179.V2

Raw Illumina reads for Microbacterium sp. str. UCD-TDU 10.6084/M9.FIGSHARE.157179.V1

Raw reads from Kocuria sp. str. UCD-OTCP genome sequencing project 10.6084/M9.FIGSHARE.157191.V1

Raw reads from genome sequencing of Leucobacter sp. str. UCD-THU 10.6084/M9.FIGSHARE.201772

24 Single Gene Alignments for Bacteria and Archaea 10.6084/M9.FIGSHARE.156111.V1

Concatenated alignment of 24 genes for bacteria and archaea 10.6084/M9.FIGSHARE.156059.V1

Eisen et al. 1995. SNF2 Evolution datasets 10.6084/M9.FIGSHARE.157190.V1

Bacterial Communities of Diverse Drosophila Species: Ecological context of a host-microbe system 10.6084/M9.FIGSHARE.106988.V1

Proteomes of genomes used in GEBA paper 10.6084/M9.FIGSHARE.106789.V1

Sequence alignment for GEBA paper 10.6084/M9.FIGSHARE.106807.V1

Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts 10.6084/M9.FIGSHARE.107011.V1

Eisen 1995 RecA Evolution 10.6084/M9.FIGSHARE.107065.V1

Treefile for GEBA paper 10.6084/M9.FIGSHARE.106806.V1

Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations ofShigella sonneiWith Increased Virulence or Fluoroquinolone Resistance 10.1101/063818

Card from Emile Zuckerkandl noting acceptance of paper 10.6084/M9.FIGSHARE.4568251.V1

Card from Emile Zuckerkandl noting acceptance of paper 10.6084/M9.FIGSHARE.4568251

My recent Twitter Analytics reports (especially for UC Davis communications group) 10.6084/M9.FIGSHARE.3205891.V1

My recent Twitter Analytics reports (especially for UC Davis communications group) 10.6084/M9.FIGSHARE.3205891

Thesis Proposal Draft June 2, 1993 10.6084/M9.FIGSHARE.3490127

Thesis Proposal Update 10.6084/M9.FIGSHARE.3490130

Communications with Journal of Bacteriology 10.6084/M9.FIGSHARE.3490136

Predicted secondary structure of Solemya velum symbiont 16S 10.6084/M9.FIGSHARE.3490142

Miscellaneous Notes for Project 10.6084/M9.FIGSHARE.3490145

Partial Lab Notebook 10.6084/M9.FIGSHARE.3490148

Cover letter 10.6084/M9.FIGSHARE.3496802

RecA and rRNA alignments used for Eisen JME 1995 10.6084/M9.FIGSHARE.3496808

RecA and rRNA trees for Eisen 1995 JME 10.6084/M9.FIGSHARE.3496811

Figures from this paper in higher resolution and (for some) in color 10.6084/M9.FIGSHARE.3496814

Gordonia tree.pdf 10.6084/M9.FIGSHARE.3466295

Proteomes of genomes used in GEBA paper 10.6084/M9.FIGSHARE.106789

Sequence alignment for GEBA paper 10.6084/M9.FIGSHARE.106807

Treefile for GEBA paper 10.6084/M9.FIGSHARE.106806

Bacterial Communities of Diverse Drosophila Species: Ecological context of a host-microbe system 10.6084/M9.FIGSHARE.106988

Yeast Communities of Diverse Drosophila Species: Comparison of Two Symbiont Groups in the Same Hosts 10.6084/M9.FIGSHARE.107011

Eisen 1995 RecA Evolution 10.6084/M9.FIGSHARE.107065

Rhesus Gastric Microbiome 10.6084/M9.FIGSHARE.153835

Data from: Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in phylogenetic trees of phylogenetic marker genes 10.5061/DRYAD.8384

Microbiome succession during ammonification in eelgrass bed sediments 10.7287/PEERJ.PREPRINTS.2956V1

Microbiome succession during ammonification in eelgrass bed sediments 10.7287/PEERJ.PREPRINTS.2956

Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota 10.7287/peerj.preprints.26912v1

Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota 10.7287/peerj.preprints.26912

American Gut: an Open Platform for Citizen Science Microbiome Research. 10.1128/msystems.00031-18

Rokubacteria: Genomic giants among the uncultured bacterial phyla 10.3389/fmicb.2017.02264

Alignment for tree of life 10.6084/M9.FIGSHARE.6916298

Metagenome-assembled genomes (MAG's) from two thermal pools in Uzon Caldera, Kamchatka, Russia 10.25338/B8N01R

Evolution of the RecA Protein: from systematics to structure 10.6084/M9.FIGSHARE.701523

The Seagrass Microbiome 10.6084/M9.FIGSHARE.1014334

rRNA gene sequence data and scripts used for PLOS Biology submission "Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota" 10.6084/M9.FIGSHARE.4789759

Genomes in the tree of life of Hug et al. (2016) - part I 10.6084/M9.FIGSHARE.6863594

Genomes in the tree of life of Hug et al. (2016) - part II 10.6084/M9.FIGSHARE.6863744

Genomes from Burgess et al. (2012) from two hot springs in Kamchatka, Russia 10.6084/M9.FIGSHARE.6863798

Genomes in the tree of life of Hug et al. (2016) - manually downloaded 10.6084/M9.FIGSHARE.6863813

Tree of life - archaea and bacteria from Hug et al.'s tree of life in 2016; MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia; and all taxa from Burgess et al. (2012) with one representative genome on NCBI (.tre file) 10.6084/M9.FIGSHARE.6874928

Table with taxa we used for the tree of life - archaea and bacteria from Hug et al.'s tree of life in 2016; MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia; and all taxa from Burgess et al. (2012) with one representative genome on NCBI. 10.6084/M9.FIGSHARE.6874934

There and back again: metagenome-assembled genomes provide new insights into two thermal pools in Kamchatka, Russia 10.1101/392308

microBEnet:  Perspectives on trying to nurture a growing MoBE field 10.6084/m9.figshare.5533540.v1

Detecting Natural Versus Unnatural DNA 10.21236/ada482115

Shotgun Sequencing of Plasmids from Marine Sediment Bacteria - Genetic Exploration 10.21236/ada398735

Gut Check: The evolution of an educational board game 10.1371/journal.pbio.2001984

Microbiome succession during ammonification in eelgrass bed sediments 10.7717/peerj.3674

Draft Genome Sequence of Arthrobacter sp. Strain UCD-GKA (Phylum Actinobacteria ) 10.1128/genomea.01599-16

Root hair-endophyte stacking (RHESt) in an ancient Afro-Indian crop creates an unusual physico-chemical barrier to trap pathogen(s) 10.1101/071548

Growth of 48 built environment bacterial isolates on board the International Space Station (ISS) 10.7287/peerj.preprints.1654

Growth of 48 built environment bacterial isolates on board the International Space Station (ISS) 10.7287/peerj.preprints.1654v1

PHYLOGENETIC DIVERSITY OF THE MICROBIAL MATS IN LAKE FRYXELL, ANTARCTICA 10.1130/abs/2016am-287206

Genome Analysis of Streptococcus pyogenes Associated with Pharyngitis and Skin Infections 10.1371/journal.pone.0168177

Draft Genome Sequence of Gordonia sp. Strain UCD-TK1 (Phylum Actinobacteria ) 10.1128/genomea.01121-16

Draft Genome Sequence of Tenacibaculum soleae UCD-KL19 10.1128/genomea.01120-16

Draft Genome Sequence of Klebsiella pneumoniae UCD-JA29 Isolated from a Patient with Sepsis 10.1128/genomea.00234-16

Root-hair endophyte stacking in finger millet creates a physicochemical barrier to trap the fungal pathogen Fusarium graminearum 10.1038/nmicrobiol.2016.167

Genes Required for the Anti-fungal Activity of a Bacterial Endophyte Isolated from a Corn Landrace Grown Continuously by Subsistence Farmers Since 1000 BC 10.3389/fmicb.2016.01548

Draft Genome Sequence of Enterococcus faecalis Strain UCD-PD3 10.1128/genomea.01386-16

Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria ) 10.1128/genomea.01040-16

Genome Sequence of a Multidrug-Resistant Strain of Bacillus pumilus , CB01, Isolated from the Feces of an American Crow, Corvus brachyrhynchos 10.1128/genomea.00807-16

A Case for Evolutionary Genomics and the Comprehensive Examination of Sequence Biodiversity 10.1093/oxfordjournals.molbev.a026278

Complete Genome Sequence of Dolosigranulum pigrum from a Patient with Interstitial Lung Disease Using Single-Molecule Real-Time Sequencing Technology 10.1128/genomea.00317-17

Complete Genome Sequence of a Paenalcaligenes hominis Strain Isolated from a Paraplegic Patient with Neurogenic Bladder Using Single-Molecule Real-Time Sequencing Technology 10.1128/genomea.00252-17

Draft Genome Sequence of Propionibacterium avidum Strain UCD-PD2 Isolated from a Feline Anal Sac 10.1128/genomea.00034-17

Global-scale structure of the eelgrass microbiome 10.1101/089797

Insights into the evolution of oxygenic photosynthesis from a phylogenetically novel, low-light cyanobacterium 10.1101/334458

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Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota 10.1371/journal.pbio.2006352

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Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. 10.1038/nbt0218-196a

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Draft genome sequences of extended-spectrum β-lactamase-producing Escherichia coli strains isolated from patients in Lebanon 10.1128/genomeA.e00123-14

Tree in Fig.2 - Archaeal and bacterial genomes used by Hug et al. in 2016 to construct a microbial tree of life; MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia; and all genomes of taxa analyzed in Burgess et al. (2012) with one representative genome on NCBI (Newick file) 10.6084/m9.figshare.6874928.v4

Sequence alignment for phylogenetic tree construction 10.6084/m9.figshare.6916298.v2

Alignment for tree of life 10.6084/m9.figshare.6916298.v1

Genomes from Burgess et al. (2012) from two hot springs in Kamchatka, Russia 10.6084/m9.figshare.6863798.v1

Genomes of taxa analyzed in Burgess et al. (2012) from two hot springs in Kamchatka, Russia 10.6084/m9.figshare.6863798.v2

Genomes used to infer a tree of life in Hug et al. (2016) - manually downloaded 10.6084/m9.figshare.6863813.v2

Genomes in the tree of life of Hug et al. (2016) - manually downloaded 10.6084/m9.figshare.6863813.v1

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Genomes used to infer a tree of life in Hug et al. (2016) II 10.6084/m9.figshare.6863744.v3

Genomes in the tree of life of Hug et al. (2016) - part I 10.6084/m9.figshare.6863594.v1

Genomes in the tree of life of Hug et al. (2016) - part II 10.6084/m9.figshare.6863744.v2

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Bacterial communities associated with cell phones and shoes 10.7287/peerj.preprints.27514

