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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 Authors Journal PubMedID Publication Date
Ethical, legal, and social considerations in conducting the Human Microbiome Project. McGuire, Amy L; Colgrove, James; Whitney, Simon N; Diaz, Christina M; Bustillos, Daniel; Versalovic, James Genome research 18971311 2008 Dec
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Langmead, Ben; Trapnell, Cole; Pop, Mihai; Salzberg, Steven L Genome biology 19261174 2009
Metagenomic pyrosequencing and microbial identification. Petrosino, Joseph F; Highlander, Sarah; Luna, Ruth Ann; Gibbs, Richard A; Versalovic, James Clinical chemistry 19264858 2009 May
Helping patients make informed choices about probiotics: a need for research. Sharp, Richard R; Achkar, Jean-Paul; Brinich, Margaret A; Farrell, Ruth M The American journal of gastroenterology 19343022 2009 Apr
Statistical methods for detecting differentially abundant features in clinical metagenomic samples. White, James Robert; Nagarajan, Niranjan; Pop, Mihai PLoS computational biology 19360128 2009 Apr
16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis. Wang, Yunwei; Hoenig, Jeanette D; Malin, Kathryn J; Qamar, Sanaa; Petrof, Elaine O; Sun, Jun; Antonopoulos, Dionysios A; Chang, Eugene B; Claud, Erika C The ISME journal 19369970 2009 Aug
Inflammation and intestinal metaplasia of the distal esophagus are associated with alterations in the microbiome. Yang, Liying; Lu, Xiaohua; Nossa, Carlos W; Francois, Fritz; Peek, Richard M; Pei, Zhiheng Gastroenterology 19394334 2009 Aug
Diversity of 23S rRNA genes within individual prokaryotic genomes. Pei, Anna; Nossa, Carlos W; Chokshi, Pooja; Blaser, Martin J; Yang, Liying; Rosmarin, David M; Pei, Zhiheng PloS one 19415112 2009
Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era. Preidis, Geoffrey A; Versalovic, James Gastroenterology 19462507 2009 May
Genome assembly reborn: recent computational challenges. Pop, Mihai Briefings in bioinformatics 19482960 2009 Jul
An ORFome assembly approach to metagenomics sequences analysis. Ye, Yuzhen; Tang, Haixu Journal of bioinformatics and computational biology 19507285 2009 Jun
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Brady, Arthur; Salzberg, Steven L Nature methods 19648916 2009 Sep
Microfluidic cell sorter with integrated piezoelectric actuator. Chen, Chun H; Cho, Sung Hwan; Tsai, Frank; Erten, Ahmet; Lo, Yu-Hwa Biomedical microdevices 19649710 2009 Dec
A method for isolating and analyzing human mRNA from newborn stool. Bennett Jr, William E; Gonzalez-Rivera, Rosbel; Shaikh, Nurmohammad; Magrini, Vincent; Boykin, Michelle; Warner, Barbara B; Hamvas, Aaron; Tarr, Phillip I Journal of immunological methods 19660464 2009 Sep 30
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes. Ye, Yuzhen; Doak, Thomas G PLoS computational biology 19680427 2009 Aug
High-fat diet determines the composition of the murine gut microbiome independently of obesity. Hildebrandt, Marie A; Hoffmann, Christian; Sherrill-Mix, Scott A; Keilbaugh, Sue A; Hamady, Micah; Chen, Ying-Yu; Knight, Rob; Ahima, Rexford S; Bushman, Frederic; Wu, Gary D Gastroenterology 19706296 2009 Nov
Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. Hamady, Micah; Lozupone, Catherine; Knight, Rob The ISME journal 19710709 2010 Jan
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing. Lazarevic, Vladimir; Whiteson, Katrine; Huse, Susan; Hernandez, David; Farinelli, Laurent; Osteras, Magne; Schrenzel, Jacques; Francois, Patrice Journal of microbiological methods 19796657 2009 Dec
Genomics. Genome project standards in a new era of sequencing. Chain, P S G; Grafham, D V; Fulton, R S; Fitzgerald, M G; Hostetler, J; Muzny, D; Ali, J; Birren, B; Bruce, D C; Buhay, C; Cole, J R; Ding, Y; Dugan, S; Field, D; Garrity, G M; Gibbs, R; Graves, T; Han, C S; Harrison, S H; Highlander, S; Hugenholtz, P; Kh Science (New York, N.Y.) 19815760 2009 Oct 9
Bacterial communities of disease vectors sampled across time, space, and species. Jones, Ryan T; Knight, Rob; Martin, Andrew P The ISME journal 19865184 2010 Feb
BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. Frank, Daniel N BMC bioinformatics 19874596 2009
What are the consequences of the disappearing human microbiota? Blaser, Martin J; Falkow, Stanley Nature reviews. Microbiology 19898491 2009 Dec
PyNAST: a flexible tool for aligning sequences to a template alignment. Caporaso, J Gregory; Bittinger, Kyle; Bushman, Frederic D; DeSantis, Todd Z; Andersen, Gary L; Knight, Rob Bioinformatics (Oxford, England) 19914921 2010 Jan 15
Searching for SNPs with cloud computing. Langmead, Ben; Schatz, Michael C; Lin, Jimmy; Pop, Mihai; Salzberg, Steven L Genome biology 19930550 2009
Micro-fabricated fluorescence-activated cell sorter. Cho, Sung Hwan; Chen, Chun H; Tsai, Frank S; Lo, Yu-Hwa Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 19965141 2009
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. Selengut, Jeremy D; Rusch, Douglas B; Haft, Daniel H BMC bioinformatics 20102603 2010
Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives. Zaneveld, Jesse R; Lozupone, Catherine; Gordon, Jeffrey I; Knight, Rob Nucleic acids research 20197316 2010 Jul
Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Huse, Susan M; Welch, David Mark; Morrison, Hilary G; Sogin, Mitchell L Environmental microbiology 20236171 2010 Jul
Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. White, James R; Navlakha, Saket; Nagarajan, Niranjan; Ghodsi, Mohammad-Reza; Kingsford, Carl; Pop, Mihai BMC bioinformatics 20334679 2010
Harnessing the power of the human microbiome. Blaser, Martin J Proceedings of the National Academy of Sciences of the United States of America 20360554 2010 Apr 6
Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. Wang, Gary P; Sherrill-Mix, Scott A; Chang, Kyong-Mi; Quince, Chris; Bushman, Frederic D Journal of virology 20375170 2010 Jun
Role of the gut microbiota in defining human health. Fujimura, Kei E; Slusher, Nicole A; Cabana, Michael D; Lynch, Susan V Expert review of anti-infective therapy 20377338 2010 Apr
Human mammalian cell sorting using a highly integrated micro-fabricated fluorescence-activated cell sorter (microFACS). Cho, Sung Hwan; Chen, Chun H; Tsai, Frank S; Godin, Jessica M; Lo, Yu-Hwa Lab on a chip 20379604 2010 Jun 21
Personal genome research : what should the participant be told? McGuire, Amy L; Lupski, James R Trends in genetics : TIG 20381895 2010 May
QIIME allows analysis of high-throughput community sequencing data. Caporaso, J Gregory; Kuczynski, Justin; Stombaugh, Jesse; Bittinger, Kyle; Bushman, Frederic D; Costello, Elizabeth K; Fierer, Noah; Pena, Antonio Gonzalez; Goodrich, Julia K; Gordon, Jeffrey I; Huttley, Gavin A; Kelley, Scott T; Knights, Dan; Koenig, Jer Nature methods 20383131 2010 May
Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples. Lauber, Christian L; Zhou, Nicholas; Gordon, Jeffrey I; Knight, Rob; Fierer, Noah FEMS microbiology letters 20412303 2010 Jun
Diversity of 16S rRNA genes within individual prokaryotic genomes. Pei, Anna Y; Oberdorf, William E; Nossa, Carlos W; Agarwal, Ankush; Chokshi, Pooja; Gerz, Erika A; Jin, Zhida; Lee, Peng; Yang, Liying; Poles, Michael; Brown, Stuart M; Sotero, Steven; Desantis, Todd; Brodie, Eoin; Nelson, Karen; Pei, Zhiheng Applied and environmental microbiology 20418441 2010 Jun
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Pati, Amrita; Ivanova, Natalia N; Mikhailova, Natalia; Ovchinnikova, Galina; Hooper, Sean D; Lykidis, Athanasios; Kyrpides, Nikos C Nature methods 20436475 2010 Jun
Informed consent in genomics and genetic research. McGuire, Amy L; Beskow, Laura M Annual review of genomics and human genetics 20477535 2010 Sep 22
A catalog of reference genomes from the human microbiome. Human Microbiome Jumpstart Reference Strains Consortium; Nelson, Karen E; Weinstock, George M; Highlander, Sarah K; Worley, Kim C; Creasy, Heather Huot; Wortman, Jennifer Russo; Rusch, Douglas B; Mitreva, Makedonka; Sodergren, Erica; Chinwalla, Asif T; Fe Science (New York, N.Y.) 20489017 2010 May 21
Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family. Haft, Daniel H; Basu, Malay Kumar; Mitchell, Douglas A BMC biology 20500830 2010
Postprandial remodeling of the gut microbiota in Burmese pythons. Costello, Elizabeth K; Gordon, Jeffrey I; Secor, Stephen M; Knight, Rob The ISME journal 20520652 2010 Nov
Vaginal microbiome of reproductive-age women. Ravel, Jacques; Gajer, Pawel; Abdo, Zaid; Schneider, G Maria; Koenig, Sara S K; McCulle, Stacey L; Karlebach, Shara; Gorle, Reshma; Russell, Jennifer; Tacket, Carol O; Brotman, Rebecca M; Davis, Catherine C; Ault, Kevin; Peralta, Ligia; Forney, Larry J Proceedings of the National Academy of Sciences of the United States of America 20534435 2011 Mar 15
Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies. Harwich Jr, Michael D; Alves, Joao M; Buck, Gregory A; Strauss 3rd, Jerome F; Patterson, Jennifer L; Oki, Aminat T; Girerd, Philippe H; Jefferson, Kimberly K BMC genomics 20540756 2010
The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Redford, Amanda J; Bowers, Robert M; Knight, Rob; Linhart, Yan; Fierer, Noah Environmental microbiology 20545741 2010 Nov
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Dominguez-Bello, Maria G; Costello, Elizabeth K; Contreras, Monica; Magris, Magda; Hidalgo, Glida; Fierer, Noah; Knight, Rob Proceedings of the National Academy of Sciences of the United States of America 20566857 2010 Jun 29
The right to ignore genetic status of late onset genetic disease in the genomic era; Prenatal testing for Huntington disease as a paradigm. Erez, A; Plunkett, K; Sutton, V R; McGuire, A L American journal of medical genetics. Part A 20583190 2010 Jul
Metagenomics: Facts and Artifacts, and Computational Challenges* Wooley, John C; Ye, Yuzhen Journal of computer science and technology 20648230 2009 Jan
Rapid fluctuation of the vaginal microbiota measured by Gram stain analysis. Brotman, Rebecca M; Ravel, Jacques; Cone, Richard A; Zenilman, Jonathan M Sexually transmitted infections 20660593 2010 Aug
Probiotics-host communication: Modulation of signaling pathways in the intestine. Thomas, Carissa M; Versalovic, James Gut microbes 20672012 2010 May-Jun
Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. Selengut, Jeremy D; Haft, Daniel H Journal of bacteriology 20675471 2010 Nov
Genome sequencing reveals widespread virulence gene exchange among human Neisseria species. Marri, Pradeep Reddy; Paniscus, Mary; Weyand, Nathan J; Rendon, Maria A; Calton, Christine M; Hernandez, Diana R; Higashi, Dustin L; Sodergren, Erica; Weinstock, George M; Rounsley, Steven D; So, Magdalene PloS one 20676376 2010
