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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
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
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
A framework for human microbiome research. Human Microbiome Project Consortium Nature 22699610 Nature 2012 Jun 13 https://www.ncbi.nlm.nih.gov/pubmed/22699610
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
'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
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
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
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
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
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, 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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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
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, 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
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
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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
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, 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
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
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
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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
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
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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
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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
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
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
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
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
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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
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
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Association of diet with circulating trimethylamine-N-oxide concentration. Hamaya R, Ivey KL, Lee DH, Wang M, Li J, Franke A, Sun Q, Rimm EB The American journal of clinical nutrition 32936862 Am J Clin Nutr 2020 Dec 10 https://www.ncbi.nlm.nih.gov/pubmed/32936862
Prevalence and Associations of Avascular Necrosis of the Hip in a Large Well-characterized Cohort of Patients With Inflammatory Bowel Disease. Rolston VS, Patel AV, Learch TJ, Li D, Karayev D, Williams C, Siddanthi ML, Targan SR, Weisman MH, McGovern DPB Journal of clinical rheumatology : practical reports on rheumatic & musculoskeletal diseases 29794876 J Clin Rheumatol 2019 Jan https://www.ncbi.nlm.nih.gov/pubmed/29794876
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C Nature microbiology 29311644 Nat Microbiol 2018 Mar https://www.ncbi.nlm.nih.gov/pubmed/29311644
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA 3rd, IBDMDB Investigators, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C Nature 31142855 Nature 2019 May https://www.ncbi.nlm.nih.gov/pubmed/31142855
HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor. Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L American journal of epidemiology 30649166 Am J Epidemiol 2019 Jun 1 https://www.ncbi.nlm.nih.gov/pubmed/30649166
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N Cell 30661755 Cell 2019 Jan 24 https://www.ncbi.nlm.nih.gov/pubmed/30661755
Profiling novel lateral gene transfer events in the human microbiome. Hsu TY, Nzabarushimana E, Wong D, Luo C, Beiko RG, Langille M, Huttenhower C, Nguyen LH, Franzosa EA bioRxiv : the preprint server for biology 37609252 bioRxiv 2023 Aug 14 https://www.ncbi.nlm.nih.gov/pubmed/37609252
The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Orešič M, Huttenhower C, Knip M, DIABIMMUNE Study Group, Xavier RJ Cell host & microbe 25662751 Cell Host Microbe 2015 Feb 11 https://www.ncbi.nlm.nih.gov/pubmed/25662751
