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Mass spectrometry searches using MASST

Mingxun Wang Alan K. Jarmusch Fernando Vargas Alexander A. Aksenov Julia M. Gauglitz Kelly Weldon Daniel Petras Ricardo da Silva Robert Quinn Alexey V. Melnik Justin J. J. van der Hooft Andrés Mauricio Caraballo-Rodríguez Louis Felix Nothias Christine M. Aceves Morgan Panitchpakdi Elizabeth Brown Francesca Di Ottavio Nicole Sikora Emmanuel O. Elijah Lara Labarta-Bajo Emily C. Gentry Shabnam Shalapour Kathleen E. Kyle Sara P. Puckett Jeramie D. Watrous Carolina S. Carpenter Amina Bouslimani Madeleine Ernst Austin D. Swafford Elina I. Zúñiga Marcy J. Balunas Jonathan L. Klassen Rohit Loomba Rob Knight Nuno Bandeira Pieter C. Dorrestein

Nature Biotechnology, 2020-1

https://doi.org/10.1038/s41587-019-0375-9

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

A lightweight, scalable grid computing framework for parallel bioinformatics applications 10.1109/HPCS.2005.7

Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probiotic effectiveness 10.1371/journal.pone.0096375

Activating and inhibiting connections in biological network dynamics 10.1186/1745-6150-3-49

Microbiota at multiple body sites during pregnancy in a rural tanzanian population and effects of Moringa-supplemented probiotic yogurt 10.1128/AEM.00780-15

Temporal variability is a personalized feature of the human microbiome 10.1186/s13059-014-0531-y

Can Your Microbiome Tell You What to Eat? 10.1016/j.cmet.2015.11.009

Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and Colon 10.1371/journal.pone.0073140

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics 10.1186/1471-2148-8-327

Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments 10.1038/ismej.2010.167

MotifCluster: An interactive online tool for clustering and visualizing sequences using shared motifs 10.1186/gb-2008-9-8-r128

Longitudinal analysis of microbial interaction between humans and the indoor environment 10.1126/science.1254529

The influence of sex, handedness, and washing on the diversity of hand surface bacteria 10.1073/pnas.0807920105

Human genetics shape the gut microbiome 10.1016/j.cell.2014.09.053

Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity 10.1128/mBio.01371-14

Environmental reservoirs of pathogenic mycobacteria across the Ethiopian biogeographical landscape 10.1371/journal.pone.0173811

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system 10.7554/eLife.01104.001

Gut microbiota from twins discordant for obesity modulate metabolism in mice 10.1126/science.1241214

Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil 10.1016/j.soilbio.2010.02.003

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags 10.1186/1471-2180-10-206

The 'rare biosphere': A reality check 10.1038/nmeth0909-636

Variable responses of human and non-human primate gut microbiomes to a Western diet 10.1186/s40168-015-0120-7

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences 10.1038/nbt.2676

Global patterns in the biogeography of bacterial taxa 10.1111/j.1462-2920.2010.02315.x

RNASTAR: An RNA structural alignment repository that provides insight into the evolution of natural and artificial RNAs 10.1261/rna.032052.111

Spatial and temporal variability of the human microbiota 10.1111/j.1469-0691.2012.03861.x

Cross-biome comparison of microbial association networks 10.3389/fmicb.2015.01200

Genetic control of obesity and gut microbiota composition in response to high-fat, high-sucrose diet in mice 10.1016/j.cmet.2012.12.007

Mass spectrometry based molecular 3D-cartography of plant metabolites 10.3389/fpls.2017.00429

Comparison of Collection Methods for Fecal Samples in Microbiome Studies 10.1093/aje/kww177

Translating the human microbiome 10.1038/nbt.2543

Specialized metabolites from the microbiome in health and disease 10.1016/j.cmet.2014.10.016

The treatment-naive microbiome in new-onset Crohn's disease 10.1016/j.chom.2014.02.005

Molecular cartography of the human skin surface in 3D 10.1073/pnas.1424409112

Reports of the death of the gene are greatly exaggerated 10.1007/s10539-006-9039-5

