We Accelerate Discovery

You are here

Human Microbiome Project (418)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips.Ma, Liang; Datta, Sujit S; Karymov, Mikhail A; Pan, Qichao; Begolo, Stefano; Ismagilov, Rustem FIntegrative biology : quantitative biosciences from nano to macro2014 Jun 23NULL24953827
The placenta harbors a unique microbiome.Aagaard, Kjersti; Ma, Jun; Antony, Kathleen M; Ganu, Radhika; Petrosino, Joseph; Versalovic, JamesScience translational medicine2014 May 21237ra6524848255
Dynamics and associations of microbial community types across the human body.Ding, Tao; Schloss, Patrick DNature2014 May 15357-6024739969
Compositional and functional features of the gastrointestinal microbiome and their effects on human health.Hollister, Emily B; Gao, Chunxu; Versalovic, JamesGastroenterology2014 May1449-5824486050
Meta'omic analytic techniques for studying the intestinal microbiome.Morgan, Xochitl C; Huttenhower, CurtisGastroenterology2014 May1437-1448.e124486053
Diet and the intestinal microbiome: associations, functions, and implications for health and disease.Albenberg, Lindsey G; Wu, Gary DGastroenterology2014 May1564-7224503132
Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets.Ma, Yingfei; Madupu, Ramana; Karaoz, Ulas; Nossa, Carlos W; Yang, Liying; Yooseph, Shibu; Yachimski, Patrick S; Brodie, Eoin L; Nelson, Karen E; Pei, ZhihengJournal of virology2014 May4786-9724522917
The microbiome in inflammatory bowel disease: current status and the future ahead.Kostic, Aleksandar D; Xavier, Ramnik J; Gevers, DirkGastroenterology2014 May1489-9924560869
Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections.Carl, Mike A; Ndao, I Malick; Springman, A Cody; Manning, Shannon D; Johnson, James R; Johnston, Brian D; Burnham, Carey-Ann D; Weinstock, Erica Sodergren; Weinstock, George M; Wylie, Todd N; Mitreva, Makedonka; Abubucker, Sahar; Zhou, Yanjiao; Stevens, HClinical infectious diseases : an official publication of the Infectious Diseases Society of America2014 May1211-824647013
Microbiome in reflux disorders and esophageal adenocarcinoma.Yang, Liying; Chaudhary, Noami; Baghdadi, Jonathan; Pei, ZhihengCancer journal (Sudbury, Mass.)2014 May-Jun207-1024855009
Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism.Tong, Maomeng; McHardy, Ian; Ruegger, Paul; Goudarzi, Maryam; Kashyap, Purna C; Haritunians, Talin; Li, Xiaoxiao; Graeber, Thomas G; Schwager, Emma; Huttenhower, Curtis; Fornace Jr, Albert J; Sonnenburg, Justin L; McGovern, Dermot Pb; Borneman, James; BraThe ISME journal2014 Apr 29NULL24781901
Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota.Campbell, Alisha G; Schwientek, Patrick; Vishnivetskaya, Tatiana; Woyke, Tanja; Levy, Shawn; Beall, Clifford J; Griffen, Ann; Leys, Eugene; Podar, MirceaEnvironmental microbiology2014 Apr 17NULL24738594
Transferable vancomycin resistance in a community-associated MRSA lineage.Rossi, Flavia; Diaz, Lorena; Wollam, Aye; Panesso, Diana; Zhou, Yanjiao; Rincon, Sandra; Narechania, Apurva; Xing, Galen; Di Gioia, Thais S R; Doi, Andre; Tran, Truc T; Reyes, Jinnethe; Munita, Jose M; Carvajal, Lina P; Hernandez-Roldan, Alejandra; BrandaThe New England journal of medicine2014 Apr 171524-3124738669
Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen.Chen, Zehua; Martinez, Diego A; Gujja, Sharvari; Sykes, Sean M; Zeng, Qiandong; Szaniszlo, Paul J; Wang, Zheng; Cuomo, Christina AG3 (Bethesda, Md.)2014 Apr561-7824496724
Pathogens and host immunity in the ancient human oral cavity.Warinner, Christina; Rodrigues, Joao F Matias; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y; Tito, Raul Y; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar-Nature genetics2014 Apr336-4424562188
The treatment-naive microbiome in new-onset Crohn's disease.Gevers, Dirk; Kugathasan, Subra; Denson, Lee A; Vazquez-Baeza, Yoshiki; Van Treuren, Will; Ren, Boyu; Schwager, Emma; Knights, Dan; Song, Se Jin; Yassour, Moran; Morgan, Xochitl C; Kostic, Aleksandar D; Luo, Chengwei; Gonzalez, Antonio; McDonald, Daniel; Cell host & microbe2014 Mar 12382-9224629344
Immune and genetic gardening of the intestinal microbiome.Jacobs, Jonathan P; Braun, JonathanFEBS letters2014 Mar 5NULL24613921
Functional and phylogenetic assembly of microbial communities in the human microbiome.Shafquat, Afrah; Joice, Regina; Simmons, Sheri L; Huttenhower, CurtisTrends in microbiology2014 Mar 4NULL24618403
Identification of a proton-chloride antiporter (EriC) by Himar1 transposon mutagenesis in Lactobacillus reuteri and its role in histamine production.Hemarajata, P; Spinler, J K; Balderas, M A; Versalovic, JAntonie van Leeuwenhoek2014 Mar579-9224488273
Early Empiric Antibiotic Use in Preterm Infants Is Associated with Lower Bacterial Diversity and Higher Relative Abundance of Enterobacter.Greenwood, Corryn; Morrow, Ardythe L; Lagomarcino, Anne J; Altaye, Mekibib; Taft, Diana H; Yu, Zhuoteng; Newburg, David S; Ward, Doyle V; Schibler, Kurt RThe Journal of pediatrics2014 Feb 13NULL24529620
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.Mason, Olivia U; Scott, Nicole M; Gonzalez, Antonio; Robbins-Pianka, Adam; Baelum, Jacob; Kimbrel, Jeffrey; Bouskill, Nicholas J; Prestat, Emmanuel; Borglin, Sharon; Joyner, Dominique C; Fortney, Julian L; Jurelevicius, Diogo; Stringfellow, William T; AlvThe ISME journal2014 Jan 23NULL24451203
Mathematical modeling of primary succession of murine intestinal microbiota.Marino, Simeone; Baxter, Nielson T; Huffnagle, Gary B; Petrosino, Joseph F; Schloss, Patrick DProceedings of the National Academy of Sciences of the United States of America2014 Jan 7439-4424367073
IMG/M 4 version of the integrated metagenome comparative analysis system.Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Pagani, Ioanna; Tringe, Susannah; Huntemann, Marcel; Billis, Konstantinos; Varghese, Neha; Tennessen, Kristin; Mavromatis, KonsNucleic acids research2014 JanD568-7324136997
MetaRef: a pan-genomic database for comparative and community microbial genomics.Huang, Katherine; Brady, Arthur; Mahurkar, Anup; White, Owen; Gevers, Dirk; Huttenhower, Curtis; Segata, NicolaNucleic acids research2014 JanD617-2424203705
Ribosomal Database Project: data and tools for high throughput rRNA analysis.Cole, James R; Wang, Qiong; Fish, Jordan A; Chai, Benli; McGarrell, Donna M; Sun, Yanni; Brown, C Titus; Porras-Alfaro, Andrea; Kuske, Cheryl R; Tiedje, James MNucleic acids research2014 JanD633-4224288368
A brave new world: the lung microbiota in an era of change.Segal, Leopoldo N; Blaser, Martin JAnnals of the American Thoracic Society2014 JanS21-724437400
Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286) and comparison to the closely related pathogen Tannerella forsythia.Beall, Clifford J; Campbell, Alisha G; Dayeh, Daniel M; Griffen, Ann L; Podar, Mircea; Leys, Eugene JPloS one2014e8939824551246
Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis.Hyde, Embriette R; Andrade, Fernando; Vaksman, Zalman; Parthasarathy, Kavitha; Jiang, Hong; Parthasarathy, Deepa K; Torregrossa, Ashley C; Tribble, Gena; Kaplan, Heidi B; Petrosino, Joseph F; Bryan, Nathan SPloS one2014e8864524670812
Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres.Swan, Brandon K; Chaffin, Mark D; Martinez-Garcia, Manuel; Morrison, Hilary G; Field, Erin K; Poulton, Nicole J; Masland, E Dashiell P; Harris, Christopher C; Sczyrba, Alexander; Chain, Patrick S G; Koren, Sergey; Woyke, Tanja; Stepanauskas, RamunasPloS one2014e9538024743558
Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data.Vital, Marius; Howe, Adina Chuang; Tiedje, James MmBio2014e0088924757212
Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls.Schubert, Alyxandria M; Rogers, Mary A M; Ring, Cathrin; Mogle, Jill; Petrosino, Joseph P; Young, Vincent B; Aronoff, David M; Schloss, Patrick DmBio2014e01021-1424803517
The prevalence of species and strains in the human microbiome: a resource for experimental efforts.Kraal, Laurens; Abubucker, Sahar; Kota, Karthik; Fischbach, Michael A; Mitreva, MakedonkaPloS one2014e9727924827833
Microfluidic platforms for single-cell protein analysis.Liu, Yanli; Singh, Anup KJournal of laboratory automation2013 Dec446-5423821679
Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data.Robertson, Charles E; Harris, J Kirk; Wagner, Brandie D; Granger, David; Browne, Kathy; Tatem, Beth; Feazel, Leah M; Park, Kristin; Pace, Norman R; Frank, Daniel NBioinformatics (Oxford, England)2013 Dec 13100-124021386
Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis.Turabelidze, George; Lawrence, Steven J; Gao, Hongyu; Sodergren, Erica; Weinstock, George M; Abubucker, Sahar; Wylie, Todd; Mitreva, Makedonka; Shaikh, Nurmohammad; Gautom, Romesh; Tarr, Phillip IJournal of clinical microbiology2013 Dec3950-424048526
Differential abundance analysis for microbial marker-gene surveys.Paulson, Joseph N; Stine, O Colin; Bravo, Hector Corrada; Pop, MihaiNature methods2013 Dec1200-224076764
Lactobacillus reuteri-specific immunoregulatory gene rsiR modulates histamine production and immunomodulation by Lactobacillus reuteri.Hemarajata, P; Gao, C; Pflughoeft, K J; Thomas, C M; Saulnier, D M; Spinler, J K; Versalovic, JJournal of bacteriology2013 Dec5567-7624123819
Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells.Gole, Jeff; Gore, Athurva; Richards, Andrew; Chiu, Yu-Jui; Fung, Ho-Lim; Bushman, Diane; Chiang, Hsin-I; Chun, Jerold; Lo, Yu-Hwa; Zhang, KunNature biotechnology2013 Dec1126-3224213699
Inferring developmental stage composition from gene expression in human malaria.Joice, Regina; Narasimhan, Vagheesh; Montgomery, Jacqui; Sidhu, Amar Bir; Oh, Keunyoung; Meyer, Evan; Pierre-Louis, Willythssa; Seydel, Karl; Milner, Danny; Williamson, Kim; Wiegand, Roger; Ndiaye, Daouda; Daily, Johanna; Wirth, Dyann; Taylor, Terrie; HutPLoS computational biology2013 Dece100339224348235
Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.Eren, A Murat; Maignien, Lois; Sul, Woo Jun; Murphy, Leslie G; Grim, Sharon L; Morrison, Hilary G; Sogin, Mitchell LMethods in ecology and evolution / British Ecological Society2013 Dec 1NULL24358444
Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem.Wendl, Michael C; Kota, Karthik; Weinstock, George M; Mitreva, MakedonkaJournal of mathematical biology2013 Nov1141-6122965653
Composition of dietary fat source shapes gut microbiota architecture and alters host inflammatory mediators in mouse adipose tissue.Huang, Edmond Y; Leone, Vanessa A; Devkota, Suzanne; Wang, Yunwei; Brady, Matthew J; Chang, Eugene BJPEN. Journal of parenteral and enteral nutrition2013 Nov746-5423639897
Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy.Brotman, Rebecca M; Shardell, Michelle D; Gajer, Pawel; Fadrosh, Doug; Chang, Kathryn; Silver, Michelle I; Viscidi, Raphael P; Burke, Anne E; Ravel, Jacques; Gravitt, Patti EMenopause (New York, N.Y.)2013 Oct 21NULL24080849
Science and regulation. Probiotics: finding the right regulatory balance.Hoffmann, D E; Fraser, C M; Palumbo, F B; Ravel, J; Rothenberg, K; Rowthorn, V; Schwartz, JScience (New York, N.Y.)2013 Oct 18314-524136953
Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota.Lee, Sunghee; Cantarel, Brandi; Henrissat, Bernard; Gevers, Dirk; Birren, Bruce W; Huttenhower, Curtis; Ko, GwangpyoThe ISME journal2013 Oct 10NULL24108330
Bringing the gut microbiota into focus through microbial culture: recent progress and future perspective.Allen-Vercoe, EmmaCurrent opinion in microbiology2013 Oct625-924148301
Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.Kozich, James J; Westcott, Sarah L; Baxter, Nielson T; Highlander, Sarah K; Schloss, Patrick DApplied and environmental microbiology2013 Sep5112-2023793624
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.Langille, Morgan G I; Zaneveld, Jesse; Caporaso, J Gregory; McDonald, Daniel; Knights, Dan; Reyes, Joshua A; Clemente, Jose C; Burkepile, Deron E; Vega Thurber, Rebecca L; Knight, Rob; Beiko, Robert G; Huttenhower, CurtisNature biotechnology2013 Sep814-2123975157
