Paperbase

Stephanie Orchanian

Orchanian Stephanie / Stephanie B. Orchanian

ORCID: 0000-0002-2491-1074

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

Genome Sequences of Cluster K Mycobacteriophages Deby, LaterM, LilPharaoh, Paola, SgtBeansprout, and Sulley. 10.1128/mra.01481-18

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science 10.7287/peerj.preprints.27295

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

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. 10.1038/s41587-019-0252-6

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science 10.7287/peerj.preprints.27295v2

High fiber, whole foods dietary intervention alters the human gut microbiome but not fecal short-chain fatty acids 10.1101/2021.02.04.429869

High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids 10.1128/mSystems.00115-21

zhenjiang xu

xu zhenjiang / Zhenjiang Zech Xu

ORCID: 0000-0003-1080-024X

https://scholar.google.com/citations?user=pR1n2NUAAAAJ&hl=en

Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor 10.4161/rna.8.3.14421

Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences 10.1093/bioinformatics/btq726

Statistical evaluation of improvement in RNA secondary structure prediction 10.1093/nar/gkr1081

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

Air proteins control differential TRAMP substrate specificity for nuclear RNA surveillance 10.1261/rna.033431.112

Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation 10.1016/j.bbrc.2015.01.074

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

Dietary effects on human gut microbiome diversity 10.1017/S0007114514004127

Subsistence strategies in traditional societies distinguish gut microbiomes 10.1038/ncomms7505

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

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

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies 10.1128/mSystems.00021-16

Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures 10.1371/journal.pone.0130200

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

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

Open-Source Sequence Clustering Methods Improve the State Of the Art 10.1128/mSystems.00003-15

Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project 10.1128/jmbe.v17i1.1034

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

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

Secondary Structure Prediction of Single Sequences Using RNAstructure 10.1007/978-1-4939-6433-8_2

Experiment-Assisted Secondary Structure Prediction with RNAstructure 10.1007/978-1-4939-6433-8_10

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

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

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns 10.1128/mSystems.00191-16

Evidence for fungal and chemodenitrification based N$_\textrm2$O flux from nitrogen impacted coastal sediments 10.1038/ncomms15595

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

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

Prediction of Secondary Structures Conserved in Multiple RNA Sequences 10.1007/978-1-4939-6433-8_3

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

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

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

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

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

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

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

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

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

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

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

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

Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems 10.1128/mSystems.00058-19

Identification of new high affinity targets for Roquin based on structural conservation 10.1093/nar/gky908

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

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

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

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

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

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

Toxicant substitutes in immunological assays for mycotoxins detection: A mini review 10.1016/j.foodchem.2020.128589

Multiple-Disease Detection and Classification across Cohorts via Microbiome Search 10.1128/mSystems.00150-20

Chlorogenic acid attenuates cadmium-induced intestinal injury in Sprague–Dawley rats 10.1016/j.fct.2019.110751

PM2RA: A Framework for Detecting and Quantifying Relationship Alterations in Microbial Community 10.1016/j.gpb.2020.07.005

Qiyun Zhu

Zhu Qiyun

ORCID: 0000-0002-3568-6271

Email: qiyunzhu@gmail.com

https://qiyunlab.github.io/

The origin of Chinese domestic horses revealed with novel mtDNA variants 10.1111/asj.12583

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

Reply to Wang and Chen: An ancient origin of magnetotactic bacteria 10.1073/pnas.1707301114

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

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

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

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

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort 10.1101/2020.09.12.20193045

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

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

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

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

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

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

Evaluating Metagenomic Prediction of the Metaproteome in a 4.5-Year Study of a Patient with Crohn's Disease. 10.1128/msystems.00337-18

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

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

Evaluating the Information Content of Shallow Shotgun Metagenomics. 10.1128/msystems.00069-18

Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea. 10.1186/s40168-018-0579-0

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

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

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

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

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

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

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

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

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

Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species. 10.1186/s12864-016-3118-z