Quantitation of major human cutaneous bacterial and fungal populations. Gao, Zhan; Perez-Perez, Guillermo I; Chen, Yu; Blaser, Martin J Journal of clinical microbiology 20702672 2010 Oct
Optofluidic Waveguides in Teflon AF-Coated PDMS Microfluidic Channels. Cho, Sung Hwan; Godin, Jessica; Lo, Yu-Hwa IEEE photonics technology letters : a publication of the IEEE Laser and Electro-optics Society. 20729984 2009 Aug 1;
METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics. Goll, Johannes; Rusch, Douglas B; Tanenbaum, David M; Thiagarajan, Mathangi; Li, Kelvin; Methe, Barbara A; Yooseph, Shibu Bioinformatics (Oxford, England) 20798169 2010 Oct 15
FragGeneScan: predicting genes in short and error-prone reads. Rho, Mina; Tang, Haixu; Ye, Yuzhen Nucleic acids research 20805240 2010 Nov
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Reeder, Jens; Knight, Rob Nature methods 20805793 2010 Sep
Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. Nossa, Carlos W; Oberdorf, William E; Yang, Liying; Aas, Jorn A; Paster, Bruce J; Desantis, Todd Z; Brodie, Eoin L; Malamud, Daniel; Poles, Michael A; Pei, Zhiheng World journal of gastroenterology : WJG 20806429 2010 Sep 7
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Kuczynski, Justin; Liu, Zongzhi; Lozupone, Catherine; McDonald, Daniel; Fierer, Noah; Knight, Rob Nature methods 20818378 2010 Oct
Molecular microbiological methods in the diagnosis of neonatal sepsis. Venkatesh, Mohan; Flores, Angela; Luna, Ruth Ann; Versalovic, James Expert review of anti-infective therapy 20818947 2010 Sep
Creation and initial evaluation of a Stool Form Scale for children. Chumpitazi, Bruno P; Lane, Mariella M; Czyzewski, Danita I; Weidler, Erica M; Swank, Paul R; Shulman, Robert J The Journal of pediatrics 20826285 2010 Oct
An algorithm for automated closure during assembly. Koren, Sergey; Miller, Jason R; Walenz, Brian P; Sutton, Granger BMC bioinformatics 20831800 2010
Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Frank, Daniel N; Robertson, Charles E; Hamm, Christina M; Kpadeh, Zegbeh; Zhang, Tianyi; Chen, Hongyan; Zhu, Wei; Sartor, R Balfour; Boedeker, Edgar C; Harpaz, Noam; Pace, Norman R; Li, Ellen Inflammatory bowel diseases 20839241 2011 Jan
Regional differences in colonic mucosa-associated microbiota determine the physiological expression of host heat shock proteins. Hu, Shien; Wang, Yunwei; Lichtenstein, Lev; Tao, Yun; Musch, Mark W; Jabri, Bana; Antonopoulos, Dionysios; Claud, Erika C; Chang, Eugene B American journal of physiology. Gastrointestinal and liver physiology 20864653 2010 Dec
Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential. Yeoman, Carl J; Yildirim, Suleyman; Thomas, Susan M; Durkin, A Scott; Torralba, Manolito; Sutton, Granger; Buhay, Christian J; Ding, Yan; Dugan-Rocha, Shannon P; Muzny, Donna M; Qin, Xiang; Gibbs, Richard A; Leigh, Steven R; Stumpf, Rebecca; White, Bryan PloS one 20865041 2010
Lab-on-a-chip flow cytometer employing color-space-time coding. Cho, Sung Hwan; Qiao, Wen; Tsai, Frank S; Yamashita, Kenichi; Lo, Yu-Hwa Applied physics letters. 20877655 2010 Aug 30;
Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Wang, Yunwei; Antonopoulos, Dionysios A; Zhu, Xiaorong; Harrell, Laura; Hanan, Ira; Alverdy, John C; Meyer, Folker; Musch, Mark W; Young, Vincent B; Chang, Eugene B Applied microbiology and biotechnology 20931185 2010 Dec
Growth and Development Symposium: promoting healthier humans through healthier livestock: animal agriculture enters the metagenomics era. Frank, D N Journal of animal science 20935136 2011 Mar
Human oral, gut, and plaque microbiota in patients with atherosclerosis. Koren, Omry; Spor, Ayme; Felin, Jenny; Fak, Frida; Stombaugh, Jesse; Tremaroli, Valentina; Behre, Carl Johan; Knight, Rob; Fagerberg, Bjorn; Ley, Ruth E; Backhed, Fredrik Proceedings of the National Academy of Sciences of the United States of America 20937873 2011 Mar 15
A comparison of methanobactins from Methylosinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions. Krentz, Benjamin D; Mulheron, Heidi J; Semrau, Jeremy D; Dispirito, Alan A; Bandow, Nathan L; Haft, Daniel H; Vuilleumier, Stephane; Murrell, J Colin; McEllistrem, Marcus T; Hartsel, Scott C; Gallagher, Warren H Biochemistry 20961038 2010 Nov 30
SmashCell: a software framework for the analysis of single-cell amplified genome sequences. Harrington, Eoghan D; Arumugam, Manimozhiyan; Raes, Jeroen; Bork, Peer; Relman, David A Bioinformatics (Oxford, England) 20966005 2010 Dec 1
Regional mucosa-associated microbiota determine physiological expression of TLR2 and TLR4 in murine colon. Wang, Yunwei; Devkota, Suzanne; Musch, Mark W; Jabri, Bana; Nagler, Cathryn; Antonopoulos, Dionysios A; Chervonsky, Alexander; Chang, Eugene B PloS one 21042588 2010
Digital MDA for enumeration of total nucleic acid contamination. Blainey, Paul C; Quake, Stephen R Nucleic acids research 21071419 2011 Mar
Probiotics, enteric and diarrheal diseases, and global health. Preidis, Geoffrey A; Hill, Colin; Guerrant, Richard L; Ramakrishna, B S; Tannock, Gerald W; Versalovic, James Gastroenterology 21075108 2011 Jan
Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. Shah, Neethu; Tang, Haixu; Doak, Thomas G; Ye, Yuzhen Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 21121044 2011
Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection. Nelson, David E; Van Der Pol, Barbara; Dong, Qunfeng; Revanna, Kashi V; Fan, Baochang; Easwaran, Shraddha; Sodergren, Erica; Weinstock, George M; Diao, Lixia; Fortenberry, J Dennis PloS one 21124791 2010
Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth. Zhou, Xia; Brotman, Rebecca M; Gajer, Pawel; Abdo, Zaid; Schuette, Ursel; Ma, Sam; Ravel, Jacques; Forney, Larry J Infectious diseases in obstetrics and gynecology 21197076 2010
Microbial diversity in saliva of oral squamous cell carcinoma. Pushalkar, Smruti; Mane, Shrinivasrao P; Ji, Xiaojie; Li, Yihong; Evans, Clive; Crasta, Oswald R; Morse, Douglas; Meagher, Robert; Singh, Anup; Saxena, Deepak FEMS immunology and medical microbiology 21205002 2011 Apr
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Haas, Brian J; Gevers, Dirk; Earl, Ashlee M; Feldgarden, Mike; Ward, Doyle V; Giannoukos, Georgia; Ciulla, Dawn; Tabbaa, Diana; Highlander, Sarah K; Sodergren, Erica; Methe, Barbara; DeSantis, Todd Z; Human Microbiome Consortium; Petrosino, Joseph F; Knig Genome research 21212162 2011 Mar
A primer on a hepatocellular carcinoma bioresource bank using the cancer genome atlas guidelines: practical issues and pitfalls. Nguyen, N Thao T; Cotton, Ron T; Harring, Theresa R; Guiteau, Jacfranz J; Gingras, Marie-Claude; Wheeler, David A; O'Mahony, Christine A; Gibbs, Richard A; Brunicardi, F Charles; Goss, John A World journal of surgery 21221581 2011 Aug
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. Haft, Daniel H BMC genomics 21223593 2011
Dielectrophoresis of Caenorhabditis elegans. Chuang, Han-Sheng; Raizen, David M; Lamb, Annesia; Dabbish, Nooreen; Bau, Haim H Lab on a chip 21225036 2011 Feb 21
Building a comprehensive genomic program for hepatocellular carcinoma. Harring, Theresa R; Guiteau, Jacfranz J; Nguyen, N Thao T; Cotton, Ron T; Gingras, Marie-Claude; Wheeler, David A; O'Mahony, Christine A; Gibbs, Richard A; Brunicardi, F Charles; Goss, John A World journal of surgery 21225260 2011 Aug
Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice. Kellermayer, Richard; Dowd, Scot E; Harris, R Alan; Balasa, Alfred; Schaible, Tiffany D; Wolcott, Randy D; Tatevian, Nina; Szigeti, Reka; Li, Zhijie; Versalovic, James; Smith, C Wayne FASEB journal : official publication of the Federation of American Societies for Experimental Biology 21228220 2011 May
Review Article: Recent advancements in optofluidic flow cytometer. Cho, Sung Hwan; Godin, Jessica M; Chen, Chun-Hao; Qiao, Wen; Lee, Hosuk; Lo, Yu-Hwa Biomicrofluidics. 21267434 2010 Dec 30;
The age of necrotizing enterocolitis onset: an application of Sartwell's incubation period model. Gonzalez-Rivera, R; Culverhouse, R C; Hamvas, A; Tarr, P I; Warner, B B Journal of perinatology : official journal of the California Perinatal Association 21273988 2011 Aug
Inexact Local Alignment Search over Suffix Arrays. Ghodsi, Mohammadreza; Pop, Mihai Proceedings. IEEE International Conference on Bioinformatics and Biomedicine 21278916 2009 Nov 1
The microbe-derived short chain fatty acid butyrate targets miRNA-dependent p21 gene expression in human colon cancer. Hu, Shien; Dong, Tien Sy; Dalal, Sushila R; Wu, Feng; Bissonnette, Marc; Kwon, John H; Chang, Eugene B PloS one 21283757 2011
The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data. Tanenbaum, David M; Goll, Johannes; Murphy, Sean; Kumar, Prateek; Zafar, Nikhat; Thiagarajan, Mathangi; Madupu, Ramana; Davidsen, Tanja; Kagan, Leonid; Kravitz, Saul; Rusch, Douglas B; Yooseph, Shibu Standards in genomic sciences. 21304707 2010 Mar 30;
Current concepts of the intestinal microbiota and the pathogenesis of infection. Wardwell, Leslie H; Huttenhower, Curtis; Garrett, Wendy S Current infectious disease reports 21308452 2011 Feb
Host and gut microbiota symbiotic factors: lessons from inflammatory bowel disease and successful symbionts. Ballal, Sonia A; Gallini, Carey Ann; Segata, Nicola; Huttenhower, Curtis; Garrett, Wendy S Cellular microbiology 21314883 2011 Apr
A randomised trial of sheathed versus standard forceps for obtaining uncontaminated biopsy specimens of microbiota from the terminal ileum. Dave, Maneesh; Johnson, Laura A; Walk, Seth T; Young, Vincent B; Stidham, Ryan W; Chaudhary, Meghana N; Funnell, Jessica; Higgins, Peter D R Gut 21317176 2011 Aug
Microdroplet-enabled highly parallel co-cultivation of microbial communities. Park, Jihyang; Kerner, Alissa; Burns, Mark A; Lin, Xiaoxia Nina PloS one 21364881 2011
Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. Blainey, Paul C; Mosier, Annika C; Potanina, Anastasia; Francis, Christopher A; Quake, Stephen R PloS one 21364937 2011
Host-associated and free-living phage communities differ profoundly in phylogenetic composition. Caporaso, J Gregory; Knight, Rob; Kelley, Scott T PloS one 21383980 2011
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. Wu, Yu-Wei; Ye, Yuzhen Journal of computational biology : a journal of computational molecular cell biology 21385052 2011 Mar
Beyond natural antibodies: the power of in vitro display technologies. Bradbury, Andrew R M; Sidhu, Sachdev; Dubel, Stefan; McCafferty, John Nature biotechnology 21390033 2011 Mar
Next generation sequence assembly with AMOS. Treangen, Todd J; Sommer, Dan D; Angly, Florent E; Koren, Sergey; Pop, Mihai Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 21400694 2011 Mar