Two-stage microbial community experimental design.Tickle, Timothy L; Segata, Nicola; Waldron, Levi; Weingart, Uri; Huttenhower, CurtisThe ISME journal2013 Aug 15NULL23949665
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes.Segata, Nicola; Bornigen, Daniela; Morgan, Xochitl C; Huttenhower, CurtisNature communications2013 Aug 14230423942190
Effects of different complementary feeding regimens on iron status and enteric microbiota in breastfed infants.Krebs, Nancy F; Sherlock, Laurie G; Westcott, Jamie; Culbertson, Diana; Hambidge, K Michael; Feazel, Leah M; Robertson, Charles E; Frank, Daniel NThe Journal of pediatrics2013 Aug416-2323452586
Gene expression profiles in febrile children with defined viral and bacterial infection.Hu, Xinran; Yu, Jinsheng; Crosby, Seth D; Storch, Gregory AProceedings of the National Academy of Sciences of the United States of America2013 Jul 3012792-723858444
Rapid evolution of the human gut virome.Minot, Samuel; Bryson, Alexandra; Chehoud, Christel; Wu, Gary D; Lewis, James D; Bushman, Frederic DProceedings of the National Academy of Sciences of the United States of America2013 Jul 2312450-523836644
Gastrointestinal viruses were not found as an aetiology of culture-negative illness in NICU patients.Melamed, Rimma; Storch, Gregory A; Warner, Barbara B; Tarr, Phillip IArchives of disease in childhood. Fetal and neonatal edition2013 JulF374-523563694
Analysis of the human gut microbiome and association with disease.Wu, Gary D; Lewis, James DClinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association2013 Jul774-723643636
Colitis-induced Bone Loss is Gender Dependent and Associated with Increased Inflammation.Irwin, Regina; Lee, Taehyung; Young, Vincent B; Parameswaran, Narayanan; McCabe, Laura RInflammatory bowel diseases2013 Jul1586-159723702805
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.Shakya, Migun; Quince, Christopher; Campbell, James H; Yang, Zamin K; Schadt, Christopher W; Podar, MirceaEnvironmental microbiology2013 Jun1882-9923387867
Culture-independent analysis of aerosol microbiology in a metropolitan subway system.Robertson, Charles E; Baumgartner, Laura K; Harris, J Kirk; Peterson, Kristen L; Stevens, Mark J; Frank, Daniel N; Pace, Norman RApplied and environmental microbiology2013 Jun3485-9323542619
Changes in cystic fibrosis airway microbiota at pulmonary exacerbation.Carmody, Lisa A; Zhao, Jiangchao; Schloss, Patrick D; Petrosino, Joseph F; Murray, Susan; Young, Vincent B; Li, Jun Z; LipPuma, John JAnnals of the American Thoracic Society2013 Jun179-8723802813
The mean and variance of phylogenetic diversity under rarefaction.Nipperess, David A; Matsen 4th, Frederick AMethods in ecology and evolution / British Ecological Society2013 Jun 1566-57223833701
Virome genomics: a tool for defining the human virome.Wylie, Kristine M; Weinstock, George M; Storch, Gregory ACurrent opinion in microbiology2013 May 2323706900
Comparison of the respiratory microbiome in healthy nonsmokers and smokers.Morris, Alison; Beck, James M; Schloss, Patrick D; Campbell, Thomas B; Crothers, Kristina; Curtis, Jeffrey L; Flores, Sonia C; Fontenot, Andrew P; Ghedin, Elodie; Huang, Laurence; Jablonski, Kathleen; Kleerup, Eric; Lynch, Susan V; Sodergren, Erica; TwiggAmerican journal of respiratory and critical care medicine2013 May 151067-7523491408
Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities.Hettich, Robert L; Pan, Chongle; Chourey, Karuna; Giannone, Richard JAnalytical chemistry2013 May 74203-1423469896
The future is now: single-cell genomics of bacteria and archaea.Blainey, Paul CFEMS microbiology reviews2013 May407-2723298390
Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.Fitzsimons, Michael S; Novotny, Mark; Lo, Chien-Chi; Dichosa, Armand E K; Yee-Greenbaum, Joyclyn L; Snook, Jeremy P; Gu, Wei; Chertkov, Olga; Davenport, Karen W; McMurry, Kim; Reitenga, Krista G; Daughton, Ashlynn R; He, Jian; Johnson, Shannon L; GleasnerGenome research2013 May878-8823493677
Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis.Koeth, Robert A; Wang, Zeneng; Levison, Bruce S; Buffa, Jennifer A; Org, Elin; Sheehy, Brendan T; Britt, Earl B; Fu, Xiaoming; Wu, Yuping; Li, Lin; Smith, Jonathan D; DiDonato, Joseph A; Chen, Jun; Li, Hongzhe; Wu, Gary D; Lewis, James D; Warrier, Manya; Nature medicine2013 May576-8523563705
A Pure L1-norm Principal Component Analysis.Brooks, Jp; Dula, Jh; Boone, ElComputational statistics & data analysis2013 May 183-9823976807
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota.Campbell, James H; O'Donoghue, Patrick; Campbell, Alisha G; Schwientek, Patrick; Sczyrba, Alexander; Woyke, Tanja; Soll, Dieter; Podar, MirceaProceedings of the National Academy of Sciences of the United States of America2013 Apr 25540-523509275
Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis.Chen, Jun; Bushman, Frederic D; Lewis, James D; Wu, Gary D; Li, HongzheBiostatistics (Oxford, England)2013 Apr244-5823074263
Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men.Redel, Henry; Gao, Zhan; Li, Huilin; Alekseyenko, Alexander V; Zhou, Yanjiao; Perez-Perez, Guillermo I; Weinstock, George; Sodergren, Erica; Blaser, Martin JThe Journal of infectious diseases2013 Apr1105-1423300163
The human gut microbiome and body metabolism: implications for obesity and diabetes.Devaraj, Sridevi; Hemarajata, Peera; Versalovic, JamesClinical chemistry2013 Apr617-2823401286
SPA: a short peptide assembler for metagenomic data.Yang, Youngik; Yooseph, ShibuNucleic acids research2013 Apre9123435317
Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players.Ursell, Luke K; Knight, RobCell metabolism2013 Mar 5317-823473028
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.Schatz, Michael C; Phillippy, Adam M; Sommer, Daniel D; Delcher, Arthur L; Puiu, Daniela; Narzisi, Giuseppe; Salzberg, Steven L; Pop, MihaiBriefings in bioinformatics2013 Mar213-2422199379
Secondary structure improves OTU assignments of 16S rRNA gene sequences.Schloss, Patrick DThe ISME journal2013 Mar457-6023018771
The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters.Aagaard, Kjersti; Petrosino, Joseph; Keitel, Wendy; Watson, Mark; Katancik, James; Garcia, Nathalia; Patel, Shital; Cutting, Mary; Madden, Tessa; Hamilton, Holli; Harris, Emily; Gevers, Dirk; Simone, Gina; McInnes, Pamela; Versalovic, JamesFASEB journal : official publication of the Federation of American Societies for Experimental Biology2013 Mar1012-2223165986
Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity.Markle, Janet G M; Frank, Daniel N; Mortin-Toth, Steven; Robertson, Charles E; Feazel, Leah M; Rolle-Kampczyk, Ulrike; von Bergen, Martin; McCoy, Kathy D; Macpherson, Andrew J; Danska, Jayne SScience (New York, N.Y.)2013 Mar 11084-823328391
Shallow breathing: bacterial life at low O(2).Morris, Rachel L; Schmidt, Thomas MNature reviews. Microbiology2013 Mar205-1223411864
Challenges in IBD research: update on progress and prioritization of the CCFA's research agenda.Denson, Lee A; Long, Millie D; McGovern, Dermot P B; Kugathasan, Subra; Wu, Gary D; Young, Vincent B; Pizarro, Theresa T; de Zoeten, Edwin F; Stappenbeck, Thaddeus S; Plevy, Scott E; Abraham, Clara; Nusrat, Asma; Jobin, Christian; McCole, Declan F; SiegelInflammatory bowel diseases2013 Mar-Apr677-8223448796
Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases.Leone, Vanessa; Chang, Eugene B; Devkota, SuzanneJournal of gastroenterology2013 Mar315-2123475322
Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences.Jiao, Dazhi; Ye, Yuzhen; Tang, HaixuPLoS computational biology2013 Mare100298123555216
Nestly--a framework for running software with nested parameter choices and aggregating results.McCoy, Connor O; Gallagher, Aaron; Hoffman, Noah G; Matsen, Frederick ABioinformatics (Oxford, England)2013 Feb 1387-823220574
Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis.Ansong, Charles; Ortega, Corrie; Payne, Samuel H; Haft, Daniel H; Chauvigne-Hines, Lacie M; Lewis, Michael P; Ollodart, Anja R; Purvine, Samuel O; Shukla, Anil K; Fortuin, Suereta; Smith, Richard D; Adkins, Joshua N; Grundner, Christoph; Wright, Aaron TChemistry & biology2013 Jan 24123-3323352146
Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne.Fitz-Gibbon, Sorel; Tomida, Shuta; Chiu, Bor-Han; Nguyen, Lin; Du, Christine; Liu, Minghsun; Elashoff, David; Erfe, Marie C; Loncaric, Anya; Kim, Jenny; Modlin, Robert L; Miller, Jeff F; Sodergren, Erica; Craft, Noah; Weinstock, George M; Li, HuiyingThe Journal of investigative dermatology2013 Jan 2123337890
Biogeography of the ecosystems of the healthy human body.Zhou, Yanjiao; Gao, Hongyu; Mihindukulasuriya, Kathie A; La Rosa, Patricio S; Wylie, Kristine M; Vishnivetskaya, Tatiana; Podar, Mircea; Warner, Barb; Tarr, Phillip I; Nelson, David E; Fortenberry, J Dennis; Holland, Martin J; Burr, Sarah E; Shannon, WillGenome biology2013 Jan 14R123316946
Genomic variation landscape of the human gut microbiome.Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi; Mitreva, Makedonka; Tap, Julien; Zhu, Ana; Waller, Alison; Mende, Daniel R; Kultima, Jens Roat; Martin, John; Kota, Karthik; Sunyaev, Shamil R; Weinstock, George M; Bork, PeerNature2013 Jan 345-5023222524
Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents.Blaser, Martin J; Dominguez-Bello, Maria G; Contreras, Monica; Magris, Magda; Hidalgo, Glida; Estrada, Isidoro; Gao, Zhan; Clemente, Jose C; Costello, Elizabeth K; Knight, RobThe ISME journal2013 Jan85-9522895161
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data.Zhu, Zhengwei; Niu, Beifang; Chen, Jing; Wu, Sitao; Sun, Shulei; Li, WeizhongBioinformatics (Oxford, England)2013 Jan 1122-323044549
Whole-genome analysis of a daptomycin-susceptible enterococcus faecium strain and its daptomycin-resistant variant arising during therapy.Tran, Truc T; Panesso, Diana; Gao, Hongyu; Roh, Jung H; Munita, Jose M; Reyes, Jinnethe; Diaz, Lorena; Lobos, Elizabeth A; Shamoo, Yousif; Mishra, Nagendra N; Bayer, Arnold S; Murray, Barbara E; Weinstock, George M; Arias, Cesar AAntimicrobial agents and chemotherapy2013 Jan261-823114757
Biodiversity and functional genomics in the human microbiome.Morgan, Xochitl C; Segata, Nicola; Huttenhower, CurtisTrends in genetics : TIG2013 Jan51-823140990
TIGRFAMs and Genome Properties in 2013.Haft, Daniel H; Selengut, Jeremy D; Richter, Roland A; Harkins, Derek; Basu, Malay K; Beck, ErinNucleic acids research2013 JanD387-9523197656
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing.Bokulich, Nicholas A; Subramanian, Sathish; Faith, Jeremiah J; Gevers, Dirk; Gordon, Jeffrey I; Knight, Rob; Mills, David A; Caporaso, J GregoryNature methods2013 Jan57-923202435
An analysis of online messages about probiotics.Brinich, Margaret A; Mercer, Mary Beth; Sharp, Richard RBMC gastroenterology2013523311418
A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets.Koren, Omry; Knights, Dan; Gonzalez, Antonio; Waldron, Levi; Segata, Nicola; Knight, Rob; Huttenhower, Curtis; Ley, Ruth EPLoS computational biology2013 Jane100286323326225
Single cell microRNA analysis using microfluidic flow cytometry.Wu, Meiye; Piccini, Matthew; Koh, Chung-Yan; Lam, Kit S; Singh, Anup KPloS one2013e5504423383050
Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes.Ballarini, Annalisa; Segata, Nicola; Huttenhower, Curtis; Jousson, OlivierPloS one2013e5576423409037
Transcriptome profiling of microRNA by Next-Gen deep sequencing reveals known and novel miRNA species in the lipid fraction of human breast milk.Munch, Erika M; Harris, R Alan; Mohammad, Mahmoud; Benham, Ashley L; Pejerrey, Sasha M; Showalter, Lori; Hu, Min; Shope, Cynthia D; Maningat, Patricia D; Gunaratne, Preethi H; Haymond, Morey; Aagaard, KjerstiPloS one2013e5056423418415
Comparative analysis of microbiome measurement platforms using latent variable structural equation modeling.Wu, Xiao; Berkow, Kathryn; Frank, Daniel N; Li, Ellen; Gulati, Ajay S; Zhu, WeiBMC bioinformatics20137923497007
Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison.Matsen 4th, Frederick A; Evans, Steven NPloS one2013e5685923505415
Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity.Campbell, Alisha G; Campbell, James H; Schwientek, Patrick; Woyke, Tanja; Sczyrba, Alexander; Allman, Steve; Beall, Clifford J; Griffen, Ann; Leys, Eugene; Podar, MirceaPloS one2013e5936123555659
Investigators' perspectives on translating human microbiome research into clinical practice.Slashinski, M J; Whitney, S N; Achenbaum, L S; Keitel, W A; McCurdy, S A; McGuire, A LPublic health genomics2013127-3323615375
Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome.Tomida, Shuta; Nguyen, Lin; Chiu, Bor-Han; Liu, Jared; Sodergren, Erica; Weinstock, George M; Li, HuiyingmBio2013e00003-1323631911
Computational meta'omics for microbial community studies.Segata, Nicola; Boernigen, Daniela; Tickle, Timothy L; Morgan, Xochitl C; Garrett, Wendy S; Huttenhower, CurtisMolecular systems biology201366623670539
Analyses of the stability and core taxonomic memberships of the human microbiome.Li, Kelvin; Bihan, Monika; Methe, Barbara APloS one2013e6313923671663
Sequencing viral genomes from a single isolated plaque.Depew, Jessica; Zhou, Bin; McCorrison, Jamison M; Wentworth, David E; Purushe, Janaki; Koroleva, Galina; Fouts, Derrick EVirology journal201318123742765
Analysis of complete genomes of Propionibacterium acnes reveals a novel plasmid and increased pseudogenes in an acne associated strain.Kasimatis, Gabriela; Fitz-Gibbon, Sorel; Tomida, Shuta; Wong, Marthew; Li, HuiyingBioMed research international201391832023762865
Carrageenan-induced colonic inflammation is reduced in Bcl10 null mice and increased in IL-10-deficient mice.Bhattacharyya, Sumit; Xue, Liquan; Devkota, Suzanne; Chang, Eugene; Morris, Stephan; Tobacman, Joanne KMediators of inflammation201339764223766559
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents.Hoffmann, Christian; Dollive, Serena; Grunberg, Stephanie; Chen, Jun; Li, Hongzhe; Wu, Gary D; Lewis, James D; Bushman, Frederic DPloS one2013e6601923799070
A filtering method to generate high quality short reads using illumina paired-end technology.Eren, A Murat; Vineis, Joseph H; Morrison, Hilary G; Sogin, Mitchell LPloS one2013e6664323799126
Urethral adenocarcinoma associated with intestinal-type metaplasia, case report and literature review.Hale, Christopher S; Huang, Hongying; Melamed, Jonathan; Xu, Ruliang; Roberts, Larry; Wieczorek, Rosemary; Pei, Zhiheng; Lee, PengInternational journal of clinical and experimental pathology20131665-7023923086
Association of gut microbiota with post-operative clinical course in Crohn's disease.Dey, Neelendu; Soergel, David A W; Repo, Susanna; Brenner, Steven EBMC gastroenterology201313123964800
De novo likelihood-based measures for comparing genome assemblies.Ghodsi, Mohammadreza; Hill, Christopher M; Astrovskaya, Irina; Lin, Henry; Sommer, Dan D; Koren, Sergey; Pop, MihaiBMC research notes201333423965294
Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment.Dollive, Serena; Chen, Ying-Yu; Grunberg, Stephanie; Bittinger, Kyle; Hoffmann, Christian; Vandivier, Lee; Cuff, Christopher; Lewis, James D; Wu, Gary D; Bushman, Frederic DPloS one2013e7180623977147
Microbiomic signatures of psoriasis: feasibility and methodology comparison.Statnikov, Alexander; Alekseyenko, Alexander V; Li, Zhiguo; Henaff, Mikael; Perez-Perez, Guillermo I; Blaser, Martin J; Aliferis, Constantin FScientific reports2013262024018484
Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool.Wang, Qiong; Quensen 3rd, John F; Fish, Jordan A; Lee, Tae Kwon; Sun, Yanni; Tiedje, James M; Cole, James RmBio2013e00592-1324045641
Optofluidic cell selection from complex microbial communities for single-genome analysis.Landry, Zachary C; Giovanonni, Stephen J; Quake, Stephen R; Blainey, Paul CMethods in enzymology201361-9024060116
A metagenomics portal for a democratized sequencing world.Wilke, Andreas; Glass, Elizabeth M; Bartels, Daniela; Bischof, Jared; Braithwaite, Daniel; D'Souza, Mark; Gerlach, Wolfgang; Harrison, Travis; Keegan, Kevin; Matthews, Hunter; Kottmann, Renzo; Paczian, Tobias; Tang, Wei; Trimble, William L; Yilmaz, Pelin;Methods in enzymology2013487-52324060134
Diet, gut enterotypes and health: is there a link?Bushman, Frederic D; Lewis, James D; Wu, Gary DNestle Nutrition Institute workshop series201365-7324107497
Interprovider variation of celiac disease testing in childhood chronic abdominal pain.Chumpitazi, Bruno Pedro; Mysore, Krupa; Tsai, Cynthia Man-Wai; Shulman, Robert JayBMC gastroenterology201315024124697
The gut microbiome modulates colon tumorigenesis.Zackular, Joseph P; Baxter, Nielson T; Iverson, Kathryn D; Sadler, William D; Petrosino, Joseph F; Chen, Grace Y; Schloss, Patrick DmBio2013e00692-1324194538
Diversified microbiota of meconium is affected by maternal diabetes status.Hu, Jianzhong; Nomura, Yoko; Bashir, Ali; Fernandez-Hernandez, Heriberto; Itzkowitz, Steven; Pei, Zhiheng; Stone, Joanne; Loudon, Holly; Peter, IngaPloS one2013e7825724223144
A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease.Tong, Maomeng; Li, Xiaoxiao; Wegener Parfrey, Laura; Roth, Bennett; Ippoliti, Andrew; Wei, Bo; Borneman, James; McGovern, Dermot P B; Frank, Daniel N; Li, Ellen; Horvath, Steve; Knight, Rob; Braun, JonathanPloS one2013e8070224260458
Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes.Close, Devin W; Ferrara, Fortunato; Dichosa, Armand E K; Kumar, Sandeep; Daughton, Ashlynn R; Daligault, Hajnalka E; Reitenga, Krista G; Velappan, Nileena; Sanchez, Timothy C; Iyer, Srinivas; Kiss, Csaba; Han, Cliff S; Bradbury, Andrew R MBMC microbiology201327024279426
More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis.Srinivasan, Sujatha; Morgan, Martin T; Liu, Congzhou; Matsen, Frederick A; Hoffman, Noah G; Fiedler, Tina L; Agnew, Kathy J; Marrazzo, Jeanne M; Fredricks, David NPloS one2013e7863324302980
The microbiome of the middle meatus in healthy adults.Ramakrishnan, Vijay R; Feazel, Leah M; Gitomer, Sarah A; Ir, Diana; Robertson, Charles E; Frank, Daniel NPloS one2013e8550724386477
Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis.Ravel, Jacques; Brotman, Rebecca M; Gajer, Pawel; Ma, Bing; Nandy, Melissa; Fadrosh, Douglas W; Sakamoto, Joyce; Koenig, Sara Sk; Fu, Li; Zhou, Xia; Hickey, Roxana J; Schwebke, Jane R; Forney, Larry JMicrobiome20132924451163
A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community.Vital, Marius; Penton, Christopher R; Wang, Qiong; Young, Vincent B; Antonopoulos, Dion A; Sogin, Mitchell L; Morrison, Hilary G; Raffals, Laura; Chang, Eugene B; Huffnagle, Gary B; Schmidt, Thomas M; Cole, James R; Tiedje, James MMicrobiome2013824451334
'Someone should oversee it': patient perspectives on the ethical issues arising with the regulation of probiotics.Harrison, Krista L; Farrell, Ruth M; Brinich, Margaret A; Highland, Janelle; Mercer, Marybeth; McCormick, Jennifer B; Tilburt, Jon; Geller, Gail; Marshall, Patricia; Sharp, Richard RHealth expectations : an international journal of public participation in health care and health policy2012 Dec 2823279082
CD-HIT: accelerated for clustering the next-generation sequencing data.Fu, Limin; Niu, Beifang; Zhu, Zhengwei; Wu, Sitao; Li, WeizhongBioinformatics (Oxford, England)2012 Dec 13150-223060610
Detection of viruses in young children with fever without an apparent source.Colvin, Joshua M; Muenzer, Jared T; Jaffe, David M; Smason, Avraham; Deych, Elena; Shannon, William D; Arens, Max Q; Buller, Richard S; Lee, Wai-Ming; Weinstock, Erica J Sodergren; Weinstock, George M; Storch, Gregory APediatrics2012 Dece1455-6223129086
Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome.Kontur, Wayne S; Schackwitz, Wendy S; Ivanova, Natalia; Martin, Joel; Labutti, Kurt; Deshpande, Shweta; Tice, Hope N; Pennacchio, Christa; Sodergren, Erica; Weinstock, George M; Noguera, Daniel R; Donohue, Timothy JJournal of bacteriology2012 Dec7016-723209255
Host genetic and environmental effects on mouse intestinal microbiota.Campbell, James H; Foster, Carmen M; Vishnivetskaya, Tatiana; Campbell, Alisha G; Yang, Zamin K; Wymore, Ann; Palumbo, Anthony V; Chesler, Elissa J; Podar, MirceaThe ISME journal2012 Nov2033-4422695862
Ultrafast clustering algorithms for metagenomic sequence analysis.Li, Weizhong; Fu, Limin; Niu, Beifang; Wu, Sitao; Wooley, JohnBriefings in bioinformatics2012 Nov656-6822772836
Dietary issues in recurrent abdominal pain.Shulman, Robert JJournal of pediatric gastroenterology and nutrition2012 NovS40-223103654
Using QIIME to analyze 16S rRNA gene sequences from microbial communities.Kuczynski, Justin; Stombaugh, Jesse; Walters, William Anton; Gonzalez, Antonio; Caporaso, J Gregory; Knight, RobCurrent protocols in microbiology2012 NovUnit 1E.5.23184592
Prevention of virus-induced type 1 diabetes with antibiotic therapy.Hara, Naoko; Alkanani, Aimon K; Ir, Diana; Robertson, Charles E; Wagner, Brandie D; Frank, Daniel N; Zipris, DannyJournal of immunology (Baltimore, Md. : 1950)2012 Oct 153805-1422988033
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts.Lozupone, Catherine; Faust, Karoline; Raes, Jeroen; Faith, Jeremiah J; Frank, Daniel N; Zaneveld, Jesse; Gordon, Jeffrey I; Knight, RobGenome research2012 Oct1974-8422665442
The microbiome of the lung.Beck, James M; Young, Vincent B; Huffnagle, Gary BTranslational research : the journal of laboratory and clinical medicine2012 Oct258-6622683412
Understanding vaginal microbiome complexity from an ecological perspective.Hickey, Roxana J; Zhou, Xia; Pierson, Jacob D; Ravel, Jacques; Forney, Larry JTranslational research : the journal of laboratory and clinical medicine2012 Oct267-8222683415
Emerging view of the human virome.Wylie, Kristine M; Weinstock, George M; Storch, Gregory ATranslational research : the journal of laboratory and clinical medicine2012 Oct283-9022683423
The world within: living with our microbial guests and guides.Janoff, Edward N; Gustafson, Claire; Frank, Daniel NTranslational research : the journal of laboratory and clinical medicine2012 Oct239-4522732305
Diversity of 5S rRNA genes within individual prokaryotic genomes.Pei, Anna; Li, Hongru; Oberdorf, William E; Alekseyenko, Alexander V; Parsons, Tamasha; Yang, Liying; Gerz, Erika A; Lee, Peng; Xiang, Charlie; Nossa, Carlos W; Pei, ZhihengFEMS microbiology letters2012 Oct11-822765222
Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women.Brotman, Rebecca M; Bradford, L Latey; Conrad, Melissa; Gajer, Pawel; Ault, Kevin; Peralta, Ligia; Forney, Larry J; Carlton, Jane M; Abdo, Zaid; Ravel, JacquesSexually transmitted diseases2012 Oct807-1223007708
Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis.Blainey, Paul C; Milla, Carlos E; Cornfield, David N; Quake, Stephen RScience translational medicine2012 Sep 26153ra13023019655
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics.Wu, Yu-Wei; Rho, Mina; Doak, Thomas G; Ye, YuzhenBioinformatics (Oxford, England)2012 Sep 15i363-i36922962453
Genomic approaches to studying the human microbiota.Weinstock, George MNature2012 Sep 13250-622972298
Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish.Semova, Ivana; Carten, Juliana D; Stombaugh, Jesse; Mackey, Lantz C; Knight, Rob; Farber, Steven A; Rawls, John FCell host & microbe2012 Sep 13277-8822980325
Host response to probiotics determined by nutritional status of rotavirus-infected neonatal mice.Preidis, Geoffrey A; Saulnier, Delphine M; Blutt, Sarah E; Mistretta, Toni-Ann; Riehle, Kevin P; Major, Angela M; Venable, Susan F; Barrish, James P; Finegold, Milton J; Petrosino, Joseph F; Guerrant, Richard L; Conner, Margaret E; Versalovic, JamesJournal of pediatric gastroenterology and nutrition2012 Sep299-30722343914
Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability.Filkins, L M; Hampton, T H; Gifford, A H; Gross, M J; Hogan, D A; Sogin, M L; Morrison, H G; Paster, B J; O'Toole, G AJournal of bacteriology2012 Sep4709-1722753064
mcaGUI: microbial community analysis R-Graphical User Interface (GUI).Copeland, Wade K; Krishnan, Vandhana; Beck, Daniel; Settles, Matt; Foster, James A; Cho, Kyu-Chul; Day, Mitch; Hickey, Roxana; Schutte, Ursel M E; Zhou, Xia; Williams, Christopher J; Forney, Larry J; Abdo, ZaidBioinformatics (Oxford, England)2012 Aug 152198-922692220
