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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 PubMedLink
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 https://www.ncbi.nlm.nih.gov/pubmed/20236171
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 https://www.ncbi.nlm.nih.gov/pubmed/21042588
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 https://www.ncbi.nlm.nih.gov/pubmed/20931185
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 https://www.ncbi.nlm.nih.gov/pubmed/23799126
DRISEE overestimates errors in metagenomic sequencing data. Eren AM, Morrison HG, Huse SM, Sogin ML Briefings in bioinformatics 23698723 Brief Bioinform 2014 Sep https://www.ncbi.nlm.nih.gov/pubmed/23698723
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 https://www.ncbi.nlm.nih.gov/pubmed/24101916
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 https://www.ncbi.nlm.nih.gov/pubmed/23702805
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 https://www.ncbi.nlm.nih.gov/pubmed/24060134
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 https://www.ncbi.nlm.nih.gov/pubmed/24045641
Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. Vital M, Howe AC, Tiedje JM mBio 24757212 mBio 2014 Apr 22 https://www.ncbi.nlm.nih.gov/pubmed/24757212
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 https://www.ncbi.nlm.nih.gov/pubmed/25343512
The gut microbiome in health and in disease. Shreiner AB, Kao JY, Young VB Current opinion in gastroenterology 25394236 Curr Opin Gastroenterol 2015 Jan https://www.ncbi.nlm.nih.gov/pubmed/25394236
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 https://www.ncbi.nlm.nih.gov/pubmed/25071935
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 https://www.ncbi.nlm.nih.gov/pubmed/22722865
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 https://www.ncbi.nlm.nih.gov/pubmed/30266729
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 https://www.ncbi.nlm.nih.gov/pubmed/21317176
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 https://www.ncbi.nlm.nih.gov/pubmed/23448796
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 https://www.ncbi.nlm.nih.gov/pubmed/23639897
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 https://www.ncbi.nlm.nih.gov/pubmed/22911969
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 https://www.ncbi.nlm.nih.gov/pubmed/22389708
The intestinal microbiota in health and disease. Young VB Current opinion in gastroenterology 22080827 Curr Opin Gastroenterol 2012 Jan https://www.ncbi.nlm.nih.gov/pubmed/22080827
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 https://www.ncbi.nlm.nih.gov/pubmed/23766559
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 https://www.ncbi.nlm.nih.gov/pubmed/24288368
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 https://www.ncbi.nlm.nih.gov/pubmed/26090504
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 https://www.ncbi.nlm.nih.gov/pubmed/24965363
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 https://www.ncbi.nlm.nih.gov/pubmed/24743558
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 https://www.ncbi.nlm.nih.gov/pubmed/25394613
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 https://www.ncbi.nlm.nih.gov/pubmed/25325381
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 https://www.ncbi.nlm.nih.gov/pubmed/24358444
Structure, function and diversity of the healthy human microbiome. Human Microbiome Project Consortium Nature 22699609 Nature 2012 Jun 13 https://www.ncbi.nlm.nih.gov/pubmed/22699609
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 https://www.ncbi.nlm.nih.gov/pubmed/22839106
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 https://www.ncbi.nlm.nih.gov/pubmed/21283757
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 https://www.ncbi.nlm.nih.gov/pubmed/19796657
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 https://www.ncbi.nlm.nih.gov/pubmed/22251411
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 https://www.ncbi.nlm.nih.gov/pubmed/24451123
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 https://www.ncbi.nlm.nih.gov/pubmed/29795209
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 https://www.ncbi.nlm.nih.gov/pubmed/25738379
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 https://www.ncbi.nlm.nih.gov/pubmed/27561676
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 https://www.ncbi.nlm.nih.gov/pubmed/21772835
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 https://www.ncbi.nlm.nih.gov/pubmed/21525143
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 https://www.ncbi.nlm.nih.gov/pubmed/20864653
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 https://www.ncbi.nlm.nih.gov/pubmed/22753064
Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance. Britton RA, Young VB Trends in microbiology 22595318 Trends Microbiol 2012 Jul https://www.ncbi.nlm.nih.gov/pubmed/22595318
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 https://www.ncbi.nlm.nih.gov/pubmed/22719824
A framework for human microbiome research. Human Microbiome Project Consortium Nature 22699610 Nature 2012 Jun 13 https://www.ncbi.nlm.nih.gov/pubmed/22699610
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 https://www.ncbi.nlm.nih.gov/pubmed/28221248
Shallow breathing: bacterial life at low O(2). Morris RL, Schmidt TM Nature reviews. Microbiology 23411864 Nat Rev Microbiol 2013 Mar https://www.ncbi.nlm.nih.gov/pubmed/23411864
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 https://www.ncbi.nlm.nih.gov/pubmed/25569221
