Human Microbiome Project (HMP)
Human Microbiome Project (HMP)
Program Publications
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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 |
|---|---|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| A framework for human microbiome research. | Human Microbiome Project Consortium | Nature | 22699610 | Nature | 2012 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/22699610 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance. | Britton RA, Young VB | Trends in microbiology | 22595318 | Trends Microbiol | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22595318 |
| A 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data. | Liu Z, Hsiao W, Cantarel BL, Drábek EF, Fraser-Liggett C | Bioinformatics (Oxford, England) | 21984758 | Bioinformatics | 2011 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/21984758 |
| Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. | Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK | PloS one | 23209564 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23209564 |
| Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. | Hettich RL, Pan C, Chourey K, Giannone RJ | Analytical chemistry | 23469896 | Anal Chem | 2013 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/23469896 |
| 'Omics' of the mammalian gut--new insights into function. | Lamendella R, VerBerkmoes N, Jansson JK | Current opinion in biotechnology | 22626866 | Curr Opin Biotechnol | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22626866 |
| 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 |
| 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 |
| 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 |
| Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. | Hollister EB, Oezguen N, Chumpitazi BP, Luna RA, Weidler EM, Rubio-Gonzales M, Dahdouli M, Cope JL, Mistretta TA, Raza S, Metcalf GA, Muzny DM, Gibbs RA, Petrosino JF, Heitkemper M, Savidge TC, Shulman RJ, Versalovic J | The Journal of molecular diagnostics : JMD | 31005411 | J Mol Diagn | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31005411 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Dietary issues in recurrent abdominal pain. | Shulman RJ | Journal of pediatric gastroenterology and nutrition | 23103654 | J Pediatr Gastroenterol Nutr | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23103654 |
| The 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 |
| 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 |
| 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 |
| Microbial Metabolism in the Mammalian Gut: Molecular Mechanisms and Clinical Implications. | Hall A, Versalovic J | Journal of pediatric gastroenterology and nutrition | 29762384 | J Pediatr Gastroenterol Nutr | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29762384 |
| 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 |
| 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 |
| Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. | Hemarajata P, Versalovic J | Therapeutic advances in gastroenterology | 23320049 | Therap Adv Gastroenterol | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23320049 |
| 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 |
| 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 |
| 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 |
| Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. | Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ, Versalovic J | Gastroenterology | 21741921 | Gastroenterology | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21741921 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Using QIIME to analyze 16S rRNA gene sequences from microbial communities. | Kuczynski J, Stombaugh J, Walters WA, González A, Caporaso JG, Knight R | Current protocols in microbiology | 23184592 | Curr Protoc Microbiol | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23184592 |
| Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. | Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, Fu X, Wu Y, Li L, Smith JD, DiDonato JA, Chen J, Li H, Wu GD, Lewis JD, Warrier M, Brown JM, Krauss RM, Tang WH, Bushman FD, Lusis AJ, Hazen SL | Nature medicine | 23563705 | Nat Med | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23563705 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison. | Ahn J, Yang L, Paster BJ, Ganly I, Morris L, Pei Z, Hayes RB | PloS one | 21829515 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21829515 |
| Simrank: Rapid and sensitive general-purpose k-mer search tool. | DeSantis TZ, Keller K, Karaoz U, Alekseyenko AV, Singh NN, Brodie EL, Pei Z, Andersen GL, Larsen N | BMC ecology | 21524302 | BMC Ecol | 2011 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/21524302 |