Tree of life (archaea and bacteria only) and MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia (tre file) 10.6084/m9.figshare.6874928.v1

Table with taxa we used for the tree of life - archaea and bacteria from Hug et al.'s tree of life in 2016, and MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia 10.6084/m9.figshare.6874934.v2

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The Seagrass Microbiome 10.6084/m9.figshare.1014334.v1

Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia 10.1038/s41598-019-39576-6

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Characterization of the mycobiome of the seagrass, Zostera marina, reveals putative associations with marine chytrids 10.1101/735050

Bacteria isolated from Bengal cat (Felis catus × Prionailurus bengalensis) anal sac secretions produce volatile compounds potentially associated with animal signaling 10.1371/journal.pone.0216846

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Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus 10.1371/journal.pone.0223033

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Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina 10.1371/journal.pone.0236135

The gut microbiome stability of a butterflyfish is disrupted on severely degraded Caribbean coral reefs 10.1101/2020.09.21.306712

Notes 1993 SSE Meeting 10.6084/m9.figshare.5705119

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Global diversity and biogeography of the Zostera marina mycobiome 10.1101/2020.10.29.361022

Teredinibacter haidensis sp. nov., Teredinibacter purpureus sp. nov. and Teredinibacter franksiae sp. nov., marine, cellulolytic endosymbiotic bacteria isolated from the gills of the wood-boring mollusc Bankia setacea (Bivalvia: Teredinidae) and emended description of the genus Teredinibacter 10.1099/ijsem.0.004627

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis 10.1101/2021.02.23.21252022

Global Diversity and Biogeography of the Zostera marina Mycobiome 10.1128/AEM.02795-20

Reconstruction of metagenome-assembled genomes from aquaria 10.1101/2021.05.28.446213

Reconstruction of Metagenome-Assembled Genomes from Aquaria 10.1128/MRA.00557-21

Matthew Jackson

Jackson Matthew / Matthew A Jackson / Matt Jackson

ORCID: 0000-0002-7891-6217

http://statsflowchart.co.uk

A large genomic island allows Neisseria meningitidis to utilize propionic acid, with implications for colonization of the human nasopharynx 10.1111/mmi.12664

Proton pump inhibitors alter the composition of the gut microbiota 10.1136/gutjnl-2015-310861

Signatures of early frailty in the gut microbiota 10.1186/s13073-016-0262-7

A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units 10.7717/peerj.2341

Genetic Determinants of the Gut Microbiome in UK Twins 10.1016/j.chom.2016.04.017

Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes 10.1371/journal.pgen.1006179

Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome 10.1016/j.cels.2016.10.004

Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain 10.1038/ijo.2017.66

Untangling the relationship between diet and visceral fat mass through blood metabolomics and gut microbiome profiling 10.1038/ijo.2017.70

Heritable components of the human fecal microbiome are associated with visceral fat 10.1080/19490976.2017.1356556

Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women 10.1038/s41598-017-10382-2

Hippurate as a metabolomic marker of gut microbiome diversity: Modulation by diet and relationship to metabolic syndrome 10.1038/s41598-017-13722-4

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations 10.7717/peerj.4303

Use of dietary indices to control for diet in human gut microbiota studies 10.1186/s40168-018-0455-y

The fecal metabolome as a functional readout of the gut microbiome 10.1038/s41588-018-0135-7

Gut microbiota associations with common diseases and prescription medications in a population-based cohort 10.1038/s41467-018-05184-7

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative 10.1186/s40168-018-0479-3

American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/msystems.00031-18

Heritable components of the human fecal microbiome are associated with visceral fat 10.1186/s13059-016-1052-7

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Response to: Population-Based Gut Microbiome Associations With Hypertension 10.1161/CIRCRESAHA.118.313913

Socioeconomic Status and the Gut Microbiome: A TwinsUK Cohort Study 10.3390/microorganisms7010017

An Investigation Into Physical Frailty as a Link Between the Gut Microbiome and Cognitive Health 10.3389/fnagi.2018.00398

A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units 10.7287/peerj.preprints.2115v1

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IL-1-driven stromal-neutrophil interaction in deep ulcers defines a pathotype of therapy non-responsive inflammatory bowel disease 10.1101/2021.02.05.429804

zhenjiang xu

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Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance 10.1261/rna.033431.112

Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation 10.1016/j.bbrc.2015.01.074

Structural basis for diversity in the SAM clan of riboswitches 10.1073/pnas.1312918111

Dietary effects on human gut microbiome diversity 10.1017/S0007114514004127

Subsistence strategies in traditional societies distinguish gut microbiomes 10.1038/ncomms7505

Ribosomal RNA, the lens into life 10.1261/rna.050799.115

Meta-analyses of human gut microbes associated with obesity and IBD 10.1016/j.febslet.2014.09.039

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies 10.1128/mSystems.00021-16

Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures 10.1371/journal.pone.0130200

Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota 10.1016/j.chom.2015.08.005

Microbial community assembly and metabolic function during mammalian corpse decomposition 10.1126/science.aad2646

Open-Source Sequence Clustering Methods Improve the State Of the Art 10.1128/mSystems.00003-15

Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project 10.1128/jmbe.v17i1.1034

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision 10.1038/ismej.2015.235

Microbiome-wide association studies link dynamic microbial consortia to disease 10.1038/nature18850

Secondary Structure Prediction of Single Sequences Using RNAstructure 10.1007/978-1-4939-6433-8_2

Experiment-Assisted Secondary Structure Prediction with RNAstructure 10.1007/978-1-4939-6433-8_10

Lifestyle chemistries from phones for individual profiling 10.1073/pnas.1610019113

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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns 10.1128/mSystems.00191-16

Evidence for fungal and chemodenitrification based N$_\textrm2$O flux from nitrogen impacted coastal sediments 10.1038/ncomms15595

A communal catalogue reveals Earth's multiscale microbial diversity 10.1038/nature24621

Guiding longitudinal sampling in IBD cohorts 10.1136/gutjnl-2017-315352

Prediction of Secondary Structures Conserved in Multiple RNA Sequences 10.1007/978-1-4939-6433-8_3

Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models 10.3390/genes9020104

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm 10.1038/s41467-018-04409-z

Exposure to toxic metals triggers unique responses from the rat gut microbiota 10.1038/s41598-018-24931-w

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information 10.1128/mSystems.00021-18

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction 10.1128/mSystems.00188-17

American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/mSystems.00031-18

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus) 10.1002/mbo3.716

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism 10.1038/s41467-018-05336-9

Microbiome Tools for Forensic Science 10.1016/j.tibtech.2017.03.006

Striped UniFrac: enabling microbiome analysis at unprecedented scale 10.1038/s41592-018-0187-8

Calour: an Interactive, Microbe-Centric Analysis Tool 10.1128/mSystems.00269-18

A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease 10.1038/s41467-019-09455-9

Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems 10.1128/mSystems.00058-19

Identification of new high affinity targets for Roquin based on structural conservation 10.1093/nar/gky908

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue 10.1111/1556-4029.13949

Best practices for analysing microbiomes 10.1038/s41579-018-0029-9

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 10.1038/s41587-019-0209-9

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads 10.1186/s13059-019-1834-9

Vitamin D metabolites and the gut microbiome in older men 10.1038/s41467-020-19793-8

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea 10.1038/s41467-019-13443-4

Toxicant substitutes in immunological assays for mycotoxins detection: A mini review 10.1016/j.foodchem.2020.128589

Multiple-Disease Detection and Classification across Cohorts via Microbiome Search 10.1128/mSystems.00150-20

Chlorogenic acid attenuates cadmium-induced intestinal injury in Sprague–Dawley rats 10.1016/j.fct.2019.110751

PM2RA: A Framework for Detecting and Quantifying Relationship Alterations in Microbial Community 10.1016/j.gpb.2020.07.005

Emily Pierce

Pierce Emily / Emily C. Pierce

ORCID: 0000-0002-9960-0270

Ketocarotenoid Production in Soybean Seeds through Metabolic Engineering 10.1371/journal.pone.0138196

Changes in the genetic requirements for microbial interactions with increasing community complexity 10.7554/elife.37072

BLANKA: an Algorithm for Blank Subtraction in Mass Spectrometry of Complex Biological Samples 10.1007/s13361-019-02185-8

Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness 10.1038/s41564-020-00800-z

High-throughput interaction screens illuminate the role of c-di-AMP in cyanobacterial nighttime survival 10.1371/journal.pgen.1007301

American Gut: an Open Platform for Citizen Science Microbiome Research. 10.1128/msystems.00031-18

A community resource for paired genomic and metabolomic data mining 10.1038/s41589-020-00724-z

Qiyun Zhu

Zhu Qiyun

ORCID: 0000-0002-3568-6271

Email: qiyunzhu@gmail.com

https://qiyunlab.github.io/

The origin of Chinese domestic horses revealed with novel mtDNA variants 10.1111/asj.12583

Origin of microbial biomineralization and magnetotaxis during the Archean 10.1073/pnas.1614654114

Reply to Wang and Chen: An ancient origin of magnetotactic bacteria 10.1073/pnas.1707301114

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota 10.1038/s41467-018-05284-4

Home chemical and microbial transitions across urbanization 10.1038/s41564-019-0593-4

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea 10.1038/s41467-019-13443-4

Microbiome analyses of blood and tissues suggest cancer diagnostic approach 10.1038/s41586-020-2095-1

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort 10.1101/2020.09.12.20193045

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QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data. 10.1002/cpbi.100

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. 10.1038/s41467-020-16366-7

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads. 10.1186/s13059-019-1834-9

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FXR Regulates Intestinal Cancer Stem Cell Proliferation. 10.1016/j.cell.2019.01.036

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease. 10.1128/msystems.00337-18

Calour: an Interactive, Microbe-Centric Analysis Tool. 10.1128/msystems.00269-18

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). 10.1002/mbo3.716

Evaluating the Information Content of Shallow Shotgun Metagenomics. 10.1128/msystems.00069-18

Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea. 10.1186/s40168-018-0579-0

Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. 10.3389/fmicb.2018.02559

Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis. 10.1016/j.eurpsy.2018.05.011

Are microbiome studies ready for hypothesis-driven research? 10.1016/j.mib.2018.07.002

Best practices for analysing microbiomes. 10.1038/s41579-018-0029-9

Methods for phylogenetic analysis of microbiome data. 10.1038/s41564-018-0156-0

American Gut: an Open Platform for Citizen Science Microbiome Research. 10.1128/msystems.00031-18

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. 10.1128/msystems.00218-17

Creating a 3D microbial and chemical snapshot of a human habitat. 10.1038/s41598-018-21541-4

A communal catalogue reveals Earth's multiscale microbial diversity. 10.1038/nature24621

Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species. 10.1186/s12864-016-3118-z

RNA: An Expanding View of Function and Evolution. 10.4137/ebo.s38105

On the probability of dinosaur fleas. 10.1186/s12862-015-0568-x

Fleas (Siphonaptera) are Cretaceous, and evolved with Theria. 10.1016/j.ympev.2015.04.027

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HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. 10.1186/1471-2164-15-717

Horizontal transfers and gene losses in the phospholipid pathway of bartonella reveal clues about early ecological niches. 10.1093/gbe/evu169

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. 10.1093/nar/gkr621

Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. 10.1016/j.devcel.2009.09.002

Recent duplication and positive selection of the GAGE gene family. 10.1007/s10709-007-9179-9

Rapid HLA-DR fluorotyping based on melting curve analysis. 10.1080/08820130701366425

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing 10.1038/s41592-020-01041-y

DEPP: Deep Learning Enables Extending Species Trees using Single Genes 10.1101/2021.01.22.427808

APPLES-2: Faster and More Accurate Distance-based Phylogenetic Placement using Divide and Conquer 10.1101/2021.02.14.431150

OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures 10.1101/2021.04.04.438427

Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes 10.1101/gr.275777.121

Luke Thompson

Thompson Luke

ORCID: 0000-0002-3911-1280

Tourmaline: a workflow for rapid and reproducible amplicon sequence analysis using QIIME 2 and Snakemake 10.1101/2021.09.15.460495

Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes. 10.1111/1462-2920.13684

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments 10.1111/j.1462-2920.2010.02280.x

Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts 10.1371/journal.pbio.0040234

Draft genome sequence of uncultured SAR324 bacterium lautmerah10, binned from a Red Sea metagenome 10.1128/genomeA.01711-15

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns 10.1128/mSystems.00191-16

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism 10.1073/pnas.1102164108

Microbial community assembly and metabolic function during mammalian corpse decomposition 10.1126/science.aad2646

Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments 10.1002/ece3.593

DNA Sequencing as a Tool to Monitor Marine Ecological Status 10.3389/fmars.2017.00107

A catalogue of 136 microbial draft genomes from Red Sea metagenomes 10.1038/sdata.2016.50

Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus 10.1371/journal.pone.0005135

Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages. 10.1093/molbev/msv149

Metagenomic covariation along densely sampled environmental gradients in the Red Sea doi:10.1038/ismej.2016.99

Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by Cyanophage 10.1371/journal.pone.0165375

A communal catalogue reveals Earth's multiscale microbial diversity. 10.1038/nature24621

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm 10.1038/s41467-018-04409-z

Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus 10.1038/s41396-018-0214-x

EMP DNA Extraction Protocol dx.doi.org/10.17504/protocols.io.nutdewn

EMP 16S Illumina Amplicon Protocol dx.doi.org/10.17504/protocols.io.nuudeww

EMP 18S Illumina Amplicon Protocol dx.doi.org/10.17504/protocols.io.nuvdew6

EMP ITS Illumina Amplicon Protocol dx.doi.org/10.17504/protocols.io.pa7dihn

EMP Sample Submission Guide dx.doi.org/10.17504/protocols.io.pfqdjmw

Species-level functional profiling of metagenomes and metatranscriptomes 10.1038/s41592-018-0176-y

A Novel Sparse Compositional Technique Reveals Microbial Perturbations 10.1128/mSystems.00016-19

Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes 10.1128/AEM.00369-19

Metagenomic Covariation Along Densely Sampled Environmental Gradients in the Red Sea 10.1101/055012

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 10.1038/s41587-019-0209-9

American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/msystems.00031-18

Hopanoid-producing bacteria in the Red Sea include the major marine nitrite oxidizers 10.1093/femsec/fiy063

The genome of a novel isolate of Prochlorococcus from the Red Sea contains transcribed genes for compatible solute biosynthesis 10.1093/femsec/fiy182

Best practices for analysing microbiomes 10.1038/s41579-018-0029-9

Distribution of Prochlorococcus Ecotypes in the Red Sea Basin Based on Analyses of rpoC1 Sequences 10.3389/fmars.2016.00104

Physiology and evolution of nitrate acquisition in Prochlorococcus 10.1038/ismej.2014.211

Distribution and diversity ofProchlorococcusecotypes in the Red Sea 10.1111/1574-6968.12490

Red Sea SAR11 and Prochlorococcus Single-cell Genomes Reflect Globally Distributed Pangenomes 10.1101/549816

Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies 10.1002/edn3.187

Multi-omics profiling of Earth’s biomes reveals that microbial and metabolite composition are shaped by the environment 10.1101/2021.06.04.446988

Optimizing an enclosed bead beating extraction method for microbial and fish environmental DNA 10.1002/edn3.251

Austin Swafford

Swafford Austin

ORCID: 0000-0001-5655-8300

Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis 10.4049/jimmunol.1800614

Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection 10.1084/jem.20192276

CD8 T cells drive anorexia, dysbiosis, and blooms of a commensal with immunosuppressive potential after viral infection 10.1073/pnas.2003656117

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment 10.1101/2020.05.12.20073577

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data 10.1111/biom.13481

OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures 10.1101/2021.04.04.438427

Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity. 10.1093/ibd/izaa262

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets. 10.1128/msystems.01216-20

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. 10.2144/btn-2020-0153

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. 10.1186/s40168-020-00960-4

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment 10.21203/rs.3.rs-56028/v2

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities 10.1101/2020.11.13.370387

Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk. 10.1016/j.bbi.2020.10.003

Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV. 10.1128/msystems.00528-20

EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets 10.1101/2020.10.06.327080

Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. 10.1128/msystems.00465-20

Context-aware dimensionality reduction deconvolutes gut microbial community dynamics. 10.1038/s41587-020-0660-7

Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity 10.1101/2020.08.17.238444

Reference data based insights expand understanding of human metabolomes 10.1101/2020.07.08.194159

High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy. 10.1128/msystems.00292-20

Microbiome analyses of blood and tissues suggest cancer diagnostic approach. 10.1038/s41586-020-2095-1

Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs. 10.1128/msystems.00635-19

Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults. 10.1016/j.bbi.2020.02.004

Human Skin, Oral, and Gut Microbiomes Predict Chronological Age. 10.1128/msystems.00630-19

Mass spectrometry searches using MASST. 10.1038/s41587-019-0375-9

In vivo evaluation of the CB₁ allosteric modulator LDK1258 reveals CB₁-receptor independent behavioral effects. 10.1016/j.pbb.2019.172840

Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs 10.1101/790063

Challenges in the construction of knowledge bases for human microbiome-disease associations. 10.1186/s40168-019-0742-2

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. 10.1038/s41587-019-0252-6

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. 10.1038/s41587-019-0209-9

Light-Induced Stress as a Primary Evolutionary Driver of Eye Origins 10.20944/preprints201904.0107.v2

Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. 10.1128/msystems.00261-19

MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data 10.1101/591016

Age and sex-dependent patterns of gut microbial diversity in human adults 10.1101/544270

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science 10.7287/peerj.preprints.27295v2

High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity. 10.1128/msystems.00166-18

Qiita: rapid, web-enabled microbiome meta-analysis. 10.1038/s41592-018-0141-9

Best practices for analysing microbiomes. 10.1038/s41579-018-0029-9

American Gut: an Open Platform for Citizen Science Microbiome Research. 10.1128/msystems.00031-18

American Gut: an Open Platform for Citizen-Science Microbiome Research 10.1101/277970

Impacts of the Human Gut Microbiome on Therapeutics. 10.1146/annurev-pharmtox-042017-031849

Inhibition of DYRK1A and GSK3B induces human β-cell proliferation. 10.1038/ncomms9372

Detection and correction of artefacts in estimation of rare copy number variants and analysis of rare deletions in type 1 diabetes. 10.1093/hmg/ddu581

An allele of IKZF1 (Ikaros) conferring susceptibility to childhood acute lymphoblastic leukemia protects against type 1 diabetes. 10.2337/db10-0446

Thermal ablation of tumor cells with antibody-functionalized single-walled carbon nanotubes. 10.1073/pnas.0803557105

Janet Jansson

Jansson Janet / J. K. Jansson

ORCID: 0000-0002-5487-4315

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications 10.1038/nbt.1823

The earth microbiome project: Meeting report of the "1 ^st EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 ^th 2010 10.4056/aigs.1443528

Use of Bromodeoxyuridine Immunocapture to Identify Active Bacteria Associated with Arbuscular Mycorrhizal Hyphae 10.1128/AEM.69.10.6208-6215.2003

Erratum: Long-term ecological impacts of antibiotic administration on the human intestinal microbiota (ISME Journal (2007) 1 (56-66) DOI: 10.1038/ismej.2007.3) 10.1038/ismej.2012.91

Temporal dynamics of CO2 and CH4 loss potentials in response to rapid hydrological shifts in tidal freshwater wetland soils 10.1016/j.ecoleng.2017.06.041

Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2 10.1186/1944-3277-9-19

Shotgun metaproteomics of the human distal gut microbiota 10.1038/ismej.2008.108

Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest 10.1038/ismej.2014.36

Attachment of different soil bacteria to arbuscular mycorrhizal fungal extraradical hyphae is determined by hyphal vitality and fungal species 10.1111/j.1574-6968.2005.00003.x

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill 10.1038/ismej.2013.254

A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes 10.1053/j.gastro.2010.08.049

Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies 10.3389/fmicb.2015.00447

Draft genome sequence of Paenibacillus polymyxa strain Mc5Re-14, an antagonistic root endophyte of Matricaria chamomilla 10.1128/genomeA.00861-15

Chitinase genes revealed and compared in bacterial isolates, DNA extracts and a metagenomic library from a phytopathogen-suppressive soil 10.1111/j.1574-6941.2009.00801.x

Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions 10.1093/femsec/fiw216

Diets high in resistant starch increase plasma levels of trimethylamine-N-oxide, a gut microbiome metabolite associated with CVD risk 10.1017/S0007114516004165

Effect of starvation and the viable-but-nonculturable state on green fluorescent protein (GFP) fluorescence in GFP-tagged Pseudomonas fluorescens A506 10.1128/AEM.66.8.3160-3165.2000

Unlocking the potential of metagenomics through replicated experimental design 10.1038/nbt.2235

Insights into the respiratory tract microbiota of patients with cystic fibrosis during early Pseudomonas aeruginosa colonization 10.1186/s40064-015-1207-0

Long-term ecological impacts of antibiotic administration on the human intestinal microbiota 10.1038/ismej.2007.3

Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses 10.3389/fmicb.2015.00399

Metagenomic and metatranscriptomic analyses reveal the structure and dynamics of a dechlorinating community containing Dehalococcoides mccartyi and corrinoidproviding microorganisms under cobalaminlimited conditions 10.1128/AEM.03508-16