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 https://www.ncbi.nlm.nih.gov/pubmed/25343515
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 https://www.ncbi.nlm.nih.gov/pubmed/25818499
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 https://www.ncbi.nlm.nih.gov/pubmed/25891358
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 https://www.ncbi.nlm.nih.gov/pubmed/27079612
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 https://www.ncbi.nlm.nih.gov/pubmed/23475322
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 https://www.ncbi.nlm.nih.gov/pubmed/22318161
History and impact of RDP: a legacy from Carl Woese to microbiology. Cole JR, Tiedje JM RNA biology 24607969 RNA Biol 2014 https://www.ncbi.nlm.nih.gov/pubmed/24607969
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 https://www.ncbi.nlm.nih.gov/pubmed/30744677
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 https://www.ncbi.nlm.nih.gov/pubmed/23469896
'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 https://www.ncbi.nlm.nih.gov/pubmed/22626866
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 https://www.ncbi.nlm.nih.gov/pubmed/22132090
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 https://www.ncbi.nlm.nih.gov/pubmed/21984758
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 https://www.ncbi.nlm.nih.gov/pubmed/23209564
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 https://www.ncbi.nlm.nih.gov/pubmed/21741921
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 https://www.ncbi.nlm.nih.gov/pubmed/21228220
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 https://www.ncbi.nlm.nih.gov/pubmed/26059898
Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Preidis GA, Versalovic J Gastroenterology 19462507 Gastroenterology 2009 May https://www.ncbi.nlm.nih.gov/pubmed/19462507
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 https://www.ncbi.nlm.nih.gov/pubmed/28275689
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 https://www.ncbi.nlm.nih.gov/pubmed/27458085
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 https://www.ncbi.nlm.nih.gov/pubmed/24486050
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 https://www.ncbi.nlm.nih.gov/pubmed/22267340
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 https://www.ncbi.nlm.nih.gov/pubmed/31005411
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 https://www.ncbi.nlm.nih.gov/pubmed/18971311
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 https://www.ncbi.nlm.nih.gov/pubmed/20826285
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 https://www.ncbi.nlm.nih.gov/pubmed/21075108
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 https://www.ncbi.nlm.nih.gov/pubmed/22343914
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 https://www.ncbi.nlm.nih.gov/pubmed/23401286
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 https://www.ncbi.nlm.nih.gov/pubmed/26104013
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 https://www.ncbi.nlm.nih.gov/pubmed/25853207
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 https://www.ncbi.nlm.nih.gov/pubmed/24989059
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 https://www.ncbi.nlm.nih.gov/pubmed/26670383
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 https://www.ncbi.nlm.nih.gov/pubmed/24124697
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 https://www.ncbi.nlm.nih.gov/pubmed/33314183
Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Hemarajata P, Versalovic J Therapeutic advances in gastroenterology 23320049 Ther Adv Gastroenterol 2013 Jan https://www.ncbi.nlm.nih.gov/pubmed/23320049
Dietary issues in recurrent abdominal pain. Shulman RJ Journal of pediatric gastroenterology and nutrition 23103654 J Pediatr Gastroenterol Nutr 2012 Nov https://www.ncbi.nlm.nih.gov/pubmed/23103654
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 https://www.ncbi.nlm.nih.gov/pubmed/23320832
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 https://www.ncbi.nlm.nih.gov/pubmed/20818947
Probiotics-host communication: Modulation of signaling pathways in the intestine. Thomas CM, Versalovic J Gut microbes 20672012 Gut Microbes 2010 May-Jun https://www.ncbi.nlm.nih.gov/pubmed/20672012
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 https://www.ncbi.nlm.nih.gov/pubmed/20377338
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 https://www.ncbi.nlm.nih.gov/pubmed/24123819
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 https://www.ncbi.nlm.nih.gov/pubmed/24488273
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 https://www.ncbi.nlm.nih.gov/pubmed/24637601
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 https://www.ncbi.nlm.nih.gov/pubmed/27025251
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 https://www.ncbi.nlm.nih.gov/pubmed/28745328
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 https://www.ncbi.nlm.nih.gov/pubmed/29762384
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 https://www.ncbi.nlm.nih.gov/pubmed/21489557
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 https://www.ncbi.nlm.nih.gov/pubmed/25197459
Luminal Conversion and Immunoregulation by Probiotics. Ganesh BP, Versalovic J Frontiers in pharmacology 26617521 Front Pharmacol 2015 https://www.ncbi.nlm.nih.gov/pubmed/26617521
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 https://www.ncbi.nlm.nih.gov/pubmed/26306392
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 https://www.ncbi.nlm.nih.gov/pubmed/21885731