| A rare case of anal carcinosarcoma with human papilloma virus infection in both biphasic tumor elements: An immunohistochemical, molecular and ultrastructural study. | Hickman RA, Bradshaw AD, Cassai N, Neto AG, Zhou D, Fu T, Lee P, Pei Z, Wieczorek R | Papillomavirus research (Amsterdam, Netherlands) | 28616595 | Papillomavirus Res | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28616595 |
| The 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 |
| 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 |
| 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 |
| Erratum to: The first microbial environment of infants born by C-section: the operating room microbes. | Shin H, Pei Z, Martinez KA 2nd, Rivera-Vinas JI, Mendez K, Cavallin H, Dominguez-Bello MG | Microbiome | 26796629 | Microbiome | 2016 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/26796629 |
| 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 |
| 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 |
| 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 |
| Sex, body mass index, and dietary fiber intake influence the human gut microbiome. | Dominianni C, Sinha R, Goedert JJ, Pei Z, Yang L, Hayes RB, Ahn J | PloS one | 25874569 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25874569 |
| Microbiome, a new dimension in cancer research. | Neto AG, Bradshaw AD, Pei Z | Annals of translational medicine | 26539446 | Ann Transl Med | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26539446 |
| MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs. | Brown SM, Chen H, Hao Y, Laungani BP, Ali TA, Dong C, Lijeron C, Kim B, Wultsch C, Pei Z, Krampis K | GigaScience | 30942867 | Gigascience | 2019 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/30942867 |
| 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 |
| Diversity of 5S rRNA genes within individual prokaryotic genomes. | Pei A, Li H, Oberdorf WE, Alekseyenko AV, Parsons T, Yang L, Gerz EA, Lee P, Xiang C, Nossa CW, Pei Z | FEMS microbiology letters | 22765222 | FEMS Microbiol Lett | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22765222 |
| SPA: a short peptide assembler for metagenomic data. | Yang Y, Yooseph S | Nucleic acids research | 23435317 | Nucleic Acids Res | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23435317 |
| 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 |
| Inflammation and intestinal metaplasia of the distal esophagus are associated with alterations in the microbiome. | Yang L, Lu X, Nossa CW, Francois F, Peek RM, Pei Z | Gastroenterology | 19394334 | Gastroenterology | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19394334 |
| Diversity of 23S rRNA genes within individual prokaryotic genomes. | Pei A, Nossa CW, Chokshi P, Blaser MJ, Yang L, Rosmarin DM, Pei Z | PloS one | 19415112 | PLoS One | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19415112 |
| 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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| Maternal activation of the EGFR prevents translocation of gut-residing pathogenic Escherichia coli in a model of late-onset neonatal sepsis. | Knoop KA, Coughlin PE, Floyd AN, Ndao IM, Hall-Moore C, Shaikh N, Gasparrini AJ, Rusconi B, Escobedo M, Good M, Warner BB, Tarr PI, Newberry RD | Proceedings of the National Academy of Sciences of the United States of America | 32179676 | Proc Natl Acad Sci U S A | 2020 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/32179676 |
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| Nonoptimal Vaginal Microbiota After Azithromycin Treatment for Chlamydia trachomatis Infection. | Tamarelle J, Ma B, Gajer P, Humphrys MS, Terplan M, Mark KS, Thiébaut ACM, Forney LJ, Brotman RM, Delarocque-Astagneau E, Bavoil PM, Ravel J | The Journal of infectious diseases | 31573603 | J Infect Dis | 2020 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/31573603 |
| Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy. | Brotman RM, Shardell MD, Gajer P, Fadrosh D, Chang K, Silver MI, Viscidi RP, Burke AE, Ravel J, Gravitt PE | Menopause (New York, N.Y.) | 24080849 | Menopause | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24080849 |
| Comparison of storage conditions for human vaginal microbiome studies. | Bai G, Gajer P, Nandy M, Ma B, Yang H, Sakamoto J, Blanchard MH, Ravel J, Brotman RM | PloS one | 22655031 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22655031 |
| Quantitative modeling predicts mechanistic links between pre-treatment microbiome composition and metronidazole efficacy in bacterial vaginosis. | Lee CY, Cheu RK, Lemke MM, Gustin AT, France MT, Hampel B, Thurman AR, Doncel GF, Ravel J, Klatt NR, Arnold KB | Nature communications | 33262350 | Nat Commun | 2020 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/33262350 |
