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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.

Title Author Journal Name PubMedID Journal Abbreviation Publication Date
Shallow breathing: bacterial life at low O(2). Morris RL, Schmidt TM Nature reviews. Microbiology 23411864 Nat Rev Microbiol 2013 Mar
Structure, function and diversity of the healthy human microbiome. Human Microbiome Project Consortium Nature 22699609 Nature 2012 Jun 13
Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments. Ozok AR, Persoon IF, Huse SM, Keijser BJ, Wesselink PR, Crielaard W, Zaura E International endodontic journal 22251411 Int Endod J 2012 Jun
Significance of the microbiome in obstructive lung disease. Han MK, Huang YJ, Lipuma JJ, Boushey HA, Boucher RC, Cookson WO, Curtis JL, Erb-Downward J, Lynch SV, Sethi S, Toews GB, Young VB, Wolfgang MC, Huffnagle GB, Martinez FJ Thorax 22318161 Thorax 2012 May
Carrageenan-induced colonic inflammation is reduced in Bcl10 null mice and increased in IL-10-deficient mice. Bhattacharyya S, Xue L, Devkota S, Chang E, Morris S, Tobacman JK Mediators of inflammation 23766559 Mediators Inflamm 2013
Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. Vital M, Howe AC, Tiedje JM mBio 24757212 mBio 2014 Apr 22
Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. Huang Y, Dalal S, Antonopoulos D, Hubert N, Raffals LH, Dolan K, Weber C, Messer JS, Jabri B, Bendelac A, Eren AM, Rubin DT, Sogin M, Chang EB Inflammatory bowel diseases 28221248 Inflamm Bowel Dis 2017 Mar
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Sun Y, Cai Y, Huse SM, Knight R, Farmerie WG, Wang X, Mai V Briefings in bioinformatics 21525143 Brief Bioinform 2012 Jan
Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting through the Growing Pains and Moving Forward. Young VB, Kahn SA, Schmidt TM, Chang EB Frontiers in microbiology 21772835 Front Microbiol 2011
Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. Devkota S, Wang Y, Musch MW, Leone V, Fehlner-Peach H, Nadimpalli A, Antonopoulos DA, Jabri B, Chang EB Nature 22722865 Nature 2012 Jul 5
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, Osterås M, Schrenzel J, François P Journal of microbiological methods 19796657 J Microbiol Methods 2009 Dec
Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility. Ward MA, Pierre JF, Leal RF, Huang Y, Shogan B, Dalal SR, Weber CR, Leone VA, Musch MW, An GC, Rao MC, Rubin DT, Raffals LE, Antonopoulos DA, Sogin ML, Hyman NH, Alverdy JC, Chang EB American journal of physiology. Gastrointestinal and liver physiology 27079612 Am J Physiol Gastrointest Liver Physiol 2016 Jun 1
Challenges in IBD research: update on progress and prioritization of the CCFA's research agenda. Denson LA, Long MD, McGovern DP, Kugathasan S, Wu GD, Young VB, Pizarro TT, de Zoeten EF, Stappenbeck TS, Plevy SE, Abraham C, Nusrat A, Jobin C, McCole DF, Siegel CA, Higgins PD, Herfarth HH, Hyams J, Sandborn WJ, Loftus EV Jr, Kappelman MD, Lewis JD, Parkos CA, Sartor RB, Challenges Workgroup Inflammatory bowel diseases 23448796 Inflamm Bowel Dis 2013 Mar-Apr
A RESTful API for accessing microbial community data for MG-RAST. Wilke A, Bischof J, Harrison T, Brettin T, D'Souza M, Gerlach W, Matthews H, Paczian T, Wilkening J, Glass EM, Desai N, Meyer F PLoS computational biology 25569221 PLoS Comput Biol 2015 Jan
Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML The ISME journal 25325381 ISME J 2015 Mar 17
The intestinal microbiota in health and disease. Young VB Current opinion in gastroenterology 22080827 Curr Opin Gastroenterol 2012 Jan
A metagenomics portal for a democratized sequencing world. Wilke A, Glass EM, Bartels D, Bischof J, Braithwaite D, D'Souza M, Gerlach W, Harrison T, Keegan K, Matthews H, Kottmann R, Paczian T, Tang W, Trimble WL, Yilmaz P, Wilkening J, Desai N, Meyer F Methods in enzymology 24060134 Methods Enzymol 2013
Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. Wang Q, Quensen JF 3rd, Fish JA, Lee TK, Sun Y, Tiedje JM, Cole JR mBio 24045641 mBio 2013 Sep 17
Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data. Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG, Sogin ML Methods in ecology and evolution 24358444 Methods Ecol Evol 2013 Dec 1
Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota. Vital M, Howe A, Bergeron N, Krauss RM, Jansson JK, Tiedje JM Applied and environmental microbiology 30266729 Appl Environ Microbiol 2018 Dec 1
Oligotyping analysis of the human oral microbiome. Eren AM, Borisy GG, Huse SM, Mark Welch JL Proceedings of the National Academy of Sciences of the United States of America 24965363 Proc Natl Acad Sci U S A 2014 Jul 15
The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention. Hampton TH, Green DM, Cutting GR, Morrison HG, Sogin ML, Gifford AH, Stanton BA, O'Toole GA Microbiome 25071935 Microbiome 2014
A framework for human microbiome research. Human Microbiome Project Consortium Nature 22699610 Nature 2012 Jun 13
Colitis-induced bone loss is gender dependent and associated with increased inflammation. Irwin R, Lee T, Young VB, Parameswaran N, McCabe LR Inflammatory bowel diseases 23702805 Inflamm Bowel Dis 2013 Jul
Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia. Vital M, Gao J, Rizzo M, Harrison T, Tiedje JM The ISME journal 25343515 ISME J 2015 Mar 17
Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Huse SM, Welch DM, Morrison HG, Sogin ML Environmental microbiology 20236171 Environ Microbiol 2010 Jul
A randomised trial of sheathed versus standard forceps for obtaining uncontaminated biopsy specimens of microbiota from the terminal ileum. Dave M, Johnson LA, Walk ST, Young VB, Stidham RW, Chaudhary MN, Funnell J, Higgins PD Gut 21317176 Gut 2011 Aug
Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. Swan BK, Chaffin MD, Martinez-Garcia M, Morrison HG, Field EK, Poulton NJ, Masland ED, Harris CC, Sczyrba A, Chain PS, Koren S, Woyke T, Stepanauskas R PloS one 24743558 PLoS One 2014
FunGene: the functional gene pipeline and repository. Fish JA, Chai B, Wang Q, Sun Y, Brown CT, Tiedje JM, Cole JR Frontiers in microbiology 24101916 Front Microbiol 2013
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 JC, Koestler DC, Stanton BA, Davidson L, Moulton LA, Housman ML, Moore JH, Guill MF, Morrison HG, Sogin ML, Hampton TH, Karagas MR, Palumbo PE, Foster JA, Hibberd PL, O'Toole GA mBio 22911969 mBio 2012
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. Trimble WL, Keegan KP, D'Souza M, Wilke A, Wilkening J, Gilbert J, Meyer F BMC bioinformatics 22839106 BMC Bioinformatics 2012 Jul 28
Composition of dietary fat source shapes gut microbiota architecture and alters host inflammatory mediators in mouse adipose tissue. Huang EY, Leone VA, Devkota S, Wang Y, Brady MJ, Chang EB JPEN. Journal of parenteral and enteral nutrition 23639897 JPEN J Parenter Enteral Nutr 2013 Nov
Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease. Vital M, Harkema JR, Rizzo M, Tiedje J, Brandenberger C Journal of immunology research 26090504 J Immunol Res 2015
The gut microbiome in health and in disease. Shreiner AB, Kao JY, Young VB Current opinion in gastroenterology 25394236 Curr Opin Gastroenterol 2015 Jan
Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases. Huang EY, Inoue T, Leone VA, Dalal S, Touw K, Wang Y, Musch MW, Theriault B, Higuchi K, Donovan S, Gilbert J, Chang EB Inflammatory bowel diseases 25738379 Inflamm Bowel Dis 2015 May
The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth. Chernikova DA, Madan JC, Housman ML, Zain-Ul-Abideen M, Lundgren SN, Morrison HG, Sogin ML, Williams SM, Moore JH, Karagas MR, Hoen AG Pediatric research 29795209 Pediatr Res 2018 Jul
Fetal exposures and perinatal influences on the stool microbiota of premature infants. Chernikova DA, Koestler DC, Hoen AG, Housman ML, Hibberd PL, Moore JH, Morrison HG, Sogin ML, Zain-Ul-Abideen M, Madan JC The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians 25394613 J Matern Fetal Neonatal Med 2016
Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Leone V, Gibbons SM, Martinez K, Hutchison AL, Huang EY, Cham CM, Pierre JF, Heneghan AF, Nadimpalli A, Hubert N, Zale E, Wang Y, Huang Y, Theriault B, Dinner AR, Musch MW, Kudsk KA, Prendergast BJ, Gilbert JA, Chang EB Cell host & microbe 25891358 Cell Host Microbe 2015 May 13
Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Wang Y, Antonopoulos DA, Zhu X, Harrell L, Hanan I, Alverdy JC, Meyer F, Musch MW, Young VB, Chang EB Applied microbiology and biotechnology 20931185 Appl Microbiol Biotechnol 2010 Dec
Regional differences in colonic mucosa-associated microbiota determine the physiological expression of host heat shock proteins. Hu S, Wang Y, Lichtenstein L, Tao Y, Musch MW, Jabri B, Antonopoulos D, Claud EC, Chang EB American journal of physiology. Gastrointestinal and liver physiology 20864653 Am J Physiol Gastrointest Liver Physiol 2010 Dec
The microbe-derived short chain fatty acid butyrate targets miRNA-dependent p21 gene expression in human colon cancer. Hu S, Dong TS, Dalal SR, Wu F, Bissonnette M, Kwon JH, Chang EB PloS one 21283757 PLoS One 2011 Jan 20
Regional mucosa-associated microbiota determine physiological expression of TLR2 and TLR4 in murine colon. Wang Y, Devkota S, Musch MW, Jabri B, Nagler C, Antonopoulos DA, Chervonsky A, Chang EB PloS one 21042588 PLoS One 2010 Oct 22
History and impact of RDP: a legacy from Carl Woese to microbiology. Cole JR, Tiedje JM RNA biology 24607969 RNA Biol 2014
A filtering method to generate high quality short reads using illumina paired-end technology. Eren AM, Vineis JH, Morrison HG, Sogin ML PloS one 23799126 PLoS One 2013
Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification. Vital M, Chai B, Østman B, Cole J, Konstantinidis KT, Tiedje JM The ISME journal 25343512 ISME J 2015 May
Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases. Leone V, Chang EB, Devkota S Journal of gastroenterology 23475322 J Gastroenterol 2013 Mar
DRISEE overestimates errors in metagenomic sequencing data. Eren AM, Morrison HG, Huse SM, Sogin ML Briefings in bioinformatics 23698723 Brief Bioinform 2014 Sep
Ribosomal Database Project: data and tools for high throughput rRNA analysis. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM Nucleic acids research 24288368 Nucleic Acids Res 2014 Jan
Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. Price KE, Hampton TH, Gifford AH, Dolben EL, Hogan DA, Morrison HG, Sogin ML, O'Toole GA Microbiome 24451123 Microbiome 2013 Nov 1
Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis. Hoen AG, Li J, Moulton LA, O'Toole GA, Housman ML, Koestler DC, Guill MF, Moore JH, Hibberd PL, Morrison HG, Sogin ML, Karagas MR, Madan JC The Journal of pediatrics 25818499 J Pediatr 2015 Jul
Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability. Filkins LM, Hampton TH, Gifford AH, Gross MJ, Hogan DA, Sogin ML, Morrison HG, Paster BJ, O'Toole GA Journal of bacteriology 22753064 J Bacteriol 2012 Sep
Standard colonic lavage alters the natural state of mucosal-associated microbiota in the human colon. Harrell L, Wang Y, Antonopoulos D, Young V, Lichtenstein L, Huang Y, Hanauer S, Chang E PloS one 22389708 PLoS One 2012
A core human microbiome as viewed through 16S rRNA sequence clusters. Huse SM, Ye Y, Zhou Y, Fodor AA PloS one 22719824 PLoS One 2012
Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance. Britton RA, Young VB Trends in microbiology 22595318 Trends Microbiol 2012 Jul
Butyrate and bioactive proteolytic form of Wnt-5a regulate colonic epithelial proliferation and spatial development. Uchiyama K, Sakiyama T, Hasebe T, Musch MW, Miyoshi H, Nakagawa Y, He TC, Lichtenstein L, Naito Y, Itoh Y, Yoshikawa T, Jabri B, Stappenbeck T, Chang EB Scientific reports 27561676 Sci Rep 2016 Aug 26
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK PloS one 23209564 PLoS One 2012
Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn's remission patients despite temporal variations in microbial taxa, genomes, and proteomes. Blakeley-Ruiz JA, Erickson AR, Cantarel BL, Xiong W, Adams R, Jansson JK, Fraser CM, Hettich RL Microbiome 30744677 Microbiome 2019 Feb 11
'Omics' of the mammalian gut--new insights into function. Lamendella R, VerBerkmoes N, Jansson JK Current opinion in biotechnology 22626866 Curr Opin Biotechnol 2012 Jun
Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. Hettich RL, Pan C, Chourey K, Giannone RJ Analytical chemistry 23469896 Anal Chem 2013 May 7
Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data. Liu Z, Hsiao W, Cantarel BL, Drábek EF, Fraser-Liggett C Bioinformatics (Oxford, England) 21984758 Bioinformatics 2011 Dec 1
Strategies for metagenomic-guided whole-community proteomics of complex microbial environments. Cantarel BL, Erickson AR, VerBerkmoes NC, Erickson BK, Carey PA, Pan C, Shah M, Mongodin EF, Jansson JK, Fraser-Liggett CM, Hettich RL PloS one 22132090 PLoS One 2011
Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Preidis GA, Versalovic J Gastroenterology 19462507 Gastroenterology 2009 May
Probiotics, enteric and diarrheal diseases, and global health. Preidis GA, Hill C, Guerrant RL, Ramakrishna BS, Tannock GW, Versalovic J Gastroenterology 21075108 Gastroenterology 2011 Jan
Host response to probiotics determined by nutritional status of rotavirus-infected neonatal mice. Preidis GA, Saulnier DM, Blutt SE, Mistretta TA, Riehle KP, Major AM, Venable SF, Barrish JP, Finegold MJ, Petrosino JF, Guerrant RL, Conner ME, Versalovic J Journal of pediatric gastroenterology and nutrition 22343914 J Pediatr Gastroenterol Nutr 2012 Sep
Interprovider variation of celiac disease testing in childhood chronic abdominal pain. Chumpitazi BP, Mysore K, Tsai CM, Shulman RJ BMC gastroenterology 24124697 BMC Gastroenterol 2013 Oct 14
Distinct Microbiome-Neuroimmune Signatures Correlate With Functional Abdominal Pain in Children With Autism Spectrum Disorder. Luna RA, Oezguen N, Balderas M, Venkatachalam A, Runge JK, Versalovic J, Veenstra-VanderWeele J, Anderson GM, Savidge T, Williams KC Cellular and molecular gastroenterology and hepatology 28275689 Cell Mol Gastroenterol Hepatol 2017 Mar
Luminal Conversion and Immunoregulation by Probiotics. Ganesh BP, Versalovic J Frontiers in pharmacology 26617521 Front Pharmacol 2015
Molecular microbiological methods in the diagnosis of neonatal sepsis. Venkatesh M, Flores A, Luna RA, Versalovic J Expert review of anti-infective therapy 20818947 Expert Rev Anti Infect Ther 2010 Sep
Dietary issues in recurrent abdominal pain. Shulman RJ Journal of pediatric gastroenterology and nutrition 23103654 J Pediatr Gastroenterol Nutr 2012 Nov
Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine. Preidis GA, Saulnier DM, Blutt SE, Mistretta TA, Riehle KP, Major AM, Venable SF, Finegold MJ, Petrosino JF, Conner ME, Versalovic J FASEB journal : official publication of the Federation of American Societies for Experimental Biology 22267340 FASEB J 2012 May
Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ, Versalovic J Gastroenterology 21741921 Gastroenterology 2011 Nov
Serial fecal microbiota transplantation alters mucosal gene expression in pediatric ulcerative colitis. Kellermayer R, Nagy-Szakal D, Harris RA, Luna RA, Pitashny M, Schady D, Mir SA, Lopez ME, Gilger MA, Belmont J, Hollister EB, Versalovic J The American journal of gastroenterology 25853207 Am J Gastroenterol 2015 Apr
Lactobacillus reuteri-specific immunoregulatory gene rsiR modulates histamine production and immunomodulation by Lactobacillus reuteri. Hemarajata P, Gao C, Pflughoeft KJ, Thomas CM, Saulnier DM, Spinler JK, Versalovic J Journal of bacteriology 24123819 J Bacteriol 2013 Dec
Structure and function of the healthy pre-adolescent pediatric gut microbiome. Hollister EB, Riehle K, Luna RA, Weidler EM, Rubio-Gonzales M, Mistretta TA, Raza S, Doddapaneni HV, Metcalf GA, Muzny DM, Gibbs RA, Petrosino JF, Shulman RJ, Versalovic J Microbiome 26306392 Microbiome 2015 Aug 26
Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation. Chehoud C, Dryga A, Hwang Y, Nagy-Szakal D, Hollister EB, Luna RA, Versalovic J, Kellermayer R, Bushman FD mBio 27025251 mBio 2016 Mar 29
Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome. Chumpitazi BP, Cope JL, Hollister EB, Tsai CM, McMeans AR, Luna RA, Versalovic J, Shulman RJ Alimentary pharmacology & therapeutics 26104013 Aliment Pharmacol Ther 2015 Aug
Lactobacillus rhamnosus L34 and Lactobacillus casei L39 suppress Clostridium difficile-induced IL-8 production by colonic epithelial cells. Boonma P, Spinler JK, Venable SF, Versalovic J, Tumwasorn S BMC microbiology 24989059 BMC Microbiol 2014 Jul 2
Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome. Chumpitazi BP, Hollister EB, Oezguen N, Tsai CM, McMeans AR, Luna RA, Savidge TC, Versalovic J, Shulman RJ Gut microbes 24637601 Gut Microbes 2014 Mar-Apr
Identification of a proton-chloride antiporter (EriC) by Himar1 transposon mutagenesis in Lactobacillus reuteri and its role in histamine production. Hemarajata P, Spinler JK, Balderas MA, Versalovic J Antonie van Leeuwenhoek 24488273 Antonie Van Leeuwenhoek 2014 Mar
The human gut microbiome and body metabolism: implications for obesity and diabetes. Devaraj S, Hemarajata P, Versalovic J Clinical chemistry 23401286 Clin Chem 2013 Apr
The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences. Riehle K, Coarfa C, Jackson A, Ma J, Tandon A, Paithankar S, Raghuraman S, Mistretta TA, Saulnier D, Raza S, Diaz MA, Shulman R, Aagaard K, Versalovic J, Milosavljevic A BMC bioinformatics 23320832 BMC Bioinformatics 2012
Fructan-sensitive children with irritable bowel syndrome have distinct gut microbiome signatures. Chumpitazi BP, Hoffman KL, Smith DP, McMeans AR, Musaad S, Versalovic J, Petrosino JF, Shulman RJ Alimentary pharmacology & therapeutics 33314183 Aliment Pharmacol Ther 2021 Feb
Creation and initial evaluation of a Stool Form Scale for children. Chumpitazi BP, Lane MM, Czyzewski DI, Weidler EM, Swank PR, Shulman RJ The Journal of pediatrics 20826285 J Pediatr 2010 Oct
Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Hemarajata P, Versalovic J Therapeutic advances in gastroenterology 23320049 Therap Adv Gastroenterol 2013 Jan
Reliability and validity of a modified Bristol Stool Form Scale for children. Lane MM, Czyzewski DI, Chumpitazi BP, Shulman RJ The Journal of pediatrics 21489557 J Pediatr 2011 Sep
Ethical, legal, and social considerations in conducting the Human Microbiome Project. McGuire AL, Colgrove J, Whitney SN, Diaz CM, Bustillos D, Versalovic J Genome research 18971311 Genome Res 2008 Dec
Compositional and functional features of the gastrointestinal microbiome and their effects on human health. Hollister EB, Gao C, Versalovic J Gastroenterology 24486050 Gastroenterology 2014 May
Diacylglycerol kinase synthesized by commensal Lactobacillus reuteri diminishes protein kinase C phosphorylation and histamine-mediated signaling in the mammalian intestinal epithelium. Ganesh BP, Hall A, Ayyaswamy S, Nelson JW, Fultz R, Major A, Haag A, Esparza M, Lugo M, Venable S, Whary M, Fox JG, Versalovic J Mucosal immunology 28745328 Mucosal Immunol 2018 Mar
Histamine H2 Receptor-Mediated Suppression of Intestinal Inflammation by Probiotic Lactobacillus reuteri. Gao C, Major A, Rendon D, Lugo M, Jackson V, Shi Z, Mori-Akiyama Y, Versalovic J mBio 26670383 mBio 2015 Dec 15
GABA-producing Bifidobacterium dentium modulates visceral sensitivity in the intestine. Pokusaeva K, Johnson C, Luk B, Uribe G, Fu Y, Oezguen N, Matsunami RK, Lugo M, Major A, Mori-Akiyama Y, Hollister EB, Dann SM, Shi XZ, Engler DA, Savidge T, Versalovic J Neurogastroenterology and motility 27458085 Neurogastroenterol Motil 2017 Jan
Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. Hollister EB, Oezguen N, Chumpitazi BP, Luna RA, Weidler EM, Rubio-Gonzales M, Dahdouli M, Cope JL, Mistretta TA, Raza S, Metcalf GA, Muzny DM, Gibbs RA, Petrosino JF, Heitkemper M, Savidge TC, Shulman RJ, Versalovic J The Journal of molecular diagnostics : JMD 31005411 J Mol Diagn 2019 May
The Fecal Microbiome in Pediatric Patients With Short Bowel Syndrome. Davidovics ZH, Carter BA, Luna RA, Hollister EB, Shulman RJ, Versalovic J JPEN. Journal of parenteral and enteral nutrition 26059898 JPEN J Parenter Enteral Nutr 2016 Nov
Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35. Boonma P, Spinler JK, Qin X, Jittaprasatsin C, Muzny DM, Doddapaneni H, Gibbs R, Petrosino J, Tumwasorn S, Versalovic J Standards in genomic sciences 25197459 Stand Genomic Sci 2014 Jun 15
Probiotics-host communication: Modulation of signaling pathways in the intestine. Thomas CM, Versalovic J Gut microbes 20672012 Gut Microbes 2010 May-Jun
Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice. Kellermayer R, Dowd SE, Harris RA, Balasa A, Schaible TD, Wolcott RD, Tatevian N, Szigeti R, Li Z, Versalovic J, Smith CW FASEB journal : official publication of the Federation of American Societies for Experimental Biology 21228220 FASEB J 2011 May
Microbial Metabolism in the Mammalian Gut: Molecular Mechanisms and Clinical Implications. Hall A, Versalovic J Journal of pediatric gastroenterology and nutrition 29762384 J Pediatr Gastroenterol Nutr 2018 Jun
Role of the gut microbiota in defining human health. Fujimura KE, Slusher NA, Cabana MD, Lynch SV Expert review of anti-infective therapy 20377338 Expert Rev Anti Infect Ther 2010 Apr
Associating microbiome composition with environmental covariates using generalized UniFrac distances. Chen J, Bittinger K, Charlson ES, Hoffmann C, Lewis J, Wu GD, Collman RG, Bushman FD, Li H Bioinformatics (Oxford, England) 22711789 Bioinformatics 2012 Aug 15
PyNAST: a flexible tool for aligning sequences to a template alignment. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R Bioinformatics (Oxford, England) 19914921 Bioinformatics 2010 Jan 15
Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R Current protocols in bioinformatics 22161565 Curr Protoc Bioinformatics 2011 Dec
Hypervariable loci in the human gut virome. Minot S, Grunberg S, Wu GD, Lewis JD, Bushman FD Proceedings of the National Academy of Sciences of the United States of America 22355105 Proc Natl Acad Sci U S A 2012 Mar 6
Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, Fu X, Wu Y, Li L, Smith JD, DiDonato JA, Chen J, Li H, Wu GD, Lewis JD, Warrier M, Brown JM, Krauss RM, Tang WH, Bushman FD, Lusis AJ, Hazen SL Nature medicine 23563705 Nat Med 2013 May
Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. Wang GP, Sherrill-Mix SA, Chang KM, Quince C, Bushman FD Journal of virology 20375170 J Virol 2010 Jun
Enterotypes in the landscape of gut microbial community composition. Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P Nature microbiology 29255284 Nat Microbiol 2018 Jan
Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts. Kelsen J, Bittinger K, Pauly-Hubbard H, Posivak L, Grunberg S, Baldassano R, Lewis JD, Wu GD, Bushman FD Inflammatory bowel diseases 26288001 Inflamm Bowel Dis 2015 Dec
A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. Dollive S, Peterfreund GL, Sherrill-Mix S, Bittinger K, Sinha R, Hoffmann C, Nabel CS, Hill DA, Artis D, Bachman MA, Custers-Allen R, Grunberg S, Wu GD, Lewis JD, Bushman FD Genome biology 22759449 Genome Biol 2012 Jul 3
Linking long-term dietary patterns with gut microbial enterotypes. Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD Science (New York, N.Y.) 21885731 Science 2011 Oct 7