Associating microbiome composition with environmental covariates using generalized UniFrac distances.Chen, Jun; Bittinger, Kyle; Charlson, Emily S; Hoffmann, Christian; Lewis, James; Wu, Gary D; Collman, Ronald G; Bushman, Frederic D; Li, HongzheBioinformatics (Oxford, England)2012 Aug 152106-1322711789
Metagenomic microbial community profiling using unique clade-specific marker genes.Segata, Nicola; Waldron, Levi; Ballarini, Annalisa; Narasimhan, Vagheesh; Jousson, Olivier; Huttenhower, CurtisNature methods2012 Aug811-422688413
Defining the human microbiome.Ursell, Luke K; Metcalf, Jessica L; Parfrey, Laura Wegener; Knight, RobNutrition reviews2012 AugS38-4422861806
Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice.Devkota, Suzanne; Wang, Yunwei; Musch, Mark W; Leone, Vanessa; Fehlner-Peach, Hannah; Nadimpalli, Anuradha; Antonopoulos, Dionysios A; Jabri, Bana; Chang, Eugene BNature2012 Jul 5104-822722865
Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences.Wang, Xiaoyu; Cai, Yunpeng; Sun, Yijun; Knight, Rob; Mai, VolkerThe ISME journal2012 Jul1277-8022170430
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences.Soergel, David A W; Dey, Neelendu; Knight, Rob; Brenner, Steven EThe ISME journal2012 Jul1440-422237546
Altered vaginal microbiota are associated with perinatal mother-to-child transmission of HIV in African women from Burkina Faso.Frank, Daniel N; Manigart, Olivier; Leroy, Valeriane; Meda, Nicolas; Valea, Diane; Zhang, Weiming; Dabis, Francois; Pace, Norman R; Van de Perre, Philippe; Janoff, Edward NJournal of acquired immune deficiency syndromes (1999)2012 Jul 1299-30622343176
Food and the gut microbiota in inflammatory bowel diseases: a critical connection.Albenberg, Lindsey G; Lewis, James D; Wu, Gary DCurrent opinion in gastroenterology2012 Jul314-2022573192
Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance.Britton, Robert A; Young, Vincent BTrends in microbiology2012 Jul313-922595318
Spatial and temporal variability of the human microbiota.Parfrey, L W; Knight, RClinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases2012 Jul8-1122647040
Stabilization of the murine gut microbiome following weaning.Schloss, Patrick D; Schubert, Alyxandria M; Zackular, Joseph P; Iverson, Kathryn D; Young, Vincent B; Petrosino, Joseph FGut microbes2012 Jul-Aug383-9322688727
Ethical Discourse about the Modification of Food for Therapeutic Purposes: How Patients with Gastrointestinal Diseases View the Good, the Bad, and the Healthy.Harrison, Krista L; Geller, Gail; Marshall, Patricia; Tilburt, Jon; Mercer, Marybeth; Brinich, Margaret A; Highland, Janelle; Farrell, Ruth M; Sharp, Richard RAJOB primary research2012 Jul 112-2022773953
Perspectives on human microbiome research ethics.McGuire, Amy L; Achenbaum, Laura S; Whitney, Simon N; Slashinski, Melody J; Versalovic, James; Keitel, Wendy A; McCurdy, Sheryl AJournal of empirical research on human research ethics : JERHRE2012 Jul1-1422850139
Structure, function and diversity of the healthy human microbiome.Human Microbiome Project ConsortiumNature2012 Jun 14207-1422699609
A framework for human microbiome research.Human Microbiome Project ConsortiumNature2012 Jun 14215-2122699610
Characterizing microbial communities through space and time.Gonzalez, Antonio; King, Andrew; Robeson 2nd, Michael S; Song, Sejin; Shade, Ashley; Metcalf, Jessica L; Knight, RobCurrent opinion in biotechnology2012 Jun431-622154467
Single cell genome sequencing.Yilmaz, Suzan; Singh, Anup KCurrent opinion in biotechnology2012 Jun437-4322154471
Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments.Ozok, A R; Persoon, I F; Huse, S M; Keijser, B J F; Wesselink, P R; Crielaard, W; Zaura, EInternational endodontic journal2012 Jun530-4122251411
Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB).Pamp, Sunje J; Harrington, Eoghan D; Quake, Stephen R; Relman, David A; Blainey, Paul CGenome research2012 Jun1107-1922434425
Alterations in the porcine colon microbiota induced by the gastrointestinal nematode Trichuris suis.Li, Robert W; Wu, Sitao; Li, Weizhong; Navarro, Karl; Couch, Robin D; Hill, Dolores; Urban Jr, Joseph FInfection and immunity2012 Jun2150-722493085
'Omics' of the mammalian gut--new insights into function.Lamendella, Regina; VerBerkmoes, Nathan; Jansson, Janet KCurrent opinion in biotechnology2012 Jun491-50022626866
A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community.Wang, Mingjie; Ye, Yuzhen; Tang, HaixuJournal of computational biology : a journal of computational molecular cell biology2012 Jun814-2522697249
The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples.Evans, Steven N; Matsen, Frederick AJournal of the Royal Statistical Society. Series B, Statistical methodology2012 Jun 1569-59222844205
Temporal dynamics of the human vaginal microbiota.Gajer, Pawel; Brotman, Rebecca M; Bai, Guoyun; Sakamoto, Joyce; Schutte, Ursel M E; Zhong, Xue; Koenig, Sara S K; Fu, Li; Ma, Zhanshan Sam; Zhou, Xia; Abdo, Zaid; Forney, Larry J; Ravel, JacquesScience translational medicine2012 May 2132ra5222553250
Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine.Preidis, Geoffrey A; Saulnier, Delphine M; Blutt, Sarah E; Mistretta, Toni-Ann; Riehle, Kevin P; Major, Angela M; Venable, Susan F; Finegold, Milton J; Petrosino, Joseph F; Conner, Margaret E; Versalovic, JamesFASEB journal : official publication of the Federation of American Societies for Experimental Biology2012 May1960-922267340
Significance of the microbiome in obstructive lung disease.Han, Meilan K; Huang, Yvonne J; Lipuma, John J; Boushey, Homer A; Boucher, Richard C; Cookson, William O; Curtis, Jeffrey L; Erb-Downward, John; Lynch, Susan V; Sethi, Sanjay; Toews, Galen B; Young, Vincent B; Wolfgang, Matthew C; Huffnagle, Gary B; MartiThorax2012 May456-6322318161
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites.Ursell, Luke K; Clemente, Jose C; Rideout, Jai Ram; Gevers, Dirk; Caporaso, J Gregory; Knight, RobThe Journal of allergy and clinical immunology2012 May1204-822541361
A new era of the vaginal microbiome: advances using next-generation sequencing.Fettweis, Jennifer M; Serrano, Myrna G; Girerd, Philippe H; Jefferson, Kimberly K; Buck, Gregory AChemistry & biodiversity2012 May965-7622589096
Molecular pathways: pathogenesis and clinical implications of microbiome alteration in esophagitis and Barrett esophagus.Yang, Liying; Francois, Fritz; Pei, ZhihengClinical cancer research : an official journal of the American Association for Cancer Research2012 Apr 152138-4422344232
Decade-long bacterial community dynamics in cystic fibrosis airways.Zhao, Jiangchao; Schloss, Patrick D; Kalikin, Linda M; Carmody, Lisa A; Foster, Bridget K; Petrosino, Joseph F; Cavalcoli, James D; VanDevanter, Donald R; Murray, Susan; Li, Jun Z; Young, Vincent B; LiPuma, John JProceedings of the National Academy of Sciences of the United States of America2012 Apr 105809-1422451929
Responses of gut microbiota to diet composition and weight loss in lean and obese mice.Ravussin, Yann; Koren, Omry; Spor, Ayme; LeDuc, Charles; Gutman, Roee; Stombaugh, Jesse; Knight, Rob; Ley, Ruth E; Leibel, Rudolph LObesity (Silver Spring, Md.)2012 Apr738-4721593810
The human microbiome: at the interface of health and disease.Cho, Ilseung; Blaser, Martin JNature reviews. Genetics2012 Apr260-7022411464
Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation.Hill, David A; Siracusa, Mark C; Abt, Michael C; Kim, Brian S; Kobuley, Dmytro; Kubo, Masato; Kambayashi, Taku; Larosa, David F; Renner, Ellen D; Orange, Jordan S; Bushman, Frederic D; Artis, DavidNature medicine2012 Apr538-4622447074
Hypervariable loci in the human gut virome.Minot, Samuel; Grunberg, Stephanie; Wu, Gary D; Lewis, James D; Bushman, Frederic DProceedings of the National Academy of Sciences of the United States of America2012 Mar 63962-622355105
Interleukin-1ýý (IL-1ýý) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis.Carvalho, Frederic A; Nalbantoglu, Ilke; Ortega-Fernandez, Sophie; Aitken, Jesse D; Su, Yueju; Koren, Omry; Walters, William A; Knight, Rob; Ley, Ruth E; Vijay-Kumar, Matam; Gewirtz, Andrew TGut2012 Mar373-8421646247
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.McDonald, Daniel; Price, Morgan N; Goodrich, Julia; Nawrocki, Eric P; DeSantis, Todd Z; Probst, Alexander; Andersen, Gary L; Knight, Rob; Hugenholtz, PhilipThe ISME journal2012 Mar610-822134646
GAGE: A critical evaluation of genome assemblies and assembly algorithms.Salzberg, Steven L; Phillippy, Adam M; Zimin, Aleksey; Puiu, Daniela; Magoc, Tanja; Koren, Sergey; Treangen, Todd J; Schatz, Michael C; Delcher, Arthur L; Roberts, Michael; Marcais, Guillaume; Pop, Mihai; Yorke, James AGenome research2012 Mar557-6722147368
Human microbiome and HIV/AIDS.Saxena, Deepak; Li, Yihong; Yang, Liying; Pei, Zhiheng; Poles, Michael; Abrams, William R; Malamud, DanielCurrent HIV/AIDS reports2012 Mar44-5122193889
Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws.Smajs, David; Norris, Steven J; Weinstock, George MInfection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases2012 Mar191-20222198325
Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice.Mei, Junjie; Liu, Yuhong; Dai, Ning; Hoffmann, Christian; Hudock, Kristin M; Zhang, Peggy; Guttentag, Susan H; Kolls, Jay K; Oliver, Paula M; Bushman, Frederic D; Worthen, G ScottThe Journal of clinical investigation2012 Mar 1974-8622326959
How patients view probiotics: findings from a multicenter study of patients with inflammatory bowel disease and irritable bowel syndrome.Mercer, MaryBeth; Brinich, Margaret A; Geller, Gail; Harrison, Krista; Highland, Janelle; James, Katherine; Marshall, Patricia; McCormick, Jennifer B; Tilburt, Jon; Achkar, Jean-Paul; Farrell, Ruth M; Sharp, Richard RJournal of clinical gastroenterology2012 Feb138-4421716123
The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, JizhongThe ISME journal2012 Feb259-7221796217
SitePainter: a tool for exploring biogeographical patterns.Gonzalez, Antonio; Stombaugh, Jesse; Lauber, Christian L; Fierer, Noah; Knight, RobBioinformatics (Oxford, England)2012 Feb 1436-822171330
Advancing analytical algorithms and pipelines for billions of microbial sequences.Gonzalez, Antonio; Knight, RobCurrent opinion in biotechnology2012 Feb64-7122172529
Single-cell protein analysis.Wu, Meiye; Singh, Anup KCurrent opinion in biotechnology2012 Feb83-822189001
Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis.Feazel, Leah M; Robertson, Charles E; Ramakrishnan, Vijay R; Frank, Daniel NThe Laryngoscope2012 Feb467-7222253013
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.Sun, Yijun; Cai, Yunpeng; Huse, Susan M; Knight, Rob; Farmerie, William G; Wang, Xiaoyu; Mai, VolkerBriefings in bioinformatics2012 Jan107-2121525143
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys.Werner, Jeffrey J; Koren, Omry; Hugenholtz, Philip; DeSantis, Todd Z; Walters, William A; Caporaso, J Gregory; Angenent, Largus T; Knight, Rob; Ley, Ruth EThe ISME journal2012 Jan94-10321716311
Antibiotic effects on bacterial profile in osteonecrosis of the jaw.Ji, X; Pushalkar, S; Li, Y; Glickman, R; Fleisher, K; Saxena, DOral diseases2012 Jan85-9521883710
Graph accordance of next-generation sequence assemblies.Yao, Guohui; Ye, Liang; Gao, Hongyu; Minx, Patrick; Warren, Wesley C; Weinstock, George MBioinformatics (Oxford, England)2012 Jan 113-622025481
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data.Zhao, Yongan; Tang, Haixu; Ye, YuzhenBioinformatics (Oxford, England)2012 Jan 1125-622039206
Epigenetic priors for identifying active transcription factor binding sites.Cuellar-Partida, Gabriel; Buske, Fabian A; McLeay, Robert C; Whitington, Tom; Noble, William Stafford; Bailey, Timothy LBioinformatics (Oxford, England)2012 Jan 156-6222072382
The intestinal microbiota in health and disease.Young, Vincent BCurrent opinion in gastroenterology2012 Jan63-922080827
