First Author



Pubmed Keywords


“Context and the human microbiome” McDonald, Daniel Microbiome 2015 American Gut Project
“ConStrains identifies microbial strains in metagenomic datasets” Luo, Chengwei Nature Biotechnology 2015 Data mining, Metagenomics, Informatics
“Genetic and environmental control of host-gut microbiota interactions” Org, Elin Genome Research 2015 Gut Microbiota
“Microbiome Studies of Carrion Decomposition” Metcalf, Jessica Carrion Ecology, Evolution, and Their Applications 2015 Carrion decomposition, genes
“Changes in vaginal microbiota following antimicrobial and probiotic therapy” Macklaim, Jean Microbial Ecology in Health and Diseases 2015 Vaginal microbiota, Lactobacillus, bacterial vaginosis, vulvovaginal candidiasis, probiotics
“Short Course in the Microbiome” Falana, Kimberly Journal of Circulating Biomarkers 2015 Bacteria, Gut microbiota
“The UniFrac significance test is sensitive to tree topography” Lozupone, Catherine A BMC Bioinformatics 2015 Unifrac, Phylogenetic tree, Microbial Community
“Effects of library size variance, sparsity, and compositionality on the analysis of microbiome data” Weiss, Sophie PeerJ 2015 Bioinformatics, Computional Biology, Ecology, Statistics
“Analysis of composition of microbiomes: a novel method for studying microbial composition” Mandal, Siddhartha Microbial Ecology in Health and Disease 2015 ANCOM
“Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses” Fuoquier, Jennifer PeerJ 2015 Ghost-tree, phylogeny
“Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity” He, Yan Microbiome 2015 OTU, Taxonomy, Operational taxonomic unit
“Molecular cartography of the human skin surface in 3D” Bouslimani, A Proceedings of the National Academy of Sciences 2015 3D mapping, Human skin, Mass spectrometry
“The microbiome of uncontacted Amerindians” Clemente, Jose ScienceAdvances 2015 Yanomami, Amerindians, AR genes
“Ribosomal RNA: the lens into life” McDonald, Daniel RNA 2015 rRNA
“Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection” Weingarden, Alexa Microbiome 2015 FMT, Fecal microbiota transplantation, CDI, Clostridium difficile,
“A standardized, extensible framework for optimizing classification improves marker-gene taxonomic assignments” Bokulich, NIcholas PeerJ 2015 Bioinformatics, Computional Biology, Ecology, Microbiology, Taxonomy
“Subsistence strategies in traditional societies distinguish gut microbiomes” Obregon-Tito, AJ Nature Communications 2015 Hunter-gatherer, Agriculturalist, Peru, Treponema succinifaciens
“Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients” McDonald, Daniel Microbial Ecology in Health and Disease 2015 ASD, autism spectrum disorder
“Seasonal variation of postmortem microbial communities.” Carter, David O. Forensic Science, Medicine, and Pathology 2015 Posmortem microbial community, decomposition
“Identifying qualitative effects of different grazing types on below-ground communities and function in a long-term field experiment” Macdonald, Katriona Environmental Microbiology 2015 Herbivores, Grazing, Soil function
“Microbial endocrinology: the interplay between the microbiota and the endocrine system.” Neuman, Hadar Oxford Journals 2015 Endocrine system, Endocrinology, Hormones
“Carcass mass has little influence on the structure of gravesoil microbial communities” Weiss, Sophie International Journal of Legal Medicine 2015 Postmortem microbial community, Decomposition, Carcass mass, Pathology
“Dietary effects on human gut microbiome diversity” Xu, Zhenjiang British Journal of Nutrition 2015 Diet, Human microbiome
“Tracking down the sources of experimental contamination in microbiome studies” Weiss, Sophie Genome Biology 2014 DNA extraction kits, Laboratory reagents
“Meeting report for the 1st skin microbiota workshop, boulder, CO October 15-16 2012” Gilbert, Jack A Standards in Genomic Sciences 2014 Skin microbiome, Bioinformatics
“Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats” Agnieszka, Mika PLoS One 2014 Exercising, Intestine
“Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013” Ravel, Jacques Microbiome 2014 Microbiome research, medical translational
“Meta-analyses of human gut microbes associated with obesity and IBD” William, Walters A FEBS Letters 2014 Obesity, IBD, Inflammatory bowel disease,
“Gut Microbes and the Brain: Paradigm Shift in Neuroscience” Mayer, Emeran A The Journal of Neuroscience 2014 Neurocine and endocrine signaling mechanisms, pathophysiological
“Human genetics shape the gut microbiome” Goodrich, Julia K Cell Press 2014 Genetics, phenotypes, twin studies, Christensenellaceae, Christensenella minuta
“Specialized Metabolites from the Microbiome in Health and Disease” Sharon, Gil Cell Press 2014 Immunity, metabolites
“Advancing the Microbiome Research Community” Huttenhower, Curtis Cell Press 2014 Microbiome research, medical translational
“Bacteria from Diverse Habitats Colonize and Compete in Mouse Gut” Seedorf, Henning Cell Press 2014 Mouse gut, xenomicrobiota
“Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity” Bolnick, Daniel I. Molecular Ecology 2014 Major Histocompatibility Class II, MHC IIb Class Polymorphism, Threespine stickleback
“Longitudinal analysis of microbial interaction between humans and the indoor environment” Lax, Simon Science 2014 Indoor microbiology, Household microbiota
“Which is more important for classifying microbial communities: who’s there or what they can do?”0 Xu, Zhenjiang The ISME Journal 2014 Phylogenetic analysis, Taxonomy, PICRUSt
“Glycan Degradation (GlyDeR) Analysis Predicts Mammalian Gut Microbiota Abundance and Host Diet-Specific Adaptations” Eilam, Omar mBio 2014 Glycans, Glycan Degradation, GlyDeR, mammalian gut
“Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity” Shade, Ashley mBio 2014 Conditionally rare taxa, CRT
“The Earth Microbiome project: successes and aspirations” Gilbert, Jack A BMC Biology 2014 Earth Microbiome Project, EMP, Biomes
“Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences” Rideout, Jai R PeerJ 2014 Bioinformatics, Microbial ecology, OTU picking, Qiime
“HLA-B27 and human β2-microglobulin affect the gut microbiota of transgenic rats.” Lin, Phoebe PLoS One 2014 HLA-B27, Human β2-microglobulin, hβ2m, Mouse gut
“Vertebrate decomposition is accelerated by soil microbes.” Lauber, CL Applied and environmental microbiology 2014 Carrion decomposition, Soil microbes, Vertebrae decomposition
“Individuals’ diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)” Bolnick, Daniel I. Ecology Letters 2014 Diet, Threespine stickleback, Eurasian perch
“SnapShot: The Human Microbiome” Gonzalez, Antonio Cell Press 2014 SnapShot, Human Microbiome Project, HMP
“Individual diet has sex-dependent effects on vertebrate gut microbiota” Bolnick, Daniel I. Nature Communications 2014 Diet, Sex-dependent, Threespine stickleback, Eurasian perch
“Satellite remote sensing data can be used to model marine microbial metabolite turnover” Larsen, Peter E The ISME Journal 2014 Bioinformatics, ecosystems
“Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.” Mason, Olivia U The ISME Journal 2014 Deepwater Horizon spill
“From microbiomes to metabolomes to function during host-microbial interactions” Dorrestein, Pieter C Immunity 2014 Metabolome, Gut microbiota
“Finding the Missing Links among Metabolites, Microbes, and the Host” Dorrestein, Pieter C Immunity 2014 Metabolome
“Genomic Standards Consortium Projects” Field, Dawn Standards in Genomic Sciences 2014 GSC, Genomic Standards Consortium
“Improved HF183 quantitative real-time PCR assay for characterization of human fecal pollution in ambient surface water samples.” Green, Hyatt C Applied and environmental microbiology 2014 HF183, qPCR
“RNA structure; X-ray crystallography; chemical probing; gene regulation; isothermal titration calorimetry” Trausch, Jeremiah PNAS 2014 RNA structure; X-ray crystallography;, Chemical probing, Gene regulation; Isothermal titration calorimetry
“Interacting symbionts and immunity in the amphibian skin mucosome predict disease risk and probioticeffectiveness.” Woodhams, Doulgas C PLoS One 2014 Probiotics, Amphibians, Antifungals, Metabolites, Batrachochytrium dendrobatidis, ,
“Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest” Neslihan, Tas The ISME Journal 2014 Carbon release, Climate change, Metagenomics
“Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus)” Loudon, Andrew H The ISME Journal 2014 Amphibians, Bacterial reservoirs, Batrachochytrium dendrobatidis, Symbiosis
“Predictive modeling of gingivitis severity and susceptibility via oral microbiota” Huang, Shi The ISME Journal 2014 Gingivitis, Plaque, Metagenomics
“The treatment-naïve microbiome in new-onset Crohn’s disease” Gevers, Dirk Cell Host & Microbe 2014 IBD, Inflammatory bowel Disease, crohn’s disease, Enterobacteriaceae, Pasteurellacaea
“The founding charter of the Genomic Observatories Network” Davies, Neil Gigascience 2014 Biodiversity, Genomics, Biocode, Earth observations
“Convergence of gut microbiomes in myrmecophagous mammals” Delsuc, Frédéric Molecular Ecology 2014 Myrmecophagous mammals, Mammalian gut
“Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet.” Manichanch, Chaysavanh Gut 2014 Colonic Bacteria, Colonic Fermentation, Colonic Microflora, Functional Bowel Disorder, Visceral Sensitivity
“What is the value of a food and drug administration investigational new drug application for fecal microbiota transplantation to treat Clostridium difficile Infection?” Hecht, Gail A Clinical Gastroenterology and Hepatology 2014 Gastroenterology, Nutrition, Clostridium difficile, Fecal microbiota
“Multilevel Research Strategies and Biological Systems” O’Malley, Maureen A PhilSci 2014 Research strategies, Microbial ecology, Systems biology
“Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity” Parfrey, Laura Wegener Frontiers in Microbiology 2014 Protist, m/icrobial ecology, /microbial diversity, Salinity, Host-associated eukaryotes, Parasites, Intestinal protozoa