Unravelling the effects of the environment and host genotype on the gut microbiome. Spor, Ayme; Koren, Omry; Ley, Ruth Nature reviews. Microbiology 21407244 2011 Apr
Overview of the development of personalized genomic medicine and surgery. Brunicardi, F Charles; Gibbs, Richard A; Wheeler, David A; Nemunaitis, John; Fisher, William; Goss, John; Chen, Changyi World journal of surgery 21424870 2011 Aug
Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. Haft, Daniel H; Basu, Malay Kumar Journal of bacteriology 21478363 2011 Jun
The mind-body-microbial continuum. Gonzalez, Antonio; Stombaugh, Jesse; Lozupone, Catherine; Turnbaugh, Peter J; Gordon, Jeffrey I; Knight, Rob Dialogues in clinical neuroscience 21485746 2011
Reliability and validity of a modified Bristol Stool Form Scale for children. Lane, Mariella M; Czyzewski, Danita I; Chumpitazi, Bruno P; Shulman, Robert J The Journal of pediatrics 21489557 2011 Sep
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. Niu, Beifang; Zhu, Zhengwei; Fu, Limin; Wu, Sitao; Li, Weizhong Bioinformatics (Oxford, England) 21505035 2011 Jun 15
Simrank: Rapid and sensitive general-purpose k-mer search tool. DeSantis, Todd Z; Keller, Keith; Karaoz, Ulas; Alekseyenko, Alexander V; Singh, Navjeet N S; Brodie, Eoin L; Pei, Zhiheng; Andersen, Gary L; Larsen, Niels BMC ecology 21524302 2011
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Sun, Yijun; Cai, Yunpeng; Huse, Susan M; Knight, Rob; Farmerie, William G; Wang, Xiaoyu; Mai, Volker Briefings in bioinformatics 21525143 2012 Jan
Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. Dominguez-Bello, Maria Gloria; Blaser, Martin J; Ley, Ruth E; Knight, Rob Gastroenterology 21530737 2011 May
Brief communication: DNA from early Holocene American dog. Tito, Raul Y; Belknap 3rd, Samuel L; Sobolik, Kristin D; Ingraham, Robert C; Cleeland, Lauren M; Lewis Jr, Cecil M American journal of physical anthropology 21541929 2011 Aug
Boulder ALignment Editor (ALE): a web-based RNA alignment tool. Stombaugh, Jesse; Widmann, Jeremy; McDonald, Daniel; Knight, Rob Bioinformatics (Oxford, England) 21546392 2011 Jun 15
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn; Knight, Rob; Cole, James R; Amaral-Zettler, Linda; Gilbert, Jack A; Karsch-Mizrachi, Ilene; Johnston, Anjanette; Cochrane, Guy; Vaughan, Robert; Hunter, Christopher; Park, Joonhong; Morrison, Norman; Rocca-Serr Nature biotechnology 21552244 2011 May
Evolution and classification of the CRISPR-Cas systems. Makarova, Kira S; Haft, Daniel H; Barrangou, Rodolphe; Brouns, Stan J J; Charpentier, Emmanuelle; Horvath, Philippe; Moineau, Sylvain; Mojica, Francisco J M; Wolf, Yuri I; Yakunin, Alexander F; van der Oost, John; Koonin, Eugene V Nature reviews. Microbiology 21552286 2011 Jun
RAPSearch: a fast protein similarity search tool for short reads. Ye, Yuzhen; Choi, Jeong-Hyeon; Tang, Haixu BMC bioinformatics 21575167 2011
Responses of gut microbiota to diet composition and weight loss in lean and obese mice. Ravussin, Yann; Koren, Omry; Spor, Ayme; LeDuc, Charles; Gutman, Roee; Stombaugh, Jesse; Knight, Rob; Ley, Ruth E; Leibel, Rudolph L Obesity (Silver Spring, Md.) 21593810 2012 Apr
The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens. Dong, Qunfeng; Nelson, David E; Toh, Evelyn; Diao, Lixia; Gao, Xiang; Fortenberry, J Dennis; Van der Pol, Barbara PloS one 21603636 2011
Mammalian Cell Sorting using ýýFACS. Cho, Sung Hwan; Chen, Chun Hao; Tsai, Frank S; Godin, Jessica; Lo, Yu-Hwa Conference on Lasers and Electro-optics : (CLEO). Conference on Lasers and Electro-optics 21614147 2010 May 16
Moving pictures of the human microbiome. Caporaso, J Gregory; Lauber, Christian L; Costello, Elizabeth K; Berg-Lyons, Donna; Gonzalez, Antonio; Stombaugh, Jesse; Knights, Dan; Gajer, Pawel; Ravel, Jacques; Fierer, Noah; Gordon, Jeffrey I; Knight, Rob Genome biology 21624126 2011
Interleukin-1ýý (IL-1ýý) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis. Carvalho, Frederic A; Nalbantoglu, Ilke; Ortega-Fernandez, Sophie; Aitken, Jesse D; Su, Yueju; Koren, Omry; Walters, William A; Knight, Rob; Ley, Ruth E; Vijay-Kumar, Matam; Gewirtz, Andrew T Gut 21646247 2012 Mar
Bacterial DNA content in the intestinal wall from infants with necrotizing enterocolitis. Bucher, Brian T; McDuffie, Lucas A; Shaikh, Nurmohammad; Tarr, Phillip I; Warner, Barbara B; Hamvas, Aaron; White, Frances V; Erwin, Christopher R; Warner, Brad W Journal of pediatric surgery 21683193 2011 Jun
UCHIME improves sensitivity and speed of chimera detection. Edgar, Robert C; Haas, Brian J; Clemente, Jose C; Quince, Christopher; Knight, Rob Bioinformatics (Oxford, England) 21700674 2011 Aug 15
Metagenomic biomarker discovery and explanation. Segata, Nicola; Izard, Jacques; Waldron, Levi; Gevers, Dirk; Miropolsky, Larisa; Garrett, Wendy S; Huttenhower, Curtis Genome biology 21702898 2011
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Challenges for case-control studies with microbiome data. Brooks, J Paul Annals of epidemiology. 27255739 2016 05;
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Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Yassour, Moran; Vatanen, Tommi; Siljander, Heli; Hämäläinen, Anu-Maaria; Härkönen, Taina; Ryhänen, Samppa J; Franzosa, Eric A; Vlamakis, Hera; Huttenhower, Curtis; Gevers, Dirk; Lander, Eric S; Knip, Mikael; DIABIMMUNE Study Group; Xavier, Ramnik J Science translational medicine. 27306663 2016 Jun 15;