IMG/M: the integrated metagenome data management and comparative analysis system.Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Pati, Amrita; Huntemann, Marcel; Liolios, Konstantinos; Pagani, Ioanna; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, NataliNucleic acids research2012 JanD123-922086953
The Human Microbiome Project: lessons from human genomics.Lewis Jr, Cecil M; Obregon-Tito, Alexandra; Tito, Raul Y; Foster, Morris W; Spicer, Paul GTrends in microbiology2012 Jan1-422112388
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata.Pagani, Ioanna; Liolios, Konstantinos; Jansson, Jakob; Chen, I-Min A; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor M; Kyrpides, Nikos CNucleic acids research2012 JanD571-922135293
CharProtDB: a database of experimentally characterized protein annotations.Madupu, Ramana; Richter, Alexander; Dodson, Robert J; Brinkac, Lauren; Harkins, Derek; Durkin, Scott; Shrivastava, Susmita; Sutton, Granger; Haft, DanielNucleic acids research2012 JanD237-4122140108
Artificial functional difference between microbial communities caused by length difference of sequencing reads.Zhang, Quan; Doak, Thomas G; Ye, YuzhenPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2012259-7022174281
Experimental and analytical tools for studying the human microbiome.Kuczynski, Justin; Lauber, Christian L; Walters, William A; Parfrey, Laura Wegener; Clemente, Jose C; Gevers, Dirk; Knight, RobNature reviews. Genetics2012 Jan47-5822179717
IMG: the Integrated Microbial Genomes database and comparative analysis system.Markowitz, Victor M; Chen, I-Min A; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, NikosNucleic acids research2012 JanD115-2222194640
Perturbation dynamics of the rumen microbiota in response to exogenous butyrate.Li, Robert W; Wu, Sitao; Baldwin 6th, Ransom L; Li, Weizhong; Li, CongjunPloS one2012e2939222253719
Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta; Pel, Joel; Marziali, AndrePloS one2012e3159722355378
A format for phylogenetic placements.Matsen, Frederick A; Hoffman, Noah G; Gallagher, Aaron; Stamatakis, AlexandrosPloS one2012e3100922383988
Standard colonic lavage alters the natural state of mucosal-associated microbiota in the human colon.Harrell, Laura; Wang, Yunwei; Antonopoulos, Dionysios; Young, Vincent; Lichtenstein, Lev; Huang, Yong; Hanauer, Stephen; Chang, EugenePloS one2012e3254522389708
Experiences of patients with chronic gastrointestinal conditions: in their own words.McCormick, Jennifer B; Hammer, Rachel R; Farrell, Ruth M; Geller, Gail; James, Katherine M; Loftus Jr, Edward V; Mercer, Mary Beth; Tilburt, Jon C; Sharp, Richard RHealth and quality of life outcomes20122522401607
AntiFam: a tool to help identify spurious ORFs in protein annotation.Eberhardt, Ruth Y; Haft, Daniel H; Punta, Marco; Martin, Maria; O'Donovan, Claire; Bateman, AlexDatabase : the journal of biological databases and curation2012bas00322434837
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.Giannoukos, Georgia; Ciulla, Dawn M; Huang, Katherine; Haas, Brian J; Izard, Jacques; Levin, Joshua Z; Livny, Jonathan; Earl, Ashlee M; Gevers, Dirk; Ward, Doyle V; Nusbaum, Chad; Birren, Bruce W; Gnirke, AndreasGenome biology2012R2322455878
Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism.Pathak, Darshankumar T; Wei, Xueming; Bucuvalas, Alex; Haft, Daniel H; Gerloff, Dietlind L; Wall, DanielPLoS genetics2012e100262622511878
Worm burden-dependent disruption of the porcine colon microbiota by Trichuris suis infection.Wu, Sitao; Li, Robert W; Li, Weizhong; Beshah, Ethiopia; Dawson, Harry D; Urban Jr, Joseph FPloS one2012e3547022532855
We are what we eat: how the diet of infants affects their gut microbiome.Pop, MihaiGenome biology201215222546514
Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing.Xiong, Xuejian; Frank, Daniel N; Robertson, Charles E; Hung, Stacy S; Markle, Janet; Canty, Angelo J; McCoy, Kathy D; Macpherson, Andrew J; Poussier, Philippe; Danska, Jayne S; Parkinson, JohnPloS one2012e3600922558305
Bacterial communities of the coronal sulcus and distal urethra of adolescent males.Nelson, David E; Dong, Qunfeng; Van der Pol, Barbara; Toh, Evelyn; Fan, Baochang; Katz, Barry P; Mi, Deming; Rong, Ruichen; Weinstock, George M; Sodergren, Erica; Fortenberry, J DennisPloS one2012e3629822606251
An ileal Crohn's disease gene signature based on whole human genome expression profiles of disease unaffected ileal mucosal biopsies.Zhang, Tianyi; Song, Bowen; Zhu, Wei; Xu, Xiao; Gong, Qing Qing; Morando, Christopher; Dassopoulos, Themistocles; Newberry, Rodney D; Hunt, Steven R; Li, EllenPloS one2012e3713922606341
Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells.Wu, Sitao; Li, Robert W; Li, Weizhong; Li, Cong-JunPloS one2012e3694022615851
Quantification of Transcriptome Responses of the Rumen Epithelium to Butyrate Infusion using RNA-seq Technology.Baldwin 6th, Ransom L; Wu, Sitao; Li, Weizhong; Li, Congjun; Bequette, Brian J; Li, Robert WGene regulation and systems biology201267-8022654504
Comparison of storage conditions for human vaginal microbiome studies.Bai, Guoyun; Gajer, Pawel; Nandy, Melissa; Ma, Bing; Yang, Hongqiu; Sakamoto, Joyce; Blanchard, May H; Ravel, Jacques; Brotman, Rebecca MPloS one2012e3693422655031
Deep sequencing of the oral microbiome reveals signatures of periodontal disease.Liu, Bo; Faller, Lina L; Klitgord, Niels; Mazumdar, Varun; Ghodsi, Mohammad; Sommer, Daniel D; Gibbons, Theodore R; Treangen, Todd J; Chang, Yi-Chien; Li, Shan; Stine, O Colin; Hasturk, Hatice; Kasif, Simon; Segre, Daniel; Pop, Mihai; Amar, SalomonPloS one2012e3791922675498
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples.Segata, Nicola; Haake, Susan Kinder; Mannon, Peter; Lemon, Katherine P; Waldron, Levi; Gevers, Dirk; Huttenhower, Curtis; Izard, JacquesGenome biology2012R4222698087
Metabolic reconstruction for metagenomic data and its application to the human microbiome.Abubucker, Sahar; Segata, Nicola; Goll, Johannes; Schubert, Alyxandria M; Izard, Jacques; Cantarel, Brandi L; Rodriguez-Mueller, Beltran; Zucker, Jeremy; Thiagarajan, Mathangi; Henrissat, Bernard; White, Owen; Kelley, Scott T; Methe, Barbara; Schloss, PatPLoS computational biology2012e100235822719234
Diverse CRISPRs evolving in human microbiomes.Rho, Mina; Wu, Yu-Wei; Tang, Haixu; Doak, Thomas G; Ye, YuzhenPLoS genetics2012e100244122719260
Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition.Li, Ellen; Hamm, Christina M; Gulati, Ajay S; Sartor, R Balfour; Chen, Hongyan; Wu, Xiao; Zhang, Tianyi; Rohlf, F James; Zhu, Wei; Gu, Chi; Robertson, Charles E; Pace, Norman R; Boedeker, Edgar C; Harpaz, Noam; Yuan, Jeffrey; Weinstock, George M; SodergrePloS one2012e2628422719818
Sequence analysis of the human virome in febrile and afebrile children.Wylie, Kristine M; Mihindukulasuriya, Kathie A; Sodergren, Erica; Weinstock, George M; Storch, Gregory APloS one2012e2773522719819
Complex carbohydrate utilization by the healthy human microbiome.Cantarel, Brandi L; Lombard, Vincent; Henrissat, BernardPloS one2012e2874222719820
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).Goll, Johannes; Thiagarajan, Mathangi; Abubucker, Sahar; Huttenhower, Curtis; Yooseph, Shibu; Methe, Barbara APloS one2012e2904422719821
Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition.Zhang, Tianyi; DeSimone, Robert A; Jiao, Xiangmin; Rohlf, F James; Zhu, Wei; Gong, Qing Qing; Hunt, Steven R; Dassopoulos, Themistocles; Newberry, Rodney D; Sodergren, Erica; Weinstock, George; Robertson, Charles E; Frank, Daniel N; Li, EllenPloS one2012e3004422719822
Analyses of the microbial diversity across the human microbiome.Li, Kelvin; Bihan, Monika; Yooseph, Shibu; Methe, Barbara APloS one2012e3211822719823
A core human microbiome as viewed through 16S rRNA sequence clusters.Huse, Susan M; Ye, Yuzhen; Zhou, Yanjiao; Fodor, Anthony APloS one2012e3424222719824
Novel bacterial taxa in the human microbiome.Wylie, Kristine M; Truty, Rebecca M; Sharpton, Thomas J; Mihindukulasuriya, Kathie A; Zhou, Yanjiao; Gao, Hongyu; Sodergren, Erica; Weinstock, George M; Pollard, Katherine SPloS one2012e3529422719826
Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities.Martin, John; Sykes, Sean; Young, Sarah; Kota, Karthik; Sanka, Ravi; Sheth, Nihar; Orvis, Joshua; Sodergren, Erica; Wang, Zhengyuan; Weinstock, George M; Mitreva, MakedonkaPloS one2012e3642722719831
A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy.Aagaard, Kjersti; Riehle, Kevin; Ma, Jun; Segata, Nicola; Mistretta, Toni-Ann; Coarfa, Cristian; Raza, Sabeen; Rosenbaum, Sean; Van den Veyver, Ignatia; Milosavljevic, Aleksandar; Gevers, Dirk; Huttenhower, Curtis; Petrosino, Joseph; Versalovic, JamesPloS one2012e3646622719832
Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria.Srinivasan, Sujatha; Hoffman, Noah G; Morgan, Martin T; Matsen, Frederick A; Fiedler, Tina L; Hall, Robert W; Ross, Frederick J; McCoy, Connor O; Bumgarner, Roger; Marrazzo, Jeanne M; Fredricks, David NPloS one2012e3781822719852
Alternative splicing regulated by butyrate in bovine epithelial cells.Wu, Sitao; Li, Congjun; Huang, Wen; Li, Weizhong; Li, Robert WPloS one2012e3918222720068
Evaluation of 16S rDNA-based community profiling for human microbiome research.Jumpstart Consortium Human Microbiome Project Data Generation Working GroupPloS one2012e3931522720093
Vaginal microbiome: rethinking health and disease.Ma, Bing; Forney, Larry J; Ravel, JacquesAnnual review of microbiology2012371-8922746335
Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes.Qin, Xiang; Galloway-Pena, Jessica R; Sillanpaa, Jouko; Roh, Jung Hyeob; Nallapareddy, Sreedhar R; Chowdhury, Shahreen; Bourgogne, Agathe; Choudhury, Tina; Muzny, Donna M; Buhay, Christian J; Ding, Yan; Dugan-Rocha, Shannon; Liu, Wen; Kovar, Christie; SodBMC microbiology201213522769602
IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project.Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Jacob, Biju; Ratner, Anna; Liolios, Konstantinos; Pagani, Ioanna; Huntemann, Marcel; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos CPloS one2012e4015122792232
Microbial co-occurrence relationships in the human microbiome.Faust, Karoline; Sathirapongsasuti, J Fah; Izard, Jacques; Segata, Nicola; Gevers, Dirk; Raes, Jeroen; Huttenhower, CurtisPLoS computational biology2012e100260622807668
Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma.Pushalkar, Smruti; Ji, Xiaojie; Li, Yihong; Estilo, Cherry; Yegnanarayana, Ramanathan; Singh, Bhuvanesh; Li, Xin; Saxena, DeepakBMC microbiology201214422817758
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal.Trimble, William L; Keegan, Kevin P; D'Souza, Mark; Wilke, Andreas; Wilkening, Jared; Gilbert, Jack; Meyer, FolkerBMC bioinformatics201218322839106
The "most wanted" taxa from the human microbiome for whole genome sequencing.Fodor, Anthony A; DeSantis, Todd Z; Wylie, Kristine M; Badger, Jonathan H; Ye, Yuzhen; Hepburn, Theresa; Hu, Ping; Sodergren, Erica; Liolios, Konstantinos; Huot-Creasy, Heather; Birren, Bruce W; Earl, Ashlee MPloS one2012e4129422848458
Conservation of gene cassettes among diverse viruses of the human gut.Minot, Samuel; Wu, Gary D; Lewis, James D; Bushman, Frederic DPloS one2012e4234222900013
The Human Microbiome Project: a community resource for the healthy human microbiome.Gevers, Dirk; Knight, Rob; Petrosino, Joseph F; Huang, Katherine; McGuire, Amy L; Birren, Bruce W; Nelson, Karen E; White, Owen; Methe, Barbara A; Huttenhower, CurtisPLoS biology2012e100137722904687
Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome.Zupancic, Margaret L; Cantarel, Brandi L; Liu, Zhenqiu; Drabek, Elliott F; Ryan, Kathleen A; Cirimotich, Shana; Jones, Cheron; Knight, Rob; Walters, William A; Knights, Daniel; Mongodin, Emmanuel F; Horenstein, Richard B; Mitchell, Braxton D; Steinle, NanPloS one2012e4305222905200
Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures.Madan, J C; Koestler, D C; Stanton, B A; Davidson, L; Moulton, L A; Housman, M L; Moore, J H; Guill, M F; Morrison, H G; Sogin, M L; Hampton, T H; Karagas, M R; Palumbo, P E; Foster, J A; Hibberd, P L; O'Toole, G AmBio201222911969