“Technology and Techniques for Microbial Ecology via DNA Sequencing” Walters, William A ATS Journals 2014 Metagenomics, Sequencing, Microbial ecology, Phylogenetics
“MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment” Glass, Elizabeth M The ISME Journal 2014 Metadata MIxS-BE
“Diversity of Rickettsiales in the Microbiome of the Lone Star Tick, Amblyomma americanum” Ponnusamy, Longanathan Applied and environmental microbiology 2014 Amblyomma americanum, Star tick, sca0 gene
“Toward Effective Probiotics for Autism and Other Neurodevelopmental Disorders” Gilbert, Jack A Cell Press 2013 ASD, autism spectrum disorder, Bacteroides fragilis
“EMPeror: a tool for visualizing high-throughput microbial community data” Vazquez-Baeza, Yoshiki Gigascience 2013 Microbial ecology, QIIME, EMPeror, Data visualization
“A Modular Organization of the Human Intestinal Mucosal Microbiota and Its Association with Inflammatory Bowel Disease” Tong, Maomeng PLoS One 2013 Crohn’s disease, CD, Ulcerative colitis (UC), IBD, Inflammatory bowel disease, Intenstinal microbiota
“A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system” Metcalf, Jessica eLife 2013 Postmortem interval, PMI, Mouse
“Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota” Kashyap, Purna C Proceedings of the National Academy of Sciences 2013 Host–microbial mutualism, Intestinal microbiota, Metabolomics
“Meta-analyses of studies of the human microbiota.” Lozupone, Catherine A Genome Research 2013 QIIME, Cross-study comparisons
“Alterations in the Gut Microbiota Associated with HIV-1 Infection” Lozupone, Catherine A Cell Host & Microbe 2013 HIV-infection, Chronic gut inflammation
“Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere” Otesen, Andrea R PLoS One 2013 Salmonella, Tomato phyllosphere
“Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and Colon” Devine, Anthony A PLoS One 2013 ICR, Ileocecal resection, Crohn’s disease, Murine jejunum, Colon, Concomitant antibiotics
“Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences” Langille, Morgan G.I. Nature Biotechnology 2013 Environmental microbiology, Gastrointestinal diseases, Microbial ecology
“The long-term stability of the human gut microbiota.” Faith, Jeremiah J Science 2013 LEA-Seq, Gut microbiota
“The ecology of microbial communities associated with Macrocystis pyrifera” Michelou, Vanessa K PLoS One 2013 Kelp forests, Macrocystis pyrifera, Gammaproteobacteria
“Nucleotides Adjacent to the Ligand-Binding Pocket are Linked to Activity Tuning in the Purine Riboswitch” Stoddard, Colby D Journal of Molecular Biology 2013 Riboswitch, RNA structure, Mutual information, Transcriptional regulation, Activity tuning
“Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)” Ottesen, Andrea R BMC Microbiology 2013 Salmonella, Solanum lycopersicum, Tomato
“Widespread Colonization of the Lung by Tropheryma whipplei in HIV Infection “ Lozupone, Catherine A ATS Journals 2013 Bronchoalveolar lavage, Lung infection, HIV infection
“Cohabiting family members share microbiota with one another and with their dogs” Song, Se Jin eLife 2013 Household microbial communities, Indoor microbiology
“Meeting Report: Fungal ITS Workshop (October 2012)” Bates, Scott T Standards in Genomic Sciences 2013 Fungal community, ITS sequence, internal transcribed spacer region, rRNA
“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” Smith, Daniel Standards in Genomic Sciences 2013 Hospital Microbiome Project, University of Chicago, Hospital-acquired infections, HAI
“A meta-analysis of changes in bacterial and archaeal communities with time” Shade, Ashley The ISME Journal 2013 Similarity-decay, Species–time relationship, Beta diversity, Turnover, High-throughput sequencing
“Biphasic assembly of the murine intestinal microbiota during early development” Pantoja-Feliciano, Ida Gisela The ISME Journal 2013 Community structure, Intestinal microbiota, Mammal development, Lactobacillus
“How delivery mode and feeding can shape the bacterial community in the infant gut” Song, Se Jin CMAJ 2013 Infant gut, Newborns
“Evidence for a persistent microbial seed bank throughout the global ocean” Gibbons, Sean M PNAS 2013 Ocean microbial community, English Channel, ICoMM, Internaitonal Census of Marine Microbes
“Global biogeography of highly diverse protistan communities in soil” Bates, Scott T The ISME Journal 2013 Soil protists, Protistan taxa, Microbial ecology
“Collaborative cloud-enabled tools allow rapid, reproducible biological insights” Ragan-Kelley, Benjamin The ISME Journal 2013 Bioinformatics, IPython
“From molecules to dynamic biological communities” McDonald, Daniel Biology & Philosophy 2013 Timeseries, Microbial community analysis, Operational taxonomic units, OTU
“Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities” Kittelmann, Sandra PLoS One 2013 Archaean biology, Anaerobic bacteria, Protozoans, rRNA, Fungi, Methanogens
“Bacterial Diversity in Two Neonatal Intensive Care Units (NICUs)” Hewitt, Krissi M PLoS One 2013 NICUs, Neonatal Intensive Care Units, Enterobacteriales