Antibiotic discovery is a walk in the park 10.1073/pnas.1618221114

Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota 10.1038/ismej.2015.64

Natural and artificial RNAs occupy the same restricted region of sequence space 10.1261/rna.1923210

Stable tRNA-based phylogenies using only 76 nucleotides 10.1261/rna.726010

The microbiome quality control project: Baseline study design and future directions 10.1186/s13059-015-0841-8

The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis 10.1371/journal.ppat.0040020

Normalization and microbial differential abundance strategies depend upon data characteristics 10.1186/s40168-017-0237-y

Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere 10.1371/journal.pone.0073079

TaskSpaces: A Software Framework for Parallel Bioinformatics on Computational Grids 10.1002/0471756504.ch26

Anal gas evacuation and colonic microbiota in patients with flatulence: Effect of diet 10.1136/gutjnl-2012-303013

Unique strain of Rickettsia parkeri associated with the hard tick Dermacentor parumapertus Neumann in the western United States 10.1128/AEM.03463-16

A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease 10.1371/journal.pone.0080702

Bringing the Dynamic Microbiome to Life with Animations 10.1016/j.chom.2016.12.009

The Human Microbiome Project 10.1038/nature06244

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota 10.1073/pnas.1306070110

Multilevel research strategies and biological systems 10.1086/677889

Microbiota and host nutrition across plant and animal kingdoms 10.1016/j.chom.2015.04.009

What is the value of a food and drug administration investigational new drug application for fecal microbiota transplantation to treat clostridium difficile infection? 10.1016/j.cgh.2013.10.009

Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns 10.1099/mic.0.2007/011833-0

Co-habiting amphibian species harbor unique skin bacterial communities in wild populations 10.1038/ismej.2011.129

Our microbial selves: What ecology can teach us 10.1038/embor.2011.137

Postprandial remodeling of the gut microbiota in Burmese pythons 10.1038/ismej.2010.71

Parallel evolution of the genetic code in arthropod mitochondrial genomes 10.1371/journal.pbio.0040127

Origin of microbial biomineralization and magnetotaxis during the Archean 10.1073/pnas.1614654114

UCHIME improves sensitivity and speed of chimera detection 10.1093/bioinformatics/btr381

Parallel mapping of antibiotic resistance alleles in Escherichia coli 10.1371/journal.pone.0146916

Individual diet has sex-dependent effects on vertebrate gut microbiota 10.1038/ncomms5500

Conducting a microbiome study 10.1016/j.cell.2014.06.037

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake 10.1101/gr.107987.110

Boulder ALignment editor (ALE): A web-based RNA alignment tool 10.1093/bioinformatics/btr258

Insights and inferences about integron evolution from genomic data 10.1186/1471-2164-9-261

CodonExplorer: An interactive online database for the analysis of codon usage and sequence composition 10.1007/978-1-59745-251-9_10

Bioinformatics Assessment of β-Myosin Mutations Reveals Myosin's High Sensitivity to Mutations 10.1016/j.tcm.2008.04.001

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea 10.1038/ismej.2011.139

The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites 10.1016/j.jaci.2012.03.010

Responses of gut microbiota to diet composition and weight loss in lean and obese mice 10.1038/oby.2011.111

Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil 10.1128/AEM.00358-07

The RNA structure alignment ontology 10.1261/rna.1601409

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch) 10.1111/ele.12301

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project 10.4056/sigs.1433550

Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota 10.1016/j.chom.2015.08.005

The genomic standards consortium: Bringing standards to life for microbial ecology 10.1038/ismej.2011.39

The long-term stability of the human gut microbiota 10.1126/science.1237439

The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins 10.1126/scitranslmed.3002701

Carcass mass has little influence on the structure of gravesoil microbial communities 10.1007/s00414-015-1206-2

Supervised classification of human microbiota 10.1111/j.1574-6976.2010.00251.x

A core gut microbiome in obese and lean twins 10.1038/nature07540

Defining seasonal marine microbial community dynamics 10.1038/ismej.2011.107

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons 10.1101/gr.112730.110

Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks 10.1016/j.mimet.2015.03.021