| High-resolution functional description of vaginal microbiomes in health and disease. | Holm JB, France MT, Gajer P, Ma B, Brotman RM, Shardell M, Forney L, Ravel J | bioRxiv : the preprint server for biology | 36993583 | bioRxiv | 2023 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/36993583 |
| Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression. | Delgado-Diaz DJ, Jesaveluk B, Hayward JA, Tyssen D, Alisoltani A, Potgieter M, Bell L, Ross E, Iranzadeh A, Allali I, Dabee S, Barnabas S, Gamieldien H, Blackburn JM, Mulder N, Smith SB, Edwards VL, Burgener AD, Bekker LG, Ravel J, Passmore JS, Masson L, Hearps AC, Tachedjian G | Microbiome | 36045402 | Microbiome | 2022 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/36045402 |
| VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. | France MT, Ma B, Gajer P, Brown S, Humphrys MS, Holm JB, Waetjen LE, Brotman RM, Ravel J | Microbiome | 33228810 | Microbiome | 2020 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/33228810 |
| Complete Genome Sequences of Ezakiella coagulans C0061C1 and Fenollaria massiliensis C0061C2. | France MT, Clifford J, Narina S, Rutt L, Ravel J | Microbiology resource announcements | 35861554 | Microbiol Resour Announc | 2022 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/35861554 |
| Factors Associated With Incidence and Spontaneous Clearance of Molecular-Bacterial Vaginosis: Results From a Longitudinal Frequent-Sampling Observational Study. | Tamarelle J, Shardell MD, Ravel J, Brotman RM | Sexually transmitted diseases | 35969846 | Sex Transm Dis | 2022 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/35969846 |
| Vaginal microbiome of reproductive-age women. | Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ | Proceedings of the National Academy of Sciences of the United States of America | 20534435 | Proc Natl Acad Sci U S A | 2011 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/20534435 |
| Vaginal Candida spp. genomes from women with vulvovaginal candidiasis. | Bradford LL, Chibucos MC, Ma B, Bruno V, Ravel J | Pathogens and disease | 28582496 | Pathog Dis | 2017 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/28582496 |
| Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis. | Noyes N, Cho KC, Ravel J, Forney LJ, Abdo Z | PloS one | 29364944 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29364944 |
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| VIRGO2: Unveiling the Functional and Ecological Complexity of the Vaginal Microbiome with an Enhanced Non-Redundant Gene Catalog. | France MT, Chaudry I, Rutt L, Quain M, Shirtliff B, McComb E, Maros A, Alizadeh M, Hussain FA, Elovitz MA, Relman DA, Rahman A, Brotman RM, Price J, Kassaro M, Holm JB, Ma B, Ravel J | bioRxiv : the preprint server for biology | 40093185 | bioRxiv | 2025 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/40093185 |
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| mcaGUI: microbial community analysis R-Graphical User Interface (GUI). | Copeland WK, Krishnan V, Beck D, Settles M, Foster JA, Cho KC, Day M, Hickey R, Schütte UM, Zhou X, Williams CJ, Forney LJ, Abdo Z | Bioinformatics (Oxford, England) | 22692220 | Bioinformatics | 2012 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/22692220 |
| New signaling pathways govern the host response to C. albicans infection in various niches. | Liu Y, Shetty AC, Schwartz JA, Bradford LL, Xu W, Phan QT, Kumari P, Mahurkar A, Mitchell AP, Ravel J, Fraser CM, Filler SG, Bruno VM | Genome research | 25858952 | Genome Res | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25858952 |
| An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. | Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J | Microbiome | 24558975 | Microbiome | 2014 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/24558975 |
| Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth. | Zhou X, Brotman RM, Gajer P, Abdo Z, Schüette U, Ma S, Ravel J, Forney LJ | Infectious diseases in obstetrics and gynecology | 21197076 | Infect Dis Obstet Gynecol | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/21197076 |
| Caring about trees in the forest: incorporating frailty in risk analysis for personalized medicine. | Ma ZS, Abdo Z, Forney LJ | Personalized medicine | 22754581 | Per Med | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22754581 |
| Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data. | France MT, Fu L, Rutt L, Yang H, Humphrys MS, Narina S, Gajer PM, Ma B, Forney LJ, Ravel J | Genome biology | 35232471 | Genome Biol | 2022 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/35232471 |
| Douching cessation and molecular bacterial vaginosis: a reanalysis of archived specimens. | Brown SE, He X, Shardell MD, Ravel J, Ghanem KG, Zenilman JM, Brotman RM | Sexually transmitted infections | 35636931 | Sex Transm Infect | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/35636931 |