Current technology in the diagnosis of developmentally related lung disorders.Hamvas, AaronNeonatology2012353-922940625
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.Morgan, Xochitl C; Tickle, Timothy L; Sokol, Harry; Gevers, Dirk; Devaney, Kathryn L; Ward, Doyle V; Reyes, Joshua A; Shah, Samir A; LeLeiko, Neal; Snapper, Scott B; Bousvaros, Athos; Korzenik, Joshua; Sands, Bruce E; Xavier, Ramnik J; Huttenhower, CurtisGenome biology2012R7923013615
The L1-norm best-fit hyperplane problem.Brooks, J P; Dula, J HApplied mathematics letters2012 Jan 151-5623024460
Succession in the gut microbiome following antibiotic and antibody therapies for Clostridium difficile.Peterfreund, Gregory L; Vandivier, Lee E; Sinha, Rohini; Marozsan, Andre J; Olson, William C; Zhu, Jun; Bushman, Frederic DPloS one2012e4696623071679
Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa.Williams, Tiffany M; Loman, Nicholas J; Ebruke, Chinelo; Musher, Daniel M; Adegbola, Richard A; Pallen, Mark J; Weinstock, George M; Antonio, MartinPloS one2012e2674223082106
"Snake-oil," "quack medicine," and "industrially cultured organisms:" biovalue and the commercialization of human microbiome research.Slashinski, Melody J; McCurdy, Sheryl A; Achenbaum, Laura S; Whitney, Simon N; McGuire, Amy LBMC medical ethics20122823110633
Estimation of distribution overlap of urn models.Hampton, Jerrad; Lladser, Manuel EPloS one2012e4236823139734
Statistical object data analysis of taxonomic trees from human microbiome data.La Rosa, Patricio S; Shands, Berkley; Deych, Elena; Zhou, Yanjiao; Sodergren, Erica; Weinstock, George; Shannon, William DPloS one2012e4899623152838
Bioinformatics for the Human Microbiome Project.Gevers, Dirk; Pop, Mihai; Schloss, Patrick D; Huttenhower, CurtisPLoS computational biology2012e100277923209389
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease.Erickson, Alison R; Cantarel, Brandi L; Lamendella, Regina; Darzi, Youssef; Mongodin, Emmanuel F; Pan, Chongle; Shah, Manesh; Halfvarson, Jonas; Tysk, Curt; Henrissat, Bernard; Raes, Jeroen; Verberkmoes, Nathan C; Fraser, Claire M; Hettich, Robert L; JansPloS one2012e4913823209564
Increased prevalence of anellovirus in pediatric patients with fever.McElvania TeKippe, Erin; Wylie, Kristine M; Deych, Elena; Sodergren, Erica; Weinstock, George; Storch, Gregory APloS one2012e5093723226428
Insights from characterizing extinct human gut microbiomes.Tito, Raul Y; Knights, Dan; Metcalf, Jessica; Obregon-Tito, Alexandra J; Cleeland, Lauren; Najar, Fares; Roe, Bruce; Reinhard, Karl; Sobolik, Kristin; Belknap, Samuel; Foster, Morris; Spicer, Paul; Knight, Rob; Lewis Jr, Cecil MPloS one2012e5114623251439
Genomic sequence analysis and characterization of Sneathia amnii sp. nov.Harwich Jr, Michael D; Serrano, Myrna G; Fettweis, Jennifer M; Alves, Joao M P; Reimers, Mark A; Vaginal Microbiome Consortium (additional members); Buck, Gregory A; Jefferson, Kimberly KBMC genomics2012S423281612
Species-level classification of the vaginal microbiome.Fettweis, Jennifer M; Serrano, Myrna G; Sheth, Nihar U; Mayer, Carly M; Glascock, Abigail L; Brooks, J Paul; Jefferson, Kimberly K; Vaginal Microbiome Consortium (additional members); Buck, Gregory ABMC genomics2012S1723282177
Hypothesis testing and power calculations for taxonomic-based human microbiome data.La Rosa, Patricio S; Brooks, J Paul; Deych, Elena; Boone, Edward L; Edwards, David J; Wang, Qin; Sodergren, Erica; Weinstock, George; Shannon, William DPloS one2012e5207823284876
Chapter 12: Human microbiome analysis.Morgan, Xochitl C; Huttenhower, CurtisPLoS computational biology2012e100280823300406
The Jeremiah Metzger lecture: Global warming redux: the disappearing microbiota and epidemic obesity.Blaser, Martin JTransactions of the American Clinical and Climatological Association2012230-8; discussion 239-4123303990
The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences.Riehle, Kevin; Coarfa, Cristian; Jackson, Andrew; Ma, Jun; Tandon, Arpit; Paithankar, Sameer; Raghuraman, Sriram; Mistretta, Toni-Ann; Saulnier, Delphine; Raza, Sabeen; Diaz, Maria Alejandra; Shulman, Robert; Aagaard, Kjersti; Versalovic, James; MilosavljBMC bioinformatics2012S1123320832
Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data.Liu, Zhenqiu; Hsiao, William; Cantarel, Brandi L; Drabek, Elliott Franco; Fraser-Liggett, ClaireBioinformatics (Oxford, England)2011 Dec 13242-921984758
Using QIIME to analyze 16S rRNA gene sequences from microbial communities.Kuczynski, Justin; Stombaugh, Jesse; Walters, William Anton; Gonzalez, Antonio; Caporaso, J Gregory; Knight, RobCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]2011 DecUnit 10.7.22161565
Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.Saulnier, Delphine M; Riehle, Kevin; Mistretta, Toni-Ann; Diaz, Maria-Alejandra; Mandal, Debasmita; Raza, Sabeen; Weidler, Erica M; Qin, Xiang; Coarfa, Cristian; Milosavljevic, Aleksandar; Petrosino, Joseph F; Highlander, Sarah; Gibbs, Richard; Lynch, SusGastroenterology2011 Nov1782-9121741921
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.Pirrung, Meg; Kennedy, Ryan; Caporaso, J Gregory; Stombaugh, Jesse; Wendel, Doug; Knight, RobBioinformatics (Oxford, England)2011 Nov 13067-921903626
Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma).Youssef, Noha H; Blainey, Paul C; Quake, Stephen R; Elshahed, Mostafa SApplied and environmental microbiology2011 Nov7804-1421908640
Bambus 2: scaffolding metagenomes.Koren, Sergey; Treangen, Todd J; Pop, MihaiBioinformatics (Oxford, England)2011 Nov 12964-7121926123
De minimis risk: a proposal for a new category of research risk.Rhodes, Rosamond; Azzouni, Jody; Baumrin, Stefan Bernard; Benkov, Keith; Blaser, Martin J; Brenner, Barbara; Dauben, Joseph W; Earle, William J; Frank, Lily; Gligorov, Nada; Goldfarb, Joseph; Hirschhorn, Kurt; Hirschhorn, Rochelle; Holzman, Ian; Indyk, DeThe American journal of bioethics : AJOB2011 Nov1-722047112
Saying privacy, meaning confidentiality.Schwab, Abraham P; Frank, Lily; Gligorov, NadaThe American journal of bioethics : AJOB2011 Nov44-522047127
Astrovirus MLB2 viremia in febrile child.Holtz, Lori R; Wylie, Kristine M; Sodergren, Erica; Jiang, Yanfang; Franz, Carl J; Weinstock, George M; Storch, Gregory A; Wang, DavidEmerging infectious diseases2011 Nov2050-222099095
Caring about trees in the forest: incorporating frailty in risk analysis for personalized medicine.Ma, Zhanshan Sam; Abdo, Zaid; Forney, Larry JPersonalized medicine2011 Nov681-68822754581
Microbiome and malignancy.Plottel, Claudia S; Blaser, Martin JCell host & microbe2011 Oct 20324-3522018233
Linking long-term dietary patterns with gut microbial enterotypes.Wu, Gary D; Chen, Jun; Hoffmann, Christian; Bittinger, Kyle; Chen, Ying-Yu; Keilbaugh, Sue A; Bewtra, Meenakshi; Knights, Dan; Walters, William A; Knight, Rob; Sinha, Rohini; Gilroy, Erin; Gupta, Kernika; Baldassano, Robert; Nessel, Lisa; Li, Hongzhe; BusScience (New York, N.Y.)2011 Oct 7105-821885731
Specific sorting of single bacterial cells with microfabricated fluorescence-activated cell sorting and tyramide signal amplification fluorescence in situ hybridization.Chen, Chun H; Cho, Sung H; Chiang, Hsin-I; Tsai, Frank; Zhang, Kun; Lo, Yu-HwaAnalytical chemistry2011 Oct 17269-7521809842
Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation.Zaneveld, Jesse R R; Parfrey, Laura Wegener; Van Treuren, Will; Lozupone, Catherine; Clemente, Jose C; Knights, Dan; Stombaugh, Jesse; Kuczynski, Justin; Knight, RobTrends in microbiology2011 Oct472-8221872475
The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment.Sczesnak, Andrew; Segata, Nicola; Qin, Xiang; Gevers, Dirk; Petrosino, Joseph F; Huttenhower, Curtis; Littman, Dan R; Ivanov, Ivaylo ICell host & microbe2011 Sep 15260-7221925113
Genetic basis for in vivo daptomycin resistance in enterococci.Arias, Cesar A; Panesso, Diana; McGrath, Danielle M; Qin, Xiang; Mojica, Maria F; Miller, Corwin; Diaz, Lorena; Tran, Truc T; Rincon, Sandra; Barbu, E Magda; Reyes, Jinnethe; Roh, Jung H; Lobos, Elizabeth; Sodergren, Erica; Pasqualini, Renata; Arap, WadihThe New England journal of medicine2011 Sep 8892-90021899450
Reliability and validity of a modified Bristol Stool Form Scale for children.Lane, Mariella M; Czyzewski, Danita I; Chumpitazi, Bruno P; Shulman, Robert JThe Journal of pediatrics2011 Sep437-441.e121489557
Bayesian community-wide culture-independent microbial source tracking.Knights, Dan; Kuczynski, Justin; Charlson, Emily S; Zaneveld, Jesse; Mozer, Michael C; Collman, Ronald G; Bushman, Frederic D; Knight, Rob; Kelley, Scott TNature methods2011 Sep761-321765408
Investigating the biological and clinical significance of human dysbioses.Frank, Daniel N; Zhu, Wei; Sartor, R Balfour; Li, EllenTrends in microbiology2011 Sep427-3421775143
Microfluidic fluorescence in situ hybridization and flow cytometry (ýýFlowFISH).Liu, Peng; Meagher, Robert J; Light, Yooli K; Yilmaz, Suzan; Chakraborty, Romy; Arkin, Adam P; Hazen, Terry C; Singh, Anup KLab on a chip2011 Aug 212673-921755095
UCHIME improves sensitivity and speed of chimera detection.Edgar, Robert C; Haas, Brian J; Clemente, Jose C; Quince, Christopher; Knight, RobBioinformatics (Oxford, England)2011 Aug 152194-20021700674
A primer on a hepatocellular carcinoma bioresource bank using the cancer genome atlas guidelines: practical issues and pitfalls.Nguyen, N Thao T; Cotton, Ron T; Harring, Theresa R; Guiteau, Jacfranz J; Gingras, Marie-Claude; Wheeler, David A; O'Mahony, Christine A; Gibbs, Richard A; Brunicardi, F Charles; Goss, John AWorld journal of surgery2011 Aug1732-721221581
Building a comprehensive genomic program for hepatocellular carcinoma.Harring, Theresa R; Guiteau, Jacfranz J; Nguyen, N Thao T; Cotton, Ron T; Gingras, Marie-Claude; Wheeler, David A; O'Mahony, Christine A; Gibbs, Richard A; Brunicardi, F Charles; Goss, John AWorld journal of surgery2011 Aug1746-5021225260
The age of necrotizing enterocolitis onset: an application of Sartwell's incubation period model.Gonzalez-Rivera, R; Culverhouse, R C; Hamvas, A; Tarr, P I; Warner, B BJournal of perinatology : official journal of the California Perinatal Association2011 Aug519-2321273988
A randomised trial of sheathed versus standard forceps for obtaining uncontaminated biopsy specimens of microbiota from the terminal ileum.Dave, Maneesh; Johnson, Laura A; Walk, Seth T; Young, Vincent B; Stidham, Ryan W; Chaudhary, Meghana N; Funnell, Jessica; Higgins, Peter D RGut2011 Aug1043-921317176
Overview of the development of personalized genomic medicine and surgery.Brunicardi, F Charles; Gibbs, Richard A; Wheeler, David A; Nemunaitis, John; Fisher, William; Goss, John; Chen, ChangyiWorld journal of surgery2011 Aug1693-921424870
Brief communication: DNA from early Holocene American dog.Tito, Raul Y; Belknap 3rd, Samuel L; Sobolik, Kristin D; Ingraham, Robert C; Cleeland, Lauren M; Lewis Jr, Cecil MAmerican journal of physical anthropology2011 Aug653-721541929
The under-recognized dominance of Verrucomicrobia in soil bacterial communities.Bergmann, Gaddy T; Bates, Scott T; Eilers, Kathryn G; Lauber, Christian L; Caporaso, J Gregory; Walters, William A; Knight, Rob; Fierer, NoahSoil biology & biochemistry2011 Jul1450-145522267877
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes.Niu, Beifang; Zhu, Zhengwei; Fu, Limin; Wu, Sitao; Li, WeizhongBioinformatics (Oxford, England)2011 Jun 151704-521505035
Boulder ALignment Editor (ALE): a web-based RNA alignment tool.Stombaugh, Jesse; Widmann, Jeremy; McDonald, Daniel; Knight, RobBioinformatics (Oxford, England)2011 Jun 151706-721546392
Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification.Haft, Daniel H; Basu, Malay KumarJournal of bacteriology2011 Jun2745-5521478363
Evolution and classification of the CRISPR-Cas systems.Makarova, Kira S; Haft, Daniel H; Barrangou, Rodolphe; Brouns, Stan J J; Charpentier, Emmanuelle; Horvath, Philippe; Moineau, Sylvain; Mojica, Francisco J M; Wolf, Yuri I; Yakunin, Alexander F; van der Oost, John; Koonin, Eugene VNature reviews. Microbiology2011 Jun467-7721552286