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 https://www.ncbi.nlm.nih.gov/pubmed/23074263
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 https://www.ncbi.nlm.nih.gov/pubmed/22900013
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 https://www.ncbi.nlm.nih.gov/pubmed/23184592
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 https://www.ncbi.nlm.nih.gov/pubmed/23563705
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 https://www.ncbi.nlm.nih.gov/pubmed/23977147
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 https://www.ncbi.nlm.nih.gov/pubmed/24312162
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 https://www.ncbi.nlm.nih.gov/pubmed/22447074
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 https://www.ncbi.nlm.nih.gov/pubmed/22355105
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 https://www.ncbi.nlm.nih.gov/pubmed/20375170
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 https://www.ncbi.nlm.nih.gov/pubmed/23071679
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 https://www.ncbi.nlm.nih.gov/pubmed/22759449
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 https://www.ncbi.nlm.nih.gov/pubmed/22161565
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 https://www.ncbi.nlm.nih.gov/pubmed/23799070
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 https://www.ncbi.nlm.nih.gov/pubmed/29255284
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 https://www.ncbi.nlm.nih.gov/pubmed/26083617
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 https://www.ncbi.nlm.nih.gov/pubmed/25970545
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 https://www.ncbi.nlm.nih.gov/pubmed/25819674
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 https://www.ncbi.nlm.nih.gov/pubmed/22573192
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 https://www.ncbi.nlm.nih.gov/pubmed/22711789
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 https://www.ncbi.nlm.nih.gov/pubmed/23836644
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 https://www.ncbi.nlm.nih.gov/pubmed/20383131
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 https://www.ncbi.nlm.nih.gov/pubmed/24107497
Diet and the intestinal microbiome: associations, functions, and implications for health and disease. Albenberg LG, Wu GD Gastroenterology 24503132 Gastroenterology 2014 May https://www.ncbi.nlm.nih.gov/pubmed/24503132
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 https://www.ncbi.nlm.nih.gov/pubmed/26468751
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 https://www.ncbi.nlm.nih.gov/pubmed/26034601
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 https://www.ncbi.nlm.nih.gov/pubmed/26081634
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 https://www.ncbi.nlm.nih.gov/pubmed/25431456
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 https://www.ncbi.nlm.nih.gov/pubmed/21552244
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 https://www.ncbi.nlm.nih.gov/pubmed/19914921
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 https://www.ncbi.nlm.nih.gov/pubmed/25597840
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 https://www.ncbi.nlm.nih.gov/pubmed/22326959
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 https://www.ncbi.nlm.nih.gov/pubmed/23643636
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 https://www.ncbi.nlm.nih.gov/pubmed/29141885
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 https://www.ncbi.nlm.nih.gov/pubmed/25046162
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 https://www.ncbi.nlm.nih.gov/pubmed/26288001
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 https://www.ncbi.nlm.nih.gov/pubmed/26098218
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 https://www.ncbi.nlm.nih.gov/pubmed/21524302
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 https://www.ncbi.nlm.nih.gov/pubmed/21829515
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 https://www.ncbi.nlm.nih.gov/pubmed/20806429
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 https://www.ncbi.nlm.nih.gov/pubmed/25874569
Microbiome, innate immunity, and esophageal adenocarcinoma. Baghdadi J, Chaudhary N, Pei Z, Yang L Clinics in laboratory medicine 25439272 Clin Lab Med 2014 Dec https://www.ncbi.nlm.nih.gov/pubmed/25439272
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 https://www.ncbi.nlm.nih.gov/pubmed/26796629
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 https://www.ncbi.nlm.nih.gov/pubmed/24223144
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 https://www.ncbi.nlm.nih.gov/pubmed/20418441
SPA: a short peptide assembler for metagenomic data. Yang Y, Yooseph S Nucleic acids research 23435317 Nucleic Acids Res 2013 Apr https://www.ncbi.nlm.nih.gov/pubmed/23435317
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 https://www.ncbi.nlm.nih.gov/pubmed/22765222
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 https://www.ncbi.nlm.nih.gov/pubmed/22134646
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 https://www.ncbi.nlm.nih.gov/pubmed/28616595
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 https://www.ncbi.nlm.nih.gov/pubmed/26620712
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 https://www.ncbi.nlm.nih.gov/pubmed/23923086
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 https://www.ncbi.nlm.nih.gov/pubmed/25126590
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 https://www.ncbi.nlm.nih.gov/pubmed/25606580
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 https://www.ncbi.nlm.nih.gov/pubmed/35751398