Monitoring physiological status of GFP-tagged Pseudomonas fluorescens SBW25 under different nutrient conditions and in soil by flow cytometry 10.1016/j.femsec.2004.07.007

Molecular analysis of the gut microbiota of identical twins with Crohn's disease 10.1038/ismej.2008.37

Interactions between arbuscular mycorrhizal fungi and bacteria and their potential for stimulating plant growth 10.1111/j.1462-2920.2005.00942.x

Impact of dietary resistant starch on the human gut Microbiome, Metaproteome, and Metabolome 10.1128/mBio.01343-17

Changes in active bacterial communities before and after dredging of highly polluted Baltic Sea sediments 10.1128/AEM.00971-06

Molecular fingerprinting of the fecal microbiota of children raised according to different lifestyles 10.1128/AEM.02223-06

Luminometry and PCR-based monitoring of gene-tagged cyanobacteria in Baltic Sea microcosms 10.1016/0378-1097(95)00133-P

Adaptation of the psychrotroph Arthrobacter chlorophenolicus A6 to growth temperature and the presence of phenols by changes in the anteiso/iso ratio of branched fatty acids 10.1111/j.1574-6968.2006.00502.x

Biomarkers for monitoring efficacy of bioremediation by microbial inoculants 10.1016/S0269-7491(99)00140-2

FOAM (Functional Ontology Assignments for Metagenomes): A Hidden Markov Model (HMM) database with environmental focus 10.1093/nar/gku702

Impact of phenolic substrate and growth temperature on the Arthrobacter chlorophenolicus proteome 10.1021/pr800897c

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes 10.1038/nature14238

Combined bromodeoxyuridine immunocapture and terminal-restriction fragment length polymorphism analysis highlights differences in the active soil bacterial metagenome due to Glomus mosseae inoculation or plant species 10.1111/j.1462-2920.2005.00868.x

Community structure of actively growing bacterial populations in plant pathogen suppressive soil 10.1007/s00248-006-9120-2

Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill 10.3389/fmicb.2014.00332

Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes 10.1007/s00248-017-1028-5

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes 10.1128/mSystems.00045-16

Microbial ecology of chlorinated solvent biodegradation 10.1111/1462-2920.12413

Microbial community structure in polluted Baltic Sea sediments 10.1111/j.1462-2920.2005.00887.x

Spotlight on... Janet K. Jansson 10.1093/femsle/fnw135

The Earth Microbiome project: Successes and aspirations 10.1186/s12915-014-0069-1

Metabolomics reveals metabolic biomarkers of Crohn's disease 10.1371/journal.pone.0006386

Molecular characterization of the stomach microbiota in patients with gastric cancer and in controls 10.1099/jmm.0.007302-0

Erratum: Tackling soil diversity with the assembly of large, complex metagenomes (Proceedings of the National Academy of Sciences of the United States of America (2014) 111, 13, (4904-4909) doi:10.1073/pnas.1402564111) 10.1073/pnas.1405719111

Advances in preservation methods: Keeping biosensor microorganisms alive and active 10.1016/j.copbio.2005.12.005

The potential of metagenomic approaches for understanding soil microbial processes 10.2136/sssaj2013.07.0287dgs

Direct cellular lysis/protein extraction protocol for soil metaproteomics 10.1021/pr100787q

Arthrobacter chlorophenolicus sp. nov., a new species capable of degrading high concentrations of 4-chlorophenol 10.1099/00207713-50-6-2083

Landscape topography structures the soil microbiome in arctic polygonal tundra 10.1038/s41467-018-03089-z

Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California 10.4056/sigs.5029016

Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments 10.1007/s00248-015-0698-0

Erratum: Marker and reporter genes: Illuminating tools for environmental microbiologists (Current Opium in Microbiology (2003) 6 (310-316) PII: S1369527403000572) 10.1016/j.mib.2003.09.011

Electron transport to nitrogenase in Rhodospirillum rubrum: The role of NAD(P)H as electron donor and the effect of fluoroacetate on nitrogenase activity 10.1016/S0378-1097(97)00127-4

Use of a novel nonantibiotic triple marker gene cassette to monitor high survival of Pseudomonas fluorescens SBW25 on winter wheat in the field 10.1111/j.1574-6941.2007.00420.x

The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments 10.3389/fmicb.2014.00108

Marker and reporter genes: Illuminating tools for environmental microbiologists 10.1016/S1369-5274(03)00057-2

Draft genome sequence of Streptomyces sp. strain Wb2n-11, a desert isolate with broadspectrum antagonism against soilborne phytopathogens 10.1128/genomeA.00860-15

Use of green fluorescent protein and luciferase biomarkers to monitor survival and activity of Arthrobacter chlorophenolicus A6 cells during degradation of 4-chlorophenol in soil 10.1046/j.1462-2920.2001.00156.x

Strategies for metagenomic-guided whole-community proteomics of complex microbial environments 10.1371/journal.pone.0027173

Meta-analyses of studies of the human microbiota 10.1101/gr.151803.112

TerraGenome: A consortium for the sequencing of a soil metagenome 10.1038/nrmicro2119

Indirect interspecies regulation: Transcriptional and physiological responses of a cyanobacterium to heterotrophic partnership 10.1128/mSystems.00181-16

Trade-offs between microbiome diversity and productivity in a stratified microbial mat 10.1038/ismej.2016.133

Active bacterial community structure along vertical redox gradients in Baltic Sea sediment. 10.1111/j.1462-2920.2008.01624.x

Fecal microbiome of growing pigs fed a cereal based diet including chicory (Cichorium intybus L.) or ribwort (Plantago lanceolata L.) forage 10.1186/s40104-015-0054-8

Novel 4-chlorophenol degradation gene cluster and degradation route via hydroxyquinol in Arthrobacter chlorophenolicus A6 10.1128/AEM.71.11.6538-6544.2005

Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill 10.1038/ismej.2017.110

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys 10.1128/mSystems.00009-15

Microbes in thawing permafrost: The unknown variable in the climate change equation 10.1038/ismej.2011.163

The soil microbiome — from metagenomics to metaphenomics 10.1016/j.mib.2018.01.013

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease 10.1371/journal.pone.0049138

Degradation of 4-chlorophenol at low temperature and during extreme temperature fluctuations by Arthrobacter chlorophenolicus A6 10.1007/s00248-003-2026-3

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill 10.1038/ismej.2012.59

Soft inertial microfluidics for high throughput separation of bacteria from human blood cells 10.1039/b817611f

Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome 10.1038/nmicrobiol.2016.221

Prospecting biotechnologically-relevant monooxygenases from cold sediment metagenomes: An in silico approach 10.3390/md15040114

Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill 10.1111/j.1462-2920.2012.02780.x

Monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism 10.1128/AEM.71.1.501-506.2005

Effect of heat stress on cell activity and cell morphology of the tropical rhizobium, Sinorhizobium arboris 10.1111/j.1574-6941.2001.tb00777.x

Specific interactions between arbuscular mycorrhizal fungi and plant growth-promoting bacteria: As revealed by different combinations 10.1111/j.1574-6968.2008.01318.x

Microbiome-wide association studies link dynamic microbial consortia to disease 10.1038/nature18850

The past, present and future of microbiome analyses 10.1038/nprot.2016.148

Stewards of a changing planet: Commentaries from ISME13 plenary lecturers 10.1038/ismej.2010.114

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw 10.1038/nature10576

Metagenomes from two microbial consortia associated with Santa Barbara seep oil 10.1016/j.margen.2014.06.003

Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments 10.1111/1462-2920.13433

Micronutrient metal speciation is controlled by competitive organic chelation in grassland soils 10.1016/j.soilbio.2018.02.018

Permafrost Meta-Omics and Climate Change 10.1146/annurev-earth-060614-105126

Advantages of the metagenomic approach for soil exploration: Reply from Vogel et al. 10.1038/nrmicro2119-c3

A unified initiative to harness Earth's microbiomes: Transition from description to causality and engineering 10.1126/science.aac8480

Complete genome sequence of Bacillus amyloliquefaciens strain Co1-6, a plant growth-promoting rhizobacterium of Calendula officinalis 10.1128/genomeA.00862-15

Development of compost maturity and Actinobacteria populations during full-scale composting of organic household waste 10.1111/j.1365-2672.2006.03271.x

Deep-sea oil plume enriches indigenous oil-degrading bacteria 10.1126/science.1195979

Gut microbial alterations associated with protection from autoimmune uveitis 10.1167/iovs.16-19733

Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies 10.1002/pmic.201300003

Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments 10.1111/j.1574-6941.2008.00513.x

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input 10.1038/srep34434

Long-term impacts of antibiotic exposure on the human intestinal microbiota 10.1099/mic.0.040618-0

The microbial ecology of permafrost 10.1038/nrmicro3262

Flow cytometric and microscopic analysis of GFP-tagged Pseudomonas fluorescens bacteria 10.1016/S0168-6496(96)00068-2

Impact of 4-chlorophenol contamination and/or inoculation with the 4-chlorophenol-degrading strain, Arthrobacter chlorophenolicus A6L, on soil bacterial community structure 10.1016/S0168-6496(02)00356-2

Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management 10.1016/j.apsoil.2010.04.003

Dynamics of the human gut microbiome in inflammatory bowel disease 10.1038/nmicrobiol.2017.4

Microbiology: The life beneath our feet 10.1038/494040a

The founding charter of the Genomic Observatories Network 10.1186/2047-217X-3-2

Impact of temperature on the physiological status of a potential bioremediation inoculant, arthrobacter chlorophenolicus A6 10.1128/AEM.70.5.2952-2958.2004

A multi-omic future for microbiome studies 10.1038/nmicrobiol.2016.49

Quantification of the Presence and Activity of Specific Microorganisms in Nature 10.1007/BF02761746

'Omics' of the mammalian gut - new insights into function 10.1016/j.copbio.2012.01.016

Tackling soil diversity with the assembly of large, complex metagenomes 10.1073/pnas.1402564111

Back to the future of soil metagenomics 10.3389/fmicb.2016.00073

Tracking genetically engineered microorganisms in nature 10.1016/0958-1669(95)80048-4

In vivo study of Trichoderma-pathogen-plant interactions, using constitutive and inducible green fluorescent protein reporter systems 10.1128/AEM.70.5.3073-3081.2004

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils 10.1111/1758-2229.12301

Omics for understanding microbial functional dynamics 10.1111/j.1462-2920.2011.02518.x

Assessment of the deepwater horizon oil spill impact on gulf coast microbial communities 10.3389/fmicb.2014.00130

Degradation of mixtures of phenolic compounds by Arthrobacter chlorophenolicus A6 10.1007/s10532-007-9154-2