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions 10.1038/nmeth0910-668b

Euphorbia plant latex is inhabited by diverse microbial communities 10.3732/ajb.1500223

Fast UniFrac: Facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data 10.1038/ismej.2009.97

Ret function in muscle stem cells points to tyrosine kinase inhibitor therapy for facioscapulohumeral muscular dystrophy 10.7554/eLife.11405.001

An ancient origin of magnetotactic bacteria 10.1073/pnas.1707301114

Global biogeography of highly diverse protistan communities in soil 10.1038/ismej.2012.147

Evolution of Symbiotic Bacteria in the Distal Human Intestine 10.1371/journal.pbio.0050156

Advancing our understanding of the human microbiome using QIIME 10.1016/B978-0-12-407863-5.00019-8

Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae 10.7554/eLife.24214

BayesFold: Rational 2° folds that combine thermodynamic, covariation; and chemical data for aligned RNA sequences 10.1261/rna.5168504

The amphibian skin-associated microbiome across species, space and life history stages 10.1111/mec.12510

Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer 10.1038/ismej.2012.26

Meta-analyses of studies of the human microbiota 10.1101/gr.151803.112

Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice 10.1073/pnas.1600324113

Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids 10.1093/nar/gki886

Comparison of the vaginal microbial communities in women with recurrent genital HSV receiving acyclovir intravaginal rings 10.1016/j.antiviral.2013.12.004

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data 10.3233/AO-2011-0082

Microbiota restoration: Natural and supplemented recovery of human microbial communities 10.1038/nrmicro2473

Occurrence of the aminoacyl-tRNA synthetases in high-molecular weight complexes correlates with the size of substrate amino acids 10.1016/j.febslet.2005.05.038

Multiple pattern matching: A Markov chain approach 10.1007/s00285-007-0109-3

Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities 10.1371/journal.pone.0047879

Microbiome Tools for Forensic Science 10.1016/j.tibtech.2017.03.006

Multiplex growth rate phenotyping of synthetic mutants in selection to engineer glucose and xylose co-utilization in Escherichia coli 10.1002/bit.26217

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys 10.1038/ismej.2011.82

Lake microbial communities are resilient after a whole-ecosystem disturbance 10.1038/ismej.2012.56

Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta) 10.1002/ajp.22555

Bacterial community structures are unique and resilient in full-scale bioenergy systems 10.1073/pnas.1015676108

Structural basis for diversity in the SAM clan of riboswitches 10.1073/pnas.1312918111

Eggshell Bacterial Load Is Related to Antimicrobial Properties of Feathers Lining Barn Swallow Nests 10.1007/s00248-013-0338-5

Microbiome-wide association studies link dynamic microbial consortia to disease 10.1038/nature18850

The Ecology of Microbial Communities Associated with Macrocystis pyrifera 10.1371/journal.pone.0067480

Does protein structure influence trypsin miscleavage? 10.1109/MEMB.2005.1436461

HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats 10.1371/journal.pone.0105684

Toward effective probiotics for autism and other neurodevelopmental disorders 10.1016/j.cell.2013.11.035

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns 10.1073/pnas.1002601107

Species divergence and the measurement of microbial diversity 10.1111/j.1574-6976.2008.00111.x

Microbial endocrinology: The interplay between the microbiota and the endocrine system 10.1093/femsre/fuu010

Reply to Putignani et al.: Vagina as a major source of natural inoculum for the newborn 10.1073/pnas.1012458107

Bayesian community-wide culture-independent microbial source tracking 10.1038/nmeth.1650

MICROBIOME. A unified initiative to harness Earth's microbiomes. 10.1126/science.aac8480

How mitochondria redefine the code 10.1007/s002390010220

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets 10.1371/journal.pcbi.1002863

Walls talk: Microbial biogeography of homes spanning urbanization 10.1126/sciadv.1501061

CodonExplorer: An online tool for analyzing codon usage and sequence composition, scaling from genes to genomes 10.1093/bioinformatics/btp141

Biphasic assembly of the murine intestinal microbiota during early development 10.1038/ismej.2013.15