RNA: An Expanding View of Function and Evolution. 10.4137/ebo.s38105

On the probability of dinosaur fleas. 10.1186/s12862-015-0568-x

Fleas (Siphonaptera) are Cretaceous, and evolved with Theria. 10.1016/j.ympev.2015.04.027

Bartonella spp. in fruit bats and blood-feeding Ectoparasites in Madagascar. 10.1371/journal.pntd.0003532

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. 10.1186/1471-2164-15-717

Horizontal transfers and gene losses in the phospholipid pathway of bartonella reveal clues about early ecological niches. 10.1093/gbe/evu169

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison. 10.1093/nar/gkr621

Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. 10.1016/j.devcel.2009.09.002

Recent duplication and positive selection of the GAGE gene family. 10.1007/s10709-007-9179-9

Rapid HLA-DR fluorotyping based on melting curve analysis. 10.1080/08820130701366425

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

DEPP: Deep Learning Enables Extending Species Trees using Single Genes 10.1101/2021.01.22.427808

APPLES-2: Faster and More Accurate Distance-based Phylogenetic Placement using Divide and Conquer 10.1101/2021.02.14.431150

OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures 10.1101/2021.04.04.438427

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

Luke Thompson

Thompson Luke

ORCID: 0000-0002-3911-1280

Tourmaline: a workflow for rapid and reproducible amplicon sequence analysis using QIIME 2 and Snakemake 10.1101/2021.09.15.460495

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

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments 10.1111/j.1462-2920.2010.02280.x

Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts 10.1371/journal.pbio.0040234

Draft genome sequence of uncultured SAR324 bacterium lautmerah10, binned from a Red Sea metagenome 10.1128/genomeA.01711-15

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns 10.1128/mSystems.00191-16

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism 10.1073/pnas.1102164108

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

Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments 10.1002/ece3.593

DNA Sequencing as a Tool to Monitor Marine Ecological Status 10.3389/fmars.2017.00107

A catalogue of 136 microbial draft genomes from Red Sea metagenomes 10.1038/sdata.2016.50

Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, Prochlorococcus 10.1371/journal.pone.0005135

Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages. 10.1093/molbev/msv149

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

Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by Cyanophage 10.1371/journal.pone.0165375

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

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

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

EMP DNA Extraction Protocol dx.doi.org/10.17504/protocols.io.nutdewn

EMP 16S Illumina Amplicon Protocol dx.doi.org/10.17504/protocols.io.nuudeww

EMP 18S Illumina Amplicon Protocol dx.doi.org/10.17504/protocols.io.nuvdew6

EMP ITS Illumina Amplicon Protocol dx.doi.org/10.17504/protocols.io.pa7dihn

EMP Sample Submission Guide dx.doi.org/10.17504/protocols.io.pfqdjmw

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

A Novel Sparse Compositional Technique Reveals Microbial Perturbations 10.1128/mSystems.00016-19

Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes 10.1128/AEM.00369-19

Metagenomic Covariation Along Densely Sampled Environmental Gradients in the Red Sea 10.1101/055012

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

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

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

The genome of a novel isolate of Prochlorococcus from the Red Sea contains transcribed genes for compatible solute biosynthesis 10.1093/femsec/fiy182

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

Distribution of Prochlorococcus Ecotypes in the Red Sea Basin Based on Analyses of rpoC1 Sequences 10.3389/fmars.2016.00104

Physiology and evolution of nitrate acquisition in Prochlorococcus 10.1038/ismej.2014.211

Distribution and diversity ofProchlorococcusecotypes in the Red Sea 10.1111/1574-6968.12490

Red Sea SAR11 and Prochlorococcus Single-cell Genomes Reflect Globally Distributed Pangenomes 10.1101/549816

Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies 10.1002/edn3.187

Multi-omics profiling of Earth’s biomes reveals that microbial and metabolite composition are shaped by the environment 10.1101/2021.06.04.446988

Optimizing an enclosed bead beating extraction method for microbial and fish environmental DNA 10.1002/edn3.251

Austin Swafford

Swafford Austin

ORCID: 0000-0001-5655-8300

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

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

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

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment 10.1101/2020.05.12.20073577