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume 10.1038/ismej.2011.91

Tools for the microbiome: Nano and beyond 10.1021/acsnano.5b07826

Rapid lab-on-a-chip profiling of human gut bacteria 10.1016/j.mimet.2007.10.011

Identification of genetic factors that modify motor performance and body weight using Collaborative Cross mice 10.1038/srep16247

Short-term antibiotic treatment has differing long- term impacts on the human throat and gut microbiome 10.1371/journal.pone.0009836

Antifungal and root surface colonization properties of GFP-tagged Paenibacillus brasilensis PB177 10.1007/s11274-005-8123-3

Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent clostridium difficile-associated diarrhea 10.1097/MCG.0b013e3181c87e02

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation 10.1128/mSystems.00013-15

Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease 10.1002/ibd.20783

Diversity, stability and resilience of the human gut microbiota 10.1038/nature11550

Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains 10.1371/journal.pbio.1001920

Clindamycin-induced enrichment and long-term persistence of resistant Bacteroides spp. and resistance genes 10.1093/jac/dkl420

Janet Jansson on the Terragenome Initiative at GSC8 10.4016/12844.01

Soil Metagenomics 10.1007/978-1-4899-7475-4_701

Soil Metagenomics 10.1007/978-1-4614-6418-1_701-4

EMP Sample Submission Guide v1 (protocols.io.pfqdjmw) 10.17504/protocols.io.pfqdjmw

Earth Microbiome Project and Global Systems Biology 10.1128/msystems.00217-17

Faculty of 1000 evaluation for Soil aggregates as massively concurrent evolutionary incubators. 10.3410/f.732730471.793543040

Current understanding of the human microbiome 10.1038/nm.4517

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities 10.1101/265132

Both the intratumoral immune and microbial microenvironment are linked to recurrence in human colon cancer: results from a prospective, multicenter nodal ultrastaging trial 10.18632/oncotarget.25276

The MPLEx Protocol for Multi-omic Analyses of Soil Samples 10.3791/57343

Agulhas Current properties shape microbial community diversity and potential functionality. 10.1038/s41598-018-28939-0

A unified conceptual framework for prediction and control of microbiomes. 10.1016/j.mib.2018.06.002

Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. 10.3389/fmicb.2018.01492

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities. 10.1093/femsec/fiy110

Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates. 10.1111/1462-2920.14348

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Addressing the Challenge of Soil Metaproteome Complexity by Improving Metaproteome Depth of Coverage 10.1016/j.soilbio.2018.07.018

Siderophore Profiling of Co-Habitating Soil Bacteria by Ultra-High Resolution Mass Spectrometry 10.1039/c8mt00252e

Metagenomic Insights into Resistant Starch Degradation by Human Gut Microbiota 10.1128/AEM.01562-18

Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States 10.3389/fmicb.2018.01775

A Probe-Enabled Approach for the Selective Isolation and Characterization of Functionally Active Subpopulations in the Gut Microbiome 10.1021/jacs.8b09668

Data access: Toward unrestricted use of public genomic data 10.1126/science.aaw1280

Spatial distribution of prokaryotic communities in hypersaline soils 10.1038/s41598-018-38339-z

Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution 10.1371/journal.pone.0207606

Tomasz Kosciolek

Kosciolek Tomasz

ORCID: 0000-0002-9915-7387

De novo structure prediction of globular proteins aided by sequence variation-derived contacts 10.1371/journal.pone.0092197

Protein binding site analysis by means of structural interaction fingerprint patterns 10.1016/j.bmcl.2011.09.027

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Impact of template choice on homology model efficiency in virtual screening 10.1021/ci500001f

Opportunities and limitations in applying coevolution-derived contacts to protein 10.1515/bams-2014-0013

Best practices for analysing microbiomes 10.1038/s41579-018-0029-9

IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis 10.1016/j.jid.2019.05.024

Structure-Based Protein Function Prediction using Graph Convolutional Networks 10.1101/786236

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea 10.1038/s41467-019-13443-4

Microbiome analyses of blood and tissues suggest cancer diagnostic approach 10.1038/s41586-020-2095-1

Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder 10.1016/j.jpsychires.2018.01.013

Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects 10.1016/j.schres.2018.09.014

The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/s12915-019-0660-6

Qiita: rapid, web-enabled microbiome meta-analysis 10.1038/s41592-018-0141-9

Docent: Transforming personal intuitions to scientific hypotheses through content learning and process training 10.1145/3231644.3231646

Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis 10.1016/j.eurpsy.2018.05.011

Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using de Novo Fragment-Based Protein Structure Predictions 10.1038/s41598-017-07156-1

Accurate contact predictions using covariation techniques and machine learning 10.1002/prot.24863

The microbiome and its potential for pharmacology 10.1007/164_2019_317

Gut instinct: Creating scientific theories with online learners 10.1145/3025453.3025769

Gut microbiome in serious mental illnesses: A systematic review and critical evaluation 10.1016/j.schres.2019.08.026

Differing salivary microbiome diversity, community and diurnal rhythmicity in association with affective state and peripheral inflammation in adults 10.1016/j.bbi.2020.02.004

Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk 10.1016/j.bbi.2020.10.003

QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data 10.1002/cpbi.100

Design and synthesis of novel cannabinoid ligands based on a 1,2,3-triazole scaffold 10.2174/157018013804725134

American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/msystems.00031-18

Justin Geier

Geier Justin

ORCID: 0000-0002-1755-1410

American Gut: an Open Platform for Citizen Science Microbiome Research. 10.1128/msystems.00031-18

Ironing out mechanisms of iron homeostasis and disorders of iron deficiency 10.1172/JCI148671

Ricardo da Silva

da Silva Ricardo

ORCID: 0000-0001-6378-0479

http://ccbl.fcfrp.usp.br

Computational Removal of Undesired Mass Spectral Features Possessing Repeat Units via a Kendrick Mass Filter 10.1007/s13361-018-2069-9

Neutrophilic proteolysis in the cystic fibrosis lung correlates with a pathogenic microbiome 10.1186/s40168-019-0636-3

A comparative venomic fingerprinting approach reveals that galling and non-galling fig wasp species have different venom profiles 10.1371/journal.pone.0207051

American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/mSystems.00031-18

Bioactivity-Based Molecular Networking for the Discovery of Drug Leads in Natural Product Bioassay-Guided Fractionation 10.1021/acs.jnatprod.7b00737

Chemical profiling of two congeneric sea mat corals along the Brazilian coast: adaptive and functional patterns 10.1039/c7cc08411k

Niche partitioning of a pathogenic microbiome driven by chemical gradients 10.1126/sciadv.aau1908

Propagating annotations of molecular networks using in silico fragmentation 10.1371/journal.pcbi.1006089

Targeted Isolation of Neuroprotective Dicoumaroyl Neolignans and Lignans from Sageretia theezans Using in Silico Molecular Network Annotation Propagation-Based Dereplication 10.1021/acs.jnatprod.8b00292

Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples 10.1021/acs.analchem.7b01381

Global chemical analysis of biology by mass spectrometry 10.1038/s41570-017-0054

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter 10.3389/fmars.2017.00405

Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols 10.1021/acsjnatprod.6b00722

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung 10.1016/j.chom.2017.10.001

Application of MALDI Mass Spectrometry in Natural Products Analysis 10.1055/s-0042-104800

From Sample to Multi-Omics Conclusions in under 48 Hours 10.1128/mSystems.00038-16

Lifestyle chemistries from phones for individual profiling 10.1073/pnas.1610019113

A metabolomic protocol for plant systematics by matrix-assisted laser-desorption/ionization time-of flight mass spectrometry 10.1016/j.aca.2015.01.002

Illuminating the dark matter in metabolomics 10.1073/pnas.1516878112

Mass spectrometry in plant metabolomics strategies: from analytical platforms to data acquisition and processing 10.1039/c3np70086k

ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics 10.1093/bioinformatics/btu019

Queen signals in a stingless bee: suppression of worker ovary activation and spatial distribution of active compounds 10.1038/srep07449

Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae 10.1111/tpj.14292

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis 10.1128/MSYSTEMS.00375-19

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages 10.1016/J.FOODCHEM.2019.125290

In silico annotation of discriminative markers of three Zanthoxylum species using molecular network derived annotation propagation 10.1016/J.FOODCHEM.2019.05.099

Investigation of Premyrsinane and Myrsinane Esters in Euphorbia cupanii and Euphobia pithyusa with MS2LDA and Combinatorial Molecular Network Annotation Propagation 10.1021/ACS.JNATPROD.8B00916

The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/S12915-019-0660-6

Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L 10.3389/FPLS.2019.00846

Initial Development toward Non-Invasive Drug Monitoring via Untargeted Mass Spectrometric Analysis of Human Skin 10.1021/ACS.ANALCHEM.8B05854

Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9

Differences in Cystic Fibrosis-Associated Burkholderia spp. Bacteria Metabolomes after Exposure to the Antibiotic Trimethoprim 10.1021/acsinfecdis.9b00513

Global chemical effects of the microbiome include new bile-acid conjugations 10.1038/s41586-020-2047-9

Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow 10.1016/j.phytochem.2020.112292

Feature-based molecular networking in the GNPS analysis environment 10.1038/s41592-020-0933-6

Time-Scale Shifting of Volatile Semiochemical Levels in Wild Type Lychnophora ericoides (Brazilian arnica) and Pollinator Records 10.1055/a-1320-4556

Distinct photo-oxidation-induced cell death pathways lead to selective killing of human breast cancer cells 10.1038/s41419-020-03275-2

A Multi-Omics Characterization of the Natural Product Potential of Tropical Filamentous Marine Cyanobacteria 10.3390/md19010020

Convergent evolution of pain-inducing defensive venom components in spitting cobras 10.1126/science.abb9303

Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden 10.1128/msystems.00601-21

REDES MOLECULARES: UMA ANÁLISE SOBRE ANOTAÇÕES E DESCOBERTA DE NOVOS ATIVOS 10.21577/0100-4042.20170777

CHAPTER 10. Perspectives for the Future 10.1039/9781788010399-00264

CHAPTER 3. Metabolomics 10.1039/9781788010399-00057

Mass Spectrometry in Chemical Biology 10.1039/9781788010399

Shyamal Peddada

Peddada Shyamal

ORCID: 0000-0002-5014-6513

Gene expression in uterine leiomyoma from tumors likely to be growing (from black women over 35) and tumors likely to be non-growing (from white women over 35). 10.1371/journal.pone.0063909

Exposures Related to House Dust Microbiota in a U.S. Farming Population. 10.1289/ehp3145

Reduced Disc Shedding and Phagocytosis of Photoreceptor Outer Segment Contributes to Kava Kava Extract-induced Retinal Degeneration in F344/N Rats. 10.1177/0192623318778796

American Gut: an Open Platform for Citizen Science Microbiome Research. 10.1128/mSystems.00031-18