SitePainter: A tool for exploring biogeographical patterns 10.1093/bioinformatics/btr685

Bacterial community variation in human body habitats across space and time 10.1126/science.1177486

Human immunodeficiency virus nef signature sequences are associated with pulmonary hypertension 10.1089/aid.2011.0021

The unifrac significance test is sensitive to tree topology 10.1186/s12859-015-0640-y

Host-associated and free-living phage communities differ profoundly in phylogenetic composition 10.1371/journal.pone.0016900

Human-associated microbial signatures: Examining their predictive value 10.1016/j.chom.2011.09.003

Key challenges in proteomics and proteoinformatics 10.1109/MEMB.2005.1436456

The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice 10.1126/scitranslmed.3000322

Toward a predictive understanding of earth’s microbiomes to address 21st century challenges 10.1128/mBio.00714-16

A preliminary survey of lichen associated eukaryotes using pyrosequencing 10.1017/S0024282911000648

The convergence of carbohydrate active gene repertoires in human gut microbes 10.1073/pnas.0807339105

Analysis of the gut microbiota in the old order amish and its relation to the metabolic syndrome 10.1371/journal.pone.0043052

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011 10.4056/sigs.2134923

Using the nucleotide substitution rate matrix to detect horizontal gene transfer 10.1186/1471-2105-7-476

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat 10.1038/ismej.2012.79

Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity 10.1098/rspb.2016.1553

Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale 10.1128/AEM.00335-09

Precision medicine in alcoholic and nonalcoholic fatty liver disease via modulating the gut microbiota 10.1152/ajpgi.00245.2016

The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's "phylogenetic beta diversity" framework 10.3390/ijms10114723

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts 10.1101/gr.138198.112

The intestinal metabolome: An intersection between microbiota and host 10.1053/j.gastro.2014.03.001

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins 10.1073/pnas.1002355107

Genomic standards consortium projects 10.4056/sigs.5559680

UniFrac: An effective distance metric for microbial community comparison 10.1038/ismej.2010.133

Let researchers try new paths 10.1038/538451a

Host-bacterial coevolution and the search for new drug targets 10.1016/j.cbpa.2008.01.015

Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients 10.1038/ismej.2011.159

Technology and techniques for microbial ecology via DNA sequencing 10.1513/AnnalsATS.201306-160MG

The Western English Channel contains a persistent microbial seed bank 10.1038/ismej.2011.162

DivergentSet, a tool for picking non-redundant sequences from large sequence collections 10.1074/mcp.T600022-MCP200

The Genomic Standards Consortium 10.1371/journal.pbio.1001088

UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context 10.1186/1471-2105-7-371

Life through a microbial lens 10.1007/s11016-009-9288-4

Why microbiome treatments could pay off soon 10.1038/518S5a

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

Correction for Gonzalez et al., "Migraines Are Correlated with Higher Levels of Nitrate-, Nitrite-, and Nitric Oxide-Reducing Oral Microbes in the American Gut Project Cohort". 10.1128/msystems.00023-17

Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease. 10.1186/s40168-017-0269-3

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. 10.1128/msystems.00195-16

Pigs, Unlike Mice, Have Two Distinct Colonic Stem Cell Populations Similar to Humans That Respond to High-Calorie Diet prior to Insulin Resistance. 10.1158/1940-6207.capr-17-0010

Intermittent Hypoxia and Hypercapnia Accelerate Atherosclerosis, Partially via Trimethylamine-Oxide. 10.1165/rcmb.2017-0086oc

Erratum for Linz et al., "Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes". 10.1128/msphere.00296-17

Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9

Oral probiotic versus placebo and the maternal microbiome during pregnancy: A randomized controlled trial 10.1016/j.ajog.2019.11.064

Using microbiome tools for estimating the postmortem interval 10.1016/B978-0-12-815379-6.00012-X

Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats. 10.1128/mbio.02901-19

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

Fructose stimulated de novo lipogenesis is promoted by inflammation 10.1038/s42255-020-0261-2

The Urinary Tract Microbiome in Older Women Exhibits Host Genetic and Environmental Influences 10.1016/j.chom.2020.06.022