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| Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women. | Brotman RM, Bradford LL, Conrad M, Gajer P, Ault K, Peralta L, Forney LJ, Carlton JM, Abdo Z, Ravel J | Sexually transmitted diseases | 23007708 | Sex Transm Dis | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23007708 |
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| Temporal dynamics of the human vaginal microbiota. | Gajer P, Brotman RM, Bai G, Sakamoto J, Schütte UM, Zhong X, Koenig SS, Fu L, Ma ZS, Zhou X, Abdo Z, Forney LJ, Ravel J | Science translational medicine | 22553250 | Sci Transl Med | 2012 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/22553250 |
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| Biogenic Amines Increase the Odds of Bacterial Vaginosis and Affect the Growth of and Lactic Acid Production by Vaginal Lactobacillus spp. | Borgogna JC, Shardell MD, Grace SG, Santori EK, Americus B, Li Z, Ulanov A, Forney L, Nelson TM, Brotman RM, Ravel J, Yeoman CJ | Applied and environmental microbiology | 33674429 | Appl Environ Microbiol | 2021 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/33674429 |
| An effective intervention to reduce intravaginal practices among HIV-1 uninfected Kenyan women. | Sivapalasingam S, McClelland RS, Ravel J, Ahmed A, Cleland CM, Gajer P, Mwamzaka M, Marshed F, Shafi J, Masese L, Fajans M, Anderson ME, Jaoko W, Kurth AE | AIDS research and human retroviruses | 25265254 | AIDS Res Hum Retroviruses | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25265254 |
| Advancing the microbiome research community. | Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, Scientists for Advancement of Microbiome Research, White O | Cell | 25303518 | Cell | 2014 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/25303518 |
| Complete Genome Sequences of Six Lactobacillus iners Strains Isolated from the Human Vagina. | France MT, Rutt L, Narina S, Arbaugh S, McComb E, Humphrys MS, Ma B, Hayward MR, Costello EK, Relman DA, Kwon DS, Ravel J | Microbiology resource announcements | 32409537 | Microbiol Resour Announc | 2020 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/32409537 |
| Asymptomatic Bacterial Vaginosis Is Associated With Depletion of Mature Superficial Cells Shed From the Vaginal Epithelium. | O'Hanlon DE, Gajer P, Brotman RM, Ravel J | Frontiers in cellular and infection microbiology | 32211347 | Front Cell Infect Microbiol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32211347 |
| Evaluation of vaginal microbiome equilibrium states identifies microbial parameters linked to resilience after menses and antibiotic therapy. | Lee CY, Diegel J, France MT, Ravel J, Arnold KB | PLoS computational biology | 37566641 | PLoS Comput Biol | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37566641 |
| Persistence and In Vivo Evolution of Vaginal Bacterial Strains over a Multiyear Time Period. | France M, Ma B, Ravel J | mSystems | 36413016 | mSystems | 2022 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/36413016 |
| Assessing the Concordance Between Urogenital and Vaginal Microbiota: Can Urine Specimens Be Used as a Proxy for Vaginal Samples? | Brown SE, Robinson CK, Shardell MD, Holm JB, Ravel J, Ghanem KG, Brotman RM | Frontiers in cellular and infection microbiology | 34268137 | Front Cell Infect Microbiol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34268137 |
| Investigating the impact of condomless vaginal intercourse and lubricant use on the vaginal metabolome: a pre-post observational study. | Borgogna JC, Grace SG, Holm JB, Aviles Zuniga T, Kadriu H, He X, McCoski SR, Ravel J, Brotman RM, Yeoman CJ | Sexually transmitted infections | 37258272 | Sex Transm Infect | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37258272 |
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| Mitochondrial DNA sequence variation is largely conserved at birth with rare de novo mutations in neonates. | Ma J, Purcell H, Showalter L, Aagaard KM | American journal of obstetrics and gynecology | 25687567 | Am J Obstet Gynecol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25687567 |
| The preterm placental microbiome varies in association with excess maternal gestational weight gain. | Antony KM, Ma J, Mitchell KB, Racusin DA, Versalovic J, Aagaard K | American journal of obstetrics and gynecology | 25557210 | Am J Obstet Gynecol | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25557210 |
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| Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis. | Hyde ER, Andrade F, Vaksman Z, Parthasarathy K, Jiang H, Parthasarathy DK, Torregrossa AC, Tribble G, Kaplan HB, Petrosino JF, Bryan NS | PloS one | 24670812 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24670812 |
| Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. | Qin X, Galloway-Peña JR, Sillanpaa J, Roh JH, Nallapareddy SR, Chowdhury S, Bourgogne A, Choudhury T, Muzny DM, Buhay CJ, Ding Y, Dugan-Rocha S, Liu W, Kovar C, Sodergren E, Highlander S, Petrosino JF, Worley KC, Gibbs RA, Weinstock GM, Murray BE | BMC microbiology | 22769602 | BMC Microbiol | 2012 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/22769602 |
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| 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 |
| 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 |
| 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 |
| Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. | Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ | Cell | 27814509 | Cell | 2016 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/27814509 |
| MetaPhlAn2 for enhanced metagenomic taxonomic profiling. | Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N | Nature methods | 26418763 | Nat Methods | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26418763 |
| Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. | Nguyen LH, Ma W, Wang DD, Cao Y, Mallick H, Gerbaba TK, Lloyd-Price J, Abu-Ali G, Hall AB, Sikavi D, Drew DA, Mehta RS, Arze C, Joshi AD, Yan Y, Branck T, DuLong C, Ivey KL, Ogino S, Rimm EB, Song M, Garrett WS, Izard J, Huttenhower C, Chan AT | Gastroenterology | 31972239 | Gastroenterology | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/31972239 |
| The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men. | Sikavi DR, Nguyen LH, Haruki K, Ugai T, Ma W, Wang DD, Thompson KN, Yan Y, Branck T, Wilkinson JE, Akimoto N, Zhong R, Lau MC, Mima K, Kosumi K, Morikawa T, Rimm EB, Garrett WS, Izard J, Cao Y, Song M, Huttenhower C, Ogino S, Chan AT | Clinical and translational gastroenterology | 34333506 | Clin Transl Gastroenterol | 2021 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/34333506 |
| Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome. | Li Y, Wang DD, Satija A, Ivey KL, Li J, Wilkinson JE, Li R, Baden M, Chan AT, Huttenhower C, Rimm EB, Hu FB, Sun Q | The Journal of nutrition | 34114015 | J Nutr | 2021 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/34114015 |
| Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. | Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N | eLife | 33944776 | Elife | 2021 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/33944776 |
| Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome. | Li Y, Wang F, Li J, Ivey KL, Wilkinson JE, Wang DD, Li R, Liu G, Eliassen HA, Chan AT, Clish CB, Huttenhower C, Hu FB, Sun Q, Rimm EB | BMC microbiology | 35350985 | BMC Microbiol | 2022 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/35350985 |
| 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 |
| Multivariable association discovery in population-scale meta-omics studies. | Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C | PLoS computational biology | 34784344 | PLoS Comput Biol | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34784344 |
| Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. | Tong M, McHardy I, Ruegger P, Goudarzi M, Kashyap PC, Haritunians T, Li X, Graeber TG, Schwager E, Huttenhower C, Fornace AJ Jr, Sonnenburg JL, McGovern DP, Borneman J, Braun J | The ISME journal | 24781901 | ISME J | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24781901 |
| Immune and genetic gardening of the intestinal microbiome. | Jacobs JP, Braun J | FEBS letters | 24613921 | FEBS Lett | 2014 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/24613921 |
| Relating the metatranscriptome and metagenome of the human gut. | Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, Izard J, Garrett WS, Chan AT, Huttenhower C | Proceedings of the National Academy of Sciences of the United States of America | 24843156 | Proc Natl Acad Sci U S A | 2014 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/24843156 |
| 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 |
| A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. | Levin BJ, Huang YY, Peck SC, Wei Y, Martínez-Del Campo A, Marks JA, Franzosa EA, Huttenhower C, Balskus EP | Science (New York, N.Y.) | 28183913 | Science | 2017 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/28183913 |
| 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 |
| Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. | Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, DIABIMMUNE Study Group, Xavier RJ | Cell | 27133167 | Cell | 2016 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/27133167 |
| 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 |
| Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. | Sinha R, Abu-Ali G, Vogtmann E, Fodor AA, Ren B, Amir A, Schwager E, Crabtree J, Ma S, Microbiome Quality Control Project Consortium, Abnet CC, Knight R, White O, Huttenhower C | Nature biotechnology | 28967885 | Nat Biotechnol | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28967885 |