“A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets” Koren, Omry PLoS Computational Biology 2013 Enterotypes, Human Microbiome Project, HMP, Meta-analysis
“Genetic Control of Obesity and Gut Microbiota Composition in Response to High-Fat, High-Sucrose Diet in Mice” Parks, Brian W Cell Metabolism 2013 Obesity, Mouse, High fat, High sucrose, Diet
“Advancing Our Understanding of the Human Microbiome Using QIIME” Navas-Molina, Jose A Methods in Enzymology 2013 Highthroughput sequencing, Microbial community analyses, QIIME
“Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle” Carey, Hannah V American Journal of Physiology 2013 Squirrel microbiota, Hibernation, Diet
“Crystal ball – 2013” Curtis, Tom Microbial Biotechnology 2013 Future of microbiology, Synthetic biology
“Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents” Blaser, Martin J The ISME Journal 2013 Venezuelan Amazon, Amerindians, Microbial diversity
“Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat” Harris, J Kirk The ISME Journal 2013 Guerrero Negro, rRNA phylogeny, Microbial mats, microbial ecology, QIIME
“Insights from Characterizing Extinct Human Gut Microbiomes” Tito, Raul Y PLoS One 2012 Extinct human microbiomes, Hinds Cave, Caserones, Rio Zape
“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” Maslanik, Thomas PLoS One 2012 Antibiotics, Cyotkines, Inflammasomes, Commensal bacteria, MAMPs, IL–1β, IL-18
“Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts” Lozupone, Catherine A Genome Research 2012 Clostridium coccoides, Eubacterium rectale, IBD, Inflammatory Bowel Disease
“Microbiota Regulate Intestinal Absorption and Metabolism of Fatty Acids in the Zebrafish” Semova, Ivana Cell Host & Microbe 2012 Intenstinal microbiota, Gnotobiotic zebrafish, Fatty acids
“Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau” Xiong, Jinbo Environmental Microbiology 2012 Tibetan Plateau, Bacterial communities, pH
“Transient Inability to Manage Proteobacteria Promotes Chronic Gut Inflammation in TLR5-Deficient Mice” Carvalho, Federic Cell Host & Microbe 2012 “TLR5, Colitis, Gut microbial diversity, Pyrosequencing, Adherent-invasive Escherichia coli”
“Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome” Zupancic, Margaret L PLoS One 2012 Obesity, Old Order Amish, Metabolism
“The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome” Gevers, Dirk PLoS Biology 2012 Human Microbiome Project, HMP, Metagenomics
“Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy” Koren, Omry Cell Press 2012 Pregnancy, Metabolic changes
“The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome” McDonald, Daniel Gigascience 2012 Biological Observation Matrix, BIOM, Bioinformatics
“Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences” Wang, Xiaoyu The ISME Journal 2012 Secondary structure, ESPIRIT-Tree, Operational taxonomic units, OTU
“RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs.” Widmann, Jeremy RNA 2012 RNA, Bioinformatics, SPuNC
“Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis” Sullam, Karen E Molecular Ecology 2012 Fish gut bacteria, Microbial ecology
“Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys” Werner, Jeffrey J The ISME Journal 2012 Illumina, Bioinformatics, Pair-ende and single-direction sequencing
“Structure, function and diversity of the healthy human microbiome” Nature 2012 Ecology, Microbiology, Genomics
“Spatial and temporal variability of the human microbiota” Parfrey, Laura Wegener Clinical Microbiology and Infection 2012 Community stability, pertubation
“Human gut microbiome viewed across age and geography” Yatsunenko, Tanya Nature 2012
“Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients” Fierer, Noah The ISME Journal 2012 Shotgun metagenomics, Pyrosequencing, Soil bacteria, Nitrogen fertilization, Soil carbon dynamics
“Responses of Gut Microbiota to Diet Composition and Weight Loss in Lean and Obese Mice” Ravussin, Yann Obesity 2012 Obseity, Mouse, Diet, Weight Loss
“Spatial and temporal dynamics of the microbial community in the Hanford unconfined aquifer” Lin, Xueju The ISME Journal 2012 Hanford Site, Columbia River
“Conceptualizing a Genomics Software Institute (GSI)” Gilber, Jack A Standards in Genomic Sciences 2012 Genomics Software Institute, GSI, Bioinformatics
“The Impact of the Gut Microbiota on Human Health: An Integrative View” Clemente, Jose C Cell Press 2012 Human health, Microbiota
“Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms” Caporaso, J Gregory The ISME Journal 2012 Illumnia HiSeq2000, QIIME, Bioinformatics
“Co-habiting amphibian species harbor unique skin bacterial communities in wild populations” McKenzie, Valerie J The ISME Journal 2012 Amphibian, Host specific, Microbial symbiots, Pond habitats
“An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea” McDonald, Daniel The ISME Journal 2012 Phylogenetics, Taxonomy, Greengenes
“SitePainter: a tool for exploring biogeographical patterns” Gonzalez, Antonio Bioinformatics 2012 SitePainter, Taxonomy, Bioinformatics