A role for bacterial urease in gut dysbiosis and Crohn's disease. Ni J, Shen TD, Chen EZ, Bittinger K, Bailey A, Roggiani M, Sirota-Madi A, Friedman ES, Chau L, Lin A, Nissim I, Scott J, Lauder A, Hoffmann C, Rivas G, Albenberg L, Baldassano RN, Braun J, Xavier RJ, Clish CB, Yudkoff M, Li H, Goulian M, Bushman FD, Lewis JD, Wu GD Science translational medicine 29141885 Sci Transl Med 2017 Nov 15
Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. Dollive S, Chen YY, Grunberg S, Bittinger K, Hoffmann C, Vandivier L, Cuff C, Lewis JD, Wu GD, Bushman FD PloS one 23977147 PLoS One 2013
Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, Bittinger K, Bailey A, Friedman ES, Hoffmann C, Albenberg L, Sinha R, Compher C, Gilroy E, Nessel L, Grant A, Chehoud C, Li H, Wu GD, Bushman FD Cell host & microbe 26468751 Cell Host Microbe 2015 Oct 14
Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9. Bryson AL, Hwang Y, Sherrill-Mix S, Wu GD, Lewis JD, Black L, Clark TA, Bushman FD mBio 26081634 mBio 2015 Jun 16
Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R Current protocols in microbiology 23184592 Curr Protoc Microbiol 2012 Nov
Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation. Hill DA, Siracusa MC, Abt MC, Kim BS, Kobuley D, Kubo M, Kambayashi T, Larosa DF, Renner ED, Orange JS, Bushman FD, Artis D Nature medicine 22447074 Nat Med 2012 Mar 25
Rapid evolution of the human gut virome. Minot S, Bryson A, Chehoud C, Wu GD, Lewis JD, Bushman FD Proceedings of the National Academy of Sciences of the United States of America 23836644 Proc Natl Acad Sci U S A 2013 Jul 23
Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Wu GD, Compher C, Chen EZ, Smith SA, Shah RD, Bittinger K, Chehoud C, Albenberg LG, Nessel L, Gilroy E, Star J, Weljie AM, Flint HJ, Metz DC, Bennett MJ, Li H, Bushman FD, Lewis JD Gut 25431456 Gut 2016 Jan
QIIME allows analysis of high-throughput community sequencing data. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R Nature methods 20383131 Nat Methods 2010 May
Diet and the intestinal microbiome: associations, functions, and implications for health and disease. Albenberg LG, Wu GD Gastroenterology 24503132 Gastroenterology 2014 May
Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis. Chen J, Bushman FD, Lewis JD, Wu GD, Li H Biostatistics (Oxford, England) 23074263 Biostatistics 2013 Apr
Conservation of gene cassettes among diverse viruses of the human gut. Minot S, Wu GD, Lewis JD, Bushman FD PloS one 22900013 PLoS One 2012
Food and the gut microbiota in inflammatory bowel diseases: a critical connection. Albenberg LG, Lewis JD, Wu GD Current opinion in gastroenterology 22573192 Curr Opin Gastroenterol 2012 Jul
Engineering the gut microbiota to treat hyperammonemia. Shen TC, Albenberg L, Bittinger K, Chehoud C, Chen YY, Judge CA, Chau L, Ni J, Sheng M, Lin A, Wilkins BJ, Buza EL, Lewis JD, Daikhin Y, Nissim I, Yudkoff M, Bushman FD, Wu GD The Journal of clinical investigation 26098218 J Clin Invest 2015 Jul 1
Inflammation-associated microbiota in pediatric eosinophilic esophagitis. Benitez AJ, Hoffmann C, Muir AB, Dods KK, Spergel JM, Bushman FD, Wang ML Microbiome 26034601 Microbiome 2015
Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD, Li H Bioinformatics (Oxford, England) 25819674 Bioinformatics 2015 Aug 1
Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease. Chehoud C, Albenberg LG, Judge C, Hoffmann C, Grunberg S, Bittinger K, Baldassano RN, Lewis JD, Bushman FD, Wu GD Inflammatory bowel diseases 26083617 Inflamm Bowel Dis 2015 Aug
Diet in the pathogenesis and treatment of inflammatory bowel diseases. Lee D, Albenberg L, Compher C, Baldassano R, Piccoli D, Lewis JD, Wu GD Gastroenterology 25597840 Gastroenterology 2015 May
Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease. Lee D, Baldassano RN, Otley AR, Albenberg L, Griffiths AM, Compher C, Chen EZ, Li H, Gilroy E, Nessel L, Grant A, Chehoud C, Bushman FD, Wu GD, Lewis JD Inflammatory bowel diseases 25970545 Inflamm Bowel Dis 2015 Aug
Diet, gut enterotypes and health: is there a link? Bushman FD, Lewis JD, Wu GD Nestle Nutrition Institute workshop series 24107497 Nestle Nutr Inst Workshop Ser 2013
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD PloS one 23799070 PLoS One 2013
Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Albenberg L, Esipova TV, Judge CP, Bittinger K, Chen J, Laughlin A, Grunberg S, Baldassano RN, Lewis JD, Li H, Thom SR, Bushman FD, Vinogradov SA, Wu GD Gastroenterology 25046162 Gastroenterology 2014 Nov
Analysis of the human gut microbiome and association with disease. Wu GD, Lewis JD Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association 23643636 Clin Gastroenterol Hepatol 2013 Jul
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, Sterk P, Arumugam M, Bailey M, Baumgartner L, Birren BW, Blaser MJ, Bonazzi V, Booth T, Bork P, Bushman FD, Buttigieg PL, Chain PS, Charlson E, Costello EK, Huot-Creasy H, Dawyndt P, DeSantis T, Fierer N, Fuhrman JA, Gallery RE, Gevers D, Gibbs RA, San Gil I, Gonzalez A, Gordon JI, Guralnick R, Hankeln W, Highlander S, Hugenholtz P, Jansson J, Kau AL, Kelley ST, Kennedy J, Knights D, Koren O, Kuczynski J, Kyrpides N, Larsen R, Lauber CL, Legg T, Ley RE, Lozupone CA, Ludwig W, Lyons D, Maguire E, Methé BA, Meyer F, Muegge B, Nakielny S, Nelson KE, Nemergut D, Neufeld JD, Newbold LK, Oliver AE, Pace NR, Palanisamy G, Peplies J, Petrosino J, Proctor L, Pruesse E, Quast C, Raes J, Ratnasingham S, Ravel J, Relman DA, Assunta-Sansone S, Schloss PD, Schriml L, Sinha R, Smith MI, Sodergren E, Spo A, Stombaugh J, Tiedje JM, Ward DV, Weinstock GM, Wendel D, White O, Whiteley A, Wilke A, Wortman JR, Yatsunenko T, Glöckner FO Nature biotechnology 21552244 Nat Biotechnol 2011 May
Succession in the gut microbiome following antibiotic and antibody therapies for Clostridium difficile. Peterfreund GL, Vandivier LE, Sinha R, Marozsan AJ, Olson WC, Zhu J, Bushman FD PloS one 23071679 PLoS One 2012
VARIABLE SELECTION FOR SPARSE DIRICHLET-MULTINOMIAL REGRESSION WITH AN APPLICATION TO MICROBIOME DATA ANALYSIS. Chen J, Li H The annals of applied statistics 24312162 Ann Appl Stat 2013 Mar 1
Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice. Mei J, Liu Y, Dai N, Hoffmann C, Hudock KM, Zhang P, Guttentag SH, Kolls JK, Oliver PM, Bushman FD, Worthen GS The Journal of clinical investigation 22326959 J Clin Invest 2012 Mar
Sex, body mass index, and dietary fiber intake influence the human gut microbiome. Dominianni C, Sinha R, Goedert JJ, Pei Z, Yang L, Hayes RB, Ahn J PloS one 25874569 PLoS One 2015
The interrelationships of the gut microbiome and inflammation in colorectal carcinogenesis. Cho M, Carter J, Harari S, Pei Z Clinics in laboratory medicine 25439270 Clin Lab Med 2014 Dec
Urethral adenocarcinoma associated with intestinal-type metaplasia, case report and literature review. Hale CS, Huang H, Melamed J, Xu R, Roberts L, Wieczorek R, Pei Z, Lee P International journal of clinical and experimental pathology 23923086 Int J Clin Exp Pathol 2013
Diversity of 23S rRNA genes within individual prokaryotic genomes. Pei A, Nossa CW, Chokshi P, Blaser MJ, Yang L, Rosmarin DM, Pei Z PloS one 19415112 PLoS One 2009
MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs. Brown SM, Chen H, Hao Y, Laungani BP, Ali TA, Dong C, Lijeron C, Kim B, Wultsch C, Pei Z, Krampis K GigaScience 30942867 Gigascience 2019 Apr 1
Erratum to: The first microbial environment of infants born by C-section: the operating room microbes. Shin H, Pei Z, Martinez KA 2nd, Rivera-Vinas JI, Mendez K, Cavallin H, Dominguez-Bello MG Microbiome 26796629 Microbiome 2016 Jan 21
HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria. Yang L, Poles MA, Fisch GS, Ma Y, Nossa C, Phelan JA, Pei Z AIDS (London, England) 26731752 AIDS 2016 Jan 2
Diversity of 16S rRNA genes within individual prokaryotic genomes. Pei AY, Oberdorf WE, Nossa CW, Agarwal A, Chokshi P, Gerz EA, Jin Z, Lee P, Yang L, Poles M, Brown SM, Sotero S, Desantis T, Brodie E, Nelson K, Pei Z Applied and environmental microbiology 20418441 Appl Environ Microbiol 2010 Jun
Simrank: Rapid and sensitive general-purpose k-mer search tool. DeSantis TZ, Keller K, Karaoz U, Alekseyenko AV, Singh NN, Brodie EL, Pei Z, Andersen GL, Larsen N BMC ecology 21524302 BMC Ecol 2011 Apr 27
Diversity of 5S rRNA genes within individual prokaryotic genomes. Pei A, Li H, Oberdorf WE, Alekseyenko AV, Parsons T, Yang L, Gerz EA, Lee P, Xiang C, Nossa CW, Pei Z FEMS microbiology letters 22765222 FEMS Microbiol Lett 2012 Oct
Human microbiome and HIV/AIDS. Saxena D, Li Y, Yang L, Pei Z, Poles M, Abrams WR, Malamud D Current HIV/AIDS reports 22193889 Curr HIV/AIDS Rep 2012 Mar
A rare case of anal carcinosarcoma with human papilloma virus infection in both biphasic tumor elements: An immunohistochemical, molecular and ultrastructural study. Hickman RA, Bradshaw AD, Cassai N, Neto AG, Zhou D, Fu T, Lee P, Pei Z, Wieczorek R Papillomavirus research (Amsterdam, Netherlands) 28616595 Papillomavirus Res 2016 Dec
Beyond infectious disease: welcome to the era of population microbiology. Pincus MR, Pei Z Clinics in laboratory medicine 25439278 Clin Lab Med 2014 Dec
Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison. Ahn J, Yang L, Paster BJ, Ganly I, Morris L, Pei Z, Hayes RB PloS one 21829515 PLoS One 2011
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, Ley RE The ISME journal 21716311 ISME J 2012 Jan
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P The ISME journal 22134646 ISME J 2012 Mar
Microbiome in reflux disorders and esophageal adenocarcinoma. Yang L, Chaudhary N, Baghdadi J, Pei Z Cancer journal (Sudbury, Mass.) 24855009 Cancer J 2014 May-Jun
Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. Nossa CW, Oberdorf WE, Yang L, Aas JA, Paster BJ, Desantis TZ, Brodie EL, Malamud D, Poles MA, Pei Z World journal of gastroenterology 20806429 World J Gastroenterol 2010 Sep 7
Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets. Ma Y, Madupu R, Karaoz U, Nossa CW, Yang L, Yooseph S, Yachimski PS, Brodie EL, Nelson KE, Pei Z Journal of virology 24522917 J Virol 2014 May
SPA: a short peptide assembler for metagenomic data. Yang Y, Yooseph S Nucleic acids research 23435317 Nucleic Acids Res 2013 Apr
Microbiome, innate immunity, and esophageal adenocarcinoma. Baghdadi J, Chaudhary N, Pei Z, Yang L Clinics in laboratory medicine 25439272 Clin Lab Med 2014 Dec
Microbiome and potential targets for chemoprevention of esophageal adenocarcinoma. Neto AG, Whitaker A, Pei Z Seminars in oncology 26970127 Semin Oncol 2016 Feb
The first microbial environment of infants born by C-section: the operating room microbes. Shin H, Pei Z, Martinez KA 2nd, Rivera-Vinas JI, Mendez K, Cavallin H, Dominguez-Bello MG Microbiome 26620712 Microbiome 2015 Dec 1
Fast disease progression in simian HIV-infected female macaque is accompanied by a robust local inflammatory innate immune and microbial response. Ren W, Ma Y, Yang L, Gettie A, Salas J, Russell K, Blanchard J, Davidow A, Pei Z, Chang TL, Cheng-Mayer C AIDS (London, England) 26035329 AIDS 2015 Jun 19
Microbiome, a new dimension in cancer research. Neto AG, Bradshaw AD, Pei Z Annals of translational medicine 26539446 Ann Transl Med 2015 Sep
Papillary urothelial carcinoma with squamous differentiation in association with human papilloma virus: case report and literature review. Guma S, Maglantay R, Lau R, Wieczorek R, Melamed J, Deng FM, Zhou M, Makarov D, Lee P, Pincus MR, Pei ZH American journal of clinical and experimental urology 27069958 Am J Clin Exp Urol 2016
Progressive dysbiosis of human orodigestive microbiota along the sequence of gastroesophageal reflux, Barrett's esophagus and esophageal adenocarcinoma. Hao Y, Karaoz U, Yang L, Yachimski PS, Tseng W, Nossa CW, Ye W, Tseng M, Poles M, Francois F, Traube M, Brown SM, Chen Y, Torralba M, Peek RM, Brodie EL, Pei Z International journal of cancer 35751398 Int J Cancer 2022 Nov 15
De novo large cell neuroendocrine carcinoma of the prostate, case report and literature review. Acosta-Gonzalez G, Qin J, Wieczorek R, Melamed J, Deng FM, Zhou M, Makarov D, Ye F, Pei Z, Pincus MR, Lee P American journal of clinical and experimental urology 25606580 Am J Clin Exp Urol 2014
Mini-review: perspective of the microbiome in the pathogenesis of urothelial carcinoma. Xu W, Yang L, Lee P, Huang WC, Nossa C, Ma Y, Deng FM, Zhou M, Melamed J, Pei Z American journal of clinical and experimental urology 25126590 Am J Clin Exp Urol 2014 Apr 15
Diversified microbiota of meconium is affected by maternal diabetes status. Hu J, Nomura Y, Bashir A, Fernandez-Hernandez H, Itzkowitz S, Pei Z, Stone J, Loudon H, Peter I PloS one 24223144 PLoS One 2013
Inflammation and intestinal metaplasia of the distal esophagus are associated with alterations in the microbiome. Yang L, Lu X, Nossa CW, Francois F, Peek RM, Pei Z Gastroenterology 19394334 Gastroenterology 2009 Aug
Molecular pathways: pathogenesis and clinical implications of microbiome alteration in esophagitis and Barrett esophagus. Yang L, Francois F, Pei Z Clinical cancer research : an official journal of the American Association for Cancer Research 22344232 Clin Cancer Res 2012 Apr 15
Bacterial communities of the coronal sulcus and distal urethra of adolescent males. Nelson DE, Dong Q, Van der Pol B, Toh E, Fan B, Katz BP, Mi D, Rong R, Weinstock GM, Sodergren E, Fortenberry JD PloS one 22606251 PLoS One 2012
The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens. Dong Q, Nelson DE, Toh E, Diao L, Gao X, Fortenberry JD, Van der Pol B PloS one 21603636 PLoS One 2011
Leveraging a relationship-based sexual health framework for sexual risk prevention in adolescent men in the United States. Hensel DJ, Bales CL, Taylor JF, Fortenberry JD Sexual health 29506642 Sex Health 2018 Jun
Biogeography of the ecosystems of the healthy human body. Zhou Y, Gao H, Mihindukulasuriya KA, La Rosa PS, Wylie KM, Vishnivetskaya T, Podar M, Warner B, Tarr PI, Nelson DE, Fortenberry JD, Holland MJ, Burr SE, Shannon WD, Sodergren E, Weinstock GM Genome biology 23316946 Genome Biol 2013 Jan 14
Necrotizing enterocolitis and preterm infant gut bacteria. Warner BB, Tarr PI Seminars in fetal & neonatal medicine 27343151 Semin Fetal Neonatal Med 2016 Dec
Statistical object data analysis of taxonomic trees from human microbiome data. La Rosa PS, Shands B, Deych E, Zhou Y, Sodergren E, Weinstock G, Shannon WD PloS one 23152838 PLoS One 2012
Hypothesis testing and power calculations for taxonomic-based human microbiome data. La Rosa PS, Brooks JP, Deych E, Boone EL, Edwards DJ, Wang Q, Sodergren E, Weinstock G, Shannon WD PloS one 23284876 PLoS One 2012
The age of necrotizing enterocolitis onset: an application of Sartwell's incubation period model. González-Rivera R, Culverhouse RC, Hamvas A, Tarr PI, Warner BB Journal of perinatology : official journal of the California Perinatal Association 21273988 J Perinatol 2011 Aug
Gastrointestinal viruses were not found as an aetiology of culture-negative illness in NICU patients. Melamed R, Storch GA, Warner BB, Tarr PI Archives of disease in childhood. Fetal and neonatal edition 23563694 Arch Dis Child Fetal Neonatal Ed 2013 Jul
A method for isolating and analyzing human mRNA from newborn stool. Bennett WE Jr, González-Rivera R, Shaikh N, Magrini V, Boykin M, Warner BB, Hamvas A, Tarr PI Journal of immunological methods 19660464 J Immunol Methods 2009 Sep 30
Maternal activation of the EGFR prevents translocation of gut-residing pathogenic Escherichia coli in a model of late-onset neonatal sepsis. Knoop KA, Coughlin PE, Floyd AN, Ndao IM, Hall-Moore C, Shaikh N, Gasparrini AJ, Rusconi B, Escobedo M, Good M, Warner BB, Tarr PI, Newberry RD Proceedings of the National Academy of Sciences of the United States of America 32179676 Proc Natl Acad Sci U S A 2020 Apr 7
Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis. Pammi M, Cope J, Tarr PI, Warner BB, Morrow AL, Mai V, Gregory KE, Kroll JS, McMurtry V, Ferris MJ, Engstrand L, Lilja HE, Hollister EB, Versalovic J, Neu J Microbiome 28274256 Microbiome 2017 Mar 9
Carriage of Cronobacter sakazakii in the Very Preterm Infant Gut. Chandrasekaran S, Burnham CD, Warner BB, Tarr PI, Wylie TN Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 29394356 Clin Infect Dis 2018 Jul 2
Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants. Thänert R, Schwartz DJ, Keen EC, Hall-Moore C, Wang B, Shaikh N, Ning J, Rouggly-Nickless LC, Thänert A, Ferreiro A, Fishbein SRS, Sullivan JE, Radmacher P, Escobedo M, Warner BB, Tarr PI, Dantas G Cell host & microbe 39317192 Cell Host Microbe 2024 Oct 9
Bacterial DNA content in the intestinal wall from infants with necrotizing enterocolitis. Bucher BT, McDuffie LA, Shaikh N, Tarr PI, Warner BB, Hamvas A, White FV, Erwin CR, Warner BW Journal of pediatric surgery 21683193 J Pediatr Surg 2011 Jun
Current technology in the diagnosis of developmentally related lung disorders. Hamvas A Neonatology 22940625 Neonatology 2012
Early pregnancy vaginal microbiome trends and preterm birth. Stout MJ, Zhou Y, Wylie KM, Tarr PI, Macones GA, Tuuli MG American journal of obstetrics and gynecology 28549981 Am J Obstet Gynecol 2017 Sep
Impact of neonatal intensive care bed configuration on rates of late-onset bacterial sepsis and methicillin-resistant Staphylococcus aureus colonization. Julian S, Burnham CA, Sellenriek P, Shannon WD, Hamvas A, Tarr PI, Warner BB Infection control and hospital epidemiology 26108888 Infect Control Hosp Epidemiol 2015 Oct
Lungs, microbes and the developing neonate. Warner BB, Hamvas A Neonatology 26044101 Neonatology 2015
Gut bacteria and late-onset neonatal bloodstream infections in preterm infants. Tarr PI, Warner BB Seminars in fetal & neonatal medicine 27345372 Semin Fetal Neonatal Med 2016 Dec
Discordant transmission of bacteria and viruses from mothers to babies at birth. Maqsood R, Rodgers R, Rodriguez C, Handley SA, Ndao IM, Tarr PI, Warner BB, Lim ES, Holtz LR Microbiome 31823811 Microbiome 2019 Dec 10
Patterned progression of bacterial populations in the premature infant gut. La Rosa PS, Warner BB, Zhou Y, Weinstock GM, Sodergren E, Hall-Moore CM, Stevens HJ, Bennett WE Jr, Shaikh N, Linneman LA, Hoffmann JA, Hamvas A, Deych E, Shands BA, Shannon WD, Tarr PI Proceedings of the National Academy of Sciences of the United States of America 25114261 Proc Natl Acad Sci U S A 2014 Aug 26
Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. Carl MA, Ndao IM, Springman AC, Manning SD, Johnson JR, Johnston BD, Burnham CA, Weinstock ES, Weinstock GM, Wylie TN, Mitreva M, Abubucker S, Zhou Y, Stevens HJ, Hall-Moore C, Julian S, Shaikh N, Warner BB, Tarr PI Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 24647013 Clin Infect Dis 2014 May
Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit. Schwartz DJ, Shalon N, Wardenburg K, DeVeaux A, Wallace MA, Hall-Moore C, Ndao IM, Sullivan JE, Radmacher P, Escobedo M, Burnham CD, Warner BB, Tarr PI, Dantas G Science translational medicine 37134153 Sci Transl Med 2023 May 3
The Microbiome and Biomarkers for Necrotizing Enterocolitis: Are We Any Closer to Prediction? Rusconi B, Good M, Warner BB The Journal of pediatrics 28669607 J Pediatr 2017 Oct
Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Gibson MK, Wang B, Ahmadi S, Burnham CA, Tarr PI, Warner BB, Dantas G Nature microbiology 27572443 Nat Microbiol 2016 Mar 7
Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. Thänert R, Thänert A, Ou J, Bajinting A, Burnham CD, Engelstad HJ, Tecos ME, Ndao IM, Hall-Moore C, Rouggly-Nickless C, Carl MA, Rubin DC, Davidson NO, Tarr PI, Warner BB, Dantas G, Warner BW Gut microbes 34264786 Gut Microbes 2021 Jan-Dec
Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants. Kaelin EA, Rodriguez C, Hall-Moore C, Hoffmann JA, Linneman LA, Ndao IM, Warner BB, Tarr PI, Holtz LR, Lim ES Nature microbiology 35449461 Nat Microbiol 2022 May
Antibiotic perturbation of the preterm infant gut microbiome and resistome. Gasparrini AJ, Crofts TS, Gibson MK, Tarr PI, Warner BB, Dantas G Gut microbes 27472377 Gut Microbes 2016 Sep 2
Early life dynamics of the human gut virome and bacterial microbiome in infants. Lim ES, Zhou Y, Zhao G, Bauer IK, Droit L, Ndao IM, Warner BB, Tarr PI, Wang D, Holtz LR Nature medicine 26366711 Nat Med 2015 Oct
Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study. Warner BB, Deych E, Zhou Y, Hall-Moore C, Weinstock GM, Sodergren E, Shaikh N, Hoffmann JA, Linneman LA, Hamvas A, Khanna G, Rouggly-Nickless LC, Ndao IM, Shands BA, Escobedo M, Sullivan JE, Radmacher PG, Shannon WD, Tarr PI Lancet (London, England) 26969089 Lancet 2016 May 7
Independence of gut bacterial content and neonatal necrotizing enterocolitis severity. Barron LK, Warner BB, Tarr PI, Shannon WD, Deych E, Warner BW Journal of pediatric surgery 28410788 J Pediatr Surg 2017 Jun
Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants. Thänert R, Schwartz DJ, Keen EC, Hall-Moore C, Wang B, Shaikh N, Ning J, Rouggly-Nickless LC, Thänert A, Ferreiro A, Fishbein SRS, Sullivan JE, Radmacher P, Escobedo M, Warner BB, Tarr PI, Dantas G Cell host & microbe 39197454 Cell Host Microbe 2024 Oct 9
Genomic sequence analysis and characterization of Sneathia amnii sp. nov. Harwich MD Jr, Serrano MG, Fettweis JM, Alves JM, Reimers MA, Vaginal Microbiome Consortium (additional members), Buck GA, Jefferson KK BMC genomics 23281612 BMC Genomics 2012
The L1-norm best-fit hyperplane problem. Brooks JP, Dulá JH Applied mathematics letters 23024460 Appl Math Lett 2012 Jan 1
Differences in vaginal microbiome in African American women versus women of European ancestry. Fettweis JM, Brooks JP, Serrano MG, Sheth NU, Girerd PH, Edwards DJ, Strauss JF, The Vaginal Microbiome Consortium, Jefferson KK, Buck GA Microbiology (Reading, England) 25073854 Microbiology (Reading) 2014 Oct
Identification of a gene in Mycoplasma hominis associated with preterm birth and microbial burden in intraamniotic infection. Allen-Daniels MJ, Serrano MG, Pflugner LP, Fettweis JM, Prestosa MA, Koparde VN, Brooks JP, Strauss JF 3rd, Romero R, Chaiworapongsa T, Eschenbach DA, Buck GA, Jefferson KK American journal of obstetrics and gynecology 25637842 Am J Obstet Gynecol 2015 Jun
Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy. Serrano MG, Parikh HI, Brooks JP, Edwards DJ, Arodz TJ, Edupuganti L, Huang B, Girerd PH, Bokhari YA, Bradley SP, Brooks JL, Dickinson MR, Drake JI, Duckworth RA 3rd, Fong SS, Glascock AL, Jean S, Jimenez NR, Khoury J, Koparde VN, Lara AM, Lee V, Matveyev AV, Milton SH, Mistry SD, Rozycki SK, Sheth NU, Smirnova E, Vivadelli SC, Wijesooriya NR, Xu J, Xu P, Chaffin DO, Sexton AL, Gravett MG, Rubens CE, Hendricks-Muñoz KD, Jefferson KK, Strauss JF 3rd, Fettweis JM, Buck GA Nature medicine 31142850 Nat Med 2019 Jun
The Integrative Human Microbiome Project. Integrative HMP (iHMP) Research Network Consortium Nature 31142853 Nature 2019 May
Relationship between vitamin D status and the vaginal microbiome during pregnancy. Jefferson KK, Parikh HI, Garcia EM, Edwards DJ, Serrano MG, Hewison M, Shary JR, Powell AM, Hollis BW, Fettweis JM, Strauss Iii JF, Buck GA, Wagner CL Journal of perinatology : official journal of the California Perinatal Association 30858609 J Perinatol 2019 Jun
Effects of combined oral contraceptives, depot medroxyprogesterone acetate and the levonorgestrel-releasing intrauterine system on the vaginal microbiome. Brooks JP, Edwards DJ, Blithe DL, Fettweis JM, Serrano MG, Sheth NU, Strauss JF 3rd, Buck GA, Jefferson KK Contraception 27913230 Contraception 2017 Apr