Bacterial DNA content in the intestinal wall from infants with necrotizing enterocolitis.Bucher, Brian T; McDuffie, Lucas A; Shaikh, Nurmohammad; Tarr, Phillip I; Warner, Barbara B; Hamvas, Aaron; White, Frances V; Erwin, Christopher R; Warner, Brad WJournal of pediatric surgery2011 Jun1029-3321683193
Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice.Kellermayer, Richard; Dowd, Scot E; Harris, R Alan; Balasa, Alfred; Schaible, Tiffany D; Wolcott, Randy D; Tatevian, Nina; Szigeti, Reka; Li, Zhijie; Versalovic, James; Smith, C WayneFASEB journal : official publication of the Federation of American Societies for Experimental Biology2011 May1449-6021228220
Development of the human gastrointestinal microbiota and insights from high-throughput sequencing.Dominguez-Bello, Maria Gloria; Blaser, Martin J; Ley, Ruth E; Knight, RobGastroenterology2011 May1713-921530737
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn; Knight, Rob; Cole, James R; Amaral-Zettler, Linda; Gilbert, Jack A; Karsch-Mizrachi, Ilene; Johnston, Anjanette; Cochrane, Guy; Vaughan, Robert; Hunter, Christopher; Park, Joonhong; Morrison, Norman; Rocca-SerrNature biotechnology2011 May415-2021552244
The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection.Reeves, Angela E; Theriot, Casey M; Bergin, Ingrid L; Huffnagle, Gary B; Schloss, Patrick D; Young, Vincent BGut microbes2011 May-Jun145-5821804357
Microbial diversity in saliva of oral squamous cell carcinoma.Pushalkar, Smruti; Mane, Shrinivasrao P; Ji, Xiaojie; Li, Yihong; Evans, Clive; Crasta, Oswald R; Morse, Douglas; Meagher, Robert; Singh, Anup; Saxena, DeepakFEMS immunology and medical microbiology2011 Apr269-7721205002
Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts.Ballal, Sonia A; Gallini, Carey Ann; Segata, Nicola; Huttenhower, Curtis; Garrett, Wendy SCellular microbiology2011 Apr508-1721314883
Unravelling the effects of the environment and host genotype on the gut microbiome.Spor, Ayme; Koren, Omry; Ley, RuthNature reviews. Microbiology2011 Apr279-9021407244
Vaginal microbiome of reproductive-age women.Ravel, Jacques; Gajer, Pawel; Abdo, Zaid; Schneider, G Maria; Koenig, Sara S K; McCulle, Stacey L; Karlebach, Shara; Gorle, Reshma; Russell, Jennifer; Tacket, Carol O; Brotman, Rebecca M; Davis, Catherine C; Ault, Kevin; Peralta, Ligia; Forney, Larry JProceedings of the National Academy of Sciences of the United States of America2011 Mar 154680-720534435
Human oral, gut, and plaque microbiota in patients with atherosclerosis.Koren, Omry; Spor, Ayme; Felin, Jenny; Fak, Frida; Stombaugh, Jesse; Tremaroli, Valentina; Behre, Carl Johan; Knight, Rob; Fagerberg, Bjorn; Ley, Ruth E; Backhed, FredrikProceedings of the National Academy of Sciences of the United States of America2011 Mar 154592-820937873
Growth and Development Symposium: promoting healthier humans through healthier livestock: animal agriculture enters the metagenomics era.Frank, D NJournal of animal science2011 Mar835-4420935136
Digital MDA for enumeration of total nucleic acid contamination.Blainey, Paul C; Quake, Stephen RNucleic acids research2011 Mare1921071419
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.Haas, Brian J; Gevers, Dirk; Earl, Ashlee M; Feldgarden, Mike; Ward, Doyle V; Giannoukos, Georgia; Ciulla, Dawn; Tabbaa, Diana; Highlander, Sarah K; Sodergren, Erica; Methe, Barbara; DeSantis, Todd Z; Human Microbiome Consortium; Petrosino, Joseph F; KnigGenome research2011 Mar494-50421212162
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.Wu, Yu-Wei; Ye, YuzhenJournal of computational biology : a journal of computational molecular cell biology2011 Mar523-3421385052
Beyond natural antibodies: the power of in vitro display technologies.Bradbury, Andrew R M; Sidhu, Sachdev; Dubel, Stefan; McCafferty, JohnNature biotechnology2011 Mar245-5421390033
Next generation sequence assembly with AMOS.Treangen, Todd J; Sommer, Dan D; Angly, Florent E; Koren, Sergey; Pop, MihaiCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]2011 MarUnit 11.821400694
Dielectrophoresis of Caenorhabditis elegans.Chuang, Han-Sheng; Raizen, David M; Lamb, Annesia; Dabbish, Nooreen; Bau, Haim HLab on a chip2011 Feb 21599-60421225036
Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment.Ye, YuzhenProceedings. IEEE International Conference on Bioinformatics and Biomedicine2011 Feb 4153-15722102981
Current concepts of the intestinal microbiota and the pathogenesis of infection.Wardwell, Leslie H; Huttenhower, Curtis; Garrett, Wendy SCurrent infectious disease reports2011 Feb28-3421308452
Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases.Frank, Daniel N; Robertson, Charles E; Hamm, Christina M; Kpadeh, Zegbeh; Zhang, Tianyi; Chen, Hongyan; Zhu, Wei; Sartor, R Balfour; Boedeker, Edgar C; Harpaz, Noam; Pace, Norman R; Li, EllenInflammatory bowel diseases2011 Jan179-8420839241
Probiotics, enteric and diarrheal diseases, and global health.Preidis, Geoffrey A; Hill, Colin; Guerrant, Richard L; Ramakrishna, B S; Tannock, Gerald W; Versalovic, JamesGastroenterology2011 Jan8-1421075108
Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics.Shah, Neethu; Tang, Haixu; Doak, Thomas G; Ye, YuzhenPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2011165-7621121044
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners.Haft, Daniel HBMC genomics20112121223593
The microbe-derived short chain fatty acid butyrate targets miRNA-dependent p21 gene expression in human colon cancer.Hu, Shien; Dong, Tien Sy; Dalal, Sushila R; Wu, Feng; Bissonnette, Marc; Kwon, John H; Chang, Eugene BPloS one2011e1622121283757
Microdroplet-enabled highly parallel co-cultivation of microbial communities.Park, Jihyang; Kerner, Alissa; Burns, Mark A; Lin, Xiaoxia NinaPloS one2011e1701921364881
Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis.Blainey, Paul C; Mosier, Annika C; Potanina, Anastasia; Francis, Christopher A; Quake, Stephen RPloS one2011e1662621364937
Host-associated and free-living phage communities differ profoundly in phylogenetic composition.Caporaso, J Gregory; Knight, Rob; Kelley, Scott TPloS one2011e1690021383980
The mind-body-microbial continuum.Gonzalez, Antonio; Stombaugh, Jesse; Lozupone, Catherine; Turnbaugh, Peter J; Gordon, Jeffrey I; Knight, RobDialogues in clinical neuroscience201155-6221485746
Simrank: Rapid and sensitive general-purpose k-mer search tool.DeSantis, Todd Z; Keller, Keith; Karaoz, Ulas; Alekseyenko, Alexander V; Singh, Navjeet N S; Brodie, Eoin L; Pei, Zhiheng; Andersen, Gary L; Larsen, NielsBMC ecology20111121524302
RAPSearch: a fast protein similarity search tool for short reads.Ye, Yuzhen; Choi, Jeong-Hyeon; Tang, HaixuBMC bioinformatics201115921575167
The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens.Dong, Qunfeng; Nelson, David E; Toh, Evelyn; Diao, Lixia; Gao, Xiang; Fortenberry, J Dennis; Van der Pol, BarbaraPloS one2011e1970921603636
Moving pictures of the human microbiome.Caporaso, J Gregory; Lauber, Christian L; Costello, Elizabeth K; Berg-Lyons, Donna; Gonzalez, Antonio; Stombaugh, Jesse; Knights, Dan; Gajer, Pawel; Ravel, Jacques; Fierer, Noah; Gordon, Jeffrey I; Knight, RobGenome biology2011R5021624126
Metagenomic biomarker discovery and explanation.Segata, Nicola; Izard, Jacques; Waldron, Levi; Gevers, Dirk; Miropolsky, Larisa; Garrett, Wendy S; Huttenhower, CurtisGenome biology2011R6021702898
DNACLUST: accurate and efficient clustering of phylogenetic marker genes.Ghodsi, Mohammadreza; Liu, Bo; Pop, MihaiBMC bioinformatics201127121718538
Extrapolation of urn models via poissonization: accurate measurements of the microbial unknown.Lladser, Manuel E; Gouet, Raul; Reeder, JensPloS one2011e2110521738613
Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting through the Growing Pains and Moving Forward.Young, Vincent B; Kahn, Stacy A; Schmidt, Thomas M; Chang, Eugene BFrontiers in microbiology201114421772835
Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.Ahn, Jiyoung; Yang, Liying; Paster, Bruce J; Ganly, Ian; Morris, Luc; Pei, Zhiheng; Hayes, Richard BPloS one2011e2278821829515
WebMGA: a customizable web server for fast metagenomic sequence analysis.Wu, Sitao; Zhu, Zhengwei; Fu, Liming; Niu, Beifang; Li, WeizhongBMC genomics201144421899761
Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies.Segata, Nicola; Huttenhower, CurtisPloS one2011e2470421931822
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.Liu, Bo; Gibbons, Theodore; Ghodsi, Mohammad; Treangen, Todd; Pop, MihaiBMC genomics2011S421989143
Fluorescent labeling of antibody fragments using split GFP.Ferrara, Fortunato; Listwan, Pawel; Waldo, Geoffrey S; Bradbury, Andrew R MPloS one2011e2572721998685
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process.Basu, Malay K; Selengut, Jeremy D; Haft, Daniel HBMC bioinformatics201143422070167
Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.Cantarel, Brandi L; Erickson, Alison R; VerBerkmoes, Nathan C; Erickson, Brian K; Carey, Patricia A; Pan, Chongle; Shah, Manesh; Mongodin, Emmanuel F; Jansson, Janet K; Fraser-Liggett, Claire M; Hettich, Robert LPloS one2011e2717322132090
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.Schloss, Patrick D; Gevers, Dirk; Westcott, Sarah LPloS one2011e2731022194782
GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease.Haft, Daniel H; Varghese, NehaPloS one2011e2888622194940
Regional differences in colonic mucosa-associated microbiota determine the physiological expression of host heat shock proteins.Hu, Shien; Wang, Yunwei; Lichtenstein, Lev; Tao, Yun; Musch, Mark W; Jabri, Bana; Antonopoulos, Dionysios; Claud, Erika C; Chang, Eugene BAmerican journal of physiology. Gastrointestinal and liver physiology2010 DecG1266-7520864653
Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon.Wang, Yunwei; Antonopoulos, Dionysios A; Zhu, Xiaorong; Harrell, Laura; Hanan, Ira; Alverdy, John C; Meyer, Folker; Musch, Mark W; Young, Vincent B; Chang, Eugene BApplied microbiology and biotechnology2010 Dec1333-4220931185
SmashCell: a software framework for the analysis of single-cell amplified genome sequences.Harrington, Eoghan D; Arumugam, Manimozhiyan; Raes, Jeroen; Bork, Peer; Relman, David ABioinformatics (Oxford, England)2010 Dec 12979-8020966005
A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions.Krentz, Benjamin D; Mulheron, Heidi J; Semrau, Jeremy D; Dispirito, Alan A; Bandow, Nathan L; Haft, Daniel H; Vuilleumier, Stephane; Murrell, J Colin; McEllistrem, Marcus T; Hartsel, Scott C; Gallagher, Warren HBiochemistry2010 Nov 3010117-3020961038
Postprandial remodeling of the gut microbiota in Burmese pythons.Costello, Elizabeth K; Gordon, Jeffrey I; Secor, Stephen M; Knight, RobThe ISME journal2010 Nov1375-8520520652
The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves.Redford, Amanda J; Bowers, Robert M; Knight, Rob; Linhart, Yan; Fierer, NoahEnvironmental microbiology2010 Nov2885-9320545741
Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.Selengut, Jeremy D; Haft, Daniel HJournal of bacteriology2010 Nov5788-9820675471
FragGeneScan: predicting genes in short and error-prone reads.Rho, Mina; Tang, Haixu; Ye, YuzhenNucleic acids research2010 Nove19120805240
METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics.Goll, Johannes; Rusch, Douglas B; Tanenbaum, David M; Thiagarajan, Mathangi; Li, Kelvin; Methe, Barbara A; Yooseph, ShibuBioinformatics (Oxford, England)2010 Oct 152631-220798169
Quantitation of major human cutaneous bacterial and fungal populations.Gao, Zhan; Perez-Perez, Guillermo I; Chen, Yu; Blaser, Martin JJournal of clinical microbiology2010 Oct3575-8120702672
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns.Kuczynski, Justin; Liu, Zongzhi; Lozupone, Catherine; McDonald, Daniel; Fierer, Noah; Knight, RobNature methods2010 Oct813-920818378
Creation and initial evaluation of a Stool Form Scale for children.Chumpitazi, Bruno P; Lane, Mariella M; Czyzewski, Danita I; Weidler, Erica M; Swank, Paul R; Shulman, Robert JThe Journal of pediatrics2010 Oct594-720826285