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Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung. Segal, Leopoldo N; Clemente, Jose C; Wu, Benjamin G; Wikoff, William R; Gao, Zhan; Li, Yonghua; Ko, Jane P; Rom, William N; Blaser, Martin J; Weiden, Michael D Thorax. 27486204 2017 Jan;
A Pleiotropic Missense Variant in SLC39A8 Is Associated With Crohn's Disease and Human Gut Microbiome Composition. Li, Dalin; Achkar, Jean-Paul; Haritunians, Talin; Jacobs, Jonathan P; Hui, Ken Y; D'Amato, Mauro; Brand, Stephan; Radford-Smith, Graham; Halfvarson, Jonas; Niess, Jan-Hendrik; Kugathasan, Subra; Büning, Carsten; Schumm, L Philip; Klei, Lambertus; Ananthakrishnan, Ashwin; Aumais, Guy; Baidoo, Leonard; Dubinsky, Marla; Fiocchi, Claudio; Glas, Jürgen; Milgrom, Raquel; Proctor, Deborah D; Regueiro, Miguel; Simms, Lisa A; Stempak, Joanne M; Targan, Stephan R; Törkvist, Leif; Sharma, Yashoda; Devlin, Bernie; Borneman, James; Hakonarson, Hakon; Xavier, Ramnik J; Daly, Mark; Brant, Steven R; Rioux, John D; Silverberg, Mark S; Cho, Judy H; Braun, Jonathan; McGovern, Dermot P B; Duerr, Richard H Gastroenterology. 27492617 2016 Oct;
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The early infant gut microbiome varies in association with a maternal high-fat diet. Chu, Derrick M; Antony, Kathleen M; Ma, Jun; Prince, Amanda L; Showalter, Lori; Moller, Michelle; Aagaard, Kjersti M Genome medicine. 27503374 2016 08 09;
Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis. Gonzalez, Mercedes E; Schaffer, Julie V; Orlow, Seth J; Gao, Zhan; Li, Huilin; Alekseyenko, Alexander V; Blaser, Martin J Journal of the American Academy of Dermatology. 27543211 2016 Sep;
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Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Gibson, Molly K; Wang, Bin; Ahmadi, Sara; Burnham, Carey-Ann D; Tarr, Phillip I; Warner, Barbara B; Dantas, Gautam Nature microbiology. 27572443 2016 Mar 07;
Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Segal, Leopoldo N; Clemente, Jose C; Tsay, Jun-Chieh J; Koralov, Sergei B; Keller, Brian C; Wu, Benjamin G; Li, Yonghua; Shen, Nan; Ghedin, Elodie; Morris, Alison; Diaz, Phillip; Huang, Laurence; Wikoff, William R; Ubeda, Carles; Artacho, Alejandro; Rom, William N; Sterman, Daniel H; Collman, Ronald G; Blaser, Martin J; Weiden, Michael D Nature microbiology. 27572644 2016;
Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Donati, Claudio; Zolfo, Moreno; Albanese, Davide; Tin Truong, Duy; Asnicar, Francesco; Iebba, Valerio; Cavalieri, Duccio; Jousson, Olivier; De Filippo, Carlotta; Huttenhower, Curtis; Segata, Nicola Nature microbiology. 27572971 2016 05 27;
Genetic Predictors of Benign Course of Ulcerative Colitis-A North American Inflammatory Bowel Disease Genetics Consortium Study. Kopylov, Uri; Boucher, Gabrielle; Waterman, Matti; Rivers, Claudia R; Patel, Mohini; Cho, Judy H; Colombel, Jean F; Duerr, Richard H; Binion, David; McGovern, Dermot P B; Schumm, Phillip P; Brant, Steven R; Silverberg, Mark S; Rioux, John D; Bitton, Alain Inflammatory bowel diseases. 27575496 2016 Oct;
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Genome Sequences of 15 Gardnerella vaginalis Strains Isolated from the Vaginas of Women with and without Bacterial Vaginosis. Robinson, Lloyd S; Perry, Justin; Lek, Sai; Wollam, Aye; Sodergren, Erica; Weinstock, George; Lewis, Warren G; Lewis, Amanda L Genome announcements. 27688326 2016 Sep 29;
Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women. Weimer, Cory M; Deitzler, Grace E; Robinson, Lloyd S; Park, SoEun; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G; Lewis, Amanda L Genome announcements. 27688327 2016 Sep 29;
Genome Sequences of 11 Human Vaginal Actinobacteria Strains. Lewis, Amanda L; Deitzler, Grace E; Ruiz, Maria J; Weimer, Cory; Park, SoEun; Robinson, Lloyd S; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G Genome announcements. 27688328 2016 Sep 29;
Genome Sequences of 14 Firmicutes Strains Isolated from the Human Vagina. Deitzler, Grace E; Ruiz, Maria J; Weimer, Cory; Park, SoEun; Robinson, Lloyd; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Amanda L; Lewis, Warren G Genome announcements. 27688329 2016 Sep 29;
Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates. Deitzler, Grace E; Ruiz, Maria J; Lu, Wendy; Weimer, Cory; Park, SoEun; Robinson, Lloyd S; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G; Lewis, Amanda L Genome announcements. 27688330 2016 Sep 29;
A New Catalog of Microbiological Tools for Women's Infectious Disease Research. Lewis, Amanda L; Lewis, Warren G Genome announcements. 27688331 2016 Sep 29;
Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Brant, Steven R; Okou, David T; Simpson, Claire L; Cutler, David J; Haritunians, Talin; Bradfield, Jonathan P; Chopra, Pankaj; Prince, Jarod; Begum, Ferdouse; Kumar, Archana; Huang, Chengrui; Venkateswaran, Suresh; Datta, Lisa W; Wei, Zhi; Thomas, Kelly; Herrinton, Lisa J; Klapproth, Jan-Micheal A; Quiros, Antonio J; Seminerio, Jenifer; Liu, Zhenqiu; Alexander, Jonathan S; Baldassano, Robert N; Dudley-Brown, Sharon; Cross, Raymond K; Dassopoulos, Themistocles; Denson, Lee A; Dhere, Tanvi A; Dryden, Gerald W; Hanson, John S; Hou, Jason K; Hussain, Sunny Z; Hyams, Jeffrey S; Isaacs, Kim L; Kader, Howard; Kappelman, Michael D; Katz, Jeffry; Kellermayer, Richard; Kirschner, Barbara S; Kuemmerle, John F; Kwon, John H; Lazarev, Mark; Li, Ellen; Mack, David; Mannon, Peter; Moulton, Dedrick E; Newberry, Rodney D; Osuntokun, Bankole O; Patel, Ashish S; Saeed, Shehzad A; Targan, Stephan R; Valentine, John F; Wang, Ming-Hsi; Zonca, Martin; Rioux, John D; Duerr, Richard H; Silverberg, Mark S; Cho, Judy H; Hakonarson, Hakon; Zwick, Michael E; McGovern, Dermot P B; Kugathasan, Subra Gastroenterology. 27693347 2017 Jan;