The association of maternal factors with the neonatal microbiota and health. Zhu B, Edwards DJ, Spaine KM, Edupuganti L, Matveyev A, Serrano MG, Buck GA Nature communications 38898021 Nat Commun 2024 Jun 19
Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. Martin J, Sykes S, Young S, Kota K, Sanka R, Sheth N, Orvis J, Sodergren E, Wang Z, Weinstock GM, Mitreva M PloS one 22719831 PLoS One 2012
The changing landscape of the vaginal microbiome. Huang B, Fettweis JM, Brooks JP, Jefferson KK, Buck GA Clinics in laboratory medicine 25439274 Clin Lab Med 2014 Dec
The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Integrative HMP (iHMP) Research Network Consortium Cell host & microbe 25211071 Cell Host Microbe 2014 Sep 10
An emerging mycoplasma associated with trichomoniasis, vaginal infection and disease. Fettweis JM, Serrano MG, Huang B, Brooks JP, Glascock AL, Sheth NU, Vaginal Microbiome Consortium, Strauss JF 3rd, Jefferson KK, Buck GA PloS one 25337710 PLoS One 2014
The vaginal microbiome and preterm birth. Fettweis JM, Serrano MG, Brooks JP, Edwards DJ, Girerd PH, Parikh HI, Huang B, Arodz TJ, Edupuganti L, Glascock AL, Xu J, Jimenez NR, Vivadelli SC, Fong SS, Sheth NU, Jean S, Lee V, Bokhari YA, Lara AM, Mistry SD, Duckworth RA 3rd, Bradley SP, Koparde VN, Orenda XV, Milton SH, Rozycki SK, Matveyev AV, Wright ML, Huzurbazar SV, Jackson EM, Smirnova E, Korlach J, Tsai YC, Dickinson MR, Brooks JL, Drake JI, Chaffin DO, Sexton AL, Gravett MG, Rubens CE, Wijesooriya NR, Hendricks-Muñoz KD, Jefferson KK, Strauss JF 3rd, Buck GA Nature medicine 31142849 Nat Med 2019 Jun
BOTUX: bayesian-like operational taxonomic unit examiner. Koparde VN, Adkins RS, Fettweis JM, Serrano MG, Buck GA, Reimers MA, Sheth NU International journal of computational biology and drug design 24878725 Int J Comput Biol Drug Des 2014
Vaginal microbiome Lactobacillus crispatus is heritable among European American women. Wright ML, Fettweis JM, Eaves LJ, Silberg JL, Neale MC, Serrano MG, Jimenez NR, Prom-Wormley E, Girerd PH, Borzelleca JF Jr, Jefferson KK, Strauss JF 3rd, York TP, Buck GA Communications biology 34354222 Commun Biol 2021 Aug 5
Sequence Comparison of Vaginolysin from Different Gardnerella Species. Garcia EM, Serrano MG, Edupuganti L, Edwards DJ, Buck GA, Jefferson KK Pathogens (Basel, Switzerland) 33498226 Pathogens 2021 Jan 20
Species-level classification of the vaginal microbiome. Fettweis JM, Serrano MG, Sheth NU, Mayer CM, Glascock AL, Brooks JP, Jefferson KK, Vaginal Microbiome Consortium (additional members), Buck GA BMC genomics 23282177 BMC Genomics 2012
Association between statin use, the vaginal microbiome, and Gardnerella vaginalis vaginolysin-mediated cytotoxicity. Abdelmaksoud AA, Girerd PH, Garcia EM, Brooks JP, Leftwich LM, Sheth NU, Bradley SP, Serrano MG, Fettweis JM, Huang B, Strauss JF 3rd, Buck GA, Jefferson KK PloS one 28846702 PLoS One 2017
Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria. Abdelmaksoud AA, Koparde VN, Sheth NU, Serrano MG, Glascock AL, Fettweis JM, Strauss JF, Buck GA, Jefferson KK Microbiology (Reading, England) 26747455 Microbiology (Reading) 2016 Mar
Impact of Herpes Simplex Virus Type 2 and Human Immunodeficiency Virus Dual Infection on Female Genital Tract Mucosal Immunity and the Vaginal Microbiome. Keller MJ, Huber A, Espinoza L, Serrano MG, Parikh HI, Buck GA, Gold JA, Wu Y, Wang T, Herold BC The Journal of infectious diseases 31111902 J Infect Dis 2019 Jul 31
The vaginal microbiome in women of reproductive age with healthy weight versus overweight/obesity. Allen NG, Edupuganti L, Edwards DJ, Jimenez NR, Buck GA, Jefferson KK, Strauss JF 3rd, Vaginal Microbiome Consortium, Wickham EP 3rd, Fettweis JM Obesity (Silver Spring, Md.) 34806323 Obesity (Silver Spring) 2022 Jan
Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies. Harwich MD Jr, Alves JM, Buck GA, Strauss JF 3rd, Patterson JL, Oki AT, Girerd PH, Jefferson KK BMC genomics 20540756 BMC Genomics 2010 Jun 11
A Pure L1-norm Principal Component Analysis. Brooks J, Dulá J, Boone E Computational statistics & data analysis 23976807 Comput Stat Data Anal 2013 May 1
A new era of the vaginal microbiome: advances using next-generation sequencing. Fettweis JM, Serrano MG, Girerd PH, Jefferson KK, Buck GA Chemistry & biodiversity 22589096 Chem Biodivers 2012 May
Unique roles of vaginal Megasphaera phylotypes in reproductive health. Glascock AL, Jimenez NR, Boundy S, Koparde VN, Brooks JP, Edwards DJ, Strauss Iii JF, Jefferson KK, Serrano MG, Buck GA, Fettweis JM Microbial genomics 34898422 Microb Genom 2021 Dec
Roles of the Microbiota of the Female Reproductive Tract in Gynecological and Reproductive Health. Zhu B, Tao Z, Edupuganti L, Serrano MG, Buck GA Microbiology and molecular biology reviews : MMBR 36222685 Microbiol Mol Biol Rev 2022 Dec 21
Does the Vaginal Microbiome Operate Differently by Race to Influence Risk of Precervical Cancer? Tossas KY, Zhu B, Perera RA, Serrano MG, Sullivan S, Sayeed S, Strauss JF 3rd, Winn RA, Buck GA, Seewaldt VL Journal of women's health (2002) 36897755 J Womens Health (Larchmt) 2023 May
An ileal Crohn's disease gene signature based on whole human genome expression profiles of disease unaffected ileal mucosal biopsies. Zhang T, Song B, Zhu W, Xu X, Gong QQ, Morando C, Dassopoulos T, Newberry RD, Hunt SR, Li E PloS one 22606341 PLoS One 2012
Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Frank DN, Robertson CE, Hamm CM, Kpadeh Z, Zhang T, Chen H, Zhu W, Sartor RB, Boedeker EC, Harpaz N, Pace NR, Li E Inflammatory bowel diseases 20839241 Inflamm Bowel Dis 2011 Jan
Growth and Development Symposium: promoting healthier humans through healthier livestock: animal agriculture enters the metagenomics era. Frank DN Journal of animal science 20935136 J Anim Sci 2011 Mar
Influence of Crohn's disease related polymorphisms in innate immune function on ileal microbiome. Li E, Zhang Y, Tian X, Wang X, Gathungu G, Wolber A, Shiekh SS, Sartor RB, Davidson NO, Ciorba MA, Zhu W, Nelson LM, Robertson CE, Frank DN PloS one 30818349 PLoS One 2019
BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. Frank DN BMC bioinformatics 19874596 BMC Bioinformatics 2009 Oct 29
Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition. Zhang T, DeSimone RA, Jiao X, Rohlf FJ, Zhu W, Gong QQ, Hunt SR, Dassopoulos T, Newberry RD, Sodergren E, Weinstock G, Robertson CE, Frank DN, Li E PloS one 22719822 PLoS One 2012
Investigating the biological and clinical significance of human dysbioses. Frank DN, Zhu W, Sartor RB, Li E Trends in microbiology 21775143 Trends Microbiol 2011 Sep
Comparative analysis of microbiome measurement platforms using latent variable structural equation modeling. Wu X, Berkow K, Frank DN, Li E, Gulati AS, Zhu W BMC bioinformatics 23497007 BMC Bioinformatics 2013 Mar 5
Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. Li E, Hamm CM, Gulati AS, Sartor RB, Chen H, Wu X, Zhang T, Rohlf FJ, Zhu W, Gu C, Robertson CE, Pace NR, Boedeker EC, Harpaz N, Yuan J, Weinstock GM, Sodergren E, Frank DN PloS one 22719818 PLoS One 2012
Association of plasma nitrite levels with obesity and metabolic syndrome in the Old Order Amish. Akram F, Fuchs D, Daue M, Nijjar G, Ryan A, Benros ME, Okusaga O, Baca-Garcia E, Brenner LA, Lowry CA, Ryan KA, Pavlovich M, Mitchell BD, Snitker S, Postolache TT Obesity science & practice 30338117 Obes Sci Pract 2018 Oct
Combing fecal microbial community data to identify consistent obesity-specific microbial signatures and shared metabolic pathways. Lin Y, Xu Z, Yeoh YK, Tun HM, Huang W, Jiang W, Chan FKL, Ng SC iScience 37096041 iScience 2023 Apr 21
Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome. Zupancic ML, Cantarel BL, Liu Z, Drabek EF, Ryan KA, Cirimotich S, Jones C, Knight R, Walters WA, Knights D, Mongodin EF, Horenstein RB, Mitchell BD, Steinle N, Snitker S, Shuldiner AR, Fraser CM PloS one 22905200 PLoS One 2012
Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis. Segal LN, Blaser MJ The Journal of pediatrics 25934071 J Pediatr 2015 Jul
Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung. Segal LN, Clemente JC, Wu BG, Wikoff WR, Gao Z, Li Y, Ko JP, Rom WN, Blaser MJ, Weiden MD Thorax 27486204 Thorax 2017 Jan
Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Segal LN, Clemente JC, Tsay JC, Koralov SB, Keller BC, Wu BG, Li Y, Shen N, Ghedin E, Morris A, Diaz P, Huang L, Wikoff WR, Ubeda C, Artacho A, Rom WN, Sterman DH, Collman RG, Blaser MJ, Weiden MD Nature microbiology 27572644 Nat Microbiol 2016 Apr 4
What are the consequences of the disappearing human microbiota? Blaser MJ, Falkow S Nature reviews. Microbiology 19898491 Nat Rev Microbiol 2009 Dec
The microbiome revolution. Blaser MJ The Journal of clinical investigation 25271724 J Clin Invest 2014 Oct
The human microbiome: at the interface of health and disease. Cho I, Blaser MJ Nature reviews. Genetics 22411464 Nat Rev Genet 2012 Mar 13
Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome. Perez Perez GI, Gao Z, Jourdain R, Ramirez J, Gany F, Clavaud C, Demaude J, Breton L, Blaser MJ PloS one 27088867 PLoS One 2016
The microbiome of uncontacted Amerindians. Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcón Ó, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG Science advances 26229982 Sci Adv 2015 Apr 3
Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men. Redel H, Gao Z, Li H, Alekseyenko AV, Zhou Y, Perez-Perez GI, Weinstock G, Sodergren E, Blaser MJ The Journal of infectious diseases 23300163 J Infect Dis 2013 Apr
The Jeremiah Metzger Lecture: Global warming redux: the disappearing microbiota and epidemic obesity. Blaser MJ Transactions of the American Clinical and Climatological Association 23303990 Trans Am Clin Climatol Assoc 2012
Microbiome and malignancy. Plottel CS, Blaser MJ Cell host & microbe 22018233 Cell Host Microbe 2011 Oct 20
The cutaneous microbiome in outpatients presenting with acute skin abscesses. Horton JM, Gao Z, Sullivan DM, Shopsin B, Perez-Perez GI, Blaser MJ The Journal of infectious diseases 25583170 J Infect Dis 2015 Jun 15
Quantitation of major human cutaneous bacterial and fungal populations. Gao Z, Perez-Perez GI, Chen Y, Blaser MJ Journal of clinical microbiology 20702672 J Clin Microbiol 2010 Oct
A brave new world: the lung microbiota in an era of change. Segal LN, Blaser MJ Annals of the American Thoracic Society 24437400 Ann Am Thorac Soc 2014 Jan
Microbiomic signatures of psoriasis: feasibility and methodology comparison. Statnikov A, Alekseyenko AV, Li Z, Henaff M, Perez-Perez GI, Blaser MJ, Aliferis CF Scientific reports 24018484 Sci Rep 2013
Harnessing the power of the human microbiome. Blaser MJ Proceedings of the National Academy of Sciences of the United States of America 20360554 Proc Natl Acad Sci U S A 2010 Apr 6
Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis. Gonzalez ME, Schaffer JV, Orlow SJ, Gao Z, Li H, Alekseyenko AV, Blaser MJ Journal of the American Academy of Dermatology 27543211 J Am Acad Dermatol 2016 Sep
The balance of metagenomic elements shapes the skin microbiome in acne and health. Barnard E, Shi B, Kang D, Craft N, Li H Scientific reports 28000755 Sci Rep 2016 Dec 21
Analysis of complete genomes of Propionibacterium acnes reveals a novel plasmid and increased pseudogenes in an acne associated strain. Kasimatis G, Fitz-Gibbon S, Tomida S, Wong M, Li H BioMed research international 23762865 Biomed Res Int 2013
Propionibacterium acnes strain populations in the human skin microbiome associated with acne. Fitz-Gibbon S, Tomida S, Chiu BH, Nguyen L, Du C, Liu M, Elashoff D, Erfe MC, Loncaric A, Kim J, Modlin RL, Miller JF, Sodergren E, Craft N, Weinstock GM, Li H The Journal of investigative dermatology 23337890 J Invest Dermatol 2013 Sep
Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome. Tomida S, Nguyen L, Chiu BH, Liu J, Sodergren E, Weinstock GM, Li H mBio 23631911 mBio 2013 Apr 30
MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data. Bangayan NJ, Shi B, Trinh J, Barnard E, Kasimatis G, Curd E, Li H Microorganisms 32397065 Microorganisms 2020 May 8
The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin. Liu J, Yan R, Zhong Q, Ngo S, Bangayan NJ, Nguyen L, Lui T, Liu M, Erfe MC, Craft N, Tomida S, Li H The ISME journal 25848871 ISME J 2015 Sep
Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis. Kang D, Shi B, Erfe MC, Craft N, Li H Science translational medicine 26109103 Sci Transl Med 2015 Jun 24
Detection of viruses in young children with fever without an apparent source. Colvin JM, Muenzer JT, Jaffe DM, Smason A, Deych E, Shannon WD, Arens MQ, Buller RS, Lee WM, Weinstock EJ, Weinstock GM, Storch GA Pediatrics 23129086 Pediatrics 2012 Dec
Increased prevalence of anellovirus in pediatric patients with fever. McElvania TeKippe E, Wylie KM, Deych E, Sodergren E, Weinstock G, Storch GA PloS one 23226428 PLoS One 2012
Gene expression profiles in febrile children with defined viral and bacterial infection. Hu X, Yu J, Crosby SD, Storch GA Proceedings of the National Academy of Sciences of the United States of America 23858444 Proc Natl Acad Sci U S A 2013 Jul 30
Astrovirus MLB2 viremia in febrile child. Holtz LR, Wylie KM, Sodergren E, Jiang Y, Franz CJ, Weinstock GM, Storch GA, Wang D Emerging infectious diseases 22099095 Emerg Infect Dis 2011 Nov
High Frequency of Detection by PCR of Viral Nucleic Acid in The Blood of Infants Presenting with Clinical Myocarditis. Simpson KE, Storch GA, Lee CK, Ward KE, Danon S, Simon CM, Delaney JW, Tong A, Canter CE Pediatric cardiology 26499513 Pediatr Cardiol 2016 Feb
Sequence analysis of the human virome in febrile and afebrile children. Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA PloS one 22719819 PLoS One 2012
Emerging view of the human virome. Wylie KM, Weinstock GM, Storch GA Translational research : the journal of laboratory and clinical medicine 22683423 Transl Res 2012 Oct
Vaginal microbiome: rethinking health and disease. Ma B, Forney LJ, Ravel J Annual review of microbiology 22746335 Annu Rev Microbiol 2012
An effective intervention to reduce intravaginal practices among HIV-1 uninfected Kenyan women. Sivapalasingam S, McClelland RS, Ravel J, Ahmed A, Cleland CM, Gajer P, Mwamzaka M, Marshed F, Shafi J, Masese L, Fajans M, Anderson ME, Jaoko W, Kurth AE AIDS research and human retroviruses 25265254 AIDS Res Hum Retroviruses 2014 Nov
An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J Microbiome 24558975 Microbiome 2014 Feb 24
Complete Genome Sequences of Ezakiella coagulans C0061C1 and Fenollaria massiliensis C0061C2. France MT, Clifford J, Narina S, Rutt L, Ravel J Microbiology resource announcements 35861554 Microbiol Resour Announc 2022 Jul 21
Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression. Delgado-Diaz DJ, Jesaveluk B, Hayward JA, Tyssen D, Alisoltani A, Potgieter M, Bell L, Ross E, Iranzadeh A, Allali I, Dabee S, Barnabas S, Gamieldien H, Blackburn JM, Mulder N, Smith SB, Edwards VL, Burgener AD, Bekker LG, Ravel J, Passmore JS, Masson L, Hearps AC, Tachedjian G Microbiome 36045402 Microbiome 2022 Aug 31
Persistence and In Vivo Evolution of Vaginal Bacterial Strains over a Multiyear Time Period. France M, Ma B, Ravel J mSystems 36413016 mSystems 2022 Dec 20
High-resolution functional description of vaginal microbiomes in health and disease. Holm JB, France MT, Gajer P, Ma B, Brotman RM, Shardell M, Forney L, Ravel J bioRxiv : the preprint server for biology 36993583 bioRxiv 2023 Mar 24
Caring about trees in the forest: incorporating frailty in risk analysis for personalized medicine. Ma ZS, Abdo Z, Forney LJ Personalized medicine 22754581 Per Med 2011 Nov
Understanding vaginal microbiome complexity from an ecological perspective. Hickey RJ, Zhou X, Pierson JD, Ravel J, Forney LJ Translational research : the journal of laboratory and clinical medicine 22683415 Transl Res 2012 Oct
Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women. Brotman RM, Bradford LL, Conrad M, Gajer P, Ault K, Peralta L, Forney LJ, Carlton JM, Abdo Z, Ravel J Sexually transmitted diseases 23007708 Sex Transm Dis 2012 Oct
mcaGUI: microbial community analysis R-Graphical User Interface (GUI). Copeland WK, Krishnan V, Beck D, Settles M, Foster JA, Cho KC, Day M, Hickey R, Schütte UM, Zhou X, Williams CJ, Forney LJ, Abdo Z Bioinformatics (Oxford, England) 22692220 Bioinformatics 2012 Aug 15
Moving pictures of the human microbiome. Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, Knights D, Gajer P, Ravel J, Fierer N, Gordon JI, Knight R Genome biology 21624126 Genome Biol 2011
Rapid fluctuation of the vaginal microbiota measured by Gram stain analysis. Brotman RM, Ravel J, Cone RA, Zenilman JM Sexually transmitted infections 20660593 Sex Transm Infect 2010 Aug
Advancing the microbiome research community. Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, Scientists for Advancement of Microbiome Research, White O Cell 25303518 Cell 2014 Oct 9
Complete Genome Sequences of Six Lactobacillus iners Strains Isolated from the Human Vagina. France MT, Rutt L, Narina S, Arbaugh S, McComb E, Humphrys MS, Ma B, Hayward MR, Costello EK, Relman DA, Kwon DS, Ravel J Microbiology resource announcements 32409537 Microbiol Resour Announc 2020 May 14
Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy. Brotman RM, Shardell MD, Gajer P, Fadrosh D, Chang K, Silver MI, Viscidi RP, Burke AE, Ravel J, Gravitt PE Menopause (New York, N.Y.) 24080849 Menopause 2014 May
Assessing the Concordance Between Urogenital and Vaginal Microbiota: Can Urine Specimens Be Used as a Proxy for Vaginal Samples? Brown SE, Robinson CK, Shardell MD, Holm JB, Ravel J, Ghanem KG, Brotman RM Frontiers in cellular and infection microbiology 34268137 Front Cell Infect Microbiol 2021
Biogenic Amines Increase the Odds of Bacterial Vaginosis and Affect the Growth of and Lactic Acid Production by Vaginal Lactobacillus spp. Borgogna JC, Shardell MD, Grace SG, Santori EK, Americus B, Li Z, Ulanov A, Forney L, Nelson TM, Brotman RM, Ravel J, Yeoman CJ Applied and environmental microbiology 33674429 Appl Environ Microbiol 2021 Apr 27
Investigating the impact of condomless vaginal intercourse and lubricant use on the vaginal metabolome: a pre-post observational study. Borgogna JC, Grace SG, Holm JB, Aviles Zuniga T, Kadriu H, He X, McCoski SR, Ravel J, Brotman RM, Yeoman CJ Sexually transmitted infections 37258272 Sex Transm Infect 2023 Nov
Vaginal microbiome of reproductive-age women. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ Proceedings of the National Academy of Sciences of the United States of America 20534435 Proc Natl Acad Sci U S A 2011 Mar 15
Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth. Zhou X, Brotman RM, Gajer P, Abdo Z, Schüette U, Ma S, Ravel J, Forney LJ Infectious diseases in obstetrics and gynecology 21197076 Infect Dis Obstet Gynecol 2010
Evaluation of vaginal microbiome equilibrium states identifies microbial parameters linked to resilience after menses and antibiotic therapy. Lee CY, Diegel J, France MT, Ravel J, Arnold KB PLoS computational biology 37566641 PLoS Comput Biol 2023 Aug
Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis. Noyes N, Cho KC, Ravel J, Forney LJ, Abdo Z PloS one 29364944 PLoS One 2018
VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. France MT, Ma B, Gajer P, Brown S, Humphrys MS, Holm JB, Waetjen LE, Brotman RM, Ravel J Microbiome 33228810 Microbiome 2020 Nov 23
Nonoptimal Vaginal Microbiota After Azithromycin Treatment for Chlamydia trachomatis Infection. Tamarelle J, Ma B, Gajer P, Humphrys MS, Terplan M, Mark KS, Thiébaut ACM, Forney LJ, Brotman RM, Delarocque-Astagneau E, Bavoil PM, Ravel J The Journal of infectious diseases 31573603 J Infect Dis 2020 Feb 3
Asymptomatic Bacterial Vaginosis Is Associated With Depletion of Mature Superficial Cells Shed From the Vaginal Epithelium. O'Hanlon DE, Gajer P, Brotman RM, Ravel J Frontiers in cellular and infection microbiology 32211347 Front Cell Infect Microbiol 2020
Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data. France MT, Fu L, Rutt L, Yang H, Humphrys MS, Narina S, Gajer PM, Ma B, Forney LJ, Ravel J Genome biology 35232471 Genome Biol 2022 Mar 1
New signaling pathways govern the host response to C. albicans infection in various niches. Liu Y, Shetty AC, Schwartz JA, Bradford LL, Xu W, Phan QT, Kumari P, Mahurkar A, Mitchell AP, Ravel J, Fraser CM, Filler SG, Bruno VM Genome research 25858952 Genome Res 2015 May
Interplay between the temporal dynamics of the vaginal microbiota and human papillomavirus detection. Brotman RM, Shardell MD, Gajer P, Tracy JK, Zenilman JM, Ravel J, Gravitt PE The Journal of infectious diseases 24943724 J Infect Dis 2014 Dec 1
Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis. Ravel J, Brotman RM, Gajer P, Ma B, Nandy M, Fadrosh DW, Sakamoto J, Koenig SS, Fu L, Zhou X, Hickey RJ, Schwebke JR, Forney LJ Microbiome 24451163 Microbiome 2013 Dec 2
Vaginal Candida spp. genomes from women with vulvovaginal candidiasis. Bradford LL, Chibucos MC, Ma B, Bruno V, Ravel J Pathogens and disease 28582496 Pathog Dis 2017 Aug 31
Temporal dynamics of the human vaginal microbiota. Gajer P, Brotman RM, Bai G, Sakamoto J, Schütte UM, Zhong X, Koenig SS, Fu L, Ma ZS, Zhou X, Abdo Z, Forney LJ, Ravel J Science translational medicine 22553250 Sci Transl Med 2012 May 2
Comparison of storage conditions for human vaginal microbiome studies. Bai G, Gajer P, Nandy M, Ma B, Yang H, Sakamoto J, Blanchard MH, Ravel J, Brotman RM PloS one 22655031 PLoS One 2012
Douching cessation and molecular bacterial vaginosis: a reanalysis of archived specimens. Brown SE, He X, Shardell MD, Ravel J, Ghanem KG, Zenilman JM, Brotman RM Sexually transmitted infections 35636931 Sex Transm Infect 2023 May
Factors Associated With Incidence and Spontaneous Clearance of Molecular-Bacterial Vaginosis: Results From a Longitudinal Frequent-Sampling Observational Study. Tamarelle J, Shardell MD, Ravel J, Brotman RM Sexually transmitted diseases 35969846 Sex Transm Dis 2022 Sep 1
Quantitative modeling predicts mechanistic links between pre-treatment microbiome composition and metronidazole efficacy in bacterial vaginosis. Lee CY, Cheu RK, Lemke MM, Gustin AT, France MT, Hampel B, Thurman AR, Doncel GF, Ravel J, Klatt NR, Arnold KB Nature communications 33262350 Nat Commun 2020 Dec 1
Integrating compositional and functional content to describe vaginal microbiomes in health and disease. Holm JB, France MT, Gajer P, Ma B, Brotman RM, Shardell M, Forney L, Ravel J Microbiome 38031142 Microbiome 2023 Nov 30
Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. Schloss PD, Jenior ML, Koumpouras CC, Westcott SL, Highlander SK PeerJ 27069806 PeerJ 2016
Metagenomic pyrosequencing and microbial identification. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J Clinical chemistry 19264858 Clin Chem 2009 May
Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. Qin X, Galloway-Peña JR, Sillanpaa J, Roh JH, Nallapareddy SR, Chowdhury S, Bourgogne A, Choudhury T, Muzny DM, Buhay CJ, Ding Y, Dugan-Rocha S, Liu W, Kovar C, Sodergren E, Highlander S, Petrosino JF, Worley KC, Gibbs RA, Weinstock GM, Murray BE BMC microbiology 22769602 BMC Microbiol 2012 Jul 7
Stabilization of the murine gut microbiome following weaning. Schloss PD, Schubert AM, Zackular JP, Iverson KD, Young VB, Petrosino JF Gut microbes 22688727 Gut Microbes 2012 Jul-Aug
The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. Aagaard K, Petrosino J, Keitel W, Watson M, Katancik J, Garcia N, Patel S, Cutting M, Madden T, Hamilton H, Harris E, Gevers D, Simone G, McInnes P, Versalovic J FASEB journal : official publication of the Federation of American Societies for Experimental Biology 23165986 FASEB J 2013 Mar