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 https://www.ncbi.nlm.nih.gov/pubmed/22344232
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 https://www.ncbi.nlm.nih.gov/pubmed/21716311
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 https://www.ncbi.nlm.nih.gov/pubmed/22193889
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 https://www.ncbi.nlm.nih.gov/pubmed/24855009
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 https://www.ncbi.nlm.nih.gov/pubmed/26731752
Microbiome and potential targets for chemoprevention of esophageal adenocarcinoma. Neto AG, Whitaker A, Pei Z Seminars in oncology 26970127 Semin Oncol 2016 Feb https://www.ncbi.nlm.nih.gov/pubmed/26970127
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 https://www.ncbi.nlm.nih.gov/pubmed/26035329
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 https://www.ncbi.nlm.nih.gov/pubmed/19394334
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 https://www.ncbi.nlm.nih.gov/pubmed/19415112
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 https://www.ncbi.nlm.nih.gov/pubmed/27069958
Beyond infectious disease: welcome to the era of population microbiology. Pincus MR, Pei Z Clinics in laboratory medicine 25439278 Clin Lab Med 2014 Dec https://www.ncbi.nlm.nih.gov/pubmed/25439278
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 https://www.ncbi.nlm.nih.gov/pubmed/25439270
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 https://www.ncbi.nlm.nih.gov/pubmed/24522917
Microbiome, a new dimension in cancer research. Neto AG, Bradshaw AD, Pei Z Annals of translational medicine 26539446 Ann Transl Med 2015 Sep https://www.ncbi.nlm.nih.gov/pubmed/26539446
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 https://www.ncbi.nlm.nih.gov/pubmed/30942867
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 https://www.ncbi.nlm.nih.gov/pubmed/23316946
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 https://www.ncbi.nlm.nih.gov/pubmed/22606251
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 https://www.ncbi.nlm.nih.gov/pubmed/21603636
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 https://www.ncbi.nlm.nih.gov/pubmed/29506642
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 https://www.ncbi.nlm.nih.gov/pubmed/21683193
Lungs, microbes and the developing neonate. Warner BB, Hamvas A Neonatology 26044101 Neonatology 2015 https://www.ncbi.nlm.nih.gov/pubmed/26044101
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 https://www.ncbi.nlm.nih.gov/pubmed/28669607
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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 https://www.ncbi.nlm.nih.gov/pubmed/24618403
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 https://www.ncbi.nlm.nih.gov/pubmed/24629344
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 https://www.ncbi.nlm.nih.gov/pubmed/24843156
Role of Autophagy in the Maintenance of Intestinal Homeostasis. Baxt LA, Xavier RJ Gastroenterology 26170139 Gastroenterology 2015 Sep https://www.ncbi.nlm.nih.gov/pubmed/26170139
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 https://www.ncbi.nlm.nih.gov/pubmed/29335555
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 https://www.ncbi.nlm.nih.gov/pubmed/29183332
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 https://www.ncbi.nlm.nih.gov/pubmed/31959971
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 https://www.ncbi.nlm.nih.gov/pubmed/31972239
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 https://www.ncbi.nlm.nih.gov/pubmed/33944776
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 https://www.ncbi.nlm.nih.gov/pubmed/25559196
High-throughput sequencing technologies. Reuter JA, Spacek DV, Snyder MP Molecular cell 26000844 Mol Cell 2015 May 21 https://www.ncbi.nlm.nih.gov/pubmed/26000844
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 https://www.ncbi.nlm.nih.gov/pubmed/27575496
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 https://www.ncbi.nlm.nih.gov/pubmed/27178263
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 https://www.ncbi.nlm.nih.gov/pubmed/27230380
Personal Omics for Precision Health. Kellogg RA, Dunn J, Snyder MP Circulation research 29700064 Circ Res 2018 Apr 27 https://www.ncbi.nlm.nih.gov/pubmed/29700064
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 https://www.ncbi.nlm.nih.gov/pubmed/30835913
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 https://www.ncbi.nlm.nih.gov/pubmed/28572688
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 https://www.ncbi.nlm.nih.gov/pubmed/39143318
Humans Are Selectively Exposed to Pneumocystis jirovecii. Cissé OH, Ma L, Jiang C, Snyder M, Kovacs JA mBio 32156824 mBio 2020 Mar 10 https://www.ncbi.nlm.nih.gov/pubmed/32156824
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 https://www.ncbi.nlm.nih.gov/pubmed/35304603
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 https://www.ncbi.nlm.nih.gov/pubmed/38479397
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 https://www.ncbi.nlm.nih.gov/pubmed/30241608
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 https://www.ncbi.nlm.nih.gov/pubmed/27705799
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 https://www.ncbi.nlm.nih.gov/pubmed/27897013
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 https://www.ncbi.nlm.nih.gov/pubmed/28081144
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 https://www.ncbi.nlm.nih.gov/pubmed/31068711
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 https://www.ncbi.nlm.nih.gov/pubmed/25787789