“Defining seasonal marine microbial community dynamics” Gilbert, Jack A The ISME Journal 2012 Operational Taxonomic Units, OTU, Microbial time-series, Plymouth, Alphaproteobacteria
“Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences” Soergel, David A W The ISME Journal 2012 Taxonomy, Phylogeny, Rtax method
“Gene discovery from a pilot study of the transcriptomes from three diverse microbial eukaryotes: Corallomyxa tenera, Chilodonella uncinata, and Subulatomonas tetraspora” Grant, Jessica R Protist Genomics 2012 RNA, Corallomyxa tenera, Chilodonella uncinata, Subulatomonas tetraspora, Phylogenetics
“A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis” Sun, Yijun Briefings in Bioinformatics 2012 Pyrosequencing, Taxonomy-independent analysis, Massive data, Clustering, Microbial diversity estimation, Bioinformatics, ESPRIT-Tree
“Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys” Werner, Jeffrey J The ISME Journal 2012 Greengenes, Naïve Bayesian classifier, Pyrosequencing, Taxonomy
“Composition of human skin microbiota affects attractiveness to malaria mosquitoes” Verhulst, Niels O PLoS One 2011 African malaria mosquito, Anopheles gambiae sensu stricto, Skin microbiota
“The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011” Gilbert, Jack A Standards in Genomic Sciences 2011 International Microbiome Project, BGI, Research projects
“Microbial biogeography of public restroom surfaces” Flores, Gilberto E PLoS One 2011 Bathroom microbiota, Indoor microbiology, Actinobacteria, Bacteriodetes, Firmicutes, Proteobacteria
“TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata” Pirrung, Meg Bioinformatics 2011 TopiaryExplorer, Phylogenetics, Bioinformatics, Taxonomy
“Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes” Wu, Gary D Science 2011 Baceteroides, Prevotella, Gut Microbial Enterotypes
“Human-Associated Microbial Signatures: Examining Their Predictive Value” Knights, Dan Cell Host & Microbe 2011 Microbial communities, Machine learning, Source tracking, Indicator species
“The genomic standards consortium: bringing standards to life for microbial ecology” Yilmaz, Pelin The ISME Journal 2011 Metagenomes, MG-RAST Annotation server, Marker studies
“Sources of Bacteria in Outdoor Air across Cities in the Midwestern United States” Bowers, Robert M Applied and environmental microbiology 2011 Bacteria, Atmosphere, Pyrosequencing, Organic aerosols
“UCHIME improves sensitivity and speed of chimera detection” Edgar, Robert C Bioinformatics 2011 Chimeric DNA, Chimeras, UCHIME, Bioinformatics
“Our microbial selves: what ecology can teach us” Gonzalez, Antonio EMBO Reports 2011 Ecological theory, Microbiota, Pathogenesis, Microbial diversity
“Sharing and archiving nucleic acid structure mapping data” Rocca-Serra, Phillippe RNA 2011 RNA struture, Chemical mapping, Secondary structure
“The Genomic Standards Consortium” Field, Dawn PLoS Biology 2011 GSC, Genomic Standards Consortium
“Moving pictures of the human microbiome” Caporaso, J Gregory Genome Biology 2011 Time series analysis, Human microbiota
“Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications Yilmaz, Pelin Nature Biotechnology 2011 GSC, Genomic Standards Consortium, MIMARKS, MIxS
“Examining the global distribution of dominant archaeal populations in soil” Bates, Scott T The ISME Journal 2011 Archaea, Crenarchaeota, Microbial ecology, Pyrosequencing, Soil
“PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers” Walters, William A Bioinformatics 2011 PrimerProspector, PCR amplication. Bioinformatics
“Meeting report of the RNA Ontology Consortium January 8-9, 2011” Birmingham, Amanda Standards in Genomic Sciences 2011 RNA Ontology Consortium, ROC, RNA-related software
“Supervised classification of microbiota mitigates mislabeling errors” Knights, Dan The ISME Journal 2011 Human Microbiome Project, HMP,
“Microbes do not follow the elevational diversity patterns of plants and animals “ Fierer, Noah ESA Journals 2011 Elevational gradient, Bacterial diveristy, Phyllosphere bacteria, Pyrosequencing, Soil bacteria
“Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments” Bowers, Robert M The ISME Journal 2011 Bioaerosol, Land-use, Ice nucleation, Pyrosequencing, Atmospheric microorganisms
“Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins” Hansen, Elizabeth E PNAS 2011 Twin studies, Methanobrevibacter smithii, Metagenomics, Horizontal gene transfer
“Human oral, gut, and plaque microbiota in patients with atherosclerosis” Koren, Omry PNAS 2011 Atherosclerosis, qPCR, Chryseomonas
“Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample” Caporaso, J Gregory PNAS 2011 Microbial communities, Microbial ecology, Next-generation sequencing
“Succession of microbial consortia in the developing infant gut microbiome” Koenig, Jeremy E PNAS 2011 Metageonmics, Community assembly, Microbial diveresity
“Bacterial community structures are unique and resilient in full-scale bioenergy systems” Werner, Jeffrey J PNAS 2011 UniFrac, Community function, Digestion, Digester, OTU, Operational Taxonomic Unit