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

OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures 10.1101/2021.04.04.438427

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

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets. 10.1128/msystems.01216-20

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

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

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment 10.21203/rs.3.rs-56028/v2

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

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

Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV. 10.1128/msystems.00528-20

EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets 10.1101/2020.10.06.327080

Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome. 10.1128/msystems.00465-20

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

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

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

High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy. 10.1128/msystems.00292-20

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

Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs. 10.1128/msystems.00635-19

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

Human Skin, Oral, and Gut Microbiomes Predict Chronological Age. 10.1128/msystems.00630-19

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

In vivo evaluation of the CB₁ allosteric modulator LDK1258 reveals CB₁-receptor independent behavioral effects. 10.1016/j.pbb.2019.172840

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

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

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. 10.1038/s41587-019-0252-6

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

Light-Induced Stress as a Primary Evolutionary Driver of Eye Origins 10.20944/preprints201904.0107.v2

Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults. 10.1128/msystems.00261-19

MASST: A Web-based Basic Mass Spectrometry Search Tool for Molecules to Search Public Data 10.1101/591016

Age and sex-dependent patterns of gut microbial diversity in human adults 10.1101/544270

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science 10.7287/peerj.preprints.27295v2

High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity. 10.1128/msystems.00166-18

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

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

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

American Gut: an Open Platform for Citizen-Science Microbiome Research 10.1101/277970

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

Inhibition of DYRK1A and GSK3B induces human β-cell proliferation. 10.1038/ncomms9372

Detection and correction of artefacts in estimation of rare copy number variants and analysis of rare deletions in type 1 diabetes. 10.1093/hmg/ddu581

An allele of IKZF1 (Ikaros) conferring susceptibility to childhood acute lymphoblastic leukemia protects against type 1 diabetes. 10.2337/db10-0446

Thermal ablation of tumor cells with antibody-functionalized single-walled carbon nanotubes. 10.1073/pnas.0803557105

Sydney Morgan

Morgan Sydney / Sydney C. Morgan

ORCID: 0000-0002-8152-1320

Email: sydney.christian.morgan@gmail.com

https://sydneycmorgan.weebly.com/

The effect of sulfur dioxide addition at crush on the fungal and bacterial communities and the sensory attributes of Pinot gris wines 10.1016/j.ijfoodmicro.2018.09.020

Sulfur dioxide addition at crush alters Saccharomyces cerevisiae strain composition in spontaneous fermentations at two Canadian wineries 10.1016/j.ijfoodmicro.2016.12.025

The interaction of two Saccharomyces cerevisiae strains affects fermentation-derived compounds in wine 10.3390/fermentation2020009

Composition of Saccharomyces cerevisiae strains in spontaneous fermentations of Pinot noir and Chardonnay https://doi.org/10.1111/ajgw.12221

Response to Sulfur Dioxide Addition by Two Commercial Saccharomyces cerevisiae Strains 10.3390/fermentation5030069

Effect of sulfite addition and pied de cuve inoculation on the microbial communities and sensory profiles of Chardonnay wines: dominance of indigenous Saccharomyces uvarum at a commercial winery 10.1093/femsyr/foz049

An indigenous Saccharomyces uvarum population with high genetic diversity dominates uninoculated Chardonnay fermentations at a Canadian winery 10.1101/838268

Yeast and bacterial inoculation practices influence the microbial communities of barrel‐fermented Chardonnay wines 10.1111/ajgw.12438

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

An indigenous Saccharomyces uvarum population with high genetic diversity dominates uninoculated Chardonnay fermentations at a Canadian winery 10.1371/journal.pone.0225615

Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer 10.1016/j.bios.2021.113111

Semi-Automated and Miniaturized SARS-CoV-2 Detection using TaqPath COVID-19 Multiplex Real-Time RT-PCR Assay dx.doi.org/10.17504/protocols.io.brhvm366

Semi-Automated Extraction of Viral RNA using the MagMax Viral Pathogen (MVPII) 96 Kit for SARS-CoV-2 Detection dx.doi.org/10.17504/protocols.io.brcvm2w6