The emergence of microbiome centres 10.1038/s41564-019-0644-x

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

Are microbiome studies ready for hypothesis-driven research? 10.1016/j.mib.2018.07.002

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

Gut microbiome in serious mental illnesses: A systematic review and critical evaluation 10.1016/j.schres.2019.08.026

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

Voices in methods development 10.1038/s41592-019-0585-6

Engineering the microbiome for animal health and conservation 10.1177/1535370219830075

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

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity 10.1186/s13059-019-1831-z

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

Reply to Sun et al., “Identifying composition novelty in microbiome studies: Improvement of prediction accuracy” 10.1128/mBio.01234-19

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

Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome 10.1128/mSystems.00901-19

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

Redbiom: A rapid sample discovery and feature characterization system 10.1128/mSystems.00215-19

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

Preserving microbial diversity. 10.1126/science.aau8816

Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis. 10.4049/jimmunol.1800614

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

Publisher Correction: The gut-liver axis and the intersection with the microbiome. 10.1038/s41575-018-0031-8

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

The microbiome and human cancer 10.1126/science.abc4552

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

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota 10.1038/s41467-018-05284-4

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

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

A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease 10.1038/s41467-019-09455-9

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

Links between gut microbiome composition and fatty liver disease in a large population sample 10.1080/19490976.2021.1888673

Docent: Transforming personal intuitions to scientific hypotheses through content learning and process training 10.1145/3231644.3231646

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

Elizabeth Brown

Brown Elizabeth

ORCID: 0000-0002-4264-8070

Reference data based insights expand understanding of human metabolomes 10.1101/2020.07.08.194159

Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages 10.1016/j.foodchem.2019.125290

Kelly Weldon

Weldon Kelly

ORCID: 0000-0003-1064-8153

Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs 10.1101/790063

Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure 10.1101/804401

Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9

Protocol for community‐created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure 10.1002/rcm.8725

Reference data based insights expand understanding of human metabolomes 10.1101/2020.07.08.194159

Targeted Neuronal Activation of the Gastrointestinal Tract Shapes the Environment of the Gut in Mice 10.1101/2021.04.12.439539

Reference data-set driven metabolomics 10.21203/rs.3.rs-654519/v1

Alexander Aksenov

Aksenov Alexander

ORCID: 0000-0002-9445-2248

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information 10.1038/s41592-019-0344-8

Repository-scale Co- and Re-analysis of Tandem Mass Spectrometry Data 10.1101/750471

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

Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9

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

Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome 10.1128/mSystems.00901-19

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

A Cutibacterium acnes antibiotic modulates human skin microbiota composition in hair follicles 10.1126/scitranslmed.aay5445

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

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

Fernando Vargas

Vargas Fernando

ORCID: 0000-0001-5847-2439

Protocol for Community-created Public MS/MS Reference Library Within the GNPS Infrastructure 10.1101/804401

ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules 10.1101/842740

Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9

Protocol for community‐created public MS/MS reference spectra within the Global Natural Products Social Molecular Networking infrastructure 10.1002/rcm.8725

Reproducible molecular networking of untargeted mass spectrometry data using GNPS 10.1038/s41596-020-0317-5

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

Justin van der Hooft

van der Hooft Justin / Justin J.J. van der Hooft

ORCID: 0000-0002-9340-5511

Structural elucidation of low abundant metabolites in complex sample matrices 10.1007/s11306-013-0519-8

Non-smoky GLYCOSYLTRANSFERASE1 prevents the release of smoky aroma from tomato fruit 10.1105/tpc.113.114231

Automatic chemical structure annotation of an LC-MSn based metabolic profile from green tea 10.1021/ac400861a

Substructure-based annotation of high-resolution multistage MSn spectral trees 10.1002/rcm.6364

Structural annotation and elucidation of conjugated phenolic compounds in black, green, and white tea extracts 10.1021/jf300297y

Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake 10.1021/ac3017339

Spectral trees as a robust annotation tool in LC-MS based metabolomics 10.1007/s11306-011-0363-7