“The mind-body-microbial continuum” Gonzalez, Antonio Dialogues in Clinical Neuroscience 2011 Higher brain function, Human microbial ecology, Gut microbiome, Metabolism, Autism, Pharmacology
“Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.” Haas, Brian J Genome Research 2011 Chimeras, Chimera Slayer, CS, BIoinformatics
“Host-Associated and Free-Living Phage Communities Differ Profoundly in Phylogenetic Composition” Caporaso, J Gregory PLoS One 2011 Phylogenetic profiling, Shotgun UniFrac
“Bacterial Communities Associated with the Lichen Symbiosis” Bates, Scott T Applied and environmental microbiology 2011 Lichens, Fungi, Algae, Chlorophyta, Cyanobacteria
“UniFrac: an effective distance metric for microbial community comparison” Lozupone, Catherine The ISME Journal 2011 UniFrac, Bioinformatics
“Closure of the NCBI SRA and implications for the long-term future of genomics data storage” GB Editorial Team Genome Biology 2011 National Center for Biotechnology Information, NCBI, Sequence Read Archive, SRA
“Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions” Parfrey, Laura Wegener Frontiers in Microbiology 2011 Intestinal protozoa, Host-associated communities, Eukaryotic diversity
“Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010” Gilbert, Jack A Standards in Genomic Sciences 2010 Metagenomics, Metadata, Metaanalysis, Models and Metainfrastructures, M5
“Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project” Gilber, Jack A Standards in Genomic Sciences 2010 Bioinformatics, Terabase Metagenomics, Illumina HiSeq 2000, Earth Microbiome Project, EMP
“The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.” Gilbert, Jack A Standards in Genomic Sciences 2010 Earth Microbiome Project, EMP, Phylogenetic diversity
“Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems” Ramirez, Kelly S ESA Journals 2010 Microbial ecology, NBItrogen, Pyrosequencing, Soil microbiology, Soil bacteria
“The bacterial microbiota in the oral mucosa of rural Amerindians” Contreras, Monica Microbiology 2010 Intestinal Microbiota, Oral Cavity, Oral mucosa, Amerindians
“Reply to Putignani et al.: Vagina as a major source of natural inoculum for the newborn” Dominguez-Bello, Maria G PNAS 2010 Vagnial microbiota, Lactobacilli, Anaerobic bacteria, Bacteroides
“A Data Analysis and Coordination Center for the Human Microbiome Project” Wortman, Jennifer Human Microbiome Project 2010 HMP, Human Microbiome Project, Data Analysis
“Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA” Majerfeld, Irene RNA 2010 SELEX, Tryptophan, RNA
“Reshaping the gut microbiome with bacterial transplantation and antibiotic intake” Manichanch, Chaysavanh Genome Research 2010 Intenstinal microbiota, Transplantation, Antibiotic intake
“Stable tRNA-based phylogenies using only 76 nucleotides” Widmann, Jeremy RNA 2010 tRNA, UniFrac, Isoacceptors, Phylogeny
“Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags” Wu, Gary D BMC Microbiology 2010 Roche pyrosequencing, 16S rRNA gene tag, Bacterial communities
“Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives” Zeneveld, Jesse R Nucleic Acids Research 2010 Mammalian gut, 16S rRNA gene sequence, Phylogenetic distances
“Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns” Dominguez-Bello, Maria G PNAS 2010 Host-microbe interactions, Neonatal bacterial assemblages, Infant gut
“Postprandial remodeling of the gut microbiota in Burmese pythons” Costello, Elizabeth K The ISME Journal 2010 Burmese python, Fasting, Host-microbe interactions, Nutrietn deprivation, REptile
“Soil bacterial and fungal communities across a pH gradient in an arable soil” Rousk, Johannes The ISME Journal 2010 Soil microbiota, pH, qPCR, Pyrosequencing, Bacterial community
“Direct sequencing of the human microbiome readily reveals community differences” Kuczynski, Justin Genome Biology 2010 Culture-independent studies
“Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins Turnbaugh, Peter J PNAS 2010 Twin studies, Microbial phylogenetic analysis, Transcriptomics, Carbohydrate active enzymes
“Forensic identification using skin bacterial communities” Fierer, Noah PNAS 2010 Bacterial forensics, Pyrosequencing, Skin microbiology, Microbial ecology
“Simple, recurring RNA binding sites for L-arginine.” Janas, Teresa RNA 2010 L-arginine, Amino acid, Genetic code, RNA
“Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples” Lauber, Christian L FEMS Microbiology Letters 2010 Storage conditions, Pyrosequencing, Microbial community, Soil, Fecal microbiota, Skin microbiota
“Natural and artificial RNAs occupy the same restricted region of sequence space” Kennedy, Ryan RNA 2010 SELEX, In vitro selection, Nucleotide composition, RNA
“Bacterial communities of disease vectors sampled across time, space, and species” Jones, Ryan T The ISME Journal 2010 Rickettsia, Bartonella, Phylogenetics, Pathogens