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
CSA13 inhibits colitis-associated intestinal fibrosis via a formyl peptide receptor like-1 mediated HMG-CoA reductase pathway. Xu C, Ghali S, Wang J, Shih DQ, Ortiz C, Mussatto CC, Lee EC, Tran DH, Jacobs JP, Lagishetty V, Fleshner P, Robbins L, Vu M, Hing TC, McGovern DPB, Koon HW Scientific reports 29180648 Sci Rep 2017 Nov 27 https://www.ncbi.nlm.nih.gov/pubmed/29180648
Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M, DIABIMMUNE Study Group, Xavier RJ Science translational medicine 27306663 Sci Transl Med 2016 Jun 15 https://www.ncbi.nlm.nih.gov/pubmed/27306663
The TNF family member TL1A induces IL-22 secretion in committed human T(h)17 cells via IL-9 induction. Thomas LS, Targan SR, Tsuda M, Yu QT, Salumbides BC, Haritunians T, Mengesha E, McGovern DP, Michelsen KS Journal of leukocyte biology 27733581 J Leukoc Biol 2017 Mar https://www.ncbi.nlm.nih.gov/pubmed/27733581
Microbial strain-level population structure and genetic diversity from metagenomes. Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N Genome research 28167665 Genome Res 2017 Apr https://www.ncbi.nlm.nih.gov/pubmed/28167665
Dynamics of the human gut microbiome in inflammatory bowel disease. Halfvarson J, Brislawn CJ, Lamendella R, Vázquez-Baeza Y, Walters WA, Bramer LM, D'Amato M, Bonfiglio F, McDonald D, Gonzalez A, McClure EE, Dunklebarger MF, Knight R, Jansson JK Nature microbiology 28191884 Nat Microbiol 2017 Feb 13 https://www.ncbi.nlm.nih.gov/pubmed/28191884
Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course. Schirmer M, Denson L, Vlamakis H, Franzosa EA, Thomas S, Gotman NM, Rufo P, Baker SS, Sauer C, Markowitz J, Pfefferkorn M, Oliva-Hemker M, Rosh J, Otley A, Boyle B, Mack D, Baldassano R, Keljo D, LeLeiko N, Heyman M, Griffiths A, Patel AS, Noe J, Kugathasan S, Walters T, Huttenhower C, Hyams J, Xavier RJ Cell host & microbe 30308161 Cell Host Microbe 2018 Oct 10 https://www.ncbi.nlm.nih.gov/pubmed/30308161
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
Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C Genome biology 25887922 Genome Biol 2015 Apr 8 https://www.ncbi.nlm.nih.gov/pubmed/25887922
An integrative view of microbiome-host interactions in inflammatory bowel diseases. Wlodarska M, Kostic AD, Xavier RJ Cell host & microbe 25974300 Cell Host Microbe 2015 May 13 https://www.ncbi.nlm.nih.gov/pubmed/25974300
Complex host genetics influence the microbiome in inflammatory bowel disease. Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ Genome medicine 25587358 Genome Med 2014 https://www.ncbi.nlm.nih.gov/pubmed/25587358
The microbiome in inflammatory bowel disease: current status and the future ahead. Kostic AD, Xavier RJ, Gevers D Gastroenterology 24560869 Gastroenterology 2014 May https://www.ncbi.nlm.nih.gov/pubmed/24560869
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. Mallick H, Franzosa EA, Mclver LJ, Banerjee S, Sirota-Madi A, Kostic AD, Clish CB, Vlamakis H, Xavier RJ, Huttenhower C Nature communications 31316056 Nat Commun 2019 Jul 17 https://www.ncbi.nlm.nih.gov/pubmed/31316056
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
High-sensitivity pattern discovery in large, paired multiomic datasets. Ghazi AR, Sucipto K, Rahnavard A, Franzosa EA, McIver LJ, Lloyd-Price J, Schwager E, Weingart G, Moon YS, Morgan XC, Waldron L, Huttenhower C Bioinformatics (Oxford, England) 35758795 Bioinformatics 2022 Jun 24 https://www.ncbi.nlm.nih.gov/pubmed/35758795
A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria. Yao L, D'Agostino GD, Park J, Hang S, Adhikari AA, Zhang Y, Li W, Avila-Pacheco J, Bae S, Clish CB, Franzosa EA, Huttenhower C, Huh JR, Devlin AS Nature microbiology 35982310 Nat Microbiol 2022 Sep https://www.ncbi.nlm.nih.gov/pubmed/35982310
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Karcher N, Pasolli E, Asnicar F, Huang KD, Tett A, Manara S, Armanini F, Bain D, Duncan SH, Louis P, Zolfo M, Manghi P, Valles-Colomer M, Raffaetà R, Rota-Stabelli O, Collado MC, Zeller G, Falush D, Maixner F, Walker AW, Huttenhower C, Segata N Genome biology 32513234 Genome Biol 2020 Jun 8 https://www.ncbi.nlm.nih.gov/pubmed/32513234
Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly. Ivey KL, Chan AT, Izard J, Cassidy A, Rogers GB, Rimm EB mBio 31551328 mBio 2019 Sep 24 https://www.ncbi.nlm.nih.gov/pubmed/31551328
The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, De Filippis F, Magnabosco C, Bonneau R, Lusingu J, Amuasi J, Reinhard K, Rattei T, Boulund F, Engstrand L, Zink A, Collado MC, Littman DR, Eibach D, Ercolini D, Rota-Stabelli O, Huttenhower C, Maixner F, Segata N Cell host & microbe 31607556 Cell Host Microbe 2019 Nov 13 https://www.ncbi.nlm.nih.gov/pubmed/31607556
Global chemical effects of the microbiome include new bile-acid conjugations. Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC Nature 32103176 Nature 2020 Mar https://www.ncbi.nlm.nih.gov/pubmed/32103176
Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. Nishiyama H, Endo H, Blanc-Mathieu R, Ogata H Microorganisms 33121006 Microorganisms 2020 Oct 27 https://www.ncbi.nlm.nih.gov/pubmed/33121006
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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Bambus 2: scaffolding metagenomes. Koren S, Treangen TJ, Pop M Bioinformatics (Oxford, England) 21926123 Bioinformatics 2011 Nov 1 https://www.ncbi.nlm.nih.gov/pubmed/21926123
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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
Deep sequencing of the oral microbiome reveals signatures of periodontal disease. Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S PloS one 22675498 PLoS One 2012 https://www.ncbi.nlm.nih.gov/pubmed/22675498
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
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DNACLUST: accurate and efficient clustering of phylogenetic marker genes. Ghodsi M, Liu B, Pop M BMC bioinformatics 21718538 BMC Bioinformatics 2011 Jun 30 https://www.ncbi.nlm.nih.gov/pubmed/21718538
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Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. Haft DH, Basu MK Journal of bacteriology 21478363 J Bacteriol 2011 Jun https://www.ncbi.nlm.nih.gov/pubmed/21478363
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TIGRFAMs and Genome Properties in 2013. Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E Nucleic acids research 23197656 Nucleic Acids Res 2013 Jan https://www.ncbi.nlm.nih.gov/pubmed/23197656
Evolution and classification of the CRISPR-Cas systems. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV Nature reviews. Microbiology 21552286 Nat Rev Microbiol 2011 Jun https://www.ncbi.nlm.nih.gov/pubmed/21552286
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Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family. Haft DH, Basu MK, Mitchell DA BMC biology 20500830 BMC Biol 2010 May 25 https://www.ncbi.nlm.nih.gov/pubmed/20500830
Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. Selengut JD, Haft DH Journal of bacteriology 20675471 J Bacteriol 2010 Nov https://www.ncbi.nlm.nih.gov/pubmed/20675471
Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. Ansong C, Ortega C, Payne SH, Haft DH, Chauvignè-Hines LM, Lewis MP, Ollodart AR, Purvine SO, Shukla AK, Fortuin S, Smith RD, Adkins JN, Grundner C, Wright AT Chemistry & biology 23352146 Chem Biol 2013 Jan 24 https://www.ncbi.nlm.nih.gov/pubmed/23352146
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Ethical Discourse about the Modification of Food for Therapeutic Purposes: How Patients with Gastrointestinal Diseases View the Good, the Bad, and the Healthy. Harrison KL, Geller G, Marshall P, Tilburt J, Mercer M, Brinich MA, Highland J, Farrell RM, Sharp RR AJOB primary research 22773953 AJOB Prim Res 2012 Jul 1 https://www.ncbi.nlm.nih.gov/pubmed/22773953
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Mammalian Cell Sorting using μFACS. Cho SH, Chen CH, Tsai FS, Godin J, Lo YH Conference on Lasers and Electro-optics : (CLEO). Conference on Lasers and Electro-optics 21614147 Conf Lasers Electro Optics 2010 May 16 https://www.ncbi.nlm.nih.gov/pubmed/21614147