Preterm infants have distinct microbiomes not explained by mode of delivery, breastfeeding duration or antibiotic exposure. 10.1093/ije/dyy064

American Gut: an Open Platform for Citizen-Science Microbiome Research 10.1101/277970

A Bootstrap Based Measure Robust to the Choice of Normalization Methods for Detecting Rhythmic Features in High Dimensional Data. 10.3389/fgene.2018.00024

Visualizing detailed postdoctoral employment trends using a new career outcome taxonomy. 10.1038/nbt.4059

Analysis of Microbiome Data in the Presence of Excess Zeros. 10.3389/fmicb.2017.02114

Seasonal change in the gut. 10.1126/science.aao2997

Structural zeros in high-dimensional data with applications to microbiome studies. 10.1093/biostatistics/kxw053

Normalization and microbial differential abundance strategies depend upon data characteristics. 10.1186/s40168-017-0237-y

Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome. 10.1002/mds.26942

The novel p53 target TNFAIP8 variant 2 is increased in cancer and offsets p53-dependent tumor suppression. 10.1038/cdd.2016.130

Fat and vitamin intakes during pregnancy have stronger relations with a pro-inflammatory maternal microbiota than does carbohydrate intake. 10.1186/s40168-016-0200-3

Order restricted inference for oscillatory systems for detecting rhythmic signals. 10.1093/nar/gkw771

DNA Methylation Score as a Biomarker in Newborns for Sustained Maternal Smoking during Pregnancy. 10.1289/EHP333

Chemical Exacerbation of Light-induced Retinal Degeneration in F344/N Rats in National Toxicology Program Rodent Bioassays. 10.1177/0192623316650050

Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice. 10.1073/pnas.1600324113

Circular piecewise regression with applications to cell-cycle data. 10.1111/biom.12512

Maternal plasma folate impacts differential DNA methylation in an epigenome-wide meta-analysis of newborns. 10.1038/ncomms10577

Renal Cell Carcinomas in Vinylidene Chloride-exposed Male B6C3F1 Mice Are Characterized by Oxidative Stress and TP53 Pathway Dysregulation. 10.1177/0192623315610820

Uterine Carcinomas in Tetrabromobisphenol A-exposed Wistar Han Rats Harbor Increased Tp53 Mutations and Mimic High-grade Type I Endometrial Carcinomas in Women. 10.1177/0192623315599256

Genomic Profiling Reveals Unique Molecular Alterations in Hepatoblastomas and Adjacent Hepatocellular Carcinomas in B6C3F1 Mice. 10.1177/0192623315599853

A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies. 10.1186/s12859-016-0937-5

Determination of Temporal Order among the Components of an Oscillatory System. 10.1371/journal.pone.0124842

Effects of library size variance, sparsity, and compositionality on the analysis of microbiome data 10.7287/peerj.preprints.1157

Analysis of composition of microbiomes: a novel method for studying microbial composition. 10.3402/mehd.v26.27663

Potential sex differences in nonmotor symptoms in early drug-naive Parkinson disease. 10.1212/WNL.0000000000001609

F344/NTac Rats Chronically Exposed to Bromodichloroacetic Acid Develop Mammary Adenocarcinomas With Mixed Luminal/Basal Phenotype and Tgfβ Dysregulation. 10.1177/0300985815571680

Biomarkers of oxidative stress study VI. Endogenous plasma antioxidants fail as useful biomarkers of endotoxin-induced oxidative stress. 10.1016/j.freeradbiomed.2015.01.006

Meta-analyses on prevalence of selected Parkinson's nonmotor symptoms before and after diagnosis. 10.1186/2047-9158-4-1

Mixed directional false discovery rate control in multiple pairwise comparisons using weighted p-values. 10.1002/bimj.201300242

Individual and joint prevalence of three nonmotor symptoms of PD in the US general population. 10.1002/mds.25950

Intraobserver variability in fibroid size measurements: estimated effects on assessing fibroid growth. 10.7863/ultra.33.7.1217

Gene expression of mesothelioma in vinylidene chloride-exposed F344/N rats reveal immune dysfunction, tissue damage, and inflammation pathways. 10.1177/0192623314537885

Maternal smoking and DNA methylation in newborns: in utero effect or epigenetic inheritance? 10.1158/1055-9965.EPI-13-1256

Neonatal genome-wide methylation patterns in relation to birth weight in the Norwegian Mother and Child Cohort. 10.1093/aje/kwt433

Linear mixed effects models under inequality constraints with applications. 10.1371/journal.pone.0084778

A systematic assessment of normalization approaches for the Infinium 450K methylation platform. 10.4161/epi.27119

Testing for the multivariate stochastic order among ordered experimental groups with application to dose-response studies. 10.1111/biom.12070

A minimal set of tissue-specific hypomethylated CpGs constitute epigenetic signatures of developmental programming. 10.1371/journal.pone.0072670

Spontaneous mesotheliomas in F344/N rats are characterized by dysregulation of cellular growth and immune function pathways. 10.1177/0192623313501894

Research on the premotor symptoms of Parkinson's disease: clinical and etiological implications. 10.1289/ehp.1306967

Novel developmental analyses identify longitudinal patterns of early gut microbiota that affect infant growth. 10.1371/journal.pcbi.1003042

Robust Analysis of High Throughput Screening (HTS) Assay Data. 10.1080/00401706.2012.749166

A HIERARCHICAL FUNCTIONAL DATA ANALYTIC APPROACH FOR ANALYZING PHYSIOLOGICALLY BASED PHARMACOKINETIC MODELS. 10.1002/env.2198

The linear stochastic order and directed inference for multivariate ordered distributions. 10.1214/12-AOS1062

Hepatocellular carcinomas in B6C3F1 mice treated with Ginkgo biloba extract for two years differ from spontaneous liver tumors in cancer gene mutations and genomic pathways. 10.1177/0192623312467520

450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy. 10.1289/ehp.1205412

Analysis of high dimensional data using pre-defined set and subset information, with applications to genomic data. 10.1186/1471-2105-13-177

Differential transcriptomic analysis of spontaneous lung tumors in B6C3F1 mice: comparison to human non-small cell lung cancer. 10.1177/0192623312447543

Gender differences in chemical carcinogenesis in National Toxicology Program 2-year bioassays. 10.1177/0192623312446527

Accounting for Uncertainty in Heteroscedasticity in Nonlinear Regression. 10.1016/j.jspi.2011.11.003

Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across species. 10.1093/nar/gkr1077

Aloe vera non-decolorized whole leaf extract-induced large intestinal tumors in F344 rats share similar molecular pathways with human sporadic colorectal tumors. 10.1177/0192623311422081

Proteomic profiling of S-acylated macrophage proteins identifies a role for palmitoylation in mitochondrial targeting of phospholipid scramblase 3. 10.1074/mcp.M110.006007

Mass spectrometric determination of IgG subclass-specific glycosylation profiles in siblings discordant for myositis syndromes. 10.1021/pr200397h

Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome. 10.1073/pnas.1105713108

Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: similarities in the molecular landscape with human liver cancer. 10.1177/0192623311407213

Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays. 10.1093/nar/gkr241

Efficacy of succimer chelation of mercury at background exposures in toddlers: a randomized trial. 10.1016/j.jpeds.2010.08.036

Comparing tumor rates in current and historical control groups in rodent cancer bioassays. 10.1198/sbr.2010.09044

Order restricted inference for multivariate binary data with application to toxicology. 10.1198/jasa.2011.tm10322

Development of gut microbiota in infants not exposed to medical interventions. 10.1111/j.1600-0463.2010.02688.x

Comparison of NTP historical control tumor incidence rates in female Harlan Sprague Dawley and Fischer 344/N Rats. 10.1177/0192623310373777

Short-term change in growth of uterine leiomyoma: tumor growth spurts. 10.1016/j.fertnstert.2010.05.011

Cellular senescence in usual type uterine leiomyoma. 10.1016/j.fertnstert.2010.04.068

Research misconduct policies of social science journals and impact factor. 10.1080/08989621003641181

A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments. 10.1186/1471-2105-10-438

Evaluating the quality of information about alternatives to research participation in oncology consent forms. 10.1016/j.cct.2009.11.001

Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle. 10.1186/1752-0509-3-93

Potential for a global historical control database for proliferative rodent lesions. 10.1177/0192623309336155

Controlling false discoveries in multidimensional directional decisions, with applications to gene expression data on ordered categories. 10.1111/j.1541-0420.2009.01292.x

Points to consider on the statistical analysis of rodent cancer bioassay data when incorporating historical control data. 10.1177/0192623309339606

Best practices for use of historical control data of proliferative rodent lesions. 10.1177/0192623309336154

The fibroid growth study: determinants of therapeutic intervention. 10.1089/jwh.2008.0903

Estimation of Parameters Subject to Order Restrictions on a Circle With Application to Estimation of Phase Angles of Cell Cycle Genes. 10.1198/jasa.2009.0120

Research misconduct policies of scientific journals. 10.1080/08989620903190299

Growth of uterine leiomyomata among premenopausal black and white women. 10.1073/pnas.0808188105

Treatment of osteomyelitis in rats by injection of degradable polymer releasing gentamicin. 10.1016/j.jconrel.2008.07.022

Adaptive choice of the number of bootstrap samples in large scale multiple testing. 10.2202/1544-6115.1360

Perceptions of ethical problems with scientific journal peer review: an exploratory study. 10.1007/s11948-008-9059-4

Genetic pathways and mutation profiles of human cancers: site- and exposure-specific patterns. 10.1093/carcin/bgm176

Order-restricted inference for ordered gene expression (ORIOGEN) data under heteroscedastic variances. 10.6026/97320630001414

Prevalence of major depressive episodes in rural women using primary care. 10.1353/hpu.2007.0010

Age and dose sensitivities in the 2-butoxyethanol F344 rat model of hemolytic anemia and disseminated thrombosis. 10.1016/j.etp.2006.11.003

Incorporating Historical Control Data When Comparing Tumor Incidence Rates. 10.1198/016214506000001356

Male sex hormones promote vagally mediated reflex airway responsiveness to cholinergic stimulation. 10.1152/ajplung.00407.2006

A survival-adjusted quantal-response test for analysis of tumor incidence rates in animal carcinogenicity studies. 10.1289/ehp.8590

Early effects of iodine on DNA synthesis in sulfur mustard-induced skin lesions. 10.1007/s00204-005-0032-6

Phase analysis of circadian-related genes in two tissues. 10.1186/1471-2105-7-87

Genetic alterations in cancer knowledge system: analysis of gene mutations in mouse and human liver and lung tumors. 10.1093/toxsci/kfj101

Hemostatic activation in a chemically induced rat model of severe hemolysis and thrombosis. 10.1016/j.thromres.2005.11.010