Metabolite identification using automated comparison of high-resolution multistage mass spectral trees 10.1021/ac2034216

Inhibitory activity of plumbagin produced by Drosera intermedia on food spoilage fungi 10.1002/jsfa.5522

A strategy for fast structural elucidation of metabolites in small volume plant extracts using automated MS-guided LC-MS-SPE-NMR 10.1002/mrc.2833

Thermal diffusivity of periderm from tomatoes of different maturity stages as determined by the concept of the frequency-domain open photoacoustic cell 10.1063/1.3530735

Polyphenol identification based on systematic and robust high-resolution accurate mass spectrometry fragmentation 10.1021/ac102546x

Iridoid and caffeoyl phenylethanoid glycosides of the endangered carnivorous plant Pinguicula lusitanica L. (Lentibulariaceae) 10.1016/j.bse.2009.05.003

Topic modeling for untargeted substructure exploration in metabolomics 10.1073/pnas.1608041113

Propagating annotations of molecular networks using in silico fragmentation 10.1371/journal.pcbi.1006089

Did a plant-herbivore arms race drive chemical diversity in Euphorbia? 10.1101/323014

Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa. 10.5702/massspectrometry.S0033

Interactions of blacktea polyphenols with human gut microbiota: implications for gut and cardiovascular health 10.3945/ajcn.113.058263

Identification of a drimenol synthase and drimenol oxidase from Persicaria hydropiper, involved in the biosynthesis of insect deterrent drimanes 10.1111/tpj.13527

Enhanced Acylcarnitine Annotation in High-Resolution Mass Spectrometry Data: Fragmentation Analysis for the Classification and Annotation of Acylcarnitines 10.3389/fbioe.2015.00026

Rapid and sustained systemic circulation of conjugated gut microbiol catabolites after single-dose black tea extract consumption 10.1021/pr5001253

In Silico Prediction and Automatic LC–MSn Annotation of Green Tea Metabolites in Urine 10.1021/ac403875b

Unexpected differential metabolic responses of Campylobacter jejuni to the abundant presence of glutamate and fucose 10.1007/s11306-018-1438-5

Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae 10.1101/463620

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra 10.1101/491506

Accelerating metabolite identification in natural product research: toward an ideal combination of LC-HRMS/MS and NMR profiling, in silico databases and chemometrics 10.1021/acs.analchem.8b05112

Untargeted Mass Spectrometry-Based Metabolomics Tracks Molecular Changes in Raw and Processed Foods and Beverages 10.1101/347716

Absorption, metabolism, distribution and excretion of (−)-epicatechin: A review of recent findings https://doi.org/10.1016/j.mam.2017.11.002

Metabolite Identification in Complex Mixtures Using Nuclear Magnetic Resonance Spectroscopy 10.1007/978-3-319-28275-6_6-2

Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry 10.1093/bioinformatics/btx582

A comprehensive evaluation of the [2-14C](–)-epicatechin metabolome in rats https://doi.org/10.1016/j.freeradbiomed.2016.08.001

The food metabolome: a window over dietary exposure 10.3945/ajcn.113.076133

Human studies on the absorption, distribution, metabolism, and excretion of tea polyphenols 10.3945/ajcn.113.058958

Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics 10.1021/acs.analchem.7b01391

A community-driven paired data platform to accelerate natural product mining by combining structural information from genomes and metabolomes 10.18174/FAIRdata2018.16286

Implementations of the chemical structural and compositional similarity metric in R and Python 10.1101/546150

Comprehensive mass spectrometry-guided phenotyping of plant specialized metabolites reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae 10.1111/tpj.14292

A genetical metabolomics approach for bioprospecting plant biosynthetic gene clusters 10.1186/s13104-019-4222-3

The Metabolomics Society—Current State of the Membership and Future Directions 10.3390/metabo9050089

Deciphering complex metabolite mixtures by unsupervised and supervised substructure discovery and semi-automated annotation from MS/MS spectra 10.1039/C8FD00235E

MolNetEnhancer: enhanced molecular networks by integrating metabolome mining and annotation tools 10.1101/654459