Optofluidic Waveguides in Teflon AF-Coated PDMS Microfluidic Channels. Cho SH, Godin J, Lo YH IEEE photonics technology letters : a publication of the IEEE Laser and Electro-optics Society 20729984 IEEE Photonics Technol Lett 2009 Aug 1 https://www.ncbi.nlm.nih.gov/pubmed/20729984
Lab-on-a-chip flow cytometer employing color-space-time coding. Cho SH, Qiao W, Tsai FS, Yamashita K, Lo YH Applied physics letters 20877655 Appl Phys Lett 2010 Aug 30 https://www.ncbi.nlm.nih.gov/pubmed/20877655
Review Article: Recent advancements in optofluidic flow cytometer. Cho SH, Godin JM, Chen CH, Qiao W, Lee H, Lo YH Biomicrofluidics 21267434 Biomicrofluidics 2010 Dec 30 https://www.ncbi.nlm.nih.gov/pubmed/21267434
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
Microfluidic cell sorter with integrated piezoelectric actuator. Chen CH, Cho SH, Tsai F, Erten A, Lo YH Biomedical microdevices 19649710 Biomed Microdevices 2009 Dec https://www.ncbi.nlm.nih.gov/pubmed/19649710
Micro-fabricated fluorescence-activated cell sorter. Cho SH, Chen CH, Tsai FS, Lo YH Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference 19965141 Annu Int Conf IEEE Eng Med Biol Soc 2009 https://www.ncbi.nlm.nih.gov/pubmed/19965141
Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Gole J, Gore A, Richards A, Chiu YJ, Fung HL, Bushman D, Chiang HI, Chun J, Lo YH, Zhang K Nature biotechnology 24213699 Nat Biotechnol 2013 Dec https://www.ncbi.nlm.nih.gov/pubmed/24213699
An optical-coding method to measure particle distribution in microfluidic devices. Wu TF, Mei Z, Pion-Tonachini L, Zhao C, Qiao W, Arianpour A, Lo YH AIP advances 22125760 AIP Adv 2011 Jun https://www.ncbi.nlm.nih.gov/pubmed/22125760
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
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
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
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
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
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
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
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
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
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
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
Extrapolation of urn models via poissonization: accurate measurements of the microbial unknown. Lladser ME, Gouet R, Reeder J PloS one 21738613 PLoS One 2011 https://www.ncbi.nlm.nih.gov/pubmed/21738613
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
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
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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
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
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
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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
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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
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 Genomics Guides Elucidation of Vitamin B(12) Biosynthesis in Novel Human-Associated Akkermansia Strains. Kirmiz N, Galindo K, Cross KL, Luna E, Rhoades N, Podar M, Flores GE Applied and environmental microbiology 31757822 Appl Environ Microbiol 2020 Jan 21 https://www.ncbi.nlm.nih.gov/pubmed/31757822
Saying privacy, meaning confidentiality. Schwab AP, Frank L, Gligorov N The American journal of bioethics : AJOB 22047127 Am J Bioeth 2011 Nov https://www.ncbi.nlm.nih.gov/pubmed/22047127
Ethical issues in microbiome research and medicine. Rhodes R BMC medicine 27729053 BMC Med 2016 Oct 12 https://www.ncbi.nlm.nih.gov/pubmed/27729053
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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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"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
Personal genome research : what should the participant be told? McGuire AL, Lupski JR Trends in genetics : TIG 20381895 Trends Genet 2010 May https://www.ncbi.nlm.nih.gov/pubmed/20381895