Nat1 Deficiency Is Associated with Mitochondrial Dysfunction and Exercise Intolerance in Mice. Chennamsetty, Indumathi; Coronado, Michael; Contrepois, Kévin; Keller, Mark P; Carcamo-Orive, Ivan; Sandin, John; Fajardo, Giovanni; Whittle, Andrew J; Fathzadeh, Mohsen; Snyder, Michael; Reaven, Gerald; Attie, Alan D; Bernstein, Daniel; Quertermous, Thomas; Knowles, Joshua W Cell reports. 27705799 2016 Oct 4;
Ethical issues in microbiome research and medicine. Rhodes, Rosamond BMC medicine. 27729053 2016 Oct 12;
The TNF family member TL1A induces IL-22 secretion in committed human Th17 cells via IL-9 induction. Thomas, Lisa S; Targan, Stephan R; Tsuda, Masato; Yu, Qi T; Salumbides, Brenda C; Haritunians, Talin; Mengesha, Emebet; McGovern, Dermot P B; Michelsen, Kathrin S Journal of leukocyte biology. 27733581 2017 03;
HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences. Danaher, Robert J; Fouts, Derrick E; Chan, Agnes P; Choi, Yongwook; DePew, Jessica; McCorrison, Jamison M; Nelson, Karen E; Wang, Chunmei; Miller, Craig S Journal of neurovirology. 27739035 2017 Apr;
Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity. Schirmer, Melanie; Smeekens, Sanne P; Vlamakis, Hera; Jaeger, Martin; Oosting, Marije; Franzosa, Eric A; Jansen, Trees; Jacobs, Liesbeth; Bonder, Marc Jan; Kurilshikov, Alexander; Fu, Jingyuan; Joosten, Leo A B; Zhernakova, Alexandra; Huttenhower, Curtis; Wijmenga, Cisca; Netea, Mihai G; Xavier, Ramnik J Cell. 27814509 2016 Nov 03;
HARNESSING BIG DATA FOR PRECISION MEDICINE: INFRASTRUCTURES AND APPLICATIONS. Yu, Kun-Hsing; Hart, Steven N; Goldfeder, Rachel; Zhang, Qiangfeng Cliff; Parker, Stephen C J; Snyder, Michael Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 27897013 2016;
MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing. Parikh, Hardik I; Koparde, Vishal N; Bradley, Steven P; Buck, Gregory A; Sheth, Nihar U BMC bioinformatics. 27905885 2016 Dec 01;
Effects of combined oral contraceptives, depot medroxyprogesterone acetate and the levonorgestrel-releasing intrauterine system on the vaginal microbiome. Brooks, J Paul; Edwards, David J; Blithe, Diana L; Fettweis, Jennifer M; Serrano, Myrna G; Sheth, Nihar U; Strauss 3rd, Jerome F; Buck, Gregory A; Jefferson, Kimberly K Contraception. 27913230 2016 Nov 29;
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Digital Health: Tracking Physiomes and Activity Using Wearable Biosensors Reveals Useful Health-Related Information. Li, Xiao; Dunn, Jessilyn; Salins, Denis; Zhou, Gao; Zhou, Wenyu; Schüssler-Fiorenza Rose, Sophia Miryam; Perelman, Dalia; Colbert, Elizabeth; Runge, Ryan; Rego, Shannon; Sonecha, Ria; Datta, Somalee; McLaughlin, Tracey; Snyder, Michael P PLoS biology. 28081144 2017 Jan;
Genome Sequence of Christensenella minuta DSM 22607T. Rosa, Bruce A; Hallsworth-Pepin, Kymberlie; Martin, John; Wollam, Aye; Mitreva, Makedonka Genome announcements. 28082495 2017 Jan 12;
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Myeloid ATG16L1 Facilitates Host-Bacteria Interactions in Maintaining Intestinal Homeostasis. Zhang, Hong; Zheng, Libo; McGovern, Dermot P B; Hamill, Ariel M; Ichikawa, Ryan; Kanazawa, Yoshitake; Luu, Justin; Kumagai, Kotaro; Cilluffo, Marianne; Fukata, Masayuki; Targan, Stephan R; Underhill, David M; Zhang, Xiaolan; Shih, David Q Journal of immunology (Baltimore, Md. : 1950). 28130498 2017 Mar 01;
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The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men. Sikavi, Daniel R; Nguyen, Long H; Haruki, Koichiro; Ugai, Tomotaka; Ma, Wenjie; Wang, Dong D; Thompson, Kelsey N; Yan, Yan; Branck, Tobyn; Wilkinson, Jeremy E; Akimoto, Naohiko; Zhong, Rong; Lau, Mai Chan; Mima, Kosuke; Kosumi, Keisuke; Morikawa, Teppei; Rimm, Eric B; Garrett, Wendy S; Izard, Jacques; Cao, Yin; Song, Mingyang; Huttenhower, Curtis; Ogino, Shuji; Chan, Andrew T Clinical and translational gastroenterology 34333506 2021 08 01
Vaginal microbiome Lactobacillus crispatus is heritable among European American women. Wright, Michelle L; Fettweis, Jennifer M; Eaves, Lindon J; Silberg, Judy L; Neale, Michael C; Serrano, Myrna G; Jimenez, Nicole R; Prom-Wormley, Elizabeth; Girerd, Philippe H; Borzelleca Jr, Joseph F; Jefferson, Kimberly K; Strauss 3rd, Jerome F; York, Timothy P; Buck, Gregory A Communications biology 34354222 2021 08 05
Complex species and strain ecology of the vaginal microbiome from pregnancy to postpartum and association with preterm birth. Pace, Ryan M; Chu, Derrick M; Prince, Amanda L; Ma, Jun; Seferovic, Maxim D; Aagaard, Kjersti M Med (New York, N.Y.) 34617072 2021 Sep 10
Metagenomic profiling of placental tissue suggests DNA virus infection of the placenta is rare. Witney, Adam A; Aller, Sean; Strang, Blair L The Journal of general virology 34723784 2021 11