Substantial extracellular metabolic differences found between phylogenetically closely related probiotic and pathogenic strains of Escherichia coli 10.3389/fmicb.2019.00252

Assessing specialized metabolite diversity in the cosmopolitan plant genus Euphorbia l. 10.3389/fpls.2019.00846

Molnetenhancer: Enhanced molecular networks by integrating metabolome mining and annotation tools 10.3390/metabo9070144

In Silico Optimization of Mass Spectrometry Fragmentation Strategies in Metabolomics 10.3390/metabo9100219

MIBiG 2.0: a repository for biosynthetic gene clusters of known function 10.1093/nar/gkz882

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages 10.1016/j.foodchem.2019.125290

The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery 10.1021/acscentsci.9b00806

Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9

Assessing specialized metabolite diversity of Alnus species by a digitized LC–MS/MS data analysis workflow 10.1016/j.phytochem.2020.112292

Microbiome-derived carnitine mimics as previously unknown mediators of gut-brain axis communication 10.1126/sciadv.aax6328

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree 10.1101/2020.05.04.077636

Linking genomics and metabolomics to chart specialized metabolic diversity 10.1039/D0CS00162G

Reproducible molecular networking of untargeted mass spectrometry data using GNPS 10.1038/s41596-020-0317-5

Decomposing metabolite set activity levels with PALS 10.1101/2020.06.07.138974

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions 10.1101/2020.06.12.148205

Phenylpropane as an Alternative Dearomatizing Unit of Indoles: Discovery of Inaequalisines A and B Using Substructure-Informed Molecular Networking 10.1021/acs.orglett.0c02153

matchms - processing and similarity evaluation of mass spectrometry data 10.1101/2020.08.06.239244

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships 10.1101/2020.08.11.245928

BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters 10.1101/2020.08.17.240838

matchms - processing and similarity evaluation of mass spectrometry data. 10.21105/joss.02411

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

Feature-based molecular networking in the GNPS analysis environment 10.1038/s41592-020-0933-6

Rapid Development of Improved Data-dependent Acquisition Strategies 10.1101/2020.09.11.293092

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

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

The ant fungus garden acts as an external digestive system 10.1101/2020.11.18.389361

BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes 10.1101/2020.12.14.422671

BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters 10.1093/gigascience/giaa154

Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs 10.1371/journal.ppat.1008932

Comparative Metabologenomics Analysis of Polar Actinomycetes 10.3390/md19020103

Ranking Metabolite Sets by Their Activity Levels 10.3390/metabo11020103

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships 10.1371/journal.pcbi.1008724

Rapid Development of Improved Data-Dependent Acquisition Strategies 10.1021/acs.analchem.0c03895

MS2DeepScore - a novel deep learning similarity measure for mass fragmentation spectrum comparisons 10.1101/2021.04.18.440324

Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions 10.1371/journal.pcbi.1008920

Metabolomics-Guided Elucidation of Plant Abiotic Stress Responses in the 4IR Era: An Overview 10.3390/metabo11070445

Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden 10.1128/mSystems.00601-21

Comprehensive Large-Scale Integrative Analysis of Omics Data To Accelerate Specialized Metabolite Discovery 10.1128/mSystems.00726-21

Lara Labarta-Bajo

Labarta-Bajo Lara

ORCID: 0000-0003-1812-6704

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

TCRα reporter mice reveal contribution of dual TCRα expression to T cell repertoire and function 10.1073/pnas.2013188117

Mass spectrometry searches using MASST. 10.1038/s41587-019-0375-9

An Unusual MHC Molecule Generates Protective CD8+ T Cell Responses to Chronic Infection. 10.3389/fimmu.2020.01464

Dangerously Fit: Extracellular ATP Aids Memory T Cell Metabolism. 10.1016/j.immuni.2018.08.009

TLR9 Sensing of Self-DNA Controls Cell-Mediated Immunity to Listeria Infection via Rapid Conversion of Conventional CD4+ T Cells to Treg. 10.1016/j.celrep.2020.01.040

TGF-β receptor maintains CD4 T helper cell identity during chronic viral infections. 10.1172/jci87041