Fluorescent labeling of antibody fragments using split GFP. Ferrara F, Listwan P, Waldo GS, Bradbury AR PloS one 21998685 PLoS One 2011 https://www.ncbi.nlm.nih.gov/pubmed/21998685
From deep sequencing to actual clones. D'Angelo S, Kumar S, Naranjo L, Ferrara F, Kiss C, Bradbury AR Protein engineering, design & selection : PEDS 25183780 Protein Eng Des Sel 2014 Oct https://www.ncbi.nlm.nih.gov/pubmed/25183780
Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes. Close DW, Ferrara F, Dichosa AE, Kumar S, Daughton AR, Daligault HE, Reitenga KG, Velappan N, Sanchez TC, Iyer S, Kiss C, Han CS, Bradbury AR BMC microbiology 24279426 BMC Microbiol 2013 Nov 27 https://www.ncbi.nlm.nih.gov/pubmed/24279426
Beyond natural antibodies: the power of in vitro display technologies. Bradbury AR, Sidhu S, Dübel S, McCafferty J Nature biotechnology 21390033 Nat Biotechnol 2011 Mar https://www.ncbi.nlm.nih.gov/pubmed/21390033
Single cell microRNA analysis using microfluidic flow cytometry. Wu M, Piccini M, Koh CY, Lam KS, Singh AK PloS one 23383050 PLoS One 2013 https://www.ncbi.nlm.nih.gov/pubmed/23383050
Single-cell protein analysis. Wu M, Singh AK Current opinion in biotechnology 22189001 Curr Opin Biotechnol 2012 Feb https://www.ncbi.nlm.nih.gov/pubmed/22189001
Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH). Liu P, Meagher RJ, Light YK, Yilmaz S, Chakraborty R, Arkin AP, Hazen TC, Singh AK Lab on a chip 21755095 Lab Chip 2011 Aug 21 https://www.ncbi.nlm.nih.gov/pubmed/21755095
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
Antibacterial and bioactive coatings on titanium implant surfaces. Kulkarni Aranya A, Pushalkar S, Zhao M, LeGeros RZ, Zhang Y, Saxena D Journal of biomedical materials research. Part A 28380669 J Biomed Mater Res A 2017 Aug https://www.ncbi.nlm.nih.gov/pubmed/28380669
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
Oral microbiota and host innate immune response in bisphosphonate-related osteonecrosis of the jaw. Pushalkar S, Li X, Kurago Z, Ramanathapuram LV, Matsumura S, Fleisher KE, Glickman R, Yan W, Li Y, Saxena D International journal of oral science 25105817 Int J Oral Sci 2014 Dec https://www.ncbi.nlm.nih.gov/pubmed/25105817
Microfluidic Flow Cytometry for Single-Cell Protein Analysis. Wu M, Singh AK Methods in molecular biology (Clifton, N.J.) 26542716 Methods Mol Biol 2015 https://www.ncbi.nlm.nih.gov/pubmed/26542716
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
Versatile on-demand droplet generation for controlled encapsulation. Rhee M, Liu P, Meagher RJ, Light YK, Singh AK Biomicrofluidics 25379072 Biomicrofluidics 2014 May https://www.ncbi.nlm.nih.gov/pubmed/25379072
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
Antibacterial property expressed by a novel calcium phosphate glass. Liu L, Pushalkar S, Saxena D, LeGeros RZ, Zhang Y Journal of biomedical materials research. Part B, Applied biomaterials 24039127 J Biomed Mater Res B Appl Biomater 2014 Apr https://www.ncbi.nlm.nih.gov/pubmed/24039127
Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma. Pushalkar S, Ji X, Li Y, Estilo C, Yegnanarayana R, Singh B, Li X, Saxena D BMC microbiology 22817758 BMC Microbiol 2012 Jul 20 https://www.ncbi.nlm.nih.gov/pubmed/22817758
Microfluidic platforms for single-cell protein analysis. Liu Y, Singh AK Journal of laboratory automation 23821679 J Lab Autom 2013 Dec https://www.ncbi.nlm.nih.gov/pubmed/23821679
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
Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples. Rhee M, Light YK, Meagher RJ, Singh AK PloS one 27144304 PLoS One 2016 https://www.ncbi.nlm.nih.gov/pubmed/27144304
Antibiotic effects on bacterial profile in osteonecrosis of the jaw. Ji X, Pushalkar S, Li Y, Glickman R, Fleisher K, Saxena D Oral diseases 21883710 Oral Dis 2012 Jan https://www.ncbi.nlm.nih.gov/pubmed/21883710
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
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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