Semi-Automated Extraction of Viral RNA using the Omega Bio-tek Mag-Bind Viral DNA/RNA 96 Kit for SARS-CoV-2 Detection dx.doi.org/10.17504/protocols.io.brqhm5t6

Dataset on optimization and development of a point-of-care glucometer-based SARS-CoV-2 detection assay using aptamers 10.1016/j.dib.2021.107278

Semi-Automated Extraction of Viral RNA using the Omega Bio-tek Mag-Bind Viral DNA/RNA 96 Kit for SARS-CoV-2 Detection v1 10.17504/protocols.io.brqhm5t6

Adam Rivers

Rivers Adam

ORCID: 0000-0002-3703-834X

https://www.tinyecology.com

An Updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3 10.1186/1944-3277-9-11

Erratum: An updated genome annotation for the model marine bacterium Ruegeria pomeroyi DSS-3 [Stand Genomic Sci. 9, (2014), (11)] DOI: 10.1186/1944-3277-9-11 10.1186/s40793-015-0107-9

Experimental identification of small non-coding RNAs in the model marine bacterium Ruegeria pomeroyi DSS-3 10.3389/fmicb.2016.00380

Individual- and assemblage-level effects of anthropogenic sedimentation on snails in Lake Tanganyika 10.1111/j.1523-1739.2005.00456.x

Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill 10.1038/ismej.2013.129

An online calculator for marine phytoplankton iron culturing experiments 10.1111/jpy.12107

A molecular and physiological survey of a diverse collection of hydrothermal vent Thermococcus and Pyrococcus isolates 10.1007/s00792-009-0278-7

Iron stress genes in marine Synechococcus and the development of a flow cytometric iron stress assay 10.1111/j.1462-2920.2008.01778.x

Spatial homogeneity of bacterial communities associated with the surface mucus layer of the reef-building coral acropora palmata 10.1371/journal.pone.0143790

Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures 10.1038/ismej.2014.206

Sizing up metatranscriptomics 10.1038/ismej.2012.94

The transcriptional response of prokaryotes to phytoplankton-derived dissolved organic matter in seawater 10.1111/1462-2920.12434

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses 10.1093/nar/gkw1030

Patterns and drivers of fungal community depth stratification in Sphagnum peat 10.1093/femsec/fix082

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

ITSxpress: Software to rapidly trim internally transcribed spacer sequences with quality scores for marker gene analysis [version 1; referees: 2 approved] 10.12688/f1000research.15704.1

AI Down on the Farm 10.1109/mitp.2020.2986104

Under-the-Radar Dengue Virus Infections in Natural Populations of Aedes aegypti Mosquitoes 10.1128/msphere.00316-20

Harnessing AI to Transform Agriculture and Inform Agricultural Research 10.1109/mitp.2020.2986124

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

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science 10.7287/peerj.preprints.27295v2

Rice Plant–Soil Microbiome Interactions Driven by Root and Shoot Biomass 10.3390/d13030125

Changes in rhizosphere soil microbial communities across plant developmental stages of high and low methane emitting rice genotypes 10.1016/j.soilbio.2021.108233

Nine new RNA viruses associated with the fire ant Solenopsis invicta from its native range 10.1007/s11262-019-01652-4

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

Irina Koester

Koester Irina

ORCID: 0000-0002-1571-882X

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

Biological Impacts of the 2013–2015 Warm-Water Anomaly in the Northeast Pacific: Winners, Losers, and the Future 10.5670/oceanog.2016.32

Mass Spectrometry-Based Visualization of Molecules Associated with Human Habitats 10.1021/acs.analchem.6b03456

High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter 10.3389/fmars.2017.00405

Short-Term Dynamics of North Sea Bacterioplankton-Dissolved Organic Matter Coherence on Molecular Level 10.3389/fmicb.2016.00321

Spatiotemporal variability in seawater carbon chemistry for a coral reef flat in Kāne‘ohe Bay, Hawai‘i 10.1002/lno.11084

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

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

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC 10.1038/s42256-020-00234-6