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 https://www.ncbi.nlm.nih.gov/pubmed/24961374
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 https://www.ncbi.nlm.nih.gov/pubmed/26960666
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 https://www.ncbi.nlm.nih.gov/pubmed/32470399
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 https://www.ncbi.nlm.nih.gov/pubmed/24561555
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 https://www.ncbi.nlm.nih.gov/pubmed/26655498
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 https://www.ncbi.nlm.nih.gov/pubmed/31932806
Personalized sequencing and the future of medicine: discovery, diagnosis and defeat of disease. Esplin ED, Oei L, Snyder MP Pharmacogenomics 25493570 Pharmacogenomics 2014 Nov https://www.ncbi.nlm.nih.gov/pubmed/25493570
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 https://www.ncbi.nlm.nih.gov/pubmed/24108091
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 https://www.ncbi.nlm.nih.gov/pubmed/26490195
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 https://www.ncbi.nlm.nih.gov/pubmed/33600772
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 https://www.ncbi.nlm.nih.gov/pubmed/34031607
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 https://www.ncbi.nlm.nih.gov/pubmed/26749064
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 https://www.ncbi.nlm.nih.gov/pubmed/26691984
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 https://www.ncbi.nlm.nih.gov/pubmed/29361466
Impact of allele-specific peptides in proteome quantification. Wu L, Snyder M Proteomics. Clinical applications 25676416 Proteomics Clin Appl 2015 Apr https://www.ncbi.nlm.nih.gov/pubmed/25676416
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 https://www.ncbi.nlm.nih.gov/pubmed/26278503
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 https://www.ncbi.nlm.nih.gov/pubmed/28658209
Gene-Environment Interaction in the Era of Precision Medicine. Li J, Li X, Zhang S, Snyder M Cell 30901546 Cell 2019 Mar 21 https://www.ncbi.nlm.nih.gov/pubmed/30901546
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 https://www.ncbi.nlm.nih.gov/pubmed/31832566
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 https://www.ncbi.nlm.nih.gov/pubmed/34301627
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 https://www.ncbi.nlm.nih.gov/pubmed/31142858
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 https://www.ncbi.nlm.nih.gov/pubmed/28478146
Personal genomes, quantitative dynamic omics and personalized medicine. Mias GI, Snyder M Quantitative biology (Beijing, China) 25798291 Quant Biol 2013 Mar https://www.ncbi.nlm.nih.gov/pubmed/25798291
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 https://www.ncbi.nlm.nih.gov/pubmed/27503255
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 https://www.ncbi.nlm.nih.gov/pubmed/27693347
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 https://www.ncbi.nlm.nih.gov/pubmed/25030927
Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California. Sailani MR, Metwally AA, Zhou W, Rose SMS, Ahadi S, Contrepois K, Mishra T, Zhang MJ, Kidziński Ł, Chu TJ, Snyder MP Nature communications 33004787 Nat Commun 2020 Oct 1 https://www.ncbi.nlm.nih.gov/pubmed/33004787
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 https://www.ncbi.nlm.nih.gov/pubmed/32742640
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 https://www.ncbi.nlm.nih.gov/pubmed/23682142
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 https://www.ncbi.nlm.nih.gov/pubmed/23493677
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 https://www.ncbi.nlm.nih.gov/pubmed/25407910
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 https://www.ncbi.nlm.nih.gov/pubmed/21304707
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 https://www.ncbi.nlm.nih.gov/pubmed/27739035
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 https://www.ncbi.nlm.nih.gov/pubmed/27258950
Analyses of the microbial diversity across the human microbiome. Li K, Bihan M, Yooseph S, Methé BA PloS one 22719823 PLoS One 2012 https://www.ncbi.nlm.nih.gov/pubmed/22719823
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 https://www.ncbi.nlm.nih.gov/pubmed/23469340
Analyses of the stability and core taxonomic memberships of the human microbiome. Li K, Bihan M, Methé BA PloS one 23671663 PLoS One 2013 https://www.ncbi.nlm.nih.gov/pubmed/23671663
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 https://www.ncbi.nlm.nih.gov/pubmed/23742765
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 https://www.ncbi.nlm.nih.gov/pubmed/20798169
An algorithm for automated closure during assembly. Koren S, Miller JR, Walenz BP, Sutton G BMC bioinformatics 20831800 BMC Bioinformatics 2010 Sep 10 https://www.ncbi.nlm.nih.gov/pubmed/20831800
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 https://www.ncbi.nlm.nih.gov/pubmed/21530737
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 https://www.ncbi.nlm.nih.gov/pubmed/21765408
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 https://www.ncbi.nlm.nih.gov/pubmed/21796217
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Reeder J, Knight R Nature methods 20805793 Nat Methods 2010 Sep https://www.ncbi.nlm.nih.gov/pubmed/20805793
Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players. Ursell LK, Knight R Cell metabolism 23473028 Cell Metab 2013 Mar 5 https://www.ncbi.nlm.nih.gov/pubmed/23473028
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 https://www.ncbi.nlm.nih.gov/pubmed/20436475