BAtCHing stem-like T cells during exhaustion 10.1038/s41590-021-00891-8

Shabnam Shalapour

Shalapour Shabnam

ORCID: 0000-0002-4743-3706

Immunotherapy, Inflammation and Colorectal Cancer 10.3390/cells9030618

Cruel to Be Kind: Epithelial, Microbial, and Immune Cell Interactions in Gastrointestinal Cancers. 10.1146/annurev-immunol-082019-081656

Mass spectrometry searches using MASST. 10.1038/s41587-019-0375-9

Pas de Deux: Control of Anti-tumor Immunity by Cancer-Associated Inflammation. 10.1016/j.immuni.2019.06.021

Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity. 10.1038/nature24302

Immunity, inflammation, and cancer: an eternal fight between good and evil. 10.1172/jci80007

Immunosuppressive plasma cells impede T-cell-dependent immunogenic chemotherapy. 10.1038/nature14395

Synergistic activity of bortezomib and HDACi in preclinical models of B-cell precursor acute lymphoblastic leukemia via modulation of p53, PI3K/AKT, and NF-κB. 10.1158/1078-0432.ccr-12-1511

Interleukin-7 links T lymphocyte and intestinal epithelial cell homeostasis. 10.1371/journal.pone.0031939

High VLA-4 expression is associated with adverse outcome and distinct gene expression changes in childhood B-cell precursor acute lymphoblastic leukemia at first relapse. 10.3324/haematol.2011.047993

The sequence of application of methotrexate and histone deacetylase inhibitors determines either a synergistic or an antagonistic response in childhood acute lymphoblastic leukemia cells. 10.1038/leu.2010.259

Commensal microflora and interferon-gamma promote steady-state interleukin-7 production in vivo. 10.1002/eji.201040441

Leukemia-associated genetic aberrations in mesenchymal stem cells of children with acute lymphoblastic leukemia. 10.1007/s00109-009-0583-8

The neglected brothers come of age: B cells and cancer 10.1016/j.smim.2021.101479

Regulation of antitumor immunity by inflammation-induced epigenetic alterations 10.1038/s41423-021-00756-y

Mauricio Caraballo

Caraballo Mauricio / Mauricio Caraballo / Andres M Caraballo-Rodriguez

ORCID: 0000-0001-5499-2728

Amphotericin B as an inducer of griseofulvin-containing guttate in the endophytic fungus Xylaria cubensis FLe9 10.1007/s00049-017-0243-3

Molecular inter-kingdom interactions of endophytes isolated from Lychnophora ericoides 10.1038/s41598-017-05532-5

Expanding the Chemical Repertoire of the Endophyte Streptomyces albospinus RLe7 Reveals Amphotericin B as an Inducer of a Fungal Phenotype 10.1021/acs.jnatprod.6b00870

Endophytic Actinobacteria from the Brazilian Medicinal PlantLychnophora ericoidesMart. and the Biological Potential of Their Secondary Metabolites 10.1002/cbdv.201500225

Protocol for Community‐created Public MS/MS Reference Spectra Within the Global Natural Products Social Molecular Networking Infrastructure 10.1002/rcm.8725

Mass spectrometry searches using MASST 10.1038/s41587-019-0375-9

Cryptic Species Account for the Seemingly Idiosyncratic Secondary Metabolism of Sarcophyton glaucum Specimens Collected in Palau 10.1021/acs.jnatprod.9b01128

Untargeted mass spectrometry-based metabolomics approach unveils molecular changes in raw and processed foods and beverages 10.1016/j.foodchem.2019.125290

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 10.1038/s41587-019-0209-9

MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools 10.3390/metabo9070144

The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization 10.1038/s41467-019-09944-x

Propagating annotations of molecular networks using in silico fragmentation 10.1371/journal.pcbi.1006089

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking 10.1038/nbt.3597

Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales 10.1016/j.ddmod.2019.08.012

Chemical signaling involved in plant–microbe interactions 10.1039/c7cs00343a

A Convolutional Neural Network-Based Approach for the Rapid Characterization of Molecularly Diverse Natural Products 10.1021/jacs.9b13786