Database-independent molecular formula annotation using Gibbs sampling through ZODIAC 10.1038/s42256-020-00259-x

Yong-Xin Liu

Liu Yong-Xin / Adam刘永鑫-中科院-宏基因组

ORCID: 0000-0003-1832-9835

Email: yxliu@genetics.ac.cn

http://blog.sciencenet.cn/u/woodcorpse

The role of genotype and diet in shaping gut microbiome in a genetic Vitamin A deficient mouse model 10.1016/j.jgg.2021.08.015

Expression of the Nitrate Transporter Gene OsNRT1.1A/OsNPF6.3 Confers High Yield and Early Maturation in Rice 10.1105/tpc.17.00809

Small RNA expression pattern in multiply inbred lines and their hybrids of maize embryo 10.1101/565911

NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice 10.1038/s41587-019-0104-4

A specialized metabolic network selectively modulates Arabidopsis root microbiota 10.1126/science.aau6389

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

Endogenous Small RNA Clusters in Plants 10.1016/j.gpb.2014.04.003

Root microbiota shift in rice correlates with resident time in the field and developmental stage 10.1007/s11427-018-9284-4

Recently duplicated sesterterpene (C25) gene clusters in Arabidopsis thaliana modulate root microbiota 10.1007/s11427-019-9521-2

Reductionist synthetic community approaches in root microbiome research 10.1016/j.mib.2019.10.010

Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome 10.1016/j.xplc.2019.100003

Methods and applications for microbiome data analysis 10.16288/j.yczz.19-222

N2O and NO emission from a biological aerated filter treating coking wastewater: Main source and microbial community 10.1016/j.jclepro.2018.12.182

Dynamic chromatin changes associated withde novocentromere formation in maize euchromatin 10.1111/tpj.13305

Genomic Analysis of MicroRNA Promoters and Their Cis-Acting Elements in Soybean 10.1016/s1671-2927(09)60252-2

In silico Detection of Novel MicroRNAs Genes in Soybean Genome 10.1016/s1671-2927(11)60126-0

MicroRNA Primary Transcripts and Promoter Elements Analysis in Soybean (Glycine max L. Merril.) 10.1016/s2095-3119(13)60500-6

A practical guide to amplicon and metagenomic analysis of microbiome data 10.1007/s13238-020-00724-8

High-throughput cultivation and identification of bacteria from the plant root microbiota 10.1038/s41596-020-00444-7

The rice histone methylation regulates hub species of the root microbiota 10.1016/j.jgg.2021.06.005

Source tracking and global distribution of the mobilized tigecycline resistant gene tet(X) 10.1101/2021.07.29.454411

EVenn: Easy to create repeatable and editable Venn diagrams and Venn networks online 10.1016/j.jgg.2021.07.007

Christian Diener

Diener Christian

ORCID: 0000-0002-7476-0868

http://cdiener.com

Baseline Gut Metagenomic Functional Gene Signature Associated with Variable Weight Loss Responses following a Healthy Lifestyle Intervention in Humans. 10.1128/msystems.00964-21

From taxonomy to metabolic output: what factors define gut microbiome health? 10.1080/19490976.2021.1907270

Yeast mating and image-based quantification of spatial pattern formation. 10.1371/journal.pcbi.1003690

Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin. 10.1074/jbc.M113.515023

Onset of immune senescence defined by unbiased pyrosequencing of human immunoglobulin mRNA repertoires. 10.1371/journal.pone.0049774

A low number of SIC1 mRNA molecules ensures a low noise level in cell cycle progression of budding yeast. 10.1039/c1mb05073g

What influences DNA replication rate in budding yeast? 10.1371/journal.pone.0010203

Effective Design of Multifunctional Peptides by Combining Compatible Functions. 10.1371/journal.pcbi.1004786

The space of enzyme regulation in HeLa cells can be inferred from its intracellular metabolome. 10.1038/srep28415

Personalized Prediction of Proliferation Rates and Metabolic Liabilities in Cancer Biopsies. 10.3389/fphys.2016.00644

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite 10.1101/350991

MICOM: metagenome-scale modeling to infer metabolic interactions in the gut microbiota 10.1101/361907