Informed consent in genomics and genetic research.McGuire, Amy L; Beskow, Laura MAnnual review of genomics and human genetics2010 Sep 22361-8120477535
Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome.Nossa, Carlos W; Oberdorf, William E; Yang, Liying; Aas, Jorn A; Paster, Bruce J; Desantis, Todd Z; Brodie, Eoin L; Malamud, Daniel; Poles, Michael A; Pei, ZhihengWorld journal of gastroenterology : WJG2010 Sep 74135-4420806429
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions.Reeder, Jens; Knight, RobNature methods2010 Sep668-920805793
Molecular microbiological methods in the diagnosis of neonatal sepsis.Venkatesh, Mohan; Flores, Angela; Luna, Ruth Ann; Versalovic, JamesExpert review of anti-infective therapy2010 Sep1037-4820818947
Rapid fluctuation of the vaginal microbiota measured by Gram stain analysis.Brotman, Rebecca M; Ravel, Jacques; Cone, Richard A; Zenilman, Jonathan MSexually transmitted infections2010 Aug297-30220660593
Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives.Zaneveld, Jesse R; Lozupone, Catherine; Gordon, Jeffrey I; Knight, RobNucleic acids research2010 Jul3869-7920197316
Ironing out the wrinkles in the rare biosphere through improved OTU clustering.Huse, Susan M; Welch, David Mark; Morrison, Hilary G; Sogin, Mitchell LEnvironmental microbiology2010 Jul1889-9820236171
The right to ignore genetic status of late onset genetic disease in the genomic era; Prenatal testing for Huntington disease as a paradigm.Erez, A; Plunkett, K; Sutton, V R; McGuire, A LAmerican journal of medical genetics. Part A2010 Jul1774-8020583190
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.Dominguez-Bello, Maria G; Costello, Elizabeth K; Contreras, Monica; Magris, Magda; Hidalgo, Glida; Fierer, Noah; Knight, RobProceedings of the National Academy of Sciences of the United States of America2010 Jun 2911971-520566857
Human mammalian cell sorting using a highly integrated micro-fabricated fluorescence-activated cell sorter (microFACS).Cho, Sung Hwan; Chen, Chun H; Tsai, Frank S; Godin, Jessica M; Lo, Yu-HwaLab on a chip2010 Jun 211567-7320379604
Hepatitis C virus transmission bottlenecks analyzed by deep sequencing.Wang, Gary P; Sherrill-Mix, Scott A; Chang, Kyong-Mi; Quince, Chris; Bushman, Frederic DJournal of virology2010 Jun6218-2820375170
Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples.Lauber, Christian L; Zhou, Nicholas; Gordon, Jeffrey I; Knight, Rob; Fierer, NoahFEMS microbiology letters2010 Jun80-620412303
Diversity of 16S rRNA genes within individual prokaryotic genomes.Pei, Anna Y; Oberdorf, William E; Nossa, Carlos W; Agarwal, Ankush; Chokshi, Pooja; Gerz, Erika A; Jin, Zhida; Lee, Peng; Yang, Liying; Poles, Michael; Brown, Stuart M; Sotero, Steven; Desantis, Todd; Brodie, Eoin; Nelson, Karen; Pei, ZhihengApplied and environmental microbiology2010 Jun3886-9720418441
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes.Pati, Amrita; Ivanova, Natalia N; Mikhailova, Natalia; Ovchinnikova, Galina; Hooper, Sean D; Lykidis, Athanasios; Kyrpides, Nikos CNature methods2010 Jun455-720436475
A catalog of reference genomes from the human microbiome.Human Microbiome Jumpstart Reference Strains Consortium; Nelson, Karen E; Weinstock, George M; Highlander, Sarah K; Worley, Kim C; Creasy, Heather Huot; Wortman, Jennifer Russo; Rusch, Douglas B; Mitreva, Makedonka; Sodergren, Erica; Chinwalla, Asif T; FeScience (New York, N.Y.)2010 May 21994-920489017
Mammalian Cell Sorting using ýýFACS.Cho, Sung Hwan; Chen, Chun Hao; Tsai, Frank S; Godin, Jessica; Lo, Yu-HwaConference on Lasers and Electro-optics : (CLEO). Conference on Lasers and Electro-optics2010 May 16CTuD121614147
Personal genome research : what should the participant be told?McGuire, Amy L; Lupski, James RTrends in genetics : TIG2010 May199-20120381895
QIIME allows analysis of high-throughput community sequencing data.Caporaso, J Gregory; Kuczynski, Justin; Stombaugh, Jesse; Bittinger, Kyle; Bushman, Frederic D; Costello, Elizabeth K; Fierer, Noah; Pena, Antonio Gonzalez; Goodrich, Julia K; Gordon, Jeffrey I; Huttley, Gavin A; Kelley, Scott T; Knights, Dan; Koenig, JerNature methods2010 May335-620383131
Probiotics-host communication: Modulation of signaling pathways in the intestine.Thomas, Carissa M; Versalovic, JamesGut microbes2010 May-Jun148-6320672012
Harnessing the power of the human microbiome.Blaser, Martin JProceedings of the National Academy of Sciences of the United States of America2010 Apr 66125-620360554
Role of the gut microbiota in defining human health.Fujimura, Kei E; Slusher, Nicole A; Cabana, Michael D; Lynch, Susan VExpert review of anti-infective therapy2010 Apr435-5420377338
Bacterial communities of disease vectors sampled across time, space, and species.Jones, Ryan T; Knight, Rob; Martin, Andrew PThe ISME journal2010 Feb223-3119865184
PyNAST: a flexible tool for aligning sequences to a template alignment.Caporaso, J Gregory; Bittinger, Kyle; Bushman, Frederic D; DeSantis, Todd Z; Andersen, Gary L; Knight, RobBioinformatics (Oxford, England)2010 Jan 15266-719914921
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data.Hamady, Micah; Lozupone, Catherine; Knight, RobThe ISME journal2010 Jan17-2719710709
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function.Selengut, Jeremy D; Rusch, Douglas B; Haft, Daniel HBMC bioinformatics20105220102603
Alignment and clustering of phylogenetic markers--implications for microbial diversity studies.White, James R; Navlakha, Saket; Nagarajan, Niranjan; Ghodsi, Mohammad-Reza; Kingsford, Carl; Pop, MihaiBMC bioinformatics201015220334679
Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family.Haft, Daniel H; Basu, Malay Kumar; Mitchell, Douglas ABMC biology20107020500830
Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies.Harwich Jr, Michael D; Alves, Joao M; Buck, Gregory A; Strauss 3rd, Jerome F; Patterson, Jennifer L; Oki, Aminat T; Girerd, Philippe H; Jefferson, Kimberly KBMC genomics201037520540756
Genome sequencing reveals widespread virulence gene exchange among human Neisseria species.Marri, Pradeep Reddy; Paniscus, Mary; Weyand, Nathan J; Rendon, Maria A; Calton, Christine M; Hernandez, Diana R; Higashi, Dustin L; Sodergren, Erica; Weinstock, George M; Rounsley, Steven D; So, MagdalenePloS one2010e1183520676376
An algorithm for automated closure during assembly.Koren, Sergey; Miller, Jason R; Walenz, Brian P; Sutton, GrangerBMC bioinformatics201045720831800
Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential.Yeoman, Carl J; Yildirim, Suleyman; Thomas, Susan M; Durkin, A Scott; Torralba, Manolito; Sutton, Granger; Buhay, Christian J; Ding, Yan; Dugan-Rocha, Shannon P; Muzny, Donna M; Qin, Xiang; Gibbs, Richard A; Leigh, Steven R; Stumpf, Rebecca; White, Bryan PloS one2010e1241120865041
Regional mucosa-associated microbiota determine physiological expression of TLR2 and TLR4 in murine colon.Wang, Yunwei; Devkota, Suzanne; Musch, Mark W; Jabri, Bana; Nagler, Cathryn; Antonopoulos, Dionysios A; Chervonsky, Alexander; Chang, Eugene BPloS one2010e1360721042588
Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection.Nelson, David E; Van Der Pol, Barbara; Dong, Qunfeng; Revanna, Kashi V; Fan, Baochang; Easwaran, Shraddha; Sodergren, Erica; Weinstock, George M; Diao, Lixia; Fortenberry, J DennisPloS one2010e1411621124791
Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth.Zhou, Xia; Brotman, Rebecca M; Gajer, Pawel; Abdo, Zaid; Schuette, Ursel; Ma, Sam; Ravel, Jacques; Forney, Larry JInfectious diseases in obstetrics and gynecology201073742521197076
Microfluidic cell sorter with integrated piezoelectric actuator.Chen, Chun H; Cho, Sung Hwan; Tsai, Frank; Erten, Ahmet; Lo, Yu-HwaBiomedical microdevices2009 Dec1223-3119649710
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.Lazarevic, Vladimir; Whiteson, Katrine; Huse, Susan; Hernandez, David; Farinelli, Laurent; Osteras, Magne; Schrenzel, Jacques; Francois, PatriceJournal of microbiological methods2009 Dec266-7119796657
What are the consequences of the disappearing human microbiota?Blaser, Martin J; Falkow, StanleyNature reviews. Microbiology2009 Dec887-9419898491
High-fat diet determines the composition of the murine gut microbiome independently of obesity.Hildebrandt, Marie A; Hoffmann, Christian; Sherrill-Mix, Scott A; Keilbaugh, Sue A; Hamady, Micah; Chen, Ying-Yu; Knight, Rob; Ahima, Rexford S; Bushman, Frederic; Wu, Gary DGastroenterology2009 Nov1716-24.e1-219706296
Inexact Local Alignment Search over Suffix Arrays.Ghodsi, Mohammadreza; Pop, MihaiProceedings. IEEE International Conference on Bioinformatics and Biomedicine2009 Nov 183-9721278916
Genomics. Genome project standards in a new era of sequencing.Chain, P S G; Grafham, D V; Fulton, R S; Fitzgerald, M G; Hostetler, J; Muzny, D; Ali, J; Birren, B; Bruce, D C; Buhay, C; Cole, J R; Ding, Y; Dugan, S; Field, D; Garrity, G M; Gibbs, R; Graves, T; Han, C S; Harrison, S H; Highlander, S; Hugenholtz, P; KhScience (New York, N.Y.)2009 Oct 9236-719815760
A method for isolating and analyzing human mRNA from newborn stool.Bennett Jr, William E; Gonzalez-Rivera, Rosbel; Shaikh, Nurmohammad; Magrini, Vincent; Boykin, Michelle; Warner, Barbara B; Hamvas, Aaron; Tarr, Phillip IJournal of immunological methods2009 Sep 3056-6019660464
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.Brady, Arthur; Salzberg, Steven LNature methods2009 Sep673-619648916
16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis.Wang, Yunwei; Hoenig, Jeanette D; Malin, Kathryn J; Qamar, Sanaa; Petrof, Elaine O; Sun, Jun; Antonopoulos, Dionysios A; Chang, Eugene B; Claud, Erika CThe ISME journal2009 Aug944-5419369970
Inflammation and intestinal metaplasia of the distal esophagus are associated with alterations in the microbiome.Yang, Liying; Lu, Xiaohua; Nossa, Carlos W; Francois, Fritz; Peek, Richard M; Pei, ZhihengGastroenterology2009 Aug588-9719394334
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.Ye, Yuzhen; Doak, Thomas GPLoS computational biology2009 Auge100046519680427
Genome assembly reborn: recent computational challenges.Pop, MihaiBriefings in bioinformatics2009 Jul354-6619482960
An ORFome assembly approach to metagenomics sequences analysis.Ye, Yuzhen; Tang, HaixuJournal of bioinformatics and computational biology2009 Jun455-7119507285
Metagenomic pyrosequencing and microbial identification.Petrosino, Joseph F; Highlander, Sarah; Luna, Ruth Ann; Gibbs, Richard A; Versalovic, JamesClinical chemistry2009 May856-6619264858
Helping patients make informed choices about probiotics: a need for research.Sharp, Richard R; Achkar, Jean-Paul; Brinich, Margaret A; Farrell, Ruth MThe American journal of gastroenterology2009 Apr809-1319343022
Statistical methods for detecting differentially abundant features in clinical metagenomic samples.White, James Robert; Nagarajan, Niranjan; Pop, MihaiPLoS computational biology2009 Apre100035219360128
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.Langmead, Ben; Trapnell, Cole; Pop, Mihai; Salzberg, Steven LGenome biology2009R2519261174
Diversity of 23S rRNA genes within individual prokaryotic genomes.Pei, Anna; Nossa, Carlos W; Chokshi, Pooja; Blaser, Martin J; Yang, Liying; Rosmarin, David M; Pei, ZhihengPloS one2009e543719415112
BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing.Frank, Daniel NBMC bioinformatics200936219874596
Searching for SNPs with cloud computing.Langmead, Ben; Schatz, Michael C; Lin, Jimmy; Pop, Mihai; Salzberg, Steven LGenome biology2009R13419930550
Micro-fabricated fluorescence-activated cell sorter.Cho, Sung Hwan; Chen, Chun H; Tsai, Frank S; Lo, Yu-HwaConference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference20091075-819965141
Metagenomics: Facts and Artifacts, and Computational Challenges*Wooley, John C; Ye, YuzhenJournal of computer science and technology2009 Jan71-8120648230
Ethical, legal, and social considerations in conducting the Human Microbiome Project.McGuire, Amy L; Colgrove, James; Whitney, Simon N; Diaz, Christina M; Bustillos, Daniel; Versalovic, JamesGenome research2008 Dec1861-418971311


Up to Top