Clusters of mutations from transient hypermutability. 10.1073/pnas.0503009102

ORIOGEN: order restricted inference for ordered gene expression data. 10.1093/bioinformatics/bti637

Mutant Brca2/p53 mice exhibit altered radiation responses in the developing mammary gland. 10.1016/j.etp.2005.06.001

Inhibition of urethane-induced genotoxicity and cell proliferation in CYP2E1-null mice. 10.1016/j.mrfmmm.2004.12.005

Mechanisms of exocrine pancreatic toxicity induced by oral treatment with 2,3,7,8-tetrachlorodibenzo-p-dioxin in female Harlan Sprague-Dawley Rats. 10.1093/toxsci/kfi121

Analysis of nonlinear regression models: a cautionary note. 10.2203/dose-response.003.03.005

2-Butoxyethanol female-rat model of hemolysis and disseminated thrombosis: X-ray characterization of osteonecrosis and growth-plate suppression. 10.1080/019262390908362

Epididymal sperm granuloma induced by chronic administration of 2-methylimidazole in B6C3F1 mice. 10.1080/01926230590922866

Reduced sulfur mustard-induced skin toxicity in cyclooxygenase-2 knockout and celecoxib-treated mice. 10.1016/j.taap.2004.03.013

Estradiol regulates the thioredoxin antioxidant system in the mouse uterus. 10.1210/en.2004-0471

Designs for single- or multiple-agent phase I trials. 10.1111/j.0006-341x.2004.00215.x

Interleukin-1beta-induced mucin production in human airway epithelium is mediated by cyclooxygenase-2, prostaglandin E2 receptors, and cyclic AMP-protein kinase A signaling. 10.1124/mol.66.2.337

Mitochondrial damage revealed by morphometric and semiquantitative analysis of mouse pup cardiomyocytes following in utero and postnatal exposure to zidovudine and lamivudine. 10.1093/toxsci/kfh208

Assessment of lead exposure and associated risk factors in urban children in Silesia, Poland. 10.1016/s0013-9351(03)00139-7

A random-periods model for expression of cell-cycle genes. 10.1073/pnas.0402285101

A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions. 10.1093/bioinformatics/bth274

Osteonecrosis in a chemically induced rat model of human hemolytic disorders associated with thrombosis--a new model for avascular necrosis of bone. 10.1007/s00223-003-0068-7

The OECD program to validate the rat uterotrophic bioassay. Phase 2: coded single-dose studies. 10.1289/ehp.5870

The OECD program to validate the rat uterotrophic bioassay. Phase 2: dose-response studies. 10.1289/ehp.5780

Forestomach tumor induction by 2,4-hexadienal in F344N rats and B6C3F1 mice. 10.1007/s00204-003-0481-8

Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference. 10.1093/bioinformatics/btg093

The hepatic endothelial carcinogen riddelliine induces endothelial apoptosis, mitosis, S phase, and p53 and hepatocytic vascular endothelial growth factor expression after short-term exposure. 10.1006/taap.2002.9485

A chemically induced rat model of hemolysis with disseminated thrombosis. 10.1007/s12012-002-0003-6

Tests for order restrictions in binary data. 10.1111/j.0006-341x.2001.01219.x

The role of oxidative stress in indium phosphide-induced lung carcinogenesis in rats. 10.1093/toxsci/64.1.28

Longitudinal assessment of hormonal and physical alterations during normal puberty in boys. VI. Modeling of growth velocity, mean growth hormone (GH mean), and serum testosterone (T) concentrations. 10.1002/1520-6300(200011/12)12:6<814::aid-ajhb9>3.0.co;2-u

Longitudinal assessment of hormonal and physical alterations during normal puberty in boys. IV: Predictions of adult height by the Bayley-Pinneau, Roche-Wainer-Thissen, and Tanner-Whitehouse methods compared. 10.1002/(sici)1520-6300(1997)9:3<371::aid-ajhb9>3.0.co;2-0

Factors affecting the thickness of the cervical prevertebral soft tissues. 10.1007/bf00206147

Some advances in constrained inference for ordered circular parameters in oscillatory systems 10.1002/9781118866641.ch4

Bootstrap confidence region estimation of the motion of rigid bodies 10.1080/01621459.1996.10476681

Qualms about BCabootstrap confidence intervals 10.1016/0167-7152(92)90288-G

A survival-adjusted quantal response test for comparing tumour incidence rates 10.1111/j.1467-9876.2005.00469.x

The role of particulate matter-associated zinc in cardiac injury in rats 10.1289/ehp.10379

CLME: An R package for linear mixed effects models under inequality constraints 10.18637/jss.v075.i01

Statistical inference in nonlinear regression under heteroscedasticity 10.1007/s13571-011-0013-0

Two non-negative estimators for the model with a common mean 10.1080/03610918908812773

Letter to the editor 10.1111/j.1467-9876.2007.00589_2.x

On The Inadmissibility Of Ridge Estimator In A Linear Model 10.1080/03610928908830110

Isocir: An R package for constrained inference using isotonic regression for circular data, with an application to cell biology 10.18637/jss.v054.i04

Confidence interval estimation under some restrictions on the parameters with non-linear boundaries 10.1016/0167-7152(93)90034-G

The exact Mean Squared Error of Stein-rule estimator in linear models 10.1016/0378-3758(88)90110-3

Comparison of some common ratio estimators using pitman measure of nearness 10.1080/03610928708829488

A chemically induced rat model of hemolysis with disseminated thrombosis 10.1385/CT:2:3:181

Tests for a simple tree order restriction with application to dose-response studies 10.1111/j.1467-9876.2006.00549.x

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Parameter estimation in linear models with heteroscedastic variances subject to order restrictions 10.1006/jmva.2001.2010

Jackknife variance estimators in linear models 10.1093/biomet/79.3.654

Statistical Analysis of Gene Expression Studies with Ordered Experimental Conditions 10.1016/B978-0-44-451875-0.00003-8

Bayesian nonparametric inference on stochastic ordering 10.1093/biomet/asn043

Comparison of Estimators of The Location Parameter Using Pitman’s Closeness Criterion 10.1080/03610929108830722

A short note on pitman’s measure of nearness 10.1080/00031305.1985.10479452

21 Jackknife variance estimation and bias reduction 10.1016/S0169-7161(05)80145-2

Entropy inequalities for some multivariate distributions 10.1016/0047-259X(91)90013-R

Testing for Inequality Constraints in Singular Models by Trimming or Winsorizing the Variance Matrix 10.1080/01621459.2017.1301258

A short note on pitman nearness for elliptically symmetric estimators 10.1016/0378-3758(87)90075-9

Classification of pixels in a noisy grayscale image of polar ice 10.1109/TGRS.2002.802517

On pitman nearness and variance of estimators 10.1080/03610928608829292

Corrections to “Least Average Residual Algorithm (LARA) for Tracking the Motion of Arctic Sea Ice”. (Ieee transactions on geoscience and remote sensing (1996) 34(5) (1288) (10.1109/TGRS.1996.536546)) 10.1109/TGRS.1996.536546

Erratum: Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome (Proceedings of the National Academy of Sciences of the United States of America (2002) 108:23 (9715-9720) DOI: 10.1073/pnas.1105713108) 10.1073/pnas.1302473110

An automated algorithm for cleaning and ordering the boundary points of a one-dimensional curve in a segmented image 10.1109/36.655340

Tanya Nguyen

Nguyen Tanya

ORCID: 0000-0002-9510-9564

Systemic Biomarkers of Accelerated Aging in Schizophrenia: A Critical Review and Future Directions. 10.1093/schbul/sbx069

Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder. 10.1016/j.jpsychires.2018.01.013

American Gut: an Open Platform for Citizen Science Microbiome Research. 10.1128/mSystems.00031-18

Successful Aging of Physicians. 10.1016/j.jagp.2017.08.003

Abnormal levels of vascular endothelial biomarkers in schizophrenia. 10.1007/s00406-017-0842-6

Steeper Slope of Age-Related Changes in White Matter Microstructure and Processing Speed in Bipolar Disorder. 10.1016/j.jagp.2017.02.014

Cerebral Cortex Regions Selectively Vulnerable to Radiation Dose-Dependent Atrophy. 10.1016/j.ijrobp.2017.01.005

Dynamic functional connectivity in bipolar disorder is associated with executive function and processing speed: A preliminary study. 10.1037/neu0000317

Randomized, double-blind, placebo-controlled clinical trial of choline supplementation in school-aged children with fetal alcohol spectrum disorders 10.3945/ajcn.116.142075

Dietary Nutrient Intake in School-Aged Children With Heavy Prenatal Alcohol Exposure. 10.1111/acer.13035

Objective assessment of ADHD core symptoms in children with heavy prenatal alcohol exposure. 10.1016/j.physbeh.2014.10.014

The Use of Open- and Closed-Loop Control During Goal-Directed Force Responses by Children with Heavy Prenatal Alcohol Exposure. 10.1111/acer.12827

The clinical utility and specificity of parent report of executive function among children with prenatal alcohol exposure. 10.1017/S1355617714000599

Children with heavy prenatal alcohol exposure experience reduced control of isotonic force. 10.1111/j.1530-0277.2012.01896.x

Children with heavy prenatal alcohol exposure have different frequency domain signal characteristics when producing isometric force. 10.1016/j.ntt.2012.11.003

Children with heavy prenatal alcohol exposure exhibit deficits when regulating isometric force. 10.1111/j.1530-0277.2011.01625.x

Fetal alcohol spectrum disorders: neuropsychological and behavioral features. 10.1007/s11065-011-9167-9

Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects. 10.1016/j.schres.2018.09.014

Identifying early diffusion imaging biomarkers of regional white matter injury as indicators of executive function decline following brain radiotherapy: A prospective clinical trial in primary brain tumor patients. 10.1016/j.radonc.2018.11.018

Positive light on schizophrenia and aging: Commentary on course and predictors of symptomatic remission in schizophrenia: A 5-year follow-up study in a Dutch psychiatric catchment area, by Lange et al. 10.1016/j.schres.2019.07.037

Quantitative imaging biomarkers of damage to ritical memory regions associated with post-radiotherapy memory performance in brain tumor patients. 10.1016/j.ijrobp.2019.08.003

Gut microbiome in serious mental illnesses: A systematic review and critical evaluation 10.1016/j.schres.2019.08.026

Beyond artificial intelligence: exploring artificial wisdom 10.1017/S1041610220000927

The Gut Microbiome, Aging, and Longevity: A Systematic Review 10.3390/nu12123759

Chemokine MCP1 is associated with cognitive flexibility in schizophrenia: A preliminary analysis 10.1016/j.jpsychires.2021.04.007

Microbes and Geriatric Mental Health: Past, Present, and Future 10.1017/S104161022100065X