Synthesis of multi-omic data and community metabolic models reveals insights into the role of hydrogen sulfide in colon cancer. 10.1016/j.ymeth.2018.04.024

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers. 10.1186/s13073-018-0586-6

Non-responder phenotype reveals microbiome-wide antibiotic resistance in the murine gut 10.1101/566190

Progressive shifts in the gut microbiome reflect prediabetes and diabetes development in a treatment-naive Mexican cohort 10.1101/710152

Use and abuse of correlation analyses in microbial ecology 10.1038/s41396-019-0459-z

Negative plant-microbiome feedback limits productivity in aquaponics 10.1101/709162

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

Artifacts for q2-micom 10.5281/zenodo.3608329

Artifacts for q2-micom 10.5281/zenodo.3608330

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota 10.1128/mSystems.00606-19

Additional databases for mbtools 10.5281/zenodo.3626228

Additional databases for mbtools 10.5281/zenodo.3626229

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. 10.1038/s41587-020-0477-4

MEMOTE for standardized genome-scale metabolic model testing. 10.1038/s41587-020-0446-y

Gut Microbiome Pattern Reflects Healthy Aging and Predicts Extended Survival in Humans 10.1101/2020.02.26.966747

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. 10.1038/s41587-019-0252-6

Distinct Microbes, Metabolites, and Ecologies Define the Microbiome in Deficient and Proficient Mismatch Repair Colorectal Cancers 10.1101/346510

Weight loss response following lifestyle intervention associated with baseline gut metagenomic signature in humans 10.1101/2021.01.05.425474

Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics 10.1371/journal.pone.0247534

Gut microbiome pattern reflects healthy ageing and predicts survival in humans. 10.1038/s42255-021-00348-0

Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut 10.1038/s42003-021-01841-8

Progressive Shifts in the Gut Microbiome Reflect Prediabetes and Diabetes Development in a Treatment-Naive Mexican Cohort. 10.3389/fendo.2020.602326

Antimicrobial Peptide against Mycobacterium Tuberculosis That Activates Autophagy Is an Effective Treatment for Tuberculosis 10.3390/pharmaceutics12111071

Sean Gibbons

Gibbons Sean / Sean M. Gibbons

ORCID: 0000-0002-8724-7916

https://www.systemsbiology.org/bio/sean-gibbons/

https://scholar.google.com/citations?user=jRChVdYAAAAJ&hl=en

https://twitter.com/gibbological

https://github.com/Gibbons-Lab

Severe plant invasions can increase mycorrhizal fungal abundance and diversity 10.1038/ismej.2013.41

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

Relative strengths of relationships between plant, microbial, and environmental parameters in heavy-metal contaminated floodplain soil 10.1016/j.pedobi.2011.07.008

Modeling microbial community structure and functional diversity across time and space 10.1111/j.1574-6968.2012.02588.x

454-sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities 10.1111/j.1365-2745.2011.01894.x

Use of microcalorimetry to determine the costs and benefits to Pseudomonas putida strain KT2440 of harboring cadmium efflux genes 10.1128/AEM.01187-10

Hyporheic microbial community development is a sensitive indicator of metal contamination 10.1021/es9005465

Ecological succession and viability of human-associated microbiota on restroom surfaces 10.1128/AEM.03117-14

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

Understanding cultivar-specificity and soil determinants of the Cannabis microbiome 10.1371/journal.pone.0099641

Human and environmental impacts on river sediment microbial communities 10.1371/journal.pone.0097435

Characterizing changes in soil bacterial community structure in response to short-term warming 10.1111/1574-6941.12289

Will different OTU delineation methods change interpretation of arbuscular mycorrhizal fungal community patterns? 10.1111/nph.12758

The role of macrobiota in structuring microbial communities along rocky shores 10.7717/peerj.631

Heavy metal tolerance genes alter cellular thermodynamics in Pseudomonas putida and river Pseudomonas spp. and influence amebal predation 10.1111/1574-6968.12226

Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples 10.1371/journal.pone.0070460