“PyNAST: a flexible tool for aligning sequences to a template alignment” Caporaso, J Gregory Bioinformatics 2010 PyNAST, Python Nearest Alignment Space Termination, Phylogenetics, Bioinformatics
“Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data” Hamady, Micah The ISME Journal 2009 Beta diversity, Community ecology, Pyrosequencing, PhyloChips, UniFrac
“The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice” Turnbaugh, Peter J Science Translational Medicine 2009 Diet, Gut microbiota, Nutrition, Gnotobiotic Mice, Metagenomic Analysis
“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” Faith, Daniel P International Journal of Molecular Sciences 2009 Bacteria, UniFrac, PD calculus, Climate change
“RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code” Yarus, Michael Journal of Molecular Evolutuion 2009 RNA, Genetic code, Crystallographic, NMR structural data
“Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat” Goodman, Andrew L Cell Host & Microbe 2009 Gut microbiota, INSeq, Mutagenic transposon, Bacteroides thetaiotaomicron
“The RNA structure alignment ontology” Brown, James W RNA 2009 Ontology, Bionformatics, RNA structure
“Characterization of airborne microbial communities at a high-elevation site and their potential to act as atmospheric ice nuclei.” Bowers, Robert M Applied and environmental microbiology 2009 Bacteria, Fungi, Burkholderiales, Moraxellaceae, Northwestern Colorado, Environmental microbiology
“Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale.” Lauber, Christian L Applied and environmental microbiology 2009 UniFrac, Soil microbiota, Pyrosequencing
“The RNA Ontology (RNAO): An Ontology for Integrating RNA Sequence and Structure Data “ Batchelor, Colin Proceedings of the International Conference on Biomedical Ontologies 2009 RNA Ontology, RNAO, RNA sequence, ROC, RNA Ontology COnsortium
“Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation” Crawford, Peter A PNAS 2009 Gnotobiotic mice, Host-microbial interaction, Gut microbiota,
“Microbial community profiling for human microbiome projects: Tools, techniques, and challenges” Hamady, Micah Genome Research 2009 Human Microbiome Project, HMP, High-throughput sequencing studies, Human microbiota
“Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale” Lauber, Christian L Applied and environmental microbiology 2009 Soil microbiota, pH, UniFrac, Acidobacteria, Actinobacteria, Bacteroidetes, phylogenetics
“CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes” Hamady, Micah Bioinformatics 2009 CodonExplorer, DNA composition, Codon usage, Bioinformatics
“RNA structure prediction from evolutionary patterns of nucleotide composition” Smit, Sandra Nucleic Acids Research 2009 RNA structure, SPuNC, Structure Prediciton using Nucleotide Composition
“A Simulated MS/MS Library for Spectrum-to-spectrum Searching in Large Scale Identification of Proteins” Yen, Chia-Yu Molecular & Cellular Proteomics 2009 Protein identification, Proteomics, Mass spectrometric fragmentation data, MS/MS spectra
“A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses” Jones, Ryan T The ISME Journal 2009 Acidobacteria, Phylogenetics, Microbial community
“Pathological rate matrices: from primates to pathogens” Schranz, Harold W BMC Bioinformatics 2008 Pathological rate matrices, Continuous-time markov models, Bioinformatics
“Activating and inhibiting connections in biological network dynamics” McDonald, Daniel Biology Direct 2008 Biological network dynamics, Activation, Inhibition
“Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics” Caporaso, J Gregory BMC Evolutionary Biology 2008 Coevolution, Phylogeny, Tree-aware method, Tree-ignorant method
“Comparison of methods for estimating the nucleotide substitution matrix” Oscamou, Maribeth BMC Bioinformatics 2008 Nucleotide substition matrix, Molecular evolution
“The influence of sex, handedness, and washing on the diversity of hand surface bacteria” Fierer, Noah PNAS 2008 Human microbiome, Pyroseequencing, Skin bacteria
“Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers” Liu, Zongzhi Nucleic Acids Research 2008 Pyrosequencing, Massively parallel pyrosequencers
“Worlds within worlds: evolution of the vertebrate gut microbiota” Ley, Ruth E Nature Reviews Microbiology 2008 Vertebrate gut microbiota, Human Microbiome Project, HMp
“The convergence of carbohydrate active gene repertoires in human gut microbes” Lozupone, Catherine PNAS 2008 Compartive genomics, Glycoside hydrolases, Gylcosyltransferases, Gut ecosystem, Microbial genome evolution
“MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs” Hamady, Micah GenomeBiology 2008 MotifCluster, Related proteins, Cluster sequences
“Insights and inferences about integron evolution from genomic data” Nemergut, Diana R BMC Genomics 2008 Integrons, Genomics, intI genes
“Information, probability, and the abundance of the simplest RNA active sites “ Kennedy, Ryan Front Biosci 2008 RNA sites, SELEX
“Species divergence and the measurement of microbial diversity” Lozupone, Catherine FEMS Microbiology Letters 2008 Alpha-diversity, Beta-diversity, Divergence, Phylogeny, Microbial communities