Advancing analytical algorithms and pipelines for billions of microbial sequences. Gonzalez A, Knight R Current opinion in biotechnology 22172529 Curr Opin Biotechnol 2012 Feb https://www.ncbi.nlm.nih.gov/pubmed/22172529
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 https://www.ncbi.nlm.nih.gov/pubmed/22170430
Complex carbohydrate utilization by the healthy human microbiome. Cantarel BL, Lombard V, Henrissat B PloS one 22719820 PLoS One 2012 https://www.ncbi.nlm.nih.gov/pubmed/22719820
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 https://www.ncbi.nlm.nih.gov/pubmed/22541361
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 https://www.ncbi.nlm.nih.gov/pubmed/22402401
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 https://www.ncbi.nlm.nih.gov/pubmed/21593810
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 https://www.ncbi.nlm.nih.gov/pubmed/22018228
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 https://www.ncbi.nlm.nih.gov/pubmed/22237546
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 https://www.ncbi.nlm.nih.gov/pubmed/22980325
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 https://www.ncbi.nlm.nih.gov/pubmed/23409217
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 https://www.ncbi.nlm.nih.gov/pubmed/22792232
Finding the missing links among metabolites, microbes, and the host. Dorrestein PC, Mazmanian SK, Knight R Immunity 24950202 Immunity 2014 Jun 19 https://www.ncbi.nlm.nih.gov/pubmed/24950202
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 https://www.ncbi.nlm.nih.gov/pubmed/26657285
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 https://www.ncbi.nlm.nih.gov/pubmed/24451203
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 https://www.ncbi.nlm.nih.gov/pubmed/24136997
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 https://www.ncbi.nlm.nih.gov/pubmed/36937228
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 https://www.ncbi.nlm.nih.gov/pubmed/22895161
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 https://www.ncbi.nlm.nih.gov/pubmed/23326225
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 https://www.ncbi.nlm.nih.gov/pubmed/23599893
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 https://www.ncbi.nlm.nih.gov/pubmed/20937873
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 https://www.ncbi.nlm.nih.gov/pubmed/19710709
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 https://www.ncbi.nlm.nih.gov/pubmed/22194640
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 https://www.ncbi.nlm.nih.gov/pubmed/22086953
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 https://www.ncbi.nlm.nih.gov/pubmed/25170151
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 https://www.ncbi.nlm.nih.gov/pubmed/28253908
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 https://www.ncbi.nlm.nih.gov/pubmed/26905627
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 https://www.ncbi.nlm.nih.gov/pubmed/21407244
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 https://www.ncbi.nlm.nih.gov/pubmed/20818378
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 https://www.ncbi.nlm.nih.gov/pubmed/21903626
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 https://www.ncbi.nlm.nih.gov/pubmed/22135293
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 https://www.ncbi.nlm.nih.gov/pubmed/22154467
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 https://www.ncbi.nlm.nih.gov/pubmed/22267877
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 https://www.ncbi.nlm.nih.gov/pubmed/22665442
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 https://www.ncbi.nlm.nih.gov/pubmed/23975157
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 https://www.ncbi.nlm.nih.gov/pubmed/26024793
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 https://www.ncbi.nlm.nih.gov/pubmed/34923581
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding. Zuo Z, Stormo GD Genetics 25209146 Genetics 2014 Nov https://www.ncbi.nlm.nih.gov/pubmed/25209146
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 https://www.ncbi.nlm.nih.gov/pubmed/25362070
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 https://www.ncbi.nlm.nih.gov/pubmed/26752632
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 https://www.ncbi.nlm.nih.gov/pubmed/22988033
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 https://www.ncbi.nlm.nih.gov/pubmed/25819063
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 https://www.ncbi.nlm.nih.gov/pubmed/22343176
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 https://www.ncbi.nlm.nih.gov/pubmed/23452586
Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis. Feazel LM, Robertson CE, Ramakrishnan VR, Frank DN The Laryngoscope 22253013 Laryngoscope 2012 Feb https://www.ncbi.nlm.nih.gov/pubmed/22253013
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 https://www.ncbi.nlm.nih.gov/pubmed/22558305
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 https://www.ncbi.nlm.nih.gov/pubmed/26068542
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 https://www.ncbi.nlm.nih.gov/pubmed/24386477
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 https://www.ncbi.nlm.nih.gov/pubmed/22732305
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 https://www.ncbi.nlm.nih.gov/pubmed/22378797
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 https://www.ncbi.nlm.nih.gov/pubmed/24021386
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 https://www.ncbi.nlm.nih.gov/pubmed/24260458