Two dynamic regimes in the human gut microbiome 10.1371/journal.pcbi.1005364

Correcting for batch effects in case-control microbiome studies 10.1101/165910

Rapid response of arbuscular mycorrhizal fungal communities to short-term fertilization in an alpine grassland on the Qinghai-Tibet Plateau 10.7717/peerj.2226

Disturbance regimes predictably alter diversity in an ecologically complex bacterial system 10.1128/mBio.01372-16

Whole-grain wheat consumption reduces inflammation in a randomized controlled trial on overweight and obese subjects with unhealthy dietary and lifestyle behaviors: Role of polyphenols bound to cereal dietary fiber 10.3945/ajcn.114.088120

Spatial scale drives patterns in soil bacterial diversity 10.1111/1462-2920.13231

Ocean acidification shows negligible impacts on high-latitude bacterial community structure in coastal pelagic mesocosms 10.5194/bg-10-555-2013

Metapopulation theory provides new insight into microbial biogeography 10.1111/1462-2920.13702

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses 10.1038/s41467-017-01973-8

Invasive plants rapidly reshape soil properties in a grassland ecosystem 10.1128/mSystems.00178-16

Arbuscular mycorrhizal fungal communities show low resistance and high resilience to wildfire disturbance 10.1007/s11104-015-2633-z

The short-chain fatty acid receptor, FFA2, contributes to gestational glucose homeostasis 10.1152/ajpendo.00171.2015

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

Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management 10.1002/zoo.21220

Designing synbiotics for improved human health 10.1111/1751-7915.12885

Function over phylogeny 10.1038/s41559-016-0032

Multi-omics analysis of periodontal pocket microbial communities pre- and posttreatment 10.1128/mSystems.00016-17

Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism 10.1016/j.chom.2015.03.006

Microbial diversity-exploration of natural ecosystems and microbiomes 10.1016/j.gde.2015.10.003

The built environment is a microbial wasteland 10.1128/mSystems.00033-16

Characterization of the salivary microbiome in patients with pancreatic cancer 10.7717/peerj.1373

Blood metabolome signature predicts gut microbiome α-diversity in health and disease 10.1101/561209

Non-responder phenotype reveals microbiome-wide antibiotic resistance in the murine gut 10.1101/566190

Defining Microbiome Health through a Host Lens 10.1128/mSystems.00155-19

Use and abuse of correlation analyses in microbial ecology 10.1038/s41396-019-0459-z

Blood metabolome predicts gut microbiome α-diversity in humans 10.1038/s41587-019-0233-9

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research 10.1038/s41591-019-0559-3

MICOM: metagenome-scale modeling to infer metabolic interactions in the gut microbiota 10.1101/361907

Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome 10.1073/pnas.1922498117

Health and disease markers correlate with gut microbiome composition across thousands of people 10.1038/s41467-020-18871-1

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

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota 10.1128/msystems.00606-19

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment. 10.1186/s40168-017-0368-1

Weight loss response following lifestyle intervention associated with baseline gut metagenomic signature in humans 10.1101/2021.01.05.425474

Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification 10.1128/mSystems.01025-20

Gut microbiome pattern reflects healthy ageing and predicts survival in humans. 10.1038/s42255-021-00348-0

Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut 10.1038/s42003-021-01841-8

Elevated rates of horizontal gene transfer in the industrialized human microbiome 10.1016/j.cell.2021.02.052

From taxonomy to metabolic output: what factors define gut microbiome health? 10.1080/19490976.2021.1907270

Baseline Gut Metagenomic Functional Gene Signature Associated with Variable Weight Loss Responses following a Healthy Lifestyle Intervention in Humans 10.1128/mSystems.00964-21

Christopher Keefe

Keefe Christopher

ORCID: 0000-0002-4289-0991

Email: chriskeefe@nau.edu

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

Developing a QIIME 2 plugin: a simple annotation for robust tools 10.6084/m9.figshare.8014976.v1

Enabling Reproducible Microbiome Science through Decentralized Provenance Tracking in QIIME 2 10.6084/m9.figshare.8014805.v1

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