“From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal” Smit, Sandra RNA 2008 Pseudonknot, RNA structure
“Host-bacterial coevolution and the search for new drug targets Zeneveld, Jesse R Current Opinion in Chemical Biology 2008 Coevolution, Genomics, Metagenomics, Symbiosis, Gnotobiotic mice
“The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis” McKenna, Philip PLoS Pathogens 2008 Rhesus macaque, Vertebrate gut, Bacterial mutualists, GI bacterial communities, Gastrointestinal
“Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns” Zeneveld, Jesse R Microbiology 2008 Horizontal gene transfer, HGT, Genomic data
“Short-Term Temporal Variability in Airborne Bacterial and Fungal Populations” Fierer, Noah Applied and environmental microbiology 2008 Airborne microbes, Fungi
“Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil” Fierer, Noah Applied and environmental microbiology 2007 Social microbiota, Bacteria, Archaea, Fungi, Viruses, OTU, Operational taxonomic unit
“The human microbiome project: exploring the microbial part of ourselves in a changing world” Turnbaugh, Peter J Nature 2007 Human Microbiome Project, HMP, Human microbiome
“Short pyrosequencing reads suffice for accurate microbial community analysis” Liu, Zongzhi Nucleic Acids Research 2007 Pyrosequencing, Microbial community,
“PyCogent: a toolkit for making sense from sequence” Knight, Rob Genome Biology 2007 PyCogent, Bioniformatics, Biological sequences
“Global patterns in bacterial diversity” Lozupone, Catherine PNAS 2007 Microbes, Microbial ecology, Phylogenetic diversity, UniFrac
“Evolution of Symbiotic Bacteria in the Distal Human Intestine” Xu, Jian PLoS Biology 2007 Human intestine, Bacteroides vulgatus, Bacteroides distasonis, Lateral gene transfer
“Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities” Lozupone, Catherine Applied and environmental microbiology 2007 Microbial diversity, UniFrac, β Diversity
“The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology” Ley, Ruth E Environmental Microbiology 2007 Human microbiome, Dichotomy
“Using the nucleotide substitution rate matrix to detect horizontal gene transfer” Hamady, Micah BMC Bioinformatics 2006 Horizontal gene transfer, HGT, Genomic data, Nucleotide substitution rate matrix, Bioinformatics
“UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context” Lozupone, Catherine BMC Bioinformatics 2006 UnifFrac, Bioinformatics
“DivergentSet, a tool for picking non-redundant sequences from large sequence collections.” Widmann, Jeremy Molecular Cell Proteomics 2006 DivergentSet, Non-redundant sequences, BIoinformatics
“Parallel Evolution of the Genetic Code in Arthropod Mitochondrial Genomes” Abascal, Federico PLoS Biology 2006 Genetic code, Metazoan mitochondrial genomes
“Fast-Find: A novel computational approach to analyzing combinatorial motifs” Hamady, Micah BMC Bioinformatics 2006 Fast-FIND, Bioinformatics
“Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories” Smit, Sandra RNA 2006 RNA secondary structure, Base composition
“UniFrac: a New Phylogenetic Method for Comparing Microbial Communities” Lozupone, Catherine Applied and environmental microbiology 2005 UniFrac, Bioinformatics
“Size, constant sequences, and optimal selection” Legiewicz, Michal RNA 2005 Amplification, Isoleucine, RNA, SELEX
“Do universal codon-usage patterns minimize the effects of mutation and translation error?” Marquez, Roberto Genome Biology 2005 Codons, Amino-acid usage, Mutation, Translation error
“Obesity alters gut microbial ecology” Ley, Ruth E PNAS 2005 Obesity, Mice, Host-microbial interactions, ob/ob mice, Phylogenetics
“Occurrence of the aminoacyl-tRNA synthetases in high-molecular weight complexes correlates with the size of substrate amino acids” Wolfson, Alexey FEMS Microbiology Letters 2005 AARSs, Aminoactyl-tRNA synthetases, ValRS, valyl-tRNA synthetase, Elongation factor, EF
“Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids” Knight, Rob Nucleic Acids Research 2005 SELEX, RNA
“BayesFold: Rational 2° folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences” Knight, Rob RNA 2004 BayesFold, Bayesian statistics, SELEX, Covariation
“Analyzing partially randomized nucleic acid pools: straight dope on doping.” Knight, Rob Nucleic Acids Research 2003 Nucleic acid pools, SELEX
“Finding specific RNA motifs: Function in a zeptomole world?” Knight, Rob RNA 2003 RNA motif, SELEX, combinatorics, Sequence motifs
“A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes” Knight, Rob Genome Biology 2001 Genome composition, Mutation, Codons
“The molecular basis of nuclear genetic code change in ciliates” Lozupone, Catherine Current Biology 2001 Nuclear genetic code, Ciliates
“The Early Evolution of the Genetic Code” Knight, Robin D Cell Press 2000 Genetic Code
“Rhyme or reason: RNA-arginine interactions and the genetic code” Knight, Robin D Chemistry & Biology 1998 RNA-arginine interactinos, Genetic code