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 https://www.ncbi.nlm.nih.gov/pubmed/25278448
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 https://www.ncbi.nlm.nih.gov/pubmed/23328391
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 https://www.ncbi.nlm.nih.gov/pubmed/23542619
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 https://www.ncbi.nlm.nih.gov/pubmed/26083474
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 https://www.ncbi.nlm.nih.gov/pubmed/25689864
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 https://www.ncbi.nlm.nih.gov/pubmed/24148301
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 https://www.ncbi.nlm.nih.gov/pubmed/21364881
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 https://www.ncbi.nlm.nih.gov/pubmed/33089329
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 https://www.ncbi.nlm.nih.gov/pubmed/22065823
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 https://www.ncbi.nlm.nih.gov/pubmed/25587411
One-Way Particle Transport Using Oscillatory Flow in Asymmetric Traps. Lee J, Burns MA Small (Weinheim an der Bergstrasse, Germany) 29377529 Small 2018 Mar https://www.ncbi.nlm.nih.gov/pubmed/29377529
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 https://www.ncbi.nlm.nih.gov/pubmed/22058976
Monodisperse alginate microgel formation in a three-dimensional microfluidic droplet generator. Lian M, Collier CP, Doktycz MJ, Retterer ST Biomicrofluidics 24198865 Biomicrofluidics 2012 https://www.ncbi.nlm.nih.gov/pubmed/24198865
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 https://www.ncbi.nlm.nih.gov/pubmed/19369970
Dielectrophoresis of Caenorhabditis elegans. Chuang HS, Raizen DM, Lamb A, Dabbish N, Bau HH Lab on a chip 21225036 Lab Chip 2011 Feb 21 https://www.ncbi.nlm.nih.gov/pubmed/21225036
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 https://www.ncbi.nlm.nih.gov/pubmed/21505035
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 https://www.ncbi.nlm.nih.gov/pubmed/22532855
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 https://www.ncbi.nlm.nih.gov/pubmed/22720068
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 https://www.ncbi.nlm.nih.gov/pubmed/23645985
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 https://www.ncbi.nlm.nih.gov/pubmed/23044549
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 https://www.ncbi.nlm.nih.gov/pubmed/23060610
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 https://www.ncbi.nlm.nih.gov/pubmed/22654504
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 https://www.ncbi.nlm.nih.gov/pubmed/22493085
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 https://www.ncbi.nlm.nih.gov/pubmed/22253719
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 https://www.ncbi.nlm.nih.gov/pubmed/21899761
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 https://www.ncbi.nlm.nih.gov/pubmed/22772836
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 https://www.ncbi.nlm.nih.gov/pubmed/22615851
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 https://www.ncbi.nlm.nih.gov/pubmed/24451366
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 https://www.ncbi.nlm.nih.gov/pubmed/24803517
Differential abundance analysis for microbial marker-gene surveys. Paulson JN, Stine OC, Bravo HC, Pop M Nature methods 24076764 Nat Methods 2013 Dec https://www.ncbi.nlm.nih.gov/pubmed/24076764
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 https://www.ncbi.nlm.nih.gov/pubmed/24995464
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 https://www.ncbi.nlm.nih.gov/pubmed/22147368
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 https://www.ncbi.nlm.nih.gov/pubmed/22199379
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 https://www.ncbi.nlm.nih.gov/pubmed/21400694
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Brady A, Salzberg SL Nature methods 19648916 Nat Methods 2009 Sep https://www.ncbi.nlm.nih.gov/pubmed/19648916
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 https://www.ncbi.nlm.nih.gov/pubmed/19261174
Reference-guided assembly of metagenomes with MetaCompass. Luan T, Cepeda-Espinoza VP, Liu B, Bowen Z, Ayyangar U, Almeida M, Koren S, Treangen TJ, Porter A, Pop M Cell reports methods 41015028 Cell Rep Methods 2025 Oct 20 https://www.ncbi.nlm.nih.gov/pubmed/41015028
We are what we eat: how the diet of infants affects their gut microbiome. Pop M Genome biology 22546514 Genome Biol 2012 https://www.ncbi.nlm.nih.gov/pubmed/22546514
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 https://www.ncbi.nlm.nih.gov/pubmed/23320958
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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 https://www.ncbi.nlm.nih.gov/pubmed/20379604
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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 https://www.ncbi.nlm.nih.gov/pubmed/21915241
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 https://www.ncbi.nlm.nih.gov/pubmed/21809842
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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 https://www.ncbi.nlm.nih.gov/pubmed/22355378
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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 https://www.ncbi.nlm.nih.gov/pubmed/21872475
Defining the human microbiome. Ursell LK, Metcalf JL, Parfrey LW, Knight R Nutrition reviews 22861806 Nutr Rev 2012 Aug https://www.ncbi.nlm.nih.gov/pubmed/22861806