Building a comprehensive genomic program for hepatocellular carcinoma. Harring TR, Guiteau JJ, Nguyen NT, Cotton RT, Gingras MC, Wheeler DA, O'Mahony CA, Gibbs RA, Brunicardi FC, Goss JA World journal of surgery 21225260 World J Surg 2011 Aug
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, Human Microbiome Consortium, Petrosino JF, Knight R, Birren BW Genome research 21212162 Genome Res 2011 Mar
Genomics. Genome project standards in a new era of sequencing. Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A, Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Detter JC Science (New York, N.Y.) 19815760 Science 2009 Oct 9
Evaluation of 16S rDNA-based community profiling for human microbiome research. Jumpstart Consortium Human Microbiome Project Data Generation Working Group PloS one 22720093 PLoS One 2012
Metagenomic profiling of placental tissue suggests DNA virus infection of the placenta is rare. Witney AA, Aller S, Strang BL The Journal of general virology 34723784 J Gen Virol 2021 Nov
Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Chu DM, Ma J, Prince AL, Antony KM, Seferovic MD, Aagaard KM Nature medicine 28112736 Nat Med 2017 Mar
Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis. Hyde ER, Andrade F, Vaksman Z, Parthasarathy K, Jiang H, Parthasarathy DK, Torregrossa AC, Tribble G, Kaplan HB, Petrosino JF, Bryan NS PloS one 24670812 PLoS One 2014
Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD Applied and environmental microbiology 23793624 Appl Environ Microbiol 2013 Sep
The early infant gut microbiome varies in association with a maternal high-fat diet. Chu DM, Antony KM, Ma J, Prince AL, Showalter L, Moller M, Aagaard KM Genome medicine 27503374 Genome Med 2016 Aug 9
From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions. Spinler JK, Sontakke A, Hollister EB, Venable SF, Oh PL, Balderas MA, Saulnier DM, Mistretta TA, Devaraj S, Walter J, Versalovic J, Highlander SK Genome biology and evolution 24951561 Genome Biol Evol 2014 Jun 19
Complex species and strain ecology of the vaginal microbiome from pregnancy to postpartum and association with preterm birth. Pace RM, Chu DM, Prince AL, Ma J, Seferovic MD, Aagaard KM Med (New York, N.Y.) 34617072 Med 2021 Sep 10
History of childhood physical abuse is associated with gut microbiota diversity among adult psychiatric inpatients. Rohr JC, Bourassa KA, Thompson DS, Fowler JC, Frueh BC, Weinstein BL, Petrosino J, Madan A Journal of affective disorders 36933668 J Affect Disord 2023 Jun 15
Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential. Yeoman CJ, Yildirim S, Thomas SM, Durkin AS, Torralba M, Sutton G, Buhay CJ, Ding Y, Dugan-Rocha SP, Muzny DM, Qin X, Gibbs RA, Leigh SR, Stumpf R, White BA, Highlander SK, Nelson KE, Wilson BA PloS one 20865041 PLoS One 2010 Aug 26
The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Sczesnak A, Segata N, Qin X, Gevers D, Petrosino JF, Huttenhower C, Littman DR, Ivanov II Cell host & microbe 21925113 Cell Host Microbe 2011 Sep 15
The placenta harbors a unique microbiome. Aagaard K, Ma J, Antony KM, Ganu R, Petrosino J, Versalovic J Science translational medicine 24848255 Sci Transl Med 2014 May 21
A primer on a hepatocellular carcinoma bioresource bank using the cancer genome atlas guidelines: practical issues and pitfalls. Nguyen NT, Cotton RT, Harring TR, Guiteau JJ, Gingras MC, Wheeler DA, O'Mahony CA, Gibbs RA, Brunicardi FC, Goss JA World journal of surgery 21221581 World J Surg 2011 Aug
The preterm placental microbiome varies in association with excess maternal gestational weight gain. Antony KM, Ma J, Mitchell KB, Racusin DA, Versalovic J, Aagaard K American journal of obstetrics and gynecology 25557210 Am J Obstet Gynecol 2015 May
Strains, functions and dynamics in the expanded Human Microbiome Project. Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, Brady A, Creasy HH, McCracken C, Giglio MG, McDonald D, Franzosa EA, Knight R, White O, Huttenhower C Nature 28953883 Nature 2017 Oct 5
Mitochondrial DNA sequence variation is largely conserved at birth with rare de novo mutations in neonates. Ma J, Purcell H, Showalter L, Aagaard KM American journal of obstetrics and gynecology 25687567 Am J Obstet Gynecol 2015 Apr
A catalog of reference genomes from the human microbiome. Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, Zhu D Science (New York, N.Y.) 20489017 Science 2010 May 21
Overview of the development of personalized genomic medicine and surgery. Brunicardi FC, Gibbs RA, Wheeler DA, Nemunaitis J, Fisher W, Goss J, Chen C World journal of surgery 21424870 World J Surg 2011 Aug
The Human Microbiome Project: a community resource for the healthy human microbiome. Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, Nelson KE, White O, Methé BA, Huttenhower C PLoS biology 22904687 PLoS Biol 2012
Differential co-expression networks of the gut microbiota are associated with depression and anxiety treatment resistance among psychiatric inpatients. Thompson DS, Fu C, Gandhi T, Fowler JC, Frueh BC, Weinstein BL, Petrosino J, Hadden JK, Carlson M, Coarfa C, Madan A Progress in neuro-psychopharmacology & biological psychiatry 36122838 Prog Neuropsychopharmacol Biol Psychiatry 2023 Jan 10
High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)). Earl AM, Desjardins CA, Fitzgerald MG, Arachchi HM, Zeng Q, Mehta T, Griggs A, Birren BW, Toney NC, Carr J, Posey J, Butler WR Standards in genomic sciences 22675588 Stand Genomic Sci 2011 Dec 31
Metabolic reconstruction for metagenomic data and its application to the human microbiome. Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C PLoS computational biology 22719234 PLoS Comput Biol 2012
MetaRef: a pan-genomic database for comparative and community microbial genomics. Huang K, Brady A, Mahurkar A, White O, Gevers D, Huttenhower C, Segata N Nucleic acids research 24203705 Nucleic Acids Res 2014 Jan
Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants. Taft DH, Ambalavanan N, Schibler KR, Yu Z, Newburg DS, Deshmukh H, Ward DV, Morrow AL PloS one 26110908 PLoS One 2015
The "most wanted" taxa from the human microbiome for whole genome sequencing. Fodor AA, DeSantis TZ, Wylie KM, Badger JH, Ye Y, Hepburn T, Hu P, Sodergren E, Liolios K, Huot-Creasy H, Birren BW, Earl AM PloS one 22848458 PLoS One 2012
A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. Aagaard K, Riehle K, Ma J, Segata N, Mistretta TA, Coarfa C, Raza S, Rosenbaum S, Van den Veyver I, Milosavljevic A, Gevers D, Huttenhower C, Petrosino J, Versalovic J PloS one 22719832 PLoS One 2012
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. Giannoukos G, Ciulla DM, Huang K, Haas BJ, Izard J, Levin JZ, Livny J, Earl AM, Gevers D, Ward DV, Nusbaum C, Birren BW, Gnirke A Genome biology 22455878 Genome Biol 2012
Identifying personal microbiomes using metagenomic codes. Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJ, Huttenhower C Proceedings of the National Academy of Sciences of the United States of America 25964341 Proc Natl Acad Sci U S A 2015 Jun 2
Evolution of invasion in a diverse set of Fusobacterium species. Manson McGuire A, Cochrane K, Griggs AD, Haas BJ, Abeel T, Zeng Q, Nice JB, MacDonald H, Birren BW, Berger BW, Allen-Vercoe E, Earl AM mBio 25370491 mBio 2014 Nov 4
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. Schloss PD, Gevers D, Westcott SL PloS one 22194782 PLoS One 2011
Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions. Liu C, Wright B, Allen-Vercoe E, Gu H, Beiko R Genome biology and evolution 30137329 Genome Biol Evol 2018 Sep 1
Bioinformatics for the Human Microbiome Project. Gevers D, Pop M, Schloss PD, Huttenhower C PLoS computational biology 23209389 PLoS Comput Biol 2012
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J Genome biology 22698087 Genome Biol 2012 Jun 14
Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium. Sizova MV, Muller PA, Stancyk D, Panikov NS, Mandalakis M, Hazen A, Hohmann T, Doerfert SN, Fowle W, Earl AM, Nelson KE, Epstein SS International journal of systematic and evolutionary microbiology 24824639 Int J Syst Evol Microbiol 2014 Aug
Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251). Cuomo CA, Rodriguez-Del Valle N, Perez-Sanchez L, Abouelleil A, Goldberg J, Young S, Zeng Q, Birren BW Genome announcements 24855299 Genome Announc 2014 May 22
Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen. Chen Z, Martinez DA, Gujja S, Sykes SM, Zeng Q, Szaniszlo PJ, Wang Z, Cuomo CA G3 (Bethesda, Md.) 24496724 G3 (Bethesda) 2014 Apr 16
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, LeLeiko N, Snapper SB, Bousvaros A, Korzenik J, Sands BE, Xavier RJ, Huttenhower C Genome biology 23013615 Genome Biol 2012 Apr 16
Microbial co-occurrence relationships in the human microbiome. Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C PLoS computational biology 22807668 PLoS Comput Biol 2012
High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae. Sizova MV, Chilaka A, Earl AM, Doerfert SN, Muller PA, Torralba M, McCorrison JM, Durkin AS, Nelson KE, Epstein SS Standards in genomic sciences 26221418 Stand Genomic Sci 2015
Host genetic variation impacts microbiome composition across human body sites. Blekhman R, Goodrich JK, Huang K, Sun Q, Bukowski R, Bell JT, Spector TD, Keinan A, Ley RE, Gevers D, Clark AG Genome biology 26374288 Genome Biol 2015 Sep 15
Evidence of extensive DNA transfer between bacteroidales species within the human gut. Coyne MJ, Zitomersky NL, McGuire AM, Earl AM, Comstock LE mBio 24939888 mBio 2014 Jun 17
Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt. Lee SC, Billmyre RB, Li A, Carson S, Sykes SM, Huh EY, Mieczkowski P, Ko DC, Cuomo CA, Heitman J mBio 25006230 mBio 2014 Jul 8
UCHIME improves sensitivity and speed of chimera detection. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R Bioinformatics (Oxford, England) 21700674 Bioinformatics 2011 Aug 15
Transcriptome profiling of microRNA by Next-Gen deep sequencing reveals known and novel miRNA species in the lipid fraction of human breast milk. Munch EM, Harris RA, Mohammad M, Benham AL, Pejerrey SM, Showalter L, Hu M, Shope CD, Maningat PD, Gunaratne PH, Haymond M, Aagaard K PloS one 23418415 PLoS One 2013
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG Nature methods 23202435 Nat Methods 2013 Jan
Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants. Ward DV, Scholz M, Zolfo M, Taft DH, Schibler KR, Tett A, Segata N, Morrow AL Cell reports 26997279 Cell Rep 2016 Mar 29
Experimental and analytical tools for studying the human microbiome. Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R Nature reviews. Genetics 22179717 Nat Rev Genet 2011 Dec 16
Emergence of Rotavirus G12P[8] in St. Louis During the 2012-2013 Rotavirus Season. Wylie KM, Weinstock GM, Storch GA Journal of the Pediatric Infectious Diseases Society 26513823 J Pediatric Infect Dis Soc 2015 Dec
The prevalence of species and strains in the human microbiome: a resource for experimental efforts. Kraal L, Abubucker S, Kota K, Fischbach MA, Mitreva M PloS one 24827833 PLoS One 2014
Genomic variation landscape of the human gut microbiome. Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P Nature 23222524 Nature 2013 Jan 3
Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. Nelson DE, Van Der Pol B, Dong Q, Revanna KV, Fan B, Easwaran S, Sodergren E, Weinstock GM, Diao L, Fortenberry JD PloS one 21124791 PLoS One 2010 Nov 24
Virome genomics: a tool for defining the human virome. Wylie KM, Weinstock GM, Storch GA Current opinion in microbiology 23706900 Curr Opin Microbiol 2013 Aug
A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2. Didion JP, Morgan AP, Clayshulte AM, Mcmullan RC, Yadgary L, Petkov PM, Bell TA, Gatti DM, Crowley JJ, Hua K, Aylor DL, Bai L, Calaway M, Chesler EJ, French JE, Geiger TR, Gooch TJ, Garland T Jr, Harrill AH, Hunter K, McMillan L, Holt M, Miller DR, O'Brien DA, Paigen K, Pan W, Rowe LB, Shaw GD, Simecek P, Sullivan PF, Svenson KL, Weinstock GM, Threadgill DW, Pomp D, Churchill GA, Pardo-Manuel de Villena F PLoS genetics 25679959 PLoS Genet 2015 Feb
Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study. Zhou Y, Shan G, Sodergren E, Weinstock G, Walker WA, Gregory KE PloS one 25741698 PLoS One 2015
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). Goll J, Thiagarajan M, Abubucker S, Huttenhower C, Yooseph S, Methé BA PloS one 22719821 PLoS One 2012
Novel bacterial taxa in the human microbiome. Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS PloS one 22719826 PLoS One 2012
Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws. Smajs D, Norris SJ, Weinstock GM Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 22198325 Infect Genet Evol 2012 Mar
Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome. Kontur WS, Schackwitz WS, Ivanova N, Martin J, Labutti K, Deshpande S, Tice HN, Pennacchio C, Sodergren E, Weinstock GM, Noguera DR, Donohue TJ Journal of bacteriology 23209255 J Bacteriol 2012 Dec
Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem. Wendl MC, Kota K, Weinstock GM, Mitreva M Journal of mathematical biology 22965653 J Math Biol 2013 Nov
Genomic approaches to studying the human microbiota. Weinstock GM Nature 22972298 Nature 2012 Sep 13
CcpA is important for growth and virulence of Enterococcus faecium. Somarajan SR, Roh JH, Singh KV, Weinstock GM, Murray BE Infection and immunity 24914215 Infect Immun 2014 Sep
Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens. Zhou Y, Wylie KM, El Feghaly RE, Mihindukulasuriya KA, Elward A, Haslam DB, Storch GA, Weinstock GM Journal of clinical microbiology 26637379 J Clin Microbiol 2016 Feb
Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women. Weimer CM, Deitzler GE, Robinson LS, Park S, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG, Lewis AL Genome announcements 27688327 Genome Announc 2016 Sep 29
Genome Sequences of 14 Firmicutes Strains Isolated from the Human Vagina. Deitzler GE, Ruiz MJ, Weimer C, Park S, Robinson L, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis AL, Lewis WG Genome announcements 27688329 Genome Announc 2016 Sep 29
Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates. Deitzler GE, Ruiz MJ, Lu W, Weimer C, Park S, Robinson LS, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG, Lewis AL Genome announcements 27688330 Genome Announc 2016 Sep 29
Genome sequencing reveals widespread virulence gene exchange among human Neisseria species. Marri PR, Paniscus M, Weyand NJ, Rendón MA, Calton CM, Hernández DR, Higashi DL, Sodergren E, Weinstock GM, Rounsley SD, So M PloS one 20676376 PLoS One 2010 Jul 28
Genetic basis for in vivo daptomycin resistance in enterococci. Arias CA, Panesso D, McGrath DM, Qin X, Mojica MF, Miller C, Diaz L, Tran TT, Rincon S, Barbu EM, Reyes J, Roh JH, Lobos E, Sodergren E, Pasqualini R, Arap W, Quinn JP, Shamoo Y, Murray BE, Weinstock GM The New England journal of medicine 21899450 N Engl J Med 2011 Sep 8
mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. Davis C, Kota K, Baldhandapani V, Gong W, Abubucker S, Becker E, Martin J, Wylie KM, Khetani R, Hudson ME, Weinstock GM, Mitreva M Journal of data mining in genomics & proteomics 26500804 J Data Mining Genomics Proteomics 2015 Aug
Genome Sequences of 15 Gardnerella vaginalis Strains Isolated from the Vaginas of Women with and without Bacterial Vaginosis. Robinson LS, Perry J, Lek S, Wollam A, Sodergren E, Weinstock G, Lewis WG, Lewis AL Genome announcements 27688326 Genome Announc 2016 Sep 29
Genome Sequences of 11 Human Vaginal Actinobacteria Strains. Lewis AL, Deitzler GE, Ruiz MJ, Weimer C, Park S, Robinson LS, Hallsworth-Pepin K, Wollam A, Mitreva M, Lewis WG Genome announcements 27688328 Genome Announc 2016 Sep 29
Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study. Zhou Y, Burnham CA, Hink T, Chen L, Shaikh N, Wollam A, Sodergren E, Weinstock GM, Tarr PI, Dubberke ER Journal of clinical microbiology 25275005 J Clin Microbiol 2014 Dec
Transferable vancomycin resistance in a community-associated MRSA lineage. Rossi F, Diaz L, Wollam A, Panesso D, Zhou Y, Rincon S, Narechania A, Xing G, Di Gioia TS, Doi A, Tran TT, Reyes J, Munita JM, Carvajal LP, Hernandez-Roldan A, Brandão D, van der Heijden IM, Murray BE, Planet PJ, Weinstock GM, Arias CA The New England journal of medicine 24738669 N Engl J Med 2014 Apr 17
The conjunctival microbiome in health and trachomatous disease: a case control study. Zhou Y, Holland MJ, Makalo P, Joof H, Roberts CH, Mabey DC, Bailey RL, Burton MJ, Weinstock GM, Burr SE Genome medicine 25484919 Genome Med 2014
High-resolution genetic mapping in the diversity outbred mouse population identifies Apobec1 as a candidate gene for atherosclerosis. Smallwood TL, Gatti DM, Quizon P, Weinstock GM, Jung KC, Zhao L, Hua K, Pomp D, Bennett BJ G3 (Bethesda, Md.) 25344410 G3 (Bethesda) 2014 Oct 23
Metagenomic analysis of double-stranded DNA viruses in healthy adults. Wylie KM, Mihindukulasuriya KA, Zhou Y, Sodergren E, Storch GA, Weinstock GM BMC biology 25212266 BMC Biol 2014 Sep 10
Genome Sequence of Christensenella minuta DSM 22607T. Rosa BA, Hallsworth-Pepin K, Martin J, Wollam A, Mitreva M Genome announcements 28082495 Genome Announc 2017 Jan 12
Improving Characterization of Understudied Human Microbiomes Using Targeted Phylogenetics. Rosa BA, Mihindukulasuriya K, Hallsworth-Pepin K, Wollam A, Martin J, Snowden C, Dunne WM Jr, Weinstock GM, Burnham CA, Mitreva M mSystems 32098835 mSystems 2020 Feb 25
Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa. Williams TM, Loman NJ, Ebruke C, Musher DM, Adegbola RA, Pallen MJ, Weinstock GM, Antonio M PloS one 23082106 PLoS One 2012
Whole-genome analysis of a daptomycin-susceptible enterococcus faecium strain and its daptomycin-resistant variant arising during therapy. Tran TT, Panesso D, Gao H, Roh JH, Munita JM, Reyes J, Diaz L, Lobos EA, Shamoo Y, Mishra NN, Bayer AS, Murray BE, Weinstock GM, Arias CA Antimicrobial agents and chemotherapy 23114757 Antimicrob Agents Chemother 2013 Jan
Graph accordance of next-generation sequence assemblies. Yao G, Ye L, Gao H, Minx P, Warren WC, Weinstock GM Bioinformatics (Oxford, England) 22025481 Bioinformatics 2012 Jan 1
Epigenetic priors for identifying active transcription factor binding sites. Cuellar-Partida G, Buske FA, McLeay RC, Whitington T, Noble WS, Bailey TL Bioinformatics (Oxford, England) 22072382 Bioinformatics 2012 Jan 1
Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis. Turabelidze G, Lawrence SJ, Gao H, Sodergren E, Weinstock GM, Abubucker S, Wylie T, Mitreva M, Shaikh N, Gautom R, Tarr PI Journal of clinical microbiology 24048526 J Clin Microbiol 2013 Dec
Community characteristics of the gut microbiomes of competitive cyclists. Petersen LM, Bautista EJ, Nguyen H, Hanson BM, Chen L, Lek SH, Sodergren E, Weinstock GM Microbiome 28797298 Microbiome 2017 Aug 10
Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, Chung J, Sohn J, Barber CM, Goldfarb DS, Raju K, Abubucker S, Zhou Y, Ruiz VE, Li H, Mitreva M, Alekseyenko AV, Weinstock GM, Sodergren E, Blaser MJ Nature communications 26123276 Nat Commun 2015 Jun 30
A New Catalog of Microbiological Tools for Women's Infectious Disease Research. Lewis AL, Lewis WG Genome announcements 27688331 Genome Announc 2016 Sep 29
PERFect: PERmutation Filtering test for microbiome data. Smirnova E, Huzurbazar S, Jafari F Biostatistics (Oxford, England) 29917060 Biostatistics 2019 Oct 1
Does the human placenta delivered at term have a microbiota? Results of cultivation, quantitative real-time PCR, 16S rRNA gene sequencing, and metagenomics. Theis KR, Romero R, Winters AD, Greenberg JM, Gomez-Lopez N, Alhousseini A, Bieda J, Maymon E, Pacora P, Fettweis JM, Buck GA, Jefferson KK, Strauss JF 3rd, Erez O, Hassan SS American journal of obstetrics and gynecology 30832984 Am J Obstet Gynecol 2019 Mar
Skin-to-Skin Care and the Development of the Preterm Infant Oral Microbiome. Hendricks-Muñoz KD, Xu J, Parikh HI, Xu P, Fettweis JM, Kim Y, Louie M, Buck GA, Thacker LR, Sheth NU American journal of perinatology 26007311 Am J Perinatol 2015 Nov
The EHEC-host interactome reveals novel targets for the translocated intimin receptor. Blasche S, Arens S, Ceol A, Siszler G, Schmidt MA, Häuser R, Schwarz F, Wuchty S, Aloy P, Uetz P, Stradal T, Koegl M Scientific reports 25519916 Sci Rep 2014 Dec 18
The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages. Mariano R, Wuchty S, Vizoso-Pinto MG, Häuser R, Uetz P Scientific reports 27103053 Sci Rep 2016 Apr 22
Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth. Liao J, Shenhav L, Urban JA, Serrano M, Zhu B, Buck GA, Korem T bioRxiv : the preprint server for biology 36711990 bioRxiv 2023 Jun 17
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. Brooks JP, Edwards DJ, Harwich MD Jr, Rivera MC, Fettweis JM, Serrano MG, Reris RA, Sheth NU, Huang B, Girerd P, Vaginal Microbiome Consortium, Strauss JF 3rd, Jefferson KK, Buck GA BMC microbiology 25880246 BMC Microbiol 2015 Mar 21
Using an in-vitro biofilm model to assess the virulence potential of bacterial vaginosis or non-bacterial vaginosis Gardnerella vaginalis isolates. Castro J, Alves P, Sousa C, Cereija T, França Â, Jefferson KK, Cerca N Scientific reports 26113465 Sci Rep 2015 Jun 26
Challenges for case-control studies with microbiome data. Brooks JP Annals of epidemiology 27255739 Ann Epidemiol 2016 May
2017 NIH-wide workshop report on "The Human Microbiome: Emerging Themes at the Horizon of the 21st Century". 2017 NIH-wide microbiome workshop writing team Microbiome 30808401 Microbiome 2019 Feb 26
MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing. Parikh HI, Koparde VN, Bradley SP, Buck GA, Sheth NU BMC bioinformatics 27905885 BMC Bioinformatics 2016 Dec 1
Identifying Hospital Antimicrobial Resistance Targets via Robust Ranking. Brooks JP, Dulá JH, Pakyz AL, Polk RE IISE transactions on healthcare systems engineering 31098436 IISE Trans Healthc Syst Eng 2017
The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins. Mehla J, Dedrick RM, Caufield JH, Siefring R, Mair M, Johnson A, Hatfull GF, Uetz P Journal of bacteriology 25986902 J Bacteriol 2015 Aug 1
HMPDACC: a Human Microbiome Project Multi-omic data resource. Creasy HH, Felix V, Aluvathingal J, Crabtree J, Ifeonu O, Matsumura J, McCracken C, Nickel L, Orvis J, Schor M, Giglio M, Mahurkar A, White O Nucleic acids research 33305317 Nucleic Acids Res 2021 Jan 8
Phase variation of poly-N-acetylglucosamine expression in Staphylococcus aureus. Brooks JL, Jefferson KK PLoS pathogens 25077798 PLoS Pathog 2014 Jul
Microdiversity of the vaginal microbiome is associated with preterm birth. Liao J, Shenhav L, Urban JA, Serrano M, Zhu B, Buck GA, Korem T Nature communications 37591872 Nat Commun 2023 Aug 17
Antibody Response to the Sneathia vaginalis Cytopathogenic Toxin A during Pregnancy. McCoy ZT, Serrano MG, Edupuganti L, Spaine KM, Edwards DJ, Buck GA, Jefferson KK ImmunoHorizons 38276916 Immunohorizons 2024 Jan 1
Early prediction of preeclampsia using the first trimester vaginal microbiome. Kindschuh WF, Austin GI, Meydan Y, Park H, Urban JA, Watters E, Pollak S, Saade GR, Chung J, Mercer BM, Grobman WA, Haas DM, Silver RM, Serrano M, Buck GA, McNeil R, Nandakumar R, Reddy U, Wapner RJ, Kav AB, Uhlemann AC, Korem T bioRxiv : the preprint server for biology 39677801 bioRxiv 2024 Dec 2
Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Donati C, Zolfo M, Albanese D, Tin Truong D, Asnicar F, Iebba V, Cavalieri D, Jousson O, De Filippo C, Huttenhower C, Segata N Nature microbiology 27572971 Nat Microbiol 2016 May 27
A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. Levin BJ, Huang YY, Peck SC, Wei Y, Martínez-Del Campo A, Marks JA, Franzosa EA, Huttenhower C, Balskus EP Science (New York, N.Y.) 28183913 Science 2017 Feb 10
Optimizing Selection of Biologics in Inflammatory Bowel Disease: Development of an Online Patient Decision Aid Using Conjoint Analysis. Almario CV, Keller MS, Chen M, Lasch K, Ursos L, Shklovskaya J, Melmed GY, Spiegel BMR The American journal of gastroenterology 29206816 Am J Gastroenterol 2018 Jan
Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. Fornelos N, Franzosa EA, Bishai J, Annand JW, Oka A, Lloyd-Price J, Arthur TD, Garner A, Avila-Pacheco J, Haiser HJ, Tolonen AC, Porter JA, Clish CB, Sartor RB, Huttenhower C, Vlamakis H, Xavier RJ Nature microbiology 31959971 Nat Microbiol 2020 Mar
The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men. Sikavi DR, Nguyen LH, Haruki K, Ugai T, Ma W, Wang DD, Thompson KN, Yan Y, Branck T, Wilkinson JE, Akimoto N, Zhong R, Lau MC, Mima K, Kosumi K, Morikawa T, Rimm EB, Garrett WS, Izard J, Cao Y, Song M, Huttenhower C, Ogino S, Chan AT Clinical and translational gastroenterology 34333506 Clin Transl Gastroenterol 2021 Aug 1
The microbiome in inflammatory bowel disease: current status and the future ahead. Kostic AD, Xavier RJ, Gevers D Gastroenterology 24560869 Gastroenterology 2014 May
Disease-specific alterations in the enteric virome in inflammatory bowel disease. Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, Stappenbeck TS, McGovern DP, Keshavarzian A, Mutlu EA, Sauk J, Gevers D, Xavier RJ, Wang D, Parkes M, Virgin HW Cell 25619688 Cell 2015 Jan 29
Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, DIABIMMUNE Study Group, Xavier RJ Cell 27133167 Cell 2016 May 5
CSA13 inhibits colitis-associated intestinal fibrosis via a formyl peptide receptor like-1 mediated HMG-CoA reductase pathway. Xu C, Ghali S, Wang J, Shih DQ, Ortiz C, Mussatto CC, Lee EC, Tran DH, Jacobs JP, Lagishetty V, Fleshner P, Robbins L, Vu M, Hing TC, McGovern DPB, Koon HW Scientific reports 29180648 Sci Rep 2017 Nov 27
Experimental design and quantitative analysis of microbial community multiomics. Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C Genome biology 29187204 Genome Biol 2017 Nov 30
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C Nature microbiology 29311644 Nat Microbiol 2018 Mar
Stability of the human faecal microbiome in a cohort of adult men. Mehta RS, Abu-Ali GS, Drew DA, Lloyd-Price J, Subramanian A, Lochhead P, Joshi AD, Ivey KL, Khalili H, Brown GT, DuLong C, Song M, Nguyen LH, Mallick H, Rimm EB, Izard J, Huttenhower C, Chan AT Nature microbiology 29335554 Nat Microbiol 2018 Mar
Metatranscriptome of human faecal microbial communities in a cohort of adult men. Abu-Ali GS, Mehta RS, Lloyd-Price J, Mallick H, Branck T, Ivey KL, Drew DA, DuLong C, Rimm E, Izard J, Chan AT, Huttenhower C Nature microbiology 29335555 Nat Microbiol 2018 Mar
Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C Genome biology 25887922 Genome Biol 2015 Apr 8
Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly. Ivey KL, Chan AT, Izard J, Cassidy A, Rogers GB, Rimm EB mBio 31551328 mBio 2019 Sep 24
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N eLife 33944776 Elife 2021 May 4
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men. Ma W, Nguyen LH, Song M, Wang DD, Franzosa EA, Cao Y, Joshi A, Drew DA, Mehta R, Ivey KL, Strate LL, Giovannucci EL, Izard J, Garrett W, Rimm EB, Huttenhower C, Chan AT Genome medicine 34140026 Genome Med 2021 Jun 17
Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis. Haberman Y, Schirmer M, Dexheimer PJ, Karns R, Braun T, Kim MO, Walters TD, Baldassano RN, Noe JD, Rosh J, Markowitz J, Crandall WV, Mack DR, Griffiths AM, Heyman MB, Baker SS, Kellermayer R, Moulton D, Patel AS, Gulati AS, Steiner SJ, LeLeiko N, Otley A, Oliva-Hemker M, Ziring D, Kirschner BS, Keljo DJ, Guthery SL, Cohen SA, Snapper S, Evans J, Dubinsky M, Aronow B, Hyams JS, Kugathasan S, Huttenhower C, Xavier RJ, Denson LA Mucosal immunology 30542108 Mucosal Immunol 2019 Mar
Determining microbial products and identifying molecular targets in the human microbiome. Joice R, Yasuda K, Shafquat A, Morgan XC, Huttenhower C Cell metabolism 25440055 Cell Metab 2014 Nov 4
A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria. Yao L, D'Agostino GD, Park J, Hang S, Adhikari AA, Zhang Y, Li W, Avila-Pacheco J, Bae S, Clish CB, Franzosa EA, Huttenhower C, Huh JR, Devlin AS Nature microbiology 35982310 Nat Microbiol 2022 Sep
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C Nature reviews. Microbiology 25915636 Nat Rev Microbiol 2015 Jun
An integrative view of microbiome-host interactions in inflammatory bowel diseases. Wlodarska M, Kostic AD, Xavier RJ Cell host & microbe 25974300 Cell Host Microbe 2015 May 13
Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. Tong M, McHardy I, Ruegger P, Goudarzi M, Kashyap PC, Haritunians T, Li X, Graeber TG, Schwager E, Huttenhower C, Fornace AJ Jr, Sonnenburg JL, McGovern DP, Borneman J, Braun J The ISME journal 24781901 ISME J 2014 Nov
Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LA The Journal of clinical investigation 25003194 J Clin Invest 2014 Aug
Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays. VanDussen KL, Marinshaw JM, Shaikh N, Miyoshi H, Moon C, Tarr PI, Ciorba MA, Stappenbeck TS Gut 25007816 Gut 2015 Jun
Inflammatory bowel disease as a model for translating the microbiome. Huttenhower C, Kostic AD, Xavier RJ Immunity 24950204 Immunity 2014 Jun 19
The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešič M, Huttenhower C, Knip M, DIABIMMUNE Study Group, Xavier RJ Cell host & microbe 25662751 Cell Host Microbe 2015 Feb 11
Complex host genetics influence the microbiome in inflammatory bowel disease. Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ Genome medicine 25587358 Genome Med 2014
Functional and phylogenetic assembly of microbial communities in the human microbiome. Shafquat A, Joice R, Simmons SL, Huttenhower C Trends in microbiology 24618403 Trends Microbiol 2014 May
Relating the metatranscriptome and metagenome of the human gut. Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, Izard J, Garrett WS, Chan AT, Huttenhower C Proceedings of the National Academy of Sciences of the United States of America 24843156 Proc Natl Acad Sci U S A 2014 Jun 3
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA 3rd, IBDMDB Investigators, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C Nature 31142855 Nature 2019 May
A Pleiotropic Missense Variant in SLC39A8 Is Associated With Crohn's Disease and Human Gut Microbiome Composition. Li D, Achkar JP, Haritunians T, Jacobs JP, Hui KY, D'Amato M, Brand S, Radford-Smith G, Halfvarson J, Niess JH, Kugathasan S, Büning C, Schumm LP, Klei L, Ananthakrishnan A, Aumais G, Baidoo L, Dubinsky M, Fiocchi C, Glas J, Milgrom R, Proctor DD, Regueiro M, Simms LA, Stempak JM, Targan SR, Törkvist L, Sharma Y, Devlin B, Borneman J, Hakonarson H, Xavier RJ, Daly M, Brant SR, Rioux JD, Silverberg MS, Cho JH, Braun J, McGovern DP, Duerr RH Gastroenterology 27492617 Gastroenterology 2016 Oct
Microbial strain-level population structure and genetic diversity from metagenomes. Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N Genome research 28167665 Genome Res 2017 Apr
Prevalence and Associations of Avascular Necrosis of the Hip in a Large Well-characterized Cohort of Patients With Inflammatory Bowel Disease. Rolston VS, Patel AV, Learch TJ, Li D, Karayev D, Williams C, Siddanthi ML, Targan SR, Weisman MH, McGovern DPB Journal of clinical rheumatology : practical reports on rheumatic & musculoskeletal diseases 29794876 J Clin Rheumatol 2019 Jan
The TNF family member TL1A induces IL-22 secretion in committed human T(h)17 cells via IL-9 induction. Thomas LS, Targan SR, Tsuda M, Yu QT, Salumbides BC, Haritunians T, Mengesha E, McGovern DP, Michelsen KS Journal of leukocyte biology 27733581 J Leukoc Biol 2017 Mar
Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ Cell 27814509 Cell 2016 Nov 3
Dissecting the human microbiome with single-cell genomics. Tolonen AC, Xavier RJ Genome medicine 28615076 Genome Med 2017 Jun 14
The protection role of Atg16l1 in CD11c(+)dendritic cells in murine colitis. Zhang H, Zheng L, Chen J, Fukata M, Ichikawa R, Shih DQ, Zhang X Immunobiology 28390705 Immunobiology 2017 Jul
Human genetic variation and the gut microbiome in disease. Hall AB, Tolonen AC, Xavier RJ Nature reviews. Genetics 28824167 Nat Rev Genet 2017 Nov
Species-level functional profiling of metagenomes and metatranscriptomes. Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C Nature methods 30377376 Nat Methods 2018 Nov
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. Mallick H, Franzosa EA, Mclver LJ, Banerjee S, Sirota-Madi A, Kostic AD, Clish CB, Vlamakis H, Xavier RJ, Huttenhower C Nature communications 31316056 Nat Commun 2019 Jul 17
The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, De Filippis F, Magnabosco C, Bonneau R, Lusingu J, Amuasi J, Reinhard K, Rattei T, Boulund F, Engstrand L, Zink A, Collado MC, Littman DR, Eibach D, Ercolini D, Rota-Stabelli O, Huttenhower C, Maixner F, Segata N Cell host & microbe 31607556 Cell Host Microbe 2019 Nov 13
Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. Nishiyama H, Endo H, Blanc-Mathieu R, Ogata H Microorganisms 33121006 Microorganisms 2020 Oct 27
Multivariable association discovery in population-scale meta-omics studies. Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C PLoS computational biology 34784344 PLoS Comput Biol 2021 Nov
Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome. Li Y, Wang F, Li J, Ivey KL, Wilkinson JE, Wang DD, Li R, Liu G, Eliassen HA, Chan AT, Clish CB, Huttenhower C, Hu FB, Sun Q, Rimm EB BMC microbiology 35350985 BMC Microbiol 2022 Mar 29
Human gut bacteria produce Τ(Η)17-modulating bile acid metabolites. Paik D, Yao L, Zhang Y, Bae S, D'Agostino GD, Zhang M, Kim E, Franzosa EA, Avila-Pacheco J, Bisanz JE, Rakowski CK, Vlamakis H, Xavier RJ, Turnbaugh PJ, Longman RS, Krout MR, Clish CB, Rastinejad F, Huttenhower C, Huh JR, Devlin AS Nature 35296854 Nature 2022 Mar
The microbiome quality control project: baseline study design and future directions. Sinha R, Abnet CC, White O, Knight R, Huttenhower C Genome biology 26653756 Genome Biol 2015 Dec 9
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M, DIABIMMUNE Study Group, Xavier RJ Science translational medicine 27306663 Sci Transl Med 2016 Jun 15
Immune and genetic gardening of the intestinal microbiome. Jacobs JP, Braun J FEBS letters 24613921 FEBS Lett 2014 Nov 17
The treatment-naive microbiome in new-onset Crohn's disease. Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ Cell host & microbe 24629344 Cell Host Microbe 2014 Mar 12
The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ Nature 30356183 Nature 2018 Oct
Gut microbiome structure and metabolic activity in inflammatory bowel disease. Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ Nature microbiology 30531976 Nat Microbiol 2019 Feb
The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. Wang DD, Nguyen LH, Li Y, Yan Y, Ma W, Rinott E, Ivey KL, Shai I, Willett WC, Hu FB, Rimm EB, Stampfer MJ, Chan AT, Huttenhower C Nature medicine 33574608 Nat Med 2021 Feb
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, Armanini F, Bain D, Duncan SH, Louis P, Zolfo M, Manghi P, Valles-Colomer M, Raffaetà R, Rota-Stabelli O, Collado MC, Zeller G, Falush D, Maixner F, Walker AW, Huttenhower C, Segata N Genome biology 32513234 Genome Biol 2020 Jun 8
Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course. Schirmer M, Denson L, Vlamakis H, Franzosa EA, Thomas S, Gotman NM, Rufo P, Baker SS, Sauer C, Markowitz J, Pfefferkorn M, Oliva-Hemker M, Rosh J, Otley A, Boyle B, Mack D, Baldassano R, Keljo D, LeLeiko N, Heyman M, Griffiths A, Patel AS, Noe J, Kugathasan S, Walters T, Huttenhower C, Hyams J, Xavier RJ Cell host & microbe 30308161 Cell Host Microbe 2018 Oct 10
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R, Bertha M, Cohen M, Garber J, Khalili H, Gevers D, Ananthakrishnan AN, Kugathasan S, Lander ES, Blainey P, Vlamakis H, Xavier RJ, Huttenhower C Genome medicine 29183332 Genome Med 2017 Nov 28
Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome. Li Y, Wang DD, Satija A, Ivey KL, Li J, Wilkinson JE, Li R, Baden M, Chan AT, Huttenhower C, Rimm EB, Hu FB, Sun Q The Journal of nutrition 34114015 J Nutr 2021 Sep 4
bioBakery: a meta'omic analysis environment. McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C Bioinformatics (Oxford, England) 29194469 Bioinformatics 2018 Apr 1
Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. Nguyen LH, Ma W, Wang DD, Cao Y, Mallick H, Gerbaba TK, Lloyd-Price J, Abu-Ali G, Hall AB, Sikavi D, Drew DA, Mehta RS, Arze C, Joshi AD, Yan Y, Branck T, DuLong C, Ivey KL, Ogino S, Rimm EB, Song M, Garrett WS, Izard J, Huttenhower C, Chan AT Gastroenterology 31972239 Gastroenterology 2020 Apr
Profiling novel lateral gene transfer events in the human microbiome. Hsu TY, Nzabarushimana E, Wong D, Luo C, Beiko RG, Langille M, Huttenhower C, Nguyen LH, Franzosa EA bioRxiv : the preprint server for biology 37609252 bioRxiv 2023 Aug 14
Profiling lateral gene transfer events in the human microbiome using WAAFLE. Hsu TY, Nzabarushimana E, Wong D, Luo C, Beiko RG, Langille M, Huttenhower C, Nguyen LH, Franzosa EA Nature microbiology 39747694 Nat Microbiol 2025 Jan
Cathelicidin suppresses lipid accumulation and hepatic steatosis by inhibition of the CD36 receptor. Hoang-Yen Tran D, Hoang-Ngoc Tran D, Mattai SA, Sallam T, Ortiz C, Lee EC, Robbins L, Ho S, Lee JE, Fisseha E, Shieh C, Sideri A, Shih DQ, Fleshner P, McGovern DP, Vu M, Hing TC, Bakirtzi K, Cheng M, Su B, Law I, Karagiannides I, Targan SR, Gallo RL, Li Z, Koon HW International journal of obesity (2005) 27163748 Int J Obes (Lond) 2016 Sep
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Sinha R, Abu-Ali G, Vogtmann E, Fodor AA, Ren B, Amir A, Schwager E, Crabtree J, Ma S, Microbiome Quality Control Project Consortium, Abnet CC, Knight R, White O, Huttenhower C Nature biotechnology 28967885 Nat Biotechnol 2017 Nov
Dynamics of the human gut microbiome in inflammatory bowel disease. Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D'Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK Nature microbiology 28191884 Nat Microbiol 2017 Feb 13
HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor. Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L American journal of epidemiology 30649166 Am J Epidemiol 2019 Jun 1
Global chemical effects of the microbiome include new bile-acid conjugations. Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC Nature 32103176 Nature 2020 Mar
Association of diet with circulating trimethylamine-N-oxide concentration. Hamaya R, Ivey KL, Lee DH, Wang M, Li J, Franke A, Sun Q, Rimm EB The American journal of clinical nutrition 32936862 Am J Clin Nutr 2020 Dec 10
Identification of Natural CRISPR Systems and Targets in the Human Microbiome. Münch PC, Franzosa EA, Stecher B, McHardy AC, Huttenhower C Cell host & microbe 33217332 Cell Host Microbe 2021 Jan 13
A Bayesian method for detecting pairwise associations in compositional data. Schwager E, Mallick H, Ventz S, Huttenhower C PLoS computational biology 29140991 PLoS Comput Biol 2017 Nov
Host genetic variation and its microbiome interactions within the Human Microbiome Project. Kolde R, Franzosa EA, Rahnavard G, Hall AB, Vlamakis H, Stevens C, Daly MJ, Xavier RJ, Huttenhower C Genome medicine 29378630 Genome Med 2018 Jan 29
PICRUSt2 for prediction of metagenome functions. Douglas GM, Maffei VJ, Zaneveld JR, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MGI Nature biotechnology 32483366 Nat Biotechnol 2020 Jun
Role of Autophagy in the Maintenance of Intestinal Homeostasis. Baxt LA, Xavier RJ Gastroenterology 26170139 Gastroenterology 2015 Sep
MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N Nature methods 26418763 Nat Methods 2015 Oct
ConStrains identifies microbial strains in metagenomic datasets. Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D Nature biotechnology 26344404 Nat Biotechnol 2015 Oct
High-sensitivity pattern discovery in large, paired multiomic datasets. Ghazi AR, Sucipto K, Rahnavard A, Franzosa EA, McIver LJ, Lloyd-Price J, Schwager E, Weingart G, Moon YS, Morgan XC, Waldron L, Huttenhower C Bioinformatics (Oxford, England) 35758795 Bioinformatics 2022 Jun 24
Myeloid ATG16L1 Facilitates Host-Bacteria Interactions in Maintaining Intestinal Homeostasis. Zhang H, Zheng L, McGovern DP, Hamill AM, Ichikawa R, Kanazawa Y, Luu J, Kumagai K, Cilluffo M, Fukata M, Targan SR, Underhill DM, Zhang X, Shih DQ Journal of immunology (Baltimore, Md. : 1950) 28130498 J Immunol 2017 Mar 1
Much ado about nothing: A qualitative study of the experiences of an average-risk population receiving results of exome sequencing. Rego S, Dagan-Rosenfeld O, Bivona SA, Snyder MP, Ormond KE Journal of genetic counseling 30835913 J Genet Couns 2019 Apr
Gene-Environment Interaction in the Era of Precision Medicine. Li J, Li X, Zhang S, Snyder M Cell 30901546 Cell 2019 Mar 21
Exerkines in health, resilience and disease. Chow LS, Gerszten RE, Taylor JM, Pedersen BK, van Praag H, Trappe S, Febbraio MA, Galis ZS, Gao Y, Haus JM, Lanza IR, Lavie CJ, Lee CH, Lucia A, Moro C, Pandey A, Robbins JM, Stanford KI, Thackray AE, Villeda S, Watt MJ, Xia A, Zierath JR, Goodpaster BH, Snyder MP Nature reviews. Endocrinology 35304603 Nat Rev Endocrinol 2022 May
Defining a personal, allele-specific, and single-molecule long-read transcriptome. Tilgner H, Grubert F, Sharon D, Snyder MP Proceedings of the National Academy of Sciences of the United States of America 24961374 Proc Natl Acad Sci U S A 2014 Jul 8
HARNESSING BIG DATA FOR PRECISION MEDICINE: INFRASTRUCTURES AND APPLICATIONS. Yu KH, Hart SN, Goldfeder R, Zhang QC, Parker SCJ, Snyder M Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 27897013 Pac Symp Biocomput 2017
Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Araya CL, Cenik C, Reuter JA, Kiss G, Pande VS, Snyder MP, Greenleaf WJ Nature genetics 26691984 Nat Genet 2016 Feb
Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL mBio 27178263 mBio 2016 May 13
Fine-mapping inflammatory bowel disease loci to single-variant resolution. Huang H, Fang M, Jostins L, Umićević Mirkov M, Boucher G, Anderson CA, Andersen V, Cleynen I, Cortes A, Crins F, D'Amato M, Deffontaine V, Dmitrieva J, Docampo E, Elansary M, Farh KK, Franke A, Gori AS, Goyette P, Halfvarson J, Haritunians T, Knight J, Lawrance IC, Lees CW, Louis E, Mariman R, Meuwissen T, Mni M, Momozawa Y, Parkes M, Spain SL, Théâtre E, Trynka G, Satsangi J, van Sommeren S, Vermeire S, Xavier RJ, International Inflammatory Bowel Disease Genetics Consortium, Weersma RK, Duerr RH, Mathew CG, Rioux JD, McGovern DPB, Cho JH, Georges M, Daly MJ, Barrett JC Nature 28658209 Nature 2017 Jul 13
Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information. Li X, Dunn J, Salins D, Zhou G, Zhou W, Schüssler-Fiorenza Rose SM, Perelman D, Colbert E, Runge R, Rego S, Sonecha R, Datta S, McLaughlin T, Snyder MP PLoS biology 28081144 PLoS Biol 2017 Jan
Serum profiling using protein microarrays to identify disease related antigens. Sharon D, Snyder M Methods in molecular biology (Clifton, N.J.) 25030927 Methods Mol Biol 2014
High-throughput sequencing technologies. Reuter JA, Spacek DV, Snyder MP Molecular cell 26000844 Mol Cell 2015 May 21
Personal genomes, quantitative dynamic omics and personalized medicine. Mias GI, Snyder M Quantitative biology (Beijing, China) 25798291 Quant Biol 2013 Mar
Characterization of genetic loci that affect susceptibility to inflammatory bowel diseases in African Americans. Huang C, Haritunians T, Okou DT, Cutler DJ, Zwick ME, Taylor KD, Datta LW, Maranville JC, Liu Z, Ellis S, Chopra P, Alexander JS, Baldassano RN, Cross RK, Dassopoulos T, Dhere TA, Duerr RH, Hanson JS, Hou JK, Hussain SZ, Isaacs KL, Kachelries KE, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kumar A, Kwon JH, Lazarev M, Mannon P, Moulton DE, Osuntokun BO, Patel A, Rioux JD, Rotter JI, Saeed S, Scherl EJ, Silverberg MS, Silverman A, Targan SR, Valentine JF, Wang MH, Simpson CL, Bridges SL, Kimberly RP, Rich SS, Cho JH, Rienzo AD, Kao LWH, McGovern DPB, Brant SR, Kugathasan S Gastroenterology 26278503 Gastroenterology 2015 Nov
Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease. Somineni HK, Nagpal S, Venkateswaran S, Cutler DJ, Okou DT, Haritunians T, Simpson CL, Begum F, Datta LW, Quiros AJ, Seminerio J, Mengesha E, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Iskandar H, Dryden GW, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kuemmerle JF, Lazarev M, Li E, Mannon P, Moulton DE, Newberry RD, Patel AS, Pekow J, Saeed SA, Valentine JF, Wang MH, McCauley JL, Abreu MT, Jester T, Molle-Rios Z, Palle S, Scherl EJ, Kwon J, Rioux JD, Duerr RH, Silverberg MS, Zwick ME, Stevens C, Daly MJ, Cho JH, Gibson G, McGovern DPB, Brant SR, Kugathasan S American journal of human genetics 33600772 Am J Hum Genet 2021 Mar 4
Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMS, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP Cell host & microbe 38479397 Cell Host Microbe 2024 Apr 10
A single-molecule long-read survey of the human transcriptome. Sharon D, Tilgner H, Grubert F, Snyder M Nature biotechnology 24108091 Nat Biotechnol 2013 Nov
Optimized Analytical Procedures for the Untargeted Metabolomic Profiling of Human Urine and Plasma by Combining Hydrophilic Interaction (HILIC) and Reverse-Phase Liquid Chromatography (RPLC)-Mass Spectrometry. Contrepois K, Jiang L, Snyder M Molecular & cellular proteomics : MCP 25787789 Mol Cell Proteomics 2015 Jun
Personalized sequencing and the future of medicine: discovery, diagnosis and defeat of disease. Esplin ED, Oei L, Snyder MP Pharmacogenomics 25493570 Pharmacogenomics 2014 Nov
Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Chu H, Khosravi A, Kusumawardhani IP, Kwon AH, Vasconcelos AC, Cunha LD, Mayer AE, Shen Y, Wu WL, Kambal A, Targan SR, Xavier RJ, Ernst PB, Green DR, McGovern DP, Virgin HW, Mazmanian SK Science (New York, N.Y.) 27230380 Science 2016 May 27
Longitudinal multi-omics of host-microbe dynamics in prediabetes. Zhou W, Sailani MR, Contrepois K, Zhou Y, Ahadi S, Leopold SR, Zhang MJ, Rao V, Avina M, Mishra T, Johnson J, Lee-McMullen B, Chen S, Metwally AA, Tran TDB, Nguyen H, Zhou X, Albright B, Hong BY, Petersen L, Bautista E, Hanson B, Chen L, Spakowicz D, Bahmani A, Salins D, Leopold B, Ashland M, Dagan-Rosenfeld O, Rego S, Limcaoco P, Colbert E, Allister C, Perelman D, Craig C, Wei E, Chaib H, Hornburg D, Dunn J, Liang L, Rose SMS, Kukurba K, Piening B, Rost H, Tse D, McLaughlin T, Sodergren E, Weinstock GM, Snyder M Nature 31142858 Nature 2019 May
A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis. Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC, UK IBD Genetics Consortium, NIDDK IBD Genetics Consortium, MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Färkkilä M, McGovern DP, Franke A, Stefansson K, Rioux JD, Xavier RJ, Daly MJ, Barrett J, de Lane K, Edwards C, Hart A, Hawkey C, Jostins L, Kennedy N, Lamb C, Lee J, Lees C, Mansfield J, Mathew C, Mowatt C, Newman B, Nimmo E, Parkes M, Pollard M, Prescott N, Randall J, Rice D, Satsangi J, Simmons A, Tremelling M, Uhlig H, Wilson D, Abraham C, Achkar JP, Bitton A, Boucher G, Croitoru K, Fleshner P, Glas J, Kugathasan S, Limbergen JV, Milgrom R, Proctor D, Regueiro M, Schumm PL, Sharma Y, Stempak JM, Targan SR, Wang MH Nature communications 27503255 Nat Commun 2016 Aug 9
Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR, Liang L, Abbott C, Gerstein M, Mardinoglu A, Smith U, Rubin DL, Pitteri S, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP Cell systems 29361466 Cell Syst 2018 Feb 28
Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium. Volkmann ER, Chang YL, Barroso N, Furst DE, Clements PJ, Gorn AH, Roth BE, Conklin JL, Getzug T, Borneman J, McGovern DP, Tong M, Jacobs JP, Braun J Arthritis & rheumatology (Hoboken, N.J.) 26749064 Arthritis Rheumatol 2016 Jun
Re: Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Misra R, Arebi N Gastroenterology 28478146 Gastroenterology 2017 Jun
Personal aging markers and ageotypes revealed by deep longitudinal profiling. Ahadi S, Zhou W, Schüssler-Fiorenza Rose SM, Sailani MR, Contrepois K, Avina M, Ashland M, Brunet A, Snyder M Nature medicine 31932806 Nat Med 2020 Jan
Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Brant SR, Okou DT, Simpson CL, Cutler DJ, Haritunians T, Bradfield JP, Chopra P, Prince J, Begum F, Kumar A, Huang C, Venkateswaran S, Datta LW, Wei Z, Thomas K, Herrinton LJ, Klapproth JA, Quiros AJ, Seminerio J, Liu Z, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Dryden GW, Hanson JS, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kwon JH, Lazarev M, Li E, Mack D, Mannon P, Moulton DE, Newberry RD, Osuntokun BO, Patel AS, Saeed SA, Targan SR, Valentine JF, Wang MH, Zonca M, Rioux JD, Duerr RH, Silverberg MS, Cho JH, Hakonarson H, Zwick ME, McGovern DP, Kugathasan S Gastroenterology 27693347 Gastroenterology 2017 Jan
Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring. Jiang C, Wang X, Li X, Inlora J, Wang T, Liu Q, Snyder M Cell 30241608 Cell 2018 Sep 20
Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz. Wagner J, Kancherla J, Braccia D, Matsumara J, Felix V, Crabtree J, Mahurkar A, Corrada Bravo H F1000Research 32742640 F1000Res 2020
Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M Nature biotechnology 26655498 Nat Biotechnol 2016 Jan
Genetic Predictors of Benign Course of Ulcerative Colitis-A North American Inflammatory Bowel Disease Genetics Consortium Study. Kopylov U, Boucher G, Waterman M, Rivers CR, Patel M, Cho JH, Colombel JF, Duerr RH, Binion D, McGovern DP, Schumm PP, Brant SR, Silverberg MS, Rioux JD, Bitton A Inflammatory bowel diseases 27575496 Inflamm Bowel Dis 2016 Oct
High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis. Goyette P, Boucher G, Mallon D, Ellinghaus E, Jostins L, Huang H, Ripke S, Gusareva ES, Annese V, Hauser SL, Oksenberg JR, Thomsen I, Leslie S, International Inflammatory Bowel Disease Genetics Consortium, Australia and New Zealand IBDGC, Belgium IBD Genetics Consortium, Italian Group for IBD Genetic Consortium, NIDDK Inflammatory Bowel Disease Genetics Consortium, United Kingdom IBDGC, Wellcome Trust Case Control Consortium, Quebec IBD Genetics Consortium, Daly MJ, Van Steen K, Duerr RH, Barrett JC, McGovern DP, Schumm LP, Traherne JA, Carrington MN, Kosmoliaptsis V, Karlsen TH, Franke A, Rioux JD Nature genetics 25559196 Nat Genet 2015 Feb
Impact of allele-specific peptides in proteome quantification. Wu L, Snyder M Proteomics. Clinical applications 25676416 Proteomics Clin Appl 2015 Apr
Personal Omics for Precision Health. Kellogg RA, Dunn J, Snyder MP Circulation research 29700064 Circ Res 2018 Apr 27
Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study. Cleynen I, Boucher G, Jostins L, Schumm LP, Zeissig S, Ahmad T, Andersen V, Andrews JM, Annese V, Brand S, Brant SR, Cho JH, Daly MJ, Dubinsky M, Duerr RH, Ferguson LR, Franke A, Gearry RB, Goyette P, Hakonarson H, Halfvarson J, Hov JR, Huang H, Kennedy NA, Kupcinskas L, Lawrance IC, Lee JC, Satsangi J, Schreiber S, Théâtre E, van der Meulen-de Jong AE, Weersma RK, Wilson DC, International Inflammatory Bowel Disease Genetics Consortium, Parkes M, Vermeire S, Rioux JD, Mansfield J, Silverberg MS, Radford-Smith G, McGovern DP, Barrett JC, Lees CW Lancet (London, England) 26490195 Lancet 2016 Jan 9
Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment. Roodgar M, Good BH, Garud NR, Martis S, Avula M, Zhou W, Lancaster SM, Lee H, Babveyh A, Nesamoney S, Pollard KS, Snyder MP Genome research 34301627 Genome Res 2021 Aug
Isolated Congenital Anosmia and CNGA2 Mutation. Sailani MR, Jingga I, MirMazlomi SH, Bitarafan F, Bernstein JA, Snyder MP, Garshasbi M Scientific reports 28572688 Sci Rep 2017 Jun 1
Can Metabolic Profiles Be Used as a Phenotypic Readout of the Genome to Enhance Precision Medicine? Contrepois K, Liang L, Snyder M Clinical chemistry 26960666 Clin Chem 2016 May
Nonlinear dynamics of multi-omics profiles during human aging. Shen X, Wang C, Zhou X, Zhou W, Hornburg D, Wu S, Snyder MP Nature aging 39143318 Nat Aging 2024 Nov
Molecular Choreography of Acute Exercise. Contrepois K, Wu S, Moneghetti KJ, Hornburg D, Ahadi S, Tsai MS, Metwally AA, Wei E, Lee-McMullen B, Quijada JV, Chen S, Christle JW, Ellenberger M, Balliu B, Taylor S, Durrant MG, Knowles DA, Choudhry H, Ashland M, Bahmani A, Enslen B, Amsallem M, Kobayashi Y, Avina M, Perelman D, Schüssler-Fiorenza Rose SM, Zhou W, Ashley EA, Montgomery SB, Chaib H, Haddad F, Snyder MP Cell 32470399 Cell 2020 May 28
A longitudinal big data approach for precision health. Schüssler-Fiorenza Rose SM, Contrepois K, Moneghetti KJ, Zhou W, Mishra T, Mataraso S, Dagan-Rosenfeld O, Ganz AB, Dunn J, Hornburg D, Rego S, Perelman D, Ahadi S, Sailani MR, Zhou Y, Leopold SR, Chen J, Ashland M, Christle JW, Avina M, Limcaoco P, Ruiz C, Tan M, Butte AJ, Weinstock GM, Slavich GM, Sodergren E, McLaughlin TL, Haddad F, Snyder MP Nature medicine 31068711 Nat Med 2019 May
Windows Into Human Health Through Wearables Data Analytics. Witt D, Kellogg R, Snyder M, Dunn J Current opinion in biomedical engineering 31832566 Curr Opin Biomed Eng 2019 Mar
Whole-genome haplotyping using long reads and statistical methods. Kuleshov V, Xie D, Chen R, Pushkarev D, Ma Z, Blauwkamp T, Kertesz M, Snyder M Nature biotechnology 24561555 Nat Biotechnol 2014 Mar
Wearable sensors enable personalized predictions of clinical laboratory measurements. Dunn J, Kidzinski L, Runge R, Witt D, Hicks JL, Schüssler-Fiorenza Rose SM, Li X, Bahmani A, Delp SL, Hastie T, Snyder MP Nature medicine 34031607 Nat Med 2021 Jun
Nat1 Deficiency Is Associated with Mitochondrial Dysfunction and Exercise Intolerance in Mice. Chennamsetty I, Coronado M, Contrepois K, Keller MP, Carcamo-Orive I, Sandin J, Fajardo G, Whittle AJ, Fathzadeh M, Snyder M, Reaven G, Attie AD, Bernstein D, Quertermous T, Knowles JW Cell reports 27705799 Cell Rep 2016 Oct 4
Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Fitzsimons MS, Novotny M, Lo CC, Dichosa AE, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, Wills PL, Parson-Quintana B, Chain PS, Detter JC, Lasken RS, Han CS Genome research 23493677 Genome Res 2013 May
HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences. Danaher RJ, Fouts DE, Chan AP, Choi Y, DePew J, McCorrison JM, Nelson KE, Wang C, Miller CS Journal of neurovirology 27739035 J Neurovirol 2017 Apr
Analyses of the stability and core taxonomic memberships of the human microbiome. Li K, Bihan M, Methé BA PloS one 23671663 PLoS One 2013
Analyses of the microbial diversity across the human microbiome. Li K, Bihan M, Yooseph S, Methé BA PloS one 22719823 PLoS One 2012
Draft Genome Sequence of Enterococcus faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces. O Cuív P, Klaassens ES, Smith WJ, Mondot S, Durkin AS, Harkins DM, Foster L, McCorrison J, Torralba M, Nelson KE, Morrison M Genome announcements 23469340 Genome Announc 2013 Jan
An algorithm for automated closure during assembly. Koren S, Miller JR, Walenz BP, Sutton G BMC bioinformatics 20831800 BMC Bioinformatics 2010 Sep 10
Sequencing viral genomes from a single isolated plaque. Depew J, Zhou B, McCorrison JM, Wentworth DE, Purushe J, Koroleva G, Fouts DE Virology journal 23742765 Virol J 2013 Jun 6
METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics. Goll J, Rusch DB, Tanenbaum DM, Thiagarajan M, Li K, Methé BA, Yooseph S Bioinformatics (Oxford, England) 20798169 Bioinformatics 2010 Oct 15
The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data. Tanenbaum DM, Goll J, Murphy S, Kumar P, Zafar N, Thiagarajan M, Madupu R, Davidsen T, Kagan L, Kravitz S, Rusch DB, Yooseph S Standards in genomic sciences 21304707 Stand Genomic Sci 2010 Mar 30
Prophages mediate defense against phage infection through diverse mechanisms. Bondy-Denomy J, Qian J, Westra ER, Buckling A, Guttman DS, Davidson AR, Maxwell KL The ISME journal 27258950 ISME J 2016 Dec
Draft Genome Sequences of Two Pairs of Human Intestinal Bifidobacterium longum subsp. longum Strains, 44B and 1-6B and 35B and 2-2B, Consecutively Isolated from Two Children after a 5-Year Time Period. Shkoporov AN, Efimov BA, Khokhlova EV, Chaplin AV, Kafarskaya LI, Durkin AS, McCorrison J, Torralba M, Gillis M, Sutton G, Weibel DB, Nelson KE, Smeianov VV Genome announcements 23682142 Genome Announc 2013 May 16
NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly. McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA BMC bioinformatics 25407910 BMC Bioinformatics 2014 Nov 19
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N, Knight R Nature methods 20818378 Nat Methods 2010 Oct
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. Soergel DA, Dey N, Knight R, Brenner SE The ISME journal 22237546 ISME J 2012 Jul
Human-associated microbial signatures: examining their predictive value. Knights D, Parfrey LW, Zaneveld J, Lozupone C, Knight R Cell host & microbe 22018228 Cell Host Microbe 2011 Oct 20
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. Hamady M, Lozupone C, Knight R The ISME journal 19710709 ISME J 2010 Jan
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. Ursell LK, Clemente JC, Rideout JR, Gevers D, Caporaso JG, Knight R The Journal of allergy and clinical immunology 22541361 J Allergy Clin Immunol 2012 May
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R Genome research 22665442 Genome Res 2012 Oct
Complex carbohydrate utilization by the healthy human microbiome. Cantarel BL, Lombard V, Henrissat B PloS one 22719820 PLoS One 2012
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. Pirrung M, Kennedy R, Caporaso JG, Stombaugh J, Wendel D, Knight R Bioinformatics (Oxford, England) 21903626 Bioinformatics 2011 Nov 1
The Microbiome and Big Data. Navas-Molina JA, Hyde ER, Sanders J, Knight R Current opinion in systems biology 36937228 Curr Opin Syst Biol 2017 Aug
IMG/M 4 version of the integrated metagenome comparative analysis system. Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Pillay M, Ratner A, Huang J, Pagani I, Tringe S, Huntemann M, Billis K, Varghese N, Tennessen K, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC Nucleic acids research 24136997 Nucleic Acids Res 2014 Jan
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C Nature biotechnology 23975157 Nat Biotechnol 2013 Sep
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R The ISME journal 22402401 ISME J 2012 Aug
Unravelling the effects of the environment and host genotype on the gut microbiome. Spor A, Koren O, Ley R Nature reviews. Microbiology 21407244 Nat Rev Microbiol 2011 Apr
A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C, Ley RE PLoS computational biology 23326225 PLoS Comput Biol 2013
Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, Knight R The ISME journal 22895161 ISME J 2013 Jan
Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Semova I, Carten JD, Stombaugh J, Mackey LC, Knight R, Farber SA, Rawls JF Cell host & microbe 22980325 Cell Host Microbe 2012 Sep 13
Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players. Ursell LK, Knight R Cell metabolism 23473028 Cell Metab 2013 Mar 5
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC Nucleic acids research 22135293 Nucleic Acids Res 2012 Jan
Finding the missing links among metabolites, microbes, and the host. Dorrestein PC, Mazmanian SK, Knight R Immunity 24950202 Immunity 2014 Jun 19
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK The ISME journal 24451203 ISME J 2014 Jul
Normalization and microbial differential abundance strategies depend upon data characteristics. Weiss S, Xu ZZ, Peddada S, Amir A, Bittinger K, Gonzalez A, Lozupone C, Zaneveld JR, Vázquez-Baeza Y, Birmingham A, Hyde ER, Knight R Microbiome 28253908 Microbiome 2017 Mar 3
Bayesian community-wide culture-independent microbial source tracking. Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, Bushman FD, Knight R, Kelley ST Nature methods 21765408 Nat Methods 2011 Jul 17
The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. He Z, Piceno Y, Deng Y, Xu M, Lu Z, Desantis T, Andersen G, Hobbie SE, Reich PB, Zhou J The ISME journal 21796217 ISME J 2012 Feb
The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness. Liolios K, Schriml L, Hirschman L, Pagani I, Nosrat B, Sterk P, White O, Rocca-Serra P, Sansone SA, Taylor C, Kyrpides NC, Field D Standards in genomic sciences 23409217 Stand Genomic Sci 2012 Jul 30
Human oral, gut, and plaque microbiota in patients with atherosclerosis. Koren O, Spor A, Felin J, Fåk F, Stombaugh J, Tremaroli V, Behre CJ, Knight R, Fagerberg B, Ley RE, Bäckhed F Proceedings of the National Academy of Sciences of the United States of America 20937873 Proc Natl Acad Sci U S A 2011 Mar 15
Characterizing microbial communities through space and time. Gonzalez A, King A, Robeson MS 2nd, Song S, Shade A, Metcalf JL, Knight R Current opinion in biotechnology 22154467 Curr Opin Biotechnol 2012 Jun
Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences. Wang X, Cai Y, Sun Y, Knight R, Mai V The ISME journal 22170430 ISME J 2012 Jul
Responses of gut microbiota to diet composition and weight loss in lean and obese mice. Ravussin Y, Koren O, Spor A, LeDuc C, Gutman R, Stombaugh J, Knight R, Ley RE, Leibel RL Obesity (Silver Spring, Md.) 21593810 Obesity (Silver Spring) 2012 Apr
Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R Gastroenterology 21530737 Gastroenterology 2011 May
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC Nature methods 20436475 Nat Methods 2010 Jun
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, Zhou J, Knight R The ISME journal 26905627 ISME J 2016 Jul
Cohabiting family members share microbiota with one another and with their dogs. Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D, Caporaso JG, Knights D, Clemente JC, Nakielny S, Gordon JI, Fierer N, Knight R eLife 23599893 Elife 2013 Apr 16
Carcass mass has little influence on the structure of gravesoil microbial communities. Weiss S, Carter DO, Metcalf JL, Knight R International journal of legal medicine 26024793 Int J Legal Med 2016 Jan
Longitudinal analysis of microbial interaction between humans and the indoor environment. Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Gibbons SM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK, Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R, Gilbert JA Science (New York, N.Y.) 25170151 Science 2014 Aug 29
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Reeder J, Knight R Nature methods 20805793 Nat Methods 2010 Sep
The under-recognized dominance of Verrucomicrobia in soil bacterial communities. Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, Knight R, Fierer N Soil biology & biochemistry 22267877 Soil Biol Biochem 2011 Jul
IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Jacob B, Ratner A, Liolios K, Pagani I, Huntemann M, Mavromatis K, Ivanova NN, Kyrpides NC PloS one 22792232 PLoS One 2012
Advancing analytical algorithms and pipelines for billions of microbial sequences. Gonzalez A, Knight R Current opinion in biotechnology 22172529 Curr Opin Biotechnol 2012 Feb
IMG/M: the integrated metagenome data management and comparative analysis system. Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, Ratner A, Jacob B, Pati A, Huntemann M, Liolios K, Pagani I, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC Nucleic acids research 22086953 Nucleic Acids Res 2012 Jan
IMG: the Integrated Microbial Genomes database and comparative analysis system. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC Nucleic acids research 22194640 Nucleic Acids Res 2012 Jan
Microbial community assembly and metabolic function during mammalian corpse decomposition. Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song SJ, Amir A, Larsen P, Sangwan N, Haarmann D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Bucheli SR, Carter DO, Knight R Science (New York, N.Y.) 26657285 Science 2016 Jan 8
A quantitative understanding of lac repressor's binding specificity and flexibility. Zuo Z, Chang Y, Stormo GD Quantitative biology (Beijing, China) 26752632 Quant Biol 2015 Jun 1
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing. Zuo Z, Chang YK, Stormo GD Briefings in functional genomics 34923581 Brief Funct Genomics 2022 Apr 11
Spec-seq: determining protein-DNA-binding specificity by sequencing. Stormo GD, Zuo Z, Chang YK Briefings in functional genomics 25362070 Brief Funct Genomics 2015 Jan
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding. Zuo Z, Stormo GD Genetics 25209146 Genetics 2014 Nov
The world within: living with our microbial guests and guides. Janoff EN, Gustafson C, Frank DN Translational research : the journal of laboratory and clinical medicine 22732305 Transl Res 2012 Oct
Of microbes and meals: the health consequences of dietary endotoxemia. Kelly CJ, Colgan SP, Frank DN Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition 22378797 Nutr Clin Pract 2012 Apr
Altered vaginal microbiota are associated with perinatal mother-to-child transmission of HIV in African women from Burkina Faso. Frank DN, Manigart O, Leroy V, Meda N, Valéa D, Zhang W, Dabis F, Pace NR, Van de Perre P, Janoff EN Journal of acquired immune deficiency syndromes (1999) 22343176 J Acquir Immune Defic Syndr 2012 Jul 1
Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. Robertson CE, Harris JK, Wagner BD, Granger D, Browne K, Tatem B, Feazel LM, Park K, Pace NR, Frank DN Bioinformatics (Oxford, England) 24021386 Bioinformatics 2013 Dec 1
Sinus culture poorly predicts resident microbiota. Hauser LJ, Feazel LM, Ir D, Fang R, Wagner BD, Robertson CE, Frank DN, Ramakrishnan VR International forum of allergy & rhinology 25278448 Int Forum Allergy Rhinol 2015 Jan
Prevention of virus-induced type 1 diabetes with antibiotic therapy. Hara N, Alkanani AK, Ir D, Robertson CE, Wagner BD, Frank DN, Zipris D Journal of immunology (Baltimore, Md. : 1950) 22988033 J Immunol 2012 Oct 15
Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Markle JG, Frank DN, Mortin-Toth S, Robertson CE, Feazel LM, Rolle-Kampczyk U, von Bergen M, McCoy KD, Macpherson AJ, Danska JS Science (New York, N.Y.) 23328391 Science 2013 Mar 1
Sinus microbiota varies among chronic rhinosinusitis phenotypes and predicts surgical outcome. Ramakrishnan VR, Hauser LJ, Feazel LM, Ir D, Robertson CE, Frank DN The Journal of allergy and clinical immunology 25819063 J Allergy Clin Immunol 2015 Aug
Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. Xiong X, Frank DN, Robertson CE, Hung SS, Markle J, Canty AJ, McCoy KD, Macpherson AJ, Poussier P, Danska JS, Parkinson J PloS one 22558305 PLoS One 2012
Effects of different complementary feeding regimens on iron status and enteric microbiota in breastfed infants. Krebs NF, Sherlock LG, Westcott J, Culbertson D, Hambidge KM, Feazel LM, Robertson CE, Frank DN The Journal of pediatrics 23452586 J Pediatr 2013 Aug
Culture-independent analysis of aerosol microbiology in a metropolitan subway system. Robertson CE, Baumgartner LK, Harris JK, Peterson KL, Stevens MJ, Frank DN, Pace NR Applied and environmental microbiology 23542619 Appl Environ Microbiol 2013 Jun
Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis. Feazel LM, Robertson CE, Ramakrishnan VR, Frank DN The Laryngoscope 22253013 Laryngoscope 2012 Feb
A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. Tong M, Li X, Wegener Parfrey L, Roth B, Ippoliti A, Wei B, Borneman J, McGovern DP, Frank DN, Li E, Horvath S, Knight R, Braun J PloS one 24260458 PLoS One 2013
The microbiome of the middle meatus in healthy adults. Ramakrishnan VR, Feazel LM, Gitomer SA, Ir D, Robertson CE, Frank DN PloS one 24386477 PLoS One 2013
Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes. Alkanani AK, Hara N, Gottlieb PA, Ir D, Robertson CE, Wagner BD, Frank DN, Zipris D Diabetes 26068542 Diabetes 2015 Oct
Effects of Vaccination with 10-Valent Pneumococcal Non-Typeable Haemophilus influenza Protein D Conjugate Vaccine (PHiD-CV) on the Nasopharyngeal Microbiome of Kenyan Toddlers. Feazel LM, Santorico SA, Robertson CE, Bashraheil M, Scott JA, Frank DN, Hammitt LL PloS one 26083474 PLoS One 2015
A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification. Bigdeli S, Dettloff RO, Frank CW, Davis RW, Crosby LD PloS one 25689864 PLoS One 2015
Bringing the gut microbiota into focus through microbial culture: recent progress and future perspective. Allen-Vercoe E Current opinion in microbiology 24148301 Curr Opin Microbiol 2013 Oct
Tetra-μ-acetato-κO:O'-bis-[(3,5-di-methyl-1H-pyrazole-κN)-copper(II)]. van Wyk J, Omondi B, Darkwa J Acta crystallographica. Section E, Structure reports online 22065823 Acta Crystallogr Sect E Struct Rep Online 2011 Sep 1
Asynchronous Magnetic Bead Rotation (AMBR) Microviscometer for Label-Free DNA Analysis. Li Y, Burke DT, Kopelman R, Burns MA Biosensors 25587411 Biosensors (Basel) 2014 Mar
Microdroplet-enabled highly parallel co-cultivation of microbial communities. Park J, Kerner A, Burns MA, Lin XN PloS one 21364881 PLoS One 2011 Feb 25
One-Way Particle Transport Using Oscillatory Flow in Asymmetric Traps. Lee J, Burns MA Small (Weinheim an der Bergstrasse, Germany) 29377529 Small 2018 Mar
Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial 'dark matter'. Tan JY, Wang S, Dick GJ, Young VB, Sherman DH, Burns MA, Lin XN Integrative biology : quantitative biosciences from nano to macro 33089329 Integr Biol (Camb) 2020 Nov 18
2,2'-Bis(meth-oxy-meth-oxy)-3-methyl-1,1'-binaphth-yl. Carrilho RM, Abreu AR, Pereira MM, Rodrigues VH Acta crystallographica. Section E, Structure reports online 22058976 Acta Crystallogr Sect E Struct Rep Online 2011 Sep 1
Monodisperse alginate microgel formation in a three-dimensional microfluidic droplet generator. Lian M, Collier CP, Doktycz MJ, Retterer ST Biomicrofluidics 24198865 Biomicrofluidics 2012
16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. Wang Y, Hoenig JD, Malin KJ, Qamar S, Petrof EO, Sun J, Antonopoulos DA, Chang EB, Claud EC The ISME journal 19369970 ISME J 2009 Aug
Dielectrophoresis of Caenorhabditis elegans. Chuang HS, Raizen DM, Lamb A, Dabbish N, Bau HH Lab on a chip 21225036 Lab Chip 2011 Feb 21
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. Niu B, Zhu Z, Fu L, Wu S, Li W Bioinformatics (Oxford, England) 21505035 Bioinformatics 2011 Jun 15
Alternative splicing regulated by butyrate in bovine epithelial cells. Wu S, Li C, Huang W, Li W, Li RW PloS one 22720068 PLoS One 2012