Wisdom as a potential antidote to loneliness in aging 10.1017/S1041610220001660

Physical frailty as an important indicator of accelerated biological aging in serious mental illnesses 10.1017/S1041610220003713

Stefan Janssen

Janssen Stefan

ORCID: 0000-0003-0955-0589

Email: stefan.janssen@uni-bielefeld.de

https://www.techfak.uni-bielefeld.de/~sjanssen/

https://scholar.google.de/citations?user=z9rJ8uwAAAAJ&hl=de

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease 10.1016/j.cell.2016.11.018

The RNA shapes studio 10.1093/bioinformatics/btu649

Ambivalent covariance models 10.1186/s12859-015-0569-1

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples 10.1128/mSystems.00218-17

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information 10.1128/mSystems.00021-18

Creating a 3D microbial and chemical snapshot of a human habitat 10.1038/s41598-018-21541-4

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software 10.1038/nmeth.4458

American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/mSystems.00031-18

Shape based indexing for faster search of RNA family databases 10.1186/1471-2105-9-131

Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction 10.1186/1471-2105-12-429

Bellman's GAP -- a Language and Compiler for Dynamic Programming in Sequence Analysis 10.1093/bioinformatics/btt022

Faster computation of exact RNA shape probabilities 10.1093/bioinformatics/btq014

Prediction of RNA Secondary Structure Including Kissing Hairpin Motifs 10.1007/978-3-642-15294-8_5

Bellman's GAP: a declarative language for dynamic programming 10.1145/2003476.2003484

A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti 10.1186/1471-2164-11-245

Qiita: rapid, web-enabled microbiome meta-analysis 10.1038/s41592-018-0141-9

Assessing taxonomic metagenome profilers with OPAL 10.1101/372680

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month 10.1186/s40168-019-0645-2

Assessing taxonomic metagenome profilers with OPAL 10.1186/s13059-019-1646-y

The impact of skin care products on skin chemistry and microbiome dynamics 10.1186/s12915-019-0660-6

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea 10.1038/s41467-019-13443-4

Infectious stimuli promote malignant B-cell acute lymphoblastic leukemia in the absence of AID 10.1038/s41467-019-13570-y

Microbiome analyses of blood and tissues suggest cancer diagnostic approach 10.1038/s41586-020-2095-1

An intact gut microbiome protects genetically predisposed mice against leukemia 10.1182/blood.2019004381

Vitamin D metabolites and the gut microbiome in older men 10.1038/s41467-020-19793-8

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets 10.1128/mSystems.01216-20

Results from a pilot study on the oral microbiome in children and adolescents with chronic nonbacterial osteomyelitis 10.1007/s00393-021-01035-x

Ashkaan Fahimipour

Fahimipour Ashkaan

ORCID: 0000-0001-9138-3593

Compensation masks trophic cascades in complex food webs 10.1007/s12080-016-0326-8

Colonisation rate and adaptive foraging control the emergence of trophic cascades. 10.1111/ele.12464

The dynamics of assembling food webs. 10.1111/ele.12264

Daylight exposure modulates bacterial communities associated with household dust 10.1186/s40168-018-0559-4

Omnivory does not preclude strong trophic cascades 10.1101/441535

Compensation masks trophic cascades in complex food webs 10.1101/068569

Global-scale structure of the eelgrass microbiome 10.1101/089797

Mapping the bacterial metabolic niche space 10.1038/s41467-020-18695-z

Body size dependent dispersal influences stability in heterogeneous metacommunities 10.1101/2021.02.08.430322

Informational constraints on predator–prey interactions 10.1111/oik.08143

Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice 10.1128/msystems.00471-21

How Light Exposure Changes Bacterial Communities in Household Dust 10.3389/frym.2019.00148

Modern models of trophic meta-communities 10.1098/rstb.2019.0455

Omnivory does not preclude strong trophic cascades 10.1002/ecs2.2800

Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors 10.1128/msystems.00200-18

American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/msystems.00031-18

Moving microbes: the dynamics of transient microbial residence on human skin 10.1101/586008

Ruth Ley

Ley Ruth

ORCID: 0000-0002-9087-1672

http://www.leylab.com

American Gut: an Open Platform for Citizen Science Microbiome Research 10.1128/mSystems.00031-18

Enterotypes in the landscape of gut microbial community composition 10.1038/s41564-017-0072-8

Genomic features of bacterial adaptation to plants 10.1038/s41588-017-0012-9

Large-scale replicated field study of maize rhizosphere identifies heritable microbes 10.1073/pnas.1800918115

Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids 10.7554/eLife.32581

Sphingolipids in host-microbial interactions 10.1016/j.mib.2017.12.011

Alterations to the Gut Microbiome Impair Bone Strength and Tissue Material Properties 10.1002/jbmr.3114

Microbiome and metabolic disease: revisiting the bacterial phylum Bacteroidetes 10.1007/s00109-016-1492-2

TGR5 contributes to glucoregulatory improvements after vertical sleeve gastrectomy in mice 10.1136/gutjnl-2015-309871

The Relationship Between the Human Genome and Microbiome Comes into View 10.1146/annurev-genet-110711-155532

Vertical sleeve gastrectomy reduces blood pressure and hypothalamic endoplasmic reticulum stress in mice 10.1242/dmm.027474

Corralling Colonic Flagellated Microbiota 10.1056/NEJMcibr1604801

Cross-species comparisons of host genetic associations with the microbiome 10.1126/science.aad9379

Crossover Control Study of the Effect of Personal Care Products Containing Triclosan on the Microbiome. 10.1128/mSphere.00056-15

Epithelial Sel1L is required for the maintenance of intestinal homeostasis 10.1091/mbc.E15-10-0724

Genetic Determinants of the Gut Microbiome in UK Twins 10.1016/j.chom.2016.04.017

Heritable components of the human fecal microbiome are associated with visceral fat 10.1186/s13059-016-1052-7

Methane Emission in a Specific Riparian-Zone Sediment Decreased with Bioelectrochemical Manipulation and Corresponded to the Microbial Community Dynamics 10.3389/fmicb.2015.01523

Novel Rhizosphere Soil Alleles for the Enzyme 1-Aminocyclopropane-1-Carboxylate Deaminase Queried for Function with an In Vivo Competition Assay 10.1128/AEM.03074-15

Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring (vol 72, pg 1962, 2015) 10.2166/wst.2016.074

Prevotella in the gut: choose carefully 10.1038/nrgastro.2016.4

Proton pump inhibitors alter the composition of the gut microbiota 10.1136/gutjnl-2015-310861

Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome 10.1186/s40168-016-0171-4

Reply to "Triclocarban and Health: the Jury Is Still Out" 10.1128/mSphere.00255-16

Signatures of early frailty in the gut microbiota 10.1186/s13073-016-0262-7

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome 10.1038/nature14232

Gut-Microbiota-Metabolite Axis in Early Renal Function Decline 10.1371/journal.pone.0134311

Host genetic variation impacts microbiome composition across human body sites 10.1186/s13059-015-0759-1

Microbiota and Host Nutrition across Plant and Animal Kingdoms 10.1016/j.chom.2015.04.009

Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring 10.2166/wst.2015.407

Selection on soil microbiomes reveals reproducible impacts on plant function 10.1038/ismej.2014.196

The gene-microbe link 10.1038/518S7a

Advancing the microbiome research community 10.1016/j.cell.2014.09.022

AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition 10.1136/gutjnl-2013-304909

Conducting a Microbiome Study 10.1016/j.cell.2014.06.037

Diet-Induced Alterations in Gut Microflora Contribute to Lethal Pulmonary Damage in TLR2/TLR4-Deficient Mice 10.1016/j.celrep.2014.05.040

Discordance between changes in the gut microbiota and pathogenicity in a mouse model of spontaneous colitis 10.4161/gmic.28622

Gut microbiota as an epigenetic regulator: pilot study based on whole-genome methylation analysis 10.1128/mBio.02113-14

Human genetics shape the gut microbiome 10.1016/j.cell.2014.09.053

Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013 10.1186/2049-2618-2-16

Intestinal epithelial cell toll-like receptor 5 regulates the intestinal microbiota to prevent low-grade inflammation and metabolic syndrome in mice 10.1053/j.gastro.2014.08.033

Linking genetic variation in human Toll-like receptor 5 genes to the gut microbiome's potential to cause inflammation 10.1016/j.imlet.2014.07.017

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets 10.1371/journal.pcbi.1002863

Diversity and heritability of the maize rhizosphere microbiome under field conditions 10.1073/pnas.1302837110

Exploring the maize rhizosphere microbiome in the field: A glimpse into a highly complex system 10.4161/cib.25177

Innate and Adaptive Immunity Interact to Quench Microbiome Flagellar Motility in the Gut 10.1016/j.chom.2013.10.009

Probiotics, prebiotics, and the host microbiome: the science of translation 10.1111/nyas.12303

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria 10.7554/eLife.01102

Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88 10.1136/gutjnl-2011-301104

Defining the core Arabidopsis thaliana root microbiome 10.1038/nature11237

Discussion from the 24th Marabou Symposium: Nutrition and the human microbiome 10.1111/j.1753-4887.2012.00501.x

Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy 10.1016/j.cell.2012.07.008

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys 10.1038/ismej.2011.82

Integrated and novel survey methods for rhinoceros populations confirm the extinction of Rhinoceros sondaicus annamiticus from Vietnam 10.1016/j.biocon.2012.06.008

Interleukin-1 beta (IL-1 beta) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis 10.1136/gut.2011.240556

Responses of Gut Microbiota to Diet Composition and Weight Loss in Lean and Obese Mice 10.1038/oby.2011.111

Transient Inability to Manage Proteobacteria Promotes Chronic Gut Inflammation in TLR5-Deficient Mice 10.1016/j.chom.2012.07.004

Branched Chain Fatty Acids Reduce the Incidence of Necrotizing Enterocolitis and Alter Gastrointestinal Microbial Ecology in a Neonatal Rat Model 10.1371/journal.pone.0029032

Development of the Human Gastrointestinal Microbiota and Insights From High-Throughput Sequencing 10.1053/j.gastro.2011.02.011

Human oral, gut, and plaque microbiota in patients with atherosclerosis 10.1073/pnas.1011383107

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications 10.1038/nbt.1823

Succession of microbial consortia in the developing infant gut microbiome 10.1073/pnas.1000081107

Supervised classification of microbiota mitigates mislabeling errors 10.1038/ismej.2010.148

The Antibacterial Lectin RegIII gamma Promotes the Spatial Segregation of Microbiota and Host in the Intestine 10.1126/science.1209791

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes 10.1146/annurev-micro-090110-102830

Unravelling the effects of the environment and host genotype on the gut microbiome 10.1038/nrmicro2540

Direct sequencing of the human microbiome readily reveals community differences 10.1186/gb-2010-11-5-210

Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5 10.1126/science.1179721