| Human gut bacteria produce Τ(Η)17-modulating bile acid metabolites. | Paik D, Yao L, Zhang Y, Bae S, D'Agostino GD, Zhang M, Kim E, Franzosa EA, Avila-Pacheco J, Bisanz JE, Rakowski CK, Vlamakis H, Xavier RJ, Turnbaugh PJ, Longman RS, Krout MR, Clish CB, Rastinejad F, Huttenhower C, Huh JR, Devlin AS | Nature | 35296854 | Nature | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35296854 |
| 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 |
| Species-level functional profiling of metagenomes and metatranscriptomes. | Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C | Nature methods | 30377376 | Nat Methods | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30377376 |
| Cathelicidin suppresses lipid accumulation and hepatic steatosis by inhibition of the CD36 receptor. | Hoang-Yen Tran D, Hoang-Ngoc Tran D, Mattai SA, Sallam T, Ortiz C, Lee EC, Robbins L, Ho S, Lee JE, Fisseha E, Shieh C, Sideri A, Shih DQ, Fleshner P, McGovern DP, Vu M, Hing TC, Bakirtzi K, Cheng M, Su B, Law I, Karagiannides I, Targan SR, Gallo RL, Li Z, Koon HW | International journal of obesity (2005) | 27163748 | Int J Obes (Lond) | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27163748 |
| 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 |
| Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. | Donati C, Zolfo M, Albanese D, Tin Truong D, Asnicar F, Iebba V, Cavalieri D, Jousson O, De Filippo C, Huttenhower C, Segata N | Nature microbiology | 27572971 | Nat Microbiol | 2016 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/27572971 |
| Optimizing Selection of Biologics in Inflammatory Bowel Disease: Development of an Online Patient Decision Aid Using Conjoint Analysis. | Almario CV, Keller MS, Chen M, Lasch K, Ursos L, Shklovskaya J, Melmed GY, Spiegel BMR | The American journal of gastroenterology | 29206816 | Am J Gastroenterol | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29206816 |
| Experimental design and quantitative analysis of microbial community multiomics. | Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C | Genome biology | 29187204 | Genome Biol | 2017 Nov 30 | https://www.ncbi.nlm.nih.gov/pubmed/29187204 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Molecular Choreography of Acute Exercise. | Contrepois K, Wu S, Moneghetti KJ, Hornburg D, Ahadi S, Tsai MS, Metwally AA, Wei E, Lee-McMullen B, Quijada JV, Chen S, Christle JW, Ellenberger M, Balliu B, Taylor S, Durrant MG, Knowles DA, Choudhry H, Ashland M, Bahmani A, Enslen B, Amsallem M, Kobayashi Y, Avina M, Perelman D, Schüssler-Fiorenza Rose SM, Zhou W, Ashley EA, Montgomery SB, Chaib H, Haddad F, Snyder MP | Cell | 32470399 | Cell | 2020 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/32470399 |
| Whole-genome 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 |
| 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 |
| Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. | Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M | Nature biotechnology | 26655498 | Nat Biotechnol | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26655498 |
| Personal 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. | Fitzsimons MS, Novotny M, Lo CC, Dichosa AE, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, Wills PL, Parson-Quintana B, Chain PS, Detter JC, Lasken RS, Han CS | Genome research | 23493677 | Genome Res | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23493677 |
| NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly. | McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA | BMC bioinformatics | 25407910 | BMC Bioinformatics | 2014 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/25407910 |
| The 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 |
| The under-recognized dominance of Verrucomicrobia in soil bacterial communities. | Bergmann GT, Bates ST, Eilers KG, Lauber CL, Caporaso JG, Walters WA, Knight R, Fierer N | Soil biology & biochemistry | 22267877 | Soil Biol Biochem | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22267877 |
| Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. | Lozupone C, Faust K, Raes J, Faith JJ, Frank DN, Zaneveld J, Gordon JI, Knight R | Genome research | 22665442 | Genome Res | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22665442 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Human-associated microbial signatures: examining their predictive value. | Knights D, Parfrey LW, Zaneveld J, Lozupone C, Knight R | Cell host & microbe | 22018228 | Cell Host Microbe | 2011 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/22018228 |
| Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. | Soergel DA, Dey N, Knight R, Brenner SE | The ISME journal | 22237546 | ISME J | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22237546 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Finding the missing links among metabolites, microbes, and the host. | Dorrestein PC, Mazmanian SK, Knight R | Immunity | 24950202 | Immunity | 2014 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/24950202 |