Ultrafast clustering algorithms for metagenomic sequence analysis. Li W, Fu L, Niu B, Wu S, Wooley J Briefings in bioinformatics 22772836 Brief Bioinform 2012 Nov
Butyrate Induced IGF2 Activation Correlated with Distinct Chromatin Signatures Due to Histone Modification. Shin JH, Li RW, Gao Y, Bickhart DM, Liu GE, Li W, Wu S, Li CJ Gene regulation and systems biology 23645985 Gene Regul Syst Bio 2013
Perturbation dynamics of the rumen microbiota in response to exogenous butyrate. Li RW, Wu S, Baldwin RL 6th, Li W, Li C PloS one 22253719 PLoS One 2012
Alterations in the porcine colon microbiota induced by the gastrointestinal nematode Trichuris suis. Li RW, Wu S, Li W, Navarro K, Couch RD, Hill D, Urban JF Jr Infection and immunity 22493085 Infect Immun 2012 Jun
CD-HIT: accelerated for clustering the next-generation sequencing data. Fu L, Niu B, Zhu Z, Wu S, Li W Bioinformatics (Oxford, England) 23060610 Bioinformatics 2012 Dec 1
WebMGA: a customizable web server for fast metagenomic sequence analysis. Wu S, Zhu Z, Fu L, Niu B, Li W BMC genomics 21899761 BMC Genomics 2011 Sep 7
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. Zhu Z, Niu B, Chen J, Wu S, Sun S, Li W Bioinformatics (Oxford, England) 23044549 Bioinformatics 2013 Jan 1
Quantification of Transcriptome Responses of the Rumen Epithelium to Butyrate Infusion using RNA-seq Technology. Baldwin RL 6th, Wu S, Li W, Li C, Bequette BJ, Li RW Gene regulation and systems biology 22654504 Gene Regul Syst Bio 2012
Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells. Wu S, Li RW, Li W, Li CJ PloS one 22615851 PLoS One 2012
Worm burden-dependent disruption of the porcine colon microbiota by Trichuris suis infection. Wu S, Li RW, Li W, Beshah E, Dawson HD, Urban JF Jr PloS one 22532855 PLoS One 2012
Secondary structure improves OTU assignments of 16S rRNA gene sequences. Schloss PD The ISME journal 23018771 ISME J 2013 Mar
The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Rogers MAM, Aronoff DM Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 26482265 Clin Microbiol Infect 2016 Feb
Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. Schubert AM, Rogers MA, Ring C, Mogle J, Petrosino JP, Young VB, Aronoff DM, Schloss PD mBio 24803517 mBio 2014 May 6
Microbiology: An integrated view of the skin microbiome. Schloss PD Nature 25279916 Nature 2014 Oct 2
The human gut microbiome as a screening tool for colorectal cancer. Zackular JP, Rogers MA, Ruffin MT 4th, Schloss PD Cancer prevention research (Philadelphia, Pa.) 25104642 Cancer Prev Res (Phila) 2014 Nov
Nurturing the microbiome field. Schloss P Science (New York, N.Y.) 26612945 Science 2015 Nov 27
Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile. Schubert AM, Sinani H, Schloss PD mBio 26173701 mBio 2015 Jul 14
Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Young VB, Raffals LH, Huse SM, Vital M, Dai D, Schloss PD, Brulc JM, Antonopoulos DA, Arrieta RL, Kwon JH, Reddy KG, Hubert NA, Grim SL, Vineis JH, Dalal S, Morrison HG, Eren AM, Meyer F, Schmidt TM, Tiedje JM, Chang EB, Sogin ML Microbiome 24451366 Microbiome 2013 Mar 4
Mathematical modeling of primary succession of murine intestinal microbiota. Marino S, Baxter NT, Huffnagle GB, Petrosino JF, Schloss PD Proceedings of the National Academy of Sciences of the United States of America 24367073 Proc Natl Acad Sci U S A 2014 Jan 7
Decade-long bacterial community dynamics in cystic fibrosis airways. Zhao J, Schloss PD, Kalikin LM, Carmody LA, Foster BK, Petrosino JF, Cavalcoli JD, VanDevanter DR, Murray S, Li JZ, Young VB, LiPuma JJ Proceedings of the National Academy of Sciences of the United States of America 22451929 Proc Natl Acad Sci U S A 2012 Apr 10
Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis. Zackular JP, Baxter NT, Chen GY, Schloss PD mSphere 27303681 mSphere 2016 Jan-Feb
Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM, Lung HIV Microbiome Project American journal of respiratory and critical care medicine 23491408 Am J Respir Crit Care Med 2013 May 15
Intra- and interindividual variations mask interspecies variation in the microbiota of sympatric peromyscus populations. Baxter NT, Wan JJ, Schubert AM, Jenior ML, Myers P, Schloss PD Applied and environmental microbiology 25362056 Appl Environ Microbiol 2015 Jan
Dynamics and associations of microbial community types across the human body. Ding T, Schloss PD Nature 24739969 Nature 2014 May 15
Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. Carmody LA, Zhao J, Schloss PD, Petrosino JF, Murray S, Young VB, Li JZ, LiPuma JJ Annals of the American Thoracic Society 23802813 Ann Am Thorac Soc 2013 Jun
The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection. Reeves AE, Theriot CM, Bergin IL, Huffnagle GB, Schloss PD, Young VB Gut microbes 21804357 Gut Microbes 2011 May-Jun
The dynamics of a family's gut microbiota reveal variations on a theme. Schloss PD, Iverson KD, Petrosino JF, Schloss SJ Microbiome 25061514 Microbiome 2014
The gut microbiome modulates colon tumorigenesis. Zackular JP, Baxter NT, Iverson KD, Sadler WD, Petrosino JF, Chen GY, Schloss PD mBio 24194538 mBio 2013 Nov 5
Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. Beck JM, Schloss PD, Venkataraman A, Twigg H 3rd, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, Frank I, Ghedin E, Huang L, Lynch SV, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB, Lung HIV Microbiome Project American journal of respiratory and critical care medicine 26247840 Am J Respir Crit Care Med 2015 Dec 1
Meta'omic analytic techniques for studying the intestinal microbiome. Morgan XC, Huttenhower C Gastroenterology 24486053 Gastroenterology 2014 May
Early empiric antibiotic use in preterm infants is associated with lower bacterial diversity and higher relative abundance of Enterobacter. Greenwood C, Morrow AL, Lagomarcino AJ, Altaye M, Taft DH, Yu Z, Newburg DS, Ward DV, Schibler KR The Journal of pediatrics 24529620 J Pediatr 2014 Jul
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. Hsu T, Joice R, Vallarino J, Abu-Ali G, Hartmann EM, Shafquat A, DuLong C, Baranowski C, Gevers D, Green JL, Morgan XC, Spengler JD, Huttenhower C mSystems 27822528 mSystems 2016 May-Jun
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. Kaminski J, Gibson MK, Franzosa EA, Segata N, Dantas G, Huttenhower C PLoS computational biology 26682918 PLoS Comput Biol 2015 Dec
Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes. Yassour M, Lim MY, Yun HS, Tickle TL, Sung J, Song YM, Lee K, Franzosa EA, Morgan XC, Gevers D, Lander ES, Xavier RJ, Birren BW, Ko G, Huttenhower C Genome medicine 26884067 Genome Med 2016 Feb 17
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Segata N, Börnigen D, Morgan XC, Huttenhower C Nature communications 23942190 Nat Commun 2013
Two-stage microbial community experimental design. Tickle TL, Segata N, Waldron L, Weingart U, Huttenhower C The ISME journal 23949665 ISME J 2013 Dec
Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes. Ballarini A, Segata N, Huttenhower C, Jousson O PloS one 23409037 PLoS One 2013
Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Yasuda K, Oh K, Ren B, Tickle TL, Franzosa EA, Wachtman LM, Miller AD, Westmoreland SV, Mansfield KG, Vallender EJ, Miller GM, Rowlett JK, Gevers D, Huttenhower C, Morgan XC Cell host & microbe 25732063 Cell Host Microbe 2015 Mar 11
Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. Segata N, Huttenhower C PloS one 21931822 PLoS One 2011
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, Rostron T, Cerundolo V, Pamer EG, Abramson SB, Huttenhower C, Littman DR eLife 24192039 Elife 2013 Nov 5
Compact graphical representation of phylogenetic data and metadata with GraPhlAn. Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N PeerJ 26157614 PeerJ 2015
Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts. Ballal SA, Gallini CA, Segata N, Huttenhower C, Garrett WS Cellular microbiology 21314883 Cell Microbiol 2011 Apr
Metagenomic biomarker discovery and explanation. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C Genome biology 21702898 Genome Biol 2011 Jun 24
Metagenomic microbial community profiling using unique clade-specific marker genes. Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C Nature methods 22688413 Nat Methods 2012 Jun 10
Current concepts of the intestinal microbiota and the pathogenesis of infection. Wardwell LH, Huttenhower C, Garrett WS Current infectious disease reports 21308452 Curr Infect Dis Rep 2011 Feb
Chapter 12: Human microbiome analysis. Morgan XC, Huttenhower C PLoS computational biology 23300406 PLoS Comput Biol 2012
Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses. Smeekens SP, Huttenhower C, Riza A, van de Veerdonk FL, Zeeuwen PL, Schalkwijk J, van der Meer JW, Xavier RJ, Netea MG, Gevers D Journal of innate immunity 23796786 J Innate Immun 2014
Wham: Identifying Structural Variants of Biological Consequence. Kronenberg ZN, Osborne EJ, Cone KR, Kennedy BJ, Domyan ET, Shapiro MD, Elde NC, Yandell M PLoS computational biology 26625158 PLoS Comput Biol 2015 Dec
Biodiversity and functional genomics in the human microbiome. Morgan XC, Segata N, Huttenhower C Trends in genetics : TIG 23140990 Trends Genet 2013 Jan
Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. Rooks MG, Veiga P, Wardwell-Scott LH, Tickle T, Segata N, Michaud M, Gallini CA, Beal C, van Hylckama-Vlieg JE, Ballal SA, Morgan XC, Glickman JN, Gevers D, Huttenhower C, Garrett WS The ISME journal 24500617 ISME J 2014 Jul
Inferring developmental stage composition from gene expression in human malaria. Joice R, Narasimhan V, Montgomery J, Sidhu AB, Oh K, Meyer E, Pierre-Louis W, Seydel K, Milner D, Williamson K, Wiegand R, Ndiaye D, Daily J, Wirth D, Taylor T, Huttenhower C, Marti M PLoS computational biology 24348235 PLoS Comput Biol 2013
Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice. Yasuda K, Hsu T, Gallini CA, Mclver LJ, Schwager E, Shi A, DuLong CR, Schwager RN, Abu-Ali GS, Franzosa EA, Garrett WS, Huttenhower C, Morgan XC mSystems 28808691 mSystems 2017 Jul-Aug
Computational meta'omics for microbial community studies. Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C Molecular systems biology 23670539 Mol Syst Biol 2013 May 14
Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota. Lee S, Cantarel B, Henrissat B, Gevers D, Birren BW, Huttenhower C, Ko G The ISME journal 24108330 ISME J 2014 Mar
A format for phylogenetic placements. Matsen FA, Hoffman NG, Gallagher A, Stamatakis A PloS one 22383988 PLoS One 2012
Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett's Esophagus Cohort. Gall A, Fero J, McCoy C, Claywell BC, Sanchez CA, Blount PL, Li X, Vaughan TL, Matsen FA, Reid BJ, Salama NR PloS one 26076489 PLoS One 2015
Nestly--a framework for running software with nested parameter choices and aggregating results. McCoy CO, Gallagher A, Hoffman NG, Matsen FA Bioinformatics (Oxford, England) 23220574 Bioinformatics 2013 Feb 1
The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples. Evans SN, Matsen FA Journal of the Royal Statistical Society. Series B, Statistical methodology 22844205 J R Stat Soc Series B Stat Methodol 2012 Jun 1
Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria. Srinivasan S, Hoffman NG, Morgan MT, Matsen FA, Fiedler TL, Hall RW, Ross FJ, McCoy CO, Bumgarner R, Marrazzo JM, Fredricks DN PloS one 22719852 PLoS One 2012
Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison. Matsen FA 4th, Evans SN PloS one 23505415 PLoS One 2013
The mean and variance of phylogenetic diversity under rarefaction. Nipperess DA, Matsen FA 4th Methods in ecology and evolution 23833701 Methods Ecol Evol 2013 Jun 1
Associations Between Vaginal Bacteria and Bacterial Vaginosis Signs and Symptoms: A Comparative Study of Kenyan and American Women. Carter KA, Balkus JE, Anzala O, Kimani J, Hoffman NG, Fiedler TL, Mochache V, Fredricks DN, McClelland RS, Srinivasan S Frontiers in cellular and infection microbiology 35310847 Front Cell Infect Microbiol 2022
Phylogenetics and the human microbiome. Matsen FA 4th Systematic biology 25102857 Syst Biol 2015 Jan
More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis. Srinivasan S, Morgan MT, Liu C, Matsen FA, Hoffman NG, Fiedler TL, Agnew KJ, Marrazzo JM, Fredricks DN PloS one 24302980 PLoS One 2013
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots. Matsen FA, Gallagher A Algorithms for molecular biology : AMB 22549005 Algorithms Mol Biol 2012 May 2
Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Yano JM, Yu K, Donaldson GP, Shastri GG, Ann P, Ma L, Nagler CR, Ismagilov RF, Mazmanian SK, Hsiao EY Cell 25860609 Cell 2015 Apr 9
Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa. Ma L, Kim J, Hatzenpichler R, Karymov MA, Hubert N, Hanan IM, Chang EB, Ismagilov RF Proceedings of the National Academy of Sciences of the United States of America 24965364 Proc Natl Acad Sci U S A 2014 Jul 8
Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips. Ma L, Datta SS, Karymov MA, Pan Q, Begolo S, Ismagilov RF Integrative biology : quantitative biosciences from nano to macro 24953827 Integr Biol (Camb) 2014 Aug
GABA-modulating bacteria of the human gut microbiota. Strandwitz P, Kim KH, Terekhova D, Liu JK, Sharma A, Levering J, McDonald D, Dietrich D, Ramadhar TR, Lekbua A, Mroue N, Liston C, Stewart EJ, Dubin MJ, Zengler K, Knight R, Gilbert JA, Clardy J, Lewis K Nature microbiology 30531975 Nat Microbiol 2019 Mar
Neurotransmitter modulation by the gut microbiota. Strandwitz P Brain research 29903615 Brain Res 2018 Aug 15
Quinones are growth factors for the human gut microbiota. Fenn K, Strandwitz P, Stewart EJ, Dimise E, Rubin S, Gurubacharya S, Clardy J, Lewis K Microbiome 29262868 Microbiome 2017 Dec 20
More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria. Srinivasan S, Munch MM, Sizova MV, Fiedler TL, Kohler CM, Hoffman NG, Liu C, Agnew KJ, Marrazzo JM, Epstein SS, Fredricks DN The Journal of infectious diseases 27449870 J Infect Dis 2016 Aug 15
Metabolic signatures of bacterial vaginosis. Srinivasan S, Morgan MT, Fiedler TL, Djukovic D, Hoffman NG, Raftery D, Marrazzo JM, Fredricks DN mBio 25873373 mBio 2015 Apr 14
Megasphaera lornae sp. nov., Megasphaera hutchinsoni sp. nov., and Megasphaera vaginalis sp. nov.: novel bacteria isolated from the female genital tract. Srinivasan S, Beamer MA, Fiedler TL, Austin MN, Sizova MV, Strenk SM, Agnew KJ, Gowda GAN, Raftery D, Epstein SS, Fredricks DN, Hillier SL International journal of systematic and evolutionary microbiology 33616513 Int J Syst Evol Microbiol 2019 Jun
Genetic Variation in Toll-Like Receptor 5 and Colonization with Flagellated Bacterial Vaginosis-Associated Bacteria. Dela Cruz EJ, Fiedler TL, Liu C, Munch MM, Kohler CM, Oot AR, Wallis JM, Wang J, Frishman A, Garcia K, Wiser A, Balkus JE, Srinivasan S, Golob JL, Sycuro LK, Marrazzo JM, Hawn TR, Fredricks DN Infection and immunity 33199356 Infect Immun 2021 Feb 16
In situ cultivation of previously uncultivable microorganisms using the ichip. Berdy B, Spoering AL, Ling LL, Epstein SS Nature protocols 29532802 Nat Protoc 2017 Oct
Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation. Noecker C, Eng A, Srinivasan S, Theriot CM, Young VB, Jansson JK, Fredricks DN, Borenstein E mSystems 27239563 mSystems 2016 Jan-Feb
Amygdalobacter indicium gen. nov., sp. nov., and Amygdalobacter nucleatus sp. nov., gen. nov.: novel bacteria from the family Oscillospiraceae isolated from the female genital tract. Srinivasan S, Austin MN, Fiedler TL, Strenk SM, Agnew KJ, Gowda GAN, Raftery D, Beamer MA, Achilles SL, Wiesenfeld HC, Fredricks DN, Hillier SL International journal of systematic and evolutionary microbiology 37787404 Int J Syst Evol Microbiol 2023 Oct
Clarifying Prehistoric Parasitism from a Complementary Morphological and Molecular Approach. Cleeland LM, Reichard MV, Tito RY, Reinhard KJ, Lewis CM Jr Journal of archaeological science 23645967 J Archaeol Sci 2013 Jul 1
Insights from characterizing extinct human gut microbiomes. Tito RY, Knights D, Metcalf J, Obregon-Tito AJ, Cleeland L, Najar F, Roe B, Reinhard K, Sobolik K, Belknap S, Foster M, Spicer P, Knight R, Lewis CM Jr PloS one 23251439 PLoS One 2012
The Human Microbiome Project: lessons from human genomics. Lewis CM Jr, Obregón-Tito A, Tito RY, Foster MW, Spicer PG Trends in microbiology 22112388 Trends Microbiol 2012 Jan
Brief communication: DNA from early Holocene American dog. Tito RY, Belknap SL 3rd, Sobolik KD, Ingraham RC, Cleeland LM, Lewis CM Jr American journal of physical anthropology 21541929 Am J Phys Anthropol 2011 Aug
Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma. Sankaranarayanan K, Ozga AT, Warinner C, Tito RY, Obregon-Tito AJ, Xu J, Gaffney PM, Jervis LL, Cox D, Stephens L, Foster M, Tallbull G, Spicer P, Lewis CM Current biology : CB 26671671 Curr Biol 2015 Dec 21
Oral microbiome diversity among Cheyenne and Arapaho individuals from Oklahoma. Ozga AT, Sankaranarayanan K, Tito RY, Obregon-Tito AJ, Foster MW, Tallbull G, Spicer P, Warinner CG, Lewis CM Jr American journal of physical anthropology 27357925 Am J Phys Anthropol 2016 Oct
Pathogens and host immunity in the ancient human oral cavity. Warinner C, Rodrigues JF, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, Speller C, Hendy J, Charlton S, Luder HU, Salazar-García DC, Eppler E, Seiler R, Hansen LH, Castruita JA, Barkow-Oesterreicher S, Teoh KY, Kelstrup CD, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis CM Jr, Collins MJ, Gilbert MT, Rühli F, Cappellini E Nature genetics 24562188 Nat Genet 2014 Apr
4,5-Diphen-oxy-benzene-1,2-dicarbo-nitrile. Foo CC, Tan AL, Wimmer FL, Mirza AH, Young DJ, Ng SW, Tiekink ER Acta crystallographica. Section E, Structure reports online 22412514 Acta Crystallogr Sect E Struct Rep Online 2012 Mar 1
Subsistence strategies in traditional societies distinguish gut microbiomes. Obregon-Tito AJ, Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC, Ursell LK, Zech Xu Z, Van Treuren W, Knight R, Gaffney PM, Spicer P, Lawson P, Marin-Reyes L, Trujillo-Villarroel O, Foster M, Guija-Poma E, Troncoso-Corzo L, Warinner C, Ozga AT, Lewis CM Nature communications 25807110 Nat Commun 2015 Mar 25
Science and regulation. Probiotics: finding the right regulatory balance. Hoffmann DE, Fraser CM, Palumbo FB, Ravel J, Rothenberg K, Rowthorn V, Schwartz J Science (New York, N.Y.) 24136953 Science 2013 Oct 18
STOPPING DECEPTIVE HEALTH CLAIMS: THE NEED FOR A PRIVATE RIGHT OF ACTION UNDER FEDERAL LAW. Hoffmann D, Schwartz J American journal of law & medicine 27263263 Am J Law Med 2016
Dichlorido{1-[N-(5-chloro-2-oxidophen-yl)carboximido-yl]naphthalen-2-olato-κO,N,O'}(methanol-κO)tin(IV). Shahverdizadeh GH, Ng SW, Tiekink ER, Mirtamizdoust B Acta crystallographica. Section E, Structure reports online 22412406 Acta Crystallogr Sect E Struct Rep Online 2012 Mar 1
Are changes to the common rule necessary to address evolving areas of research? A case study focusing on the human microbiome project. Hoffmann DE, Fortenberry JD, Ravel J The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics 23802897 J Law Med Ethics 2013 Summer
Probiotics: achieving a better regulatory fit. Hoffmann DE, Fraser CM, Palumbo F, Ravel J, Rowthorn V, Schwartz J Food and drug law journal 25163211 Food Drug Law J 2014
Artificial functional difference between microbial communities caused by length difference of sequencing reads. Zhang Q, Doak TG, Ye Y Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 22174281 Pac Symp Biocomput 2012
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. Wu YW, Rho M, Doak TG, Ye Y Bioinformatics (Oxford, England) 22962453 Bioinformatics 2012 Sep 15
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. Wu YW, Ye Y Journal of computational biology : a journal of computational molecular cell biology 21385052 J Comput Biol 2011 Mar
Metagenomics: Facts and Artifacts, and Computational Challenges*. Wooley JC, Ye Y Journal of computer science and technology 20648230 J Comput Sci Technol 2009 Jan
FragGeneScan: predicting genes in short and error-prone reads. Rho M, Tang H, Ye Y Nucleic acids research 20805240 Nucleic Acids Res 2010 Nov
RAPSearch: a fast protein similarity search tool for short reads. Ye Y, Choi JH, Tang H BMC bioinformatics 21575167 BMC Bioinformatics 2011 May 15
An ORFome assembly approach to metagenomics sequences analysis. Ye Y, Tang H Journal of bioinformatics and computational biology 19507285 J Bioinform Comput Biol 2009 Jun
A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community. Wang M, Ye Y, Tang H Journal of computational biology : a journal of computational molecular cell biology 22697249 J Comput Biol 2012 Jun
Diverse CRISPRs evolving in human microbiomes. Rho M, Wu YW, Tang H, Doak TG, Ye Y PLoS genetics 22719260 PLoS Genet 2012
Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Shah N, Tang H, Doak TG, Ye Y Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 21121044 Pac Symp Biocomput 2011
Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences. Jiao D, Ye Y, Tang H PLoS computational biology 23555216 PLoS Comput Biol 2013
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Zhao Y, Tang H, Ye Y Bioinformatics (Oxford, England) 22039206 Bioinformatics 2012 Jan 1
Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment. Ye Y Proceedings. IEEE International Conference on Bioinformatics and Biomedicine 22102981 Proceedings (IEEE Int Conf Bioinformatics Biomed) 2011 Feb 4
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. Ye Y, Doak TG PLoS computational biology 19680427 PLoS Comput Biol 2009 Aug
The microbiome of the lung. Beck JM, Young VB, Huffnagle GB Translational research : the journal of laboratory and clinical medicine 22683412 Transl Res 2012 Oct
Engineering Values Into Genetic Engineering: A Proposed Analytic Framework for Scientific Social Responsibility. Sankar PL, Cho MK The American journal of bioethics : AJOB 26632356 Am J Bioeth 2015
"What is the FDA Going to Think?": Negotiating Values through Reflective and Strategic Category Work in Microbiome Science. Darling KW, Boyce AM, Cho MK, Sankar PL Science, technology & human values 36119463 Sci Technol Human Values 2015 Jan
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Langmead B, Trapnell C, Pop M, Salzberg SL Genome biology 19261174 Genome Biol 2009
We are what we eat: how the diet of infants affects their gut microbiome. Pop M Genome biology 22546514 Genome Biol 2012
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, Hossain MA, Oundo J, Tamboura B, Mai V, Astrovskaya I, Corrada Bravo H, Rance R, Stares M, Levine MM, Panchalingam S, Kotloff K, Ikumapayi UN, Ebruke C, Adeyemi M, Ahmed D, Ahmed F, Alam MT, Amin R, Siddiqui S, Ochieng JB, Ouma E, Juma J, Mailu E, Omore R, Morris JG, Breiman RF, Saha D, Parkhill J, Nataro JP, Stine OC Genome biology 24995464 Genome Biol 2014 Jun 27
De novo likelihood-based measures for comparing genome assemblies. Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M BMC research notes 23965294 BMC Res Notes 2013 Aug 22
Bambus 2: scaffolding metagenomes. Koren S, Treangen TJ, Pop M Bioinformatics (Oxford, England) 21926123 Bioinformatics 2011 Nov 1
Inexact Local Alignment Search over Suffix Arrays. Ghodsi M, Pop M Proceedings. IEEE International Conference on Bioinformatics and Biomedicine 21278916 Proceedings (IEEE Int Conf Bioinformatics Biomed) 2009 Nov 1
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M Genome biology 23320958 Genome Biol 2013 Jan 15
Deep sequencing of the oral microbiome reveals signatures of periodontal disease. Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S PloS one 22675498 PLoS One 2012