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 https://www.ncbi.nlm.nih.gov/pubmed/23964800
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 https://www.ncbi.nlm.nih.gov/pubmed/24995004
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 https://www.ncbi.nlm.nih.gov/pubmed/20566857
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 https://www.ncbi.nlm.nih.gov/pubmed/20520652
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 https://www.ncbi.nlm.nih.gov/pubmed/20412303
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 https://www.ncbi.nlm.nih.gov/pubmed/21383980
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 https://www.ncbi.nlm.nih.gov/pubmed/21485746
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 https://www.ncbi.nlm.nih.gov/pubmed/22424233
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 https://www.ncbi.nlm.nih.gov/pubmed/22678395
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 https://www.ncbi.nlm.nih.gov/pubmed/22645380
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 https://www.ncbi.nlm.nih.gov/pubmed/22647040
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 https://www.ncbi.nlm.nih.gov/pubmed/20197316
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 https://www.ncbi.nlm.nih.gov/pubmed/30059804
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 https://www.ncbi.nlm.nih.gov/pubmed/30275573
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 https://www.ncbi.nlm.nih.gov/pubmed/20545741
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 https://www.ncbi.nlm.nih.gov/pubmed/19865184
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 https://www.ncbi.nlm.nih.gov/pubmed/19706296
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 https://www.ncbi.nlm.nih.gov/pubmed/21546392
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 https://www.ncbi.nlm.nih.gov/pubmed/21646247
Estimation of distribution overlap of urn models. Hampton J, Lladser ME PloS one 23139734 PLoS One 2012 https://www.ncbi.nlm.nih.gov/pubmed/23139734
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 https://www.ncbi.nlm.nih.gov/pubmed/22171330
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 https://www.ncbi.nlm.nih.gov/pubmed/25307765
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 https://www.ncbi.nlm.nih.gov/pubmed/25036628
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 https://www.ncbi.nlm.nih.gov/pubmed/26257300
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 https://www.ncbi.nlm.nih.gov/pubmed/28576788
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 https://www.ncbi.nlm.nih.gov/pubmed/21908640
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 https://www.ncbi.nlm.nih.gov/pubmed/21364937
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 https://www.ncbi.nlm.nih.gov/pubmed/23019655
The future is now: single-cell genomics of bacteria and archaea. Blainey PC FEMS microbiology reviews 23298390 FEMS Microbiol Rev 2013 May https://www.ncbi.nlm.nih.gov/pubmed/23298390
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 https://www.ncbi.nlm.nih.gov/pubmed/20966005
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 https://www.ncbi.nlm.nih.gov/pubmed/24060116
Digital MDA for enumeration of total nucleic acid contamination. Blainey PC, Quake SR Nucleic acids research 21071419 Nucleic Acids Res 2011 Mar https://www.ncbi.nlm.nih.gov/pubmed/21071419
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 https://www.ncbi.nlm.nih.gov/pubmed/22434425
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 https://www.ncbi.nlm.nih.gov/pubmed/26601305
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 https://www.ncbi.nlm.nih.gov/pubmed/22695862
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 https://www.ncbi.nlm.nih.gov/pubmed/23555659
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 https://www.ncbi.nlm.nih.gov/pubmed/29105370
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 https://www.ncbi.nlm.nih.gov/pubmed/23509275
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 https://www.ncbi.nlm.nih.gov/pubmed/24738594
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 https://www.ncbi.nlm.nih.gov/pubmed/24551246
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 https://www.ncbi.nlm.nih.gov/pubmed/28787424
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 https://www.ncbi.nlm.nih.gov/pubmed/23387867
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"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 https://www.ncbi.nlm.nih.gov/pubmed/23110633
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 https://www.ncbi.nlm.nih.gov/pubmed/23615375
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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 https://www.ncbi.nlm.nih.gov/pubmed/27409808
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 https://www.ncbi.nlm.nih.gov/pubmed/25027027
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 https://www.ncbi.nlm.nih.gov/pubmed/25270338
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 https://www.ncbi.nlm.nih.gov/pubmed/21205002
Single cell genome sequencing. Yilmaz S, Singh AK Current opinion in biotechnology 22154471 Curr Opin Biotechnol 2012 Jun https://www.ncbi.nlm.nih.gov/pubmed/22154471
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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 https://www.ncbi.nlm.nih.gov/pubmed/25218391
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 https://www.ncbi.nlm.nih.gov/pubmed/29138425

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