| Microbial community assembly and metabolic function during mammalian corpse decomposition. | Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, Song SJ, Amir A, Larsen P, Sangwan N, Haarmann D, Humphrey GC, Ackermann G, Thompson LR, Lauber C, Bibat A, Nicholas C, Gebert MJ, Petrosino JF, Reed SC, Gilbert JA, Lynne AM, Bucheli SR, Carter DO, Knight R | Science (New York, N.Y.) | 26657285 | Science | 2016 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/26657285 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| A quantitative understanding of lac repressor's binding specificity and flexibility. | Zuo Z, Chang Y, Stormo GD | Quantitative biology (Beijing, China) | 26752632 | Quant Biol | 2015 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/26752632 |
| Prevention of virus-induced type 1 diabetes with antibiotic therapy. | Hara N, Alkanani AK, Ir D, Robertson CE, Wagner BD, Frank DN, Zipris D | Journal of immunology (Baltimore, Md. : 1950) | 22988033 | J Immunol | 2012 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/22988033 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The gut microbiota in human energy homeostasis and obesity. | Rosenbaum M, Knight R, Leibel RL | Trends in endocrinology and metabolism: TEM | 26257300 | Trends Endocrinol Metab | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26257300 |
| Pigs, Unlike Mice, Have Two Distinct Colonic Stem Cell Populations Similar to Humans That Respond to High-Calorie Diet prior to Insulin Resistance. | Charepalli V, Reddivari L, Radhakrishnan S, Eriksson E, Xiao X, Kim SW, Shen F, Vijay-Kumar M, Li Q, Bhat VB, Knight R, Vanamala JKP | Cancer prevention research (Philadelphia, Pa.) | 28576788 | Cancer Prev Res (Phila) | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28576788 |
| Defining the human microbiome. | Ursell LK, Metcalf JL, Parfrey LW, Knight R | Nutrition reviews | 22861806 | Nutr Rev | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22861806 |
| Estimation of distribution overlap of urn models. | Hampton J, Lladser ME | PloS one | 23139734 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23139734 |
| Spatial and temporal variability of the human microbiota. | Parfrey LW, Knight R | Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases | 22647040 | Clin Microbiol Infect | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22647040 |
| 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 |
| 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 |
| SitePainter: a tool for exploring biogeographical patterns. | Gonzalez A, Stombaugh J, Lauber CL, Fierer N, Knight R | Bioinformatics (Oxford, England) | 22171330 | Bioinformatics | 2012 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/22171330 |
| 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 |
| 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 |
| Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. | Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R | Frontiers in microbiology | 24995004 | Front Microbiol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24995004 |
| Association of gut microbiota with post-operative clinical course in Crohn's disease. | Dey N, Soergel DA, Repo S, Brenner SE | BMC gastroenterology | 23964800 | BMC Gastroenterol | 2013 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/23964800 |
| 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 |
| 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 |
| Conducting a microbiome study. | Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE | Cell | 25036628 | Cell | 2014 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/25036628 |
| 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 |
| 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 |
| 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 |
| Are microbiome studies ready for hypothesis-driven research? | Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song SJ, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R | Current opinion in microbiology | 30059804 | Curr Opin Microbiol | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30059804 |
| Qiita: rapid, web-enabled microbiome meta-analysis. | Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R | Nature methods | 30275573 | Nat Methods | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30275573 |
| The 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 |
| Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. | Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR | PloS one | 21364937 | PLoS One | 2011 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/21364937 |
| Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis. | Blainey PC, Milla CE, Cornfield DN, Quake SR | Science translational medicine | 23019655 | Sci Transl Med | 2012 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/23019655 |
| 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 |
| 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 |
| 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 |
| Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. | Campbell AG, Schwientek P, Vishnivetskaya T, Woyke T, Levy S, Beall CJ, Griffen A, Leys E, Podar M | Environmental microbiology | 24738594 | Environ Microbiol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24738594 |
| Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286) and comparison to the closely related pathogen Tannerella forsythia. | Beall CJ, Campbell AG, Dayeh DM, Griffen AL, Podar M, Leys EJ | PloS one | 24551246 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24551246 |
| Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity. | Campbell AG, Campbell JH, Schwientek P, Woyke T, Sczyrba A, Allman S, Beall CJ, Griffen A, Leys E, Podar M | PloS one | 23555659 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23555659 |
| Cultivation of Peptidiphaga gingivicola from subgingival plaque: The first representative of a novel genus of Actinomycetaceae. | Beall CJ, Mokrzan EM, Griffen AL, Leys EJ | Molecular oral microbiology | 29105370 | Mol Oral Microbiol | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29105370 |
| 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 |
| Toward unrestricted use of public genomic data. | Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I | Science (New York, N.Y.) | 30679363 | Science | 2019 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/30679363 |
| Single-Cell Genomics and the Oral Microbiome. | Balachandran M, Cross KL, Podar M | Journal of dental research | 32091935 | J Dent Res | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32091935 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| De minimis risk: a proposal for a new category of research risk. | Rhodes R, Azzouni J, Baumrin SB, Benkov K, Blaser MJ, Brenner B, Dauben JW, Earle WJ, Frank L, Gligorov N, Goldfarb J, Hirschhorn K, Hirschhorn R, Holzman I, Indyk D, Jabs EW, Lackey DP, Moros DA, Philpott S, Rhodes ME, Richardson LD, Sacks HS, Schwab A, Sperling R, Trusko B, Zweig A | The American journal of bioethics : AJOB | 22047112 | Am J Bioeth | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22047112 |
| 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 |
| 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 |
| Perspectives on human microbiome research ethics. | McGuire AL, Achenbaum LS, Whitney SN, Slashinski MJ, Versalovic J, Keitel WA, McCurdy SA | Journal of empirical research on human research ethics : JERHRE | 22850139 | J Empir Res Hum Res Ethics | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22850139 |
| The right to ignore genetic status of late onset genetic disease in the genomic era; Prenatal testing for Huntington disease as a paradigm. | Erez A, Plunkett K, Sutton VR, McGuire AL | American journal of medical genetics. Part A | 20583190 | Am J Med Genet A | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20583190 |
| "Snake-oil," "quack medicine," and "industrially cultured organisms:" biovalue and the commercialization of human microbiome research. | Slashinski MJ, McCurdy SA, Achenbaum LS, Whitney SN, McGuire AL | BMC medical ethics | 23110633 | BMC Med Ethics | 2012 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/23110633 |
| Investigators' perspectives on translating human microbiome research into clinical practice. | Slashinski MJ, Whitney SN, Achenbaum LS, Keitel WA, McCurdy SA, McGuire AL | Public health genomics | 23615375 | Public Health Genomics | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23615375 |
| Informed consent in genomics and genetic research. | McGuire AL, Beskow LM | Annual review of genomics and human genetics | 20477535 | Annu Rev Genomics Hum Genet | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20477535 |
| 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 |
| 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 |
| 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 |
| 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 |
| Microbial diversity in saliva of oral squamous cell carcinoma. | Pushalkar S, Mane SP, Ji X, Li Y, Evans C, Crasta OR, Morse D, Meagher R, Singh A, Saxena D | FEMS immunology and medical microbiology | 21205002 | FEMS Immunol Med Microbiol | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21205002 |
| Single-cell protein analysis. | Wu M, Singh AK | Current opinion in biotechnology | 22189001 | Curr Opin Biotechnol | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22189001 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