Genome assembly reborn: recent computational challenges. Pop M Briefings in bioinformatics 19482960 Brief Bioinform 2009 Jul
Searching for SNPs with cloud computing. Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL Genome biology 19930550 Genome Biol 2009
Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers. Davison M, Treangen TJ, Koren S, Pop M, Bhaya D PloS one 27611571 PLoS One 2016
MetaCompass: Reference-guided Assembly of Metagenomes. Luan T, Cepeda V, Liu B, Bowen Z, Ayyangar U, Almeida M, Hill CM, Koren S, Treangen TJ, Porter A, Pop M ArXiv 38903742 ArXiv 2024 Mar 3
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Brady A, Salzberg SL Nature methods 19648916 Nat Methods 2009 Sep
GAGE: A critical evaluation of genome assemblies and assembly algorithms. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA Genome research 22147368 Genome Res 2012 Mar
DNACLUST: accurate and efficient clustering of phylogenetic marker genes. Ghodsi M, Liu B, Pop M BMC bioinformatics 21718538 BMC Bioinformatics 2011 Jun 30
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M BMC genomics 21989143 BMC Genomics 2011
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Olson ND, Treangen TJ, Hill CM, Cepeda-Espinoza V, Ghurye J, Koren S, Pop M Briefings in bioinformatics 28968737 Brief Bioinform 2019 Jul 19
Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. White JR, Navlakha S, Nagarajan N, Ghodsi MR, Kingsford C, Pop M BMC bioinformatics 20334679 BMC Bioinformatics 2010 Mar 24
Statistical methods for detecting differentially abundant features in clinical metagenomic samples. White JR, Nagarajan N, Pop M PLoS computational biology 19360128 PLoS Comput Biol 2009 Apr
Next generation sequence assembly with AMOS. Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M Current protocols in bioinformatics 21400694 Curr Protoc Bioinformatics 2011 Mar
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M Briefings in bioinformatics 22199379 Brief Bioinform 2013 Mar
Differential abundance analysis for microbial marker-gene surveys. Paulson JN, Stine OC, Bravo HC, Pop M Nature methods 24076764 Nat Methods 2013 Dec
Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family. Haft DH, Basu MK, Mitchell DA BMC biology 20500830 BMC Biol 2010 May 25
Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. Selengut JD, Haft DH Journal of bacteriology 20675471 J Bacteriol 2010 Nov
GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease. Haft DH, Varghese N PloS one 22194940 PLoS One 2011
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. Haft DH BMC genomics 21223593 BMC Genomics 2011 Jan 11
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 BD, Mulheron HJ, Semrau JD, Dispirito AA, Bandow NL, Haft DH, Vuilleumier S, Murrell JC, McEllistrem MT, Hartsel SC, Gallagher WH Biochemistry 20961038 Biochemistry 2010 Nov 30
Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. Ansong C, Ortega C, Payne SH, Haft DH, Chauvignè-Hines LM, Lewis MP, Ollodart AR, Purvine SO, Shukla AK, Fortuin S, Smith RD, Adkins JN, Grundner C, Wright AT Chemistry & biology 23352146 Chem Biol 2013 Jan 24
TIGRFAMs and Genome Properties in 2013. Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E Nucleic acids research 23197656 Nucleic Acids Res 2013 Jan
AntiFam: a tool to help identify spurious ORFs in protein annotation. Eberhardt RY, Haft DH, Punta M, Martin M, O'Donovan C, Bateman A Database : the journal of biological databases and curation 22434837 Database (Oxford) 2012
Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism. Pathak DT, Wei X, Bucuvalas A, Haft DH, Gerloff DL, Wall D PLoS genetics 22511878 PLoS Genet 2012
Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. Haft DH, Basu MK Journal of bacteriology 21478363 J Bacteriol 2011 Jun
CharProtDB: a database of experimentally characterized protein annotations. Madupu R, Richter A, Dodson RJ, Brinkac L, Harkins D, Durkin S, Shrivastava S, Sutton G, Haft D Nucleic acids research 22140108 Nucleic Acids Res 2012 Jan
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. Selengut JD, Rusch DB, Haft DH BMC bioinformatics 20102603 BMC Bioinformatics 2010 Jan 26
Evolution and classification of the CRISPR-Cas systems. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV Nature reviews. Microbiology 21552286 Nat Rev Microbiol 2011 Jun
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. Basu MK, Selengut JD, Haft DH BMC bioinformatics 22070167 BMC Bioinformatics 2011 Nov 9
Ethical Discourse about the Modification of Food for Therapeutic Purposes: How Patients with Gastrointestinal Diseases View the Good, the Bad, and the Healthy. Harrison KL, Geller G, Marshall P, Tilburt J, Mercer M, Brinich MA, Highland J, Farrell RM, Sharp RR AJOB primary research 22773953 AJOB Prim Res 2012 Jul 1
How patients view probiotics: findings from a multicenter study of patients with inflammatory bowel disease and irritable bowel syndrome. Mercer M, Brinich MA, Geller G, Harrison K, Highland J, James K, Marshall P, McCormick JB, Tilburt J, Achkar JP, Farrell RM, Sharp RR Journal of clinical gastroenterology 21716123 J Clin Gastroenterol 2012 Feb
'Someone should oversee it': patient perspectives on the ethical issues arising with the regulation of probiotics. Harrison KL, Farrell RM, Brinich MA, Highland J, Mercer M, McCormick JB, Tilburt J, Geller G, Marshall P, Sharp RR Health expectations : an international journal of public participation in health care and health policy 23279082 Health Expect 2015 Apr
An analysis of online messages about probiotics. Brinich MA, Mercer MB, Sharp RR BMC gastroenterology 23311418 BMC Gastroenterol 2013 Jan 11
Helping patients make informed choices about probiotics: a need for research. Sharp RR, Achkar JP, Brinich MA, Farrell RM The American journal of gastroenterology 19343022 Am J Gastroenterol 2009 Apr
Experiences of patients with chronic gastrointestinal conditions: in their own words. McCormick JB, Hammer RR, Farrell RM, Geller G, James KM, Loftus EV Jr, Mercer MB, Tilburt JC, Sharp RR Health and quality of life outcomes 22401607 Health Qual Life Outcomes 2012 Mar 8
Mammalian Cell Sorting using μFACS. Cho SH, Chen CH, Tsai FS, Godin J, Lo YH Conference on Lasers and Electro-optics : (CLEO). Conference on Lasers and Electro-optics 21614147 Conf Lasers Electro Optics 2010 May 16
Lab-on-a-chip flow cytometer employing color-space-time coding. Cho SH, Qiao W, Tsai FS, Yamashita K, Lo YH Applied physics letters 20877655 Appl Phys Lett 2010 Aug 30
Review Article: Recent advancements in optofluidic flow cytometer. Cho SH, Godin JM, Chen CH, Qiao W, Lee H, Lo YH Biomicrofluidics 21267434 Biomicrofluidics 2010 Dec 30
Micro-fabricated fluorescence-activated cell sorter. Cho SH, Chen CH, Tsai FS, Lo YH Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference 19965141 Annu Int Conf IEEE Eng Med Biol Soc 2009
Optofluidic Waveguides in Teflon AF-Coated PDMS Microfluidic Channels. Cho SH, Godin J, Lo YH IEEE photonics technology letters : a publication of the IEEE Laser and Electro-optics Society 20729984 IEEE Photonics Technol Lett 2009 Aug 1
Microfluidic cell sorter with integrated piezoelectric actuator. Chen CH, Cho SH, Tsai F, Erten A, Lo YH Biomedical microdevices 19649710 Biomed Microdevices 2009 Dec
Human mammalian cell sorting using a highly integrated micro-fabricated fluorescence-activated cell sorter (microFACS). Cho SH, Chen CH, Tsai FS, Godin JM, Lo YH Lab on a chip 20379604 Lab Chip 2010 Jun 21
Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Gole J, Gore A, Richards A, Chiu YJ, Fung HL, Bushman D, Chiang HI, Chun J, Lo YH, Zhang K Nature biotechnology 24213699 Nat Biotechnol 2013 Dec
Specific sorting of single bacterial cells with microfabricated fluorescence-activated cell sorting and tyramide signal amplification fluorescence in situ hybridization. Chen CH, Cho SH, Chiang HI, Tsai F, Zhang K, Lo YH Analytical chemistry 21809842 Anal Chem 2011 Oct 1
An optical-coding method to measure particle distribution in microfluidic devices. Wu TF, Mei Z, Pion-Tonachini L, Zhao C, Qiao W, Arianpour A, Lo YH AIP advances 22125760 AIP Adv 2011 Jun
Applying an optical space-time coding method to enhance light scattering signals in microfluidic devices. Mei Z, Wu TF, Pion-Tonachini L, Qiao W, Zhao C, Liu Z, Lo YH Biomicrofluidics 21915241 Biomicrofluidics 2011 Sep
Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment. Thompson JD, Shibahara G, Rajan S, Pel J, Marziali A PloS one 22355378 PLoS One 2012
SitePainter: a tool for exploring biogeographical patterns. Gonzalez A, Stombaugh J, Lauber CL, Fierer N, Knight R Bioinformatics (Oxford, England) 22171330 Bioinformatics 2012 Feb 1
The mind-body-microbial continuum. Gonzalez A, Stombaugh J, Lozupone C, Turnbaugh PJ, Gordon JI, Knight R Dialogues in clinical neuroscience 21485746 Dialogues Clin Neurosci 2011
Bacterial communities of disease vectors sampled across time, space, and species. Jones RT, Knight R, Martin AP The ISME journal 19865184 ISME J 2010 Feb
Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives. Zaneveld JR, Lozupone C, Gordon JI, Knight R Nucleic acids research 20197316 Nucleic Acids Res 2010 Jul
Spatial and temporal variability of the human microbiota. Parfrey LW, Knight R Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 22647040 Clin Microbiol Infect 2012 Jul
The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N Environmental microbiology 20545741 Environ Microbiol 2010 Nov
Qiita: rapid, web-enabled microbiome meta-analysis. Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R Nature methods 30275573 Nat Methods 2018 Oct
Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. Zaneveld JR, Parfrey LW, Van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, Knight R Trends in microbiology 21872475 Trends Microbiol 2011 Oct
Interleukin-1β (IL-1β) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis. Carvalho FA, Nalbantoglu I, Ortega-Fernandez S, Aitken JD, Su Y, Koren O, Walters WA, Knight R, Ley RE, Vijay-Kumar M, Gewirtz AT Gut 21646247 Gut 2012 Mar
Extrapolation of urn models via poissonization: accurate measurements of the microbial unknown. Lladser ME, Gouet R, Reeder J PloS one 21738613 PLoS One 2011
Host-associated and free-living phage communities differ profoundly in phylogenetic composition. Caporaso JG, Knight R, Kelley ST PloS one 21383980 PLoS One 2011 Feb 24
Boulder ALignment Editor (ALE): a web-based RNA alignment tool. Stombaugh J, Widmann J, McDonald D, Knight R Bioinformatics (Oxford, England) 21546392 Bioinformatics 2011 Jun 15
Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R Frontiers in microbiology 24995004 Front Microbiol 2014
Association of gut microbiota with post-operative clinical course in Crohn's disease. Dey N, Soergel DA, Repo S, Brenner SE BMC gastroenterology 23964800 BMC Gastroenterol 2013 Aug 22
High-fat diet determines the composition of the murine gut microbiome independently of obesity. Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen YY, Knight R, Ahima RS, Bushman F, Wu GD Gastroenterology 19706296 Gastroenterology 2009 Nov
Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. Lauber CL, Zhou N, Gordon JI, Knight R, Fierer N FEMS microbiology letters 20412303 FEMS Microbiol Lett 2010 Jun
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R Proceedings of the National Academy of Sciences of the United States of America 20566857 Proc Natl Acad Sci U S A 2010 Jun 29
The impact of the gut microbiota on human health: an integrative view. Clemente JC, Ursell LK, Parfrey LW, Knight R Cell 22424233 Cell 2012 Mar 16
Conducting a microbiome study. Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE Cell 25036628 Cell 2014 Jul 17
Meta-analyses of human gut microbes associated with obesity and IBD. Walters WA, Xu Z, Knight R FEBS letters 25307765 FEBS Lett 2014 Nov 17
Pigs, Unlike Mice, Have Two Distinct Colonic Stem Cell Populations Similar to Humans That Respond to High-Calorie Diet prior to Insulin Resistance. Charepalli V, Reddivari L, Radhakrishnan S, Eriksson E, Xiao X, Kim SW, Shen F, Vijay-Kumar M, Li Q, Bhat VB, Knight R, Vanamala JKP Cancer prevention research (Philadelphia, Pa.) 28576788 Cancer Prev Res (Phila) 2017 Aug
Postprandial remodeling of the gut microbiota in Burmese pythons. Costello EK, Gordon JI, Secor SM, Knight R The ISME journal 20520652 ISME J 2010 Nov
Unlocking the potential of metagenomics through replicated experimental design. Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, Hugenholtz P, van der Lelie D, Meyer F, Stevens R, Bailey MJ, Gordon JI, Kowalchuk GA, Gilbert JA Nature biotechnology 22678395 Nat Biotechnol 2012 Jun 7
RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. Widmann J, Stombaugh J, McDonald D, Chocholousova J, Gardner P, Iyer MK, Liu Z, Lozupone CA, Quinn J, Smit S, Wikman S, Zaneveld JR, Knight R RNA (New York, N.Y.) 22645380 RNA 2012 Jul
Estimation of distribution overlap of urn models. Hampton J, Lladser ME PloS one 23139734 PLoS One 2012
Defining the human microbiome. Ursell LK, Metcalf JL, Parfrey LW, Knight R Nutrition reviews 22861806 Nutr Rev 2012 Aug
Are microbiome studies ready for hypothesis-driven research? Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song SJ, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R Current opinion in microbiology 30059804 Curr Opin Microbiol 2018 Aug
The gut microbiota in human energy homeostasis and obesity. Rosenbaum M, Knight R, Leibel RL Trends in endocrinology and metabolism: TEM 26257300 Trends Endocrinol Metab 2015 Sep
Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis. Blainey PC, Milla CE, Cornfield DN, Quake SR Science translational medicine 23019655 Sci Transl Med 2012 Sep 26
Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). Youssef NH, Blainey PC, Quake SR, Elshahed MS Applied and environmental microbiology 21908640 Appl Environ Microbiol 2011 Nov
Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR PloS one 21364937 PLoS One 2011 Feb 22
Optofluidic cell selection from complex microbial communities for single-genome analysis. Landry ZC, Giovanonni SJ, Quake SR, Blainey PC Methods in enzymology 24060116 Methods Enzymol 2013
Digital MDA for enumeration of total nucleic acid contamination. Blainey PC, Quake SR Nucleic acids research 21071419 Nucleic Acids Res 2011 Mar
Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Pamp SJ, Harrington ED, Quake SR, Relman DA, Blainey PC Genome research 22434425 Genome Res 2012 Jun
The future is now: single-cell genomics of bacteria and archaea. Blainey PC FEMS microbiology reviews 23298390 FEMS Microbiol Rev 2013 May
SmashCell: a software framework for the analysis of single-cell amplified genome sequences. Harrington ED, Arumugam M, Raes J, Bork P, Relman DA Bioinformatics (Oxford, England) 20966005 Bioinformatics 2010 Dec 1
Host genetic and environmental effects on mouse intestinal microbiota. Campbell JH, Foster CM, Vishnivetskaya T, Campbell AG, Yang ZK, Wymore A, Palumbo AV, Chesler EJ, Podar M The ISME journal 22695862 ISME J 2012 Nov
Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. Campbell AG, Schwientek P, Vishnivetskaya T, Woyke T, Levy S, Beall CJ, Griffen A, Leys E, Podar M Environmental microbiology 24738594 Environ Microbiol 2014 Sep
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Shakya M, Quince C, Campbell JH, Yang ZK, Schadt CW, Podar M Environmental microbiology 23387867 Environ Microbiol 2013 Jun
Comparative Genomics Guides Elucidation of Vitamin B(12) Biosynthesis in Novel Human-Associated Akkermansia Strains. Kirmiz N, Galindo K, Cross KL, Luna E, Rhoades N, Podar M, Flores GE Applied and environmental microbiology 31757822 Appl Environ Microbiol 2020 Jan 21
Cultivation of Peptidiphaga gingivicola from subgingival plaque: The first representative of a novel genus of Actinomycetaceae. Beall CJ, Mokrzan EM, Griffen AL, Leys EJ Molecular oral microbiology 29105370 Mol Oral Microbiol 2018 Feb
Single-Cell Genomics and the Oral Microbiome. Balachandran M, Cross KL, Podar M Journal of dental research 32091935 J Dent Res 2020 Jun
Global prevalence and distribution of genes and microorganisms involved in mercury methylation. Podar M, Gilmour CC, Brandt CC, Soren A, Brown SD, Crable BR, Palumbo AV, Somenahally AC, Elias DA Science advances 26601305 Sci Adv 2015 Oct
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Söll D, Podar M Proceedings of the National Academy of Sciences of the United States of America 23509275 Proc Natl Acad Sci U S A 2013 Apr 2
Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286) and comparison to the closely related pathogen Tannerella forsythia. Beall CJ, Campbell AG, Dayeh DM, Griffen AL, Podar M, Leys EJ PloS one 24551246 PLoS One 2014
Toward unrestricted use of public genomic data. Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I Science (New York, N.Y.) 30679363 Science 2019 Jan 25
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C, Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T Nature biotechnology 28787424 Nat Biotechnol 2017 Aug 8
Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity. Campbell AG, Campbell JH, Schwientek P, Woyke T, Sczyrba A, Allman S, Beall CJ, Griffen A, Leys E, Podar M PloS one 23555659 PLoS One 2013
De minimis risk: a proposal for a new category of research risk. Rhodes R, Azzouni J, Baumrin SB, Benkov K, Blaser MJ, Brenner B, Dauben JW, Earle WJ, Frank L, Gligorov N, Goldfarb J, Hirschhorn K, Hirschhorn R, Holzman I, Indyk D, Jabs EW, Lackey DP, Moros DA, Philpott S, Rhodes ME, Richardson LD, Sacks HS, Schwab A, Sperling R, Trusko B, Zweig A The American journal of bioethics : AJOB 22047112 Am J Bioeth 2011 Nov
Saying privacy, meaning confidentiality. Schwab AP, Frank L, Gligorov N The American journal of bioethics : AJOB 22047127 Am J Bioeth 2011 Nov
Ethical issues in microbiome research and medicine. Rhodes R BMC medicine 27729053 BMC Med 2016 Oct 12
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 VR, McGuire AL American journal of medical genetics. Part A 20583190 Am J Med Genet A 2010 Jul
Perspectives on human microbiome research ethics. McGuire AL, Achenbaum LS, Whitney SN, Slashinski MJ, Versalovic J, Keitel WA, McCurdy SA Journal of empirical research on human research ethics : JERHRE 22850139 J Empir Res Hum Res Ethics 2012 Jul
"Snake-oil," "quack medicine," and "industrially cultured organisms:" biovalue and the commercialization of human microbiome research. Slashinski MJ, McCurdy SA, Achenbaum LS, Whitney SN, McGuire AL BMC medical ethics 23110633 BMC Med Ethics 2012 Oct 30
Personal genome research : what should the participant be told? McGuire AL, Lupski JR Trends in genetics : TIG 20381895 Trends Genet 2010 May
Informed consent in genomics and genetic research. McGuire AL, Beskow LM Annual review of genomics and human genetics 20477535 Annu Rev Genomics Hum Genet 2010
Investigators' perspectives on translating human microbiome research into clinical practice. Slashinski MJ, Whitney SN, Achenbaum LS, Keitel WA, McCurdy SA, McGuire AL Public health genomics 23615375 Public Health Genomics 2013
Beyond natural antibodies: the power of in vitro display technologies. Bradbury AR, Sidhu S, Dübel S, McCafferty J Nature biotechnology 21390033 Nat Biotechnol 2011 Mar
Fluorescent labeling of antibody fragments using split GFP. Ferrara F, Listwan P, Waldo GS, Bradbury AR PloS one 21998685 PLoS One 2011
From deep sequencing to actual clones. D'Angelo S, Kumar S, Naranjo L, Ferrara F, Kiss C, Bradbury AR Protein engineering, design & selection : PEDS 25183780 Protein Eng Des Sel 2014 Oct
Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes. Close DW, Ferrara F, Dichosa AE, Kumar S, Daughton AR, Daligault HE, Reitenga KG, Velappan N, Sanchez TC, Iyer S, Kiss C, Han CS, Bradbury AR BMC microbiology 24279426 BMC Microbiol 2013 Nov 27
Single cell genome sequencing. Yilmaz S, Singh AK Current opinion in biotechnology 22154471 Curr Opin Biotechnol 2012 Jun
Antibacterial property expressed by a novel calcium phosphate glass. Liu L, Pushalkar S, Saxena D, LeGeros RZ, Zhang Y Journal of biomedical materials research. Part B, Applied biomaterials 24039127 J Biomed Mater Res B Appl Biomater 2014 Apr
Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems. Rhee M, Light YK, Yilmaz S, Adams PD, Saxena D, Meagher RJ, Singh AK Lab on a chip 25270338 Lab Chip 2014 Dec 7
Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples. Rhee M, Light YK, Meagher RJ, Singh AK PloS one 27144304 PLoS One 2016
Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation. Harmon B, Chylek LA, Liu Y, Mitra ED, Mahajan A, Saada EA, Schudel BR, Holowka DA, Baird BA, Wilson BS, Hlavacek WS, Singh AK Scientific reports 29138425 Sci Rep 2017 Nov 14
Microfluidic platforms for single-cell protein analysis. Liu Y, Singh AK Journal of laboratory automation 23821679 J Lab Autom 2013 Dec
Antibiotic effects on bacterial profile in osteonecrosis of the jaw. Ji X, Pushalkar S, Li Y, Glickman R, Fleisher K, Saxena D Oral diseases 21883710 Oral Dis 2012 Jan
Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma. Pushalkar S, Ji X, Li Y, Estilo C, Yegnanarayana R, Singh B, Li X, Saxena D BMC microbiology 22817758 BMC Microbiol 2012 Jul 20
Microfluidic Flow Cytometry for Single-Cell Protein Analysis. Wu M, Singh AK Methods in molecular biology (Clifton, N.J.) 26542716 Methods Mol Biol 2015
Mobile genes in the human microbiome are structured from global to individual scales. Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, Naisilisili W, Tamminen M, Smillie CS, Wortman JR, Birren BW, Xavier RJ, Blainey PC, Singh AK, Gevers D, Alm EJ Nature 27409808 Nature 2016 Jul 21
Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH). Liu P, Meagher RJ, Light YK, Yilmaz S, Chakraborty R, Arkin AP, Hazen TC, Singh AK Lab on a chip 21755095 Lab Chip 2011 Aug 21
Single-cell protein analysis. Wu M, Singh AK Current opinion in biotechnology 22189001 Curr Opin Biotechnol 2012 Feb
Microfluidic molecular assay platform for the detection of miRNAs, mRNAs, proteins, and posttranslational modifications at single-cell resolution. Wu M, Singh AK Journal of laboratory automation 25027027 J Lab Autom 2014 Dec
Oral microbiota and host innate immune response in bisphosphonate-related osteonecrosis of the jaw. Pushalkar S, Li X, Kurago Z, Ramanathapuram LV, Matsumura S, Fleisher KE, Glickman R, Yan W, Li Y, Saxena D International journal of oral science 25105817 Int J Oral Sci 2014 Dec
Microbial diversity in saliva of oral squamous cell carcinoma. Pushalkar S, Mane SP, Ji X, Li Y, Evans C, Crasta OR, Morse D, Meagher R, Singh A, Saxena D FEMS immunology and medical microbiology 21205002 FEMS Immunol Med Microbiol 2011 Apr
Single cell microRNA analysis using microfluidic flow cytometry. Wu M, Piccini M, Koh CY, Lam KS, Singh AK PloS one 23383050 PLoS One 2013
Versatile on-demand droplet generation for controlled encapsulation. Rhee M, Liu P, Meagher RJ, Light YK, Singh AK Biomicrofluidics 25379072 Biomicrofluidics 2014 May
MiRNA detection at single-cell resolution using microfluidic LNA flow-FISH. Wu M, Piccini ME, Singh AK Methods in molecular biology (Clifton, N.J.) 25218391 Methods Mol Biol 2014
Antibacterial and bioactive coatings on titanium implant surfaces. Kulkarni Aranya A, Pushalkar S, Zhao M, LeGeros RZ, Zhang Y, Saxena D Journal of biomedical materials research. Part A 28380669 J Biomed Mater Res A 2017 Aug

This page last reviewed on March 13, 2025

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