Multivariable association discovery in population-scale meta-omics studies. Mallick, Himel; Rahnavard, Ali; McIver, Lauren J; Ma, Siyuan; Zhang, Yancong; Nguyen, Long H; Tickle, Timothy L; Weingart, George; Ren, Boyu; Schwager, Emma H; Chatterjee, Suvo; Thompson, Kelsey N; Wilkinson, Jeremy E; Subramanian, Ayshwarya; Lu, Yiren; Waldron, Levi; Paulson, Joseph N; Franzosa, Eric A; Bravo, Hector Corrada; Huttenhower, Curtis PLoS computational biology 34784344 2021 11
The vaginal microbiome in women of reproductive age with healthy weight versus overweight/obesity. Allen, Natalie G; Edupuganti, Laahirie; Edwards, David J; Jimenez, Nicole R; Buck, Gregory A; Jefferson, Kimberly K; Strauss 3rd, Jerome F; Vaginal Microbiome Consortium; Wickham 3rd, Edmond P; Fettweis, Jennifer M Obesity (Silver Spring, Md.) 34806323 2022 01
Unique roles of vaginal Megasphaera phylotypes in reproductive health. Glascock, Abigail L; Jimenez, Nicole R; Boundy, Sam; Koparde, Vishal N; Brooks, J Paul; Edwards, David J; Strauss Iii, Jerome F; Jefferson, Kimberly K; Serrano, Myrna G; Buck, Gregory A; Fettweis, Jennifer M Microbial genomics 34898422 2021 12
Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing. Zuo, Zheng; Chang, Yiming Kenny; Stormo, Gary D Briefings in functional genomics 34923581 2022 Apr 11
Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data. France, Michael T; Fu, Li; Rutt, Lindsay; Yang, Hongqiu; Humphrys, Michael S; Narina, Shilpa; Gajer, Pawel M; Ma, Bing; Forney, Larry J; Ravel, Jacques Genome biology 35232471 2022 Mar 01
Human gut bacteria produce ΤΗ17-modulating bile acid metabolites. Paik, Donggi; Yao, Lina; Zhang, Yancong; Bae, Sena; D'Agostino, Gabriel D; Zhang, Minghao; Kim, Eunha; Franzosa, Eric A; Avila-Pacheco, Julian; Bisanz, Jordan E; Rakowski, Christopher K; Vlamakis, Hera; Xavier, Ramnik J; Turnbaugh, Peter J; Longman, Randy S; Krout, Michael R; Clish, Clary B; Rastinejad, Fraydoon; Huttenhower, Curtis; Huh, Jun R; Devlin, A Sloan Nature 35296854 2022 03
Exerkines in health, resilience and disease. Chow, Lisa S; Gerszten, Robert E; Taylor, Joan M; Pedersen, Bente K; van Praag, Henriette; Trappe, Scott; Febbraio, Mark A; Galis, Zorina S; Gao, Yunling; Haus, Jacob M; Lanza, Ian R; Lavie, Carl J; Lee, Chih-Hao; Lucia, Alejandro; Moro, Cedric; Pandey, Ambarish; Robbins, Jeremy M; Stanford, Kristin I; Thackray, Alice E; Villeda, Saul; Watt, Matthew J; Xia, Ashley; Zierath, Juleen R; Goodpaster, Bret H; Snyder, Michael P Nature reviews. Endocrinology 35304603 2022 05
Associations Between Vaginal Bacteria and Bacterial Vaginosis Signs and Symptoms: A Comparative Study of Kenyan and American Women. Carter, Kayla A; Balkus, Jennifer E; Anzala, Omu; Kimani, Joshua; Hoffman, Noah G; Fiedler, Tina L; Mochache, Vernon; Fredricks, David N; McClelland, Raymond Scott; Srinivasan, Sujatha Frontiers in cellular and infection microbiology 35310847 2022
Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome. Li, Yanping; Wang, Fenglei; Li, Jun; Ivey, Kerry L; Wilkinson, Jeremy E; Wang, Dong D; Li, Ruifeng; Liu, Gang; Eliassen, Heather A; Chan, Andrew T; Clish, Clary B; Huttenhower, Curtis; Hu, Frank B; Sun, Qi; Rimm, Eric B BMC microbiology 35350985 2022 03 29
Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants. Kaelin, Emily A; Rodriguez, Cynthia; Hall-Moore, Carla; Hoffmann, Julie A; Linneman, Laura A; Ndao, I Malick; Warner, Barbara B; Tarr, Phillip I; Holtz, Lori R; Lim, Efrem S Nature microbiology 35449461 2022 May
Douching cessation and molecular bacterial vaginosis: a reanalysis of archived specimens. Brown, Sarah Elizabeth; He, Xin; Shardell, Michelle D; Ravel, Jacques; Ghanem, Khalil G; Zenilman, Jonathan M; Brotman, Rebecca M Sexually transmitted infections 35636931 2022 May 30
Progressive dysbiosis of human orodigestive microbiota along the sequence of gastroesophageal reflux, Barrett's esophagus and esophageal adenocarcinoma. Hao, Yuhan; Karaoz, Ulas; Yang, Liying; Yachimski, Patrick S; Tseng, Wenzhi; Nossa, Carlos W; Ye, Weimin; Tseng, Mengkao; Poles, Michael; Francois, Fritz; Traube, Morris; Brown, Stuart M; Chen, Yu; Torralba, Manolito; Peek, Richard M; Brodie, Eoin L; Pei, Zhiheng International journal of cancer 35751398 2022 Jun 24
High-sensitivity pattern discovery in large, paired multiomic datasets. Ghazi, Andrew R; Sucipto, Kathleen; Rahnavard, Ali; Franzosa, Eric A; McIver, Lauren J; Lloyd-Price, Jason; Schwager, Emma; Weingart, George; Moon, Yo Sup; Morgan, Xochitl C; Waldron, Levi; Huttenhower, Curtis Bioinformatics (Oxford, England) 35758795 2022 06 24
Complete Genome Sequences of Ezakiella coagulans C0061C1 and Fenollaria massiliensis C0061C2. France, Michael T; Clifford, Jack; Narina, Shilpa; Rutt, Lindsay; Ravel, Jacques Microbiology resource announcements 35861554 2022 Jul 21
Factors Associated With Incidence and Spontaneous Clearance of Molecular-Bacterial Vaginosis: Results From a Longitudinal Frequent-Sampling Observational Study. Tamarelle, Jeanne; Shardell, Michelle D; Ravel, Jacques; Brotman, Rebecca M Sexually transmitted diseases 35969846 2022 Sep 01
A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria. Yao, Lina; D'Agostino, Gabriel D; Park, Jinseok; Hang, Saiyu; Adhikari, Arijit A; Zhang, Yancong; Li, Wei; Avila-Pacheco, Julian; Bae, Sena; Clish, Clary B; Franzosa, Eric A; Huttenhower, Curtis; Huh, Jun R; Devlin, A Sloan Nature microbiology 35982310 2022 09
Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression. Delgado-Diaz, David Jose; Jesaveluk, Brianna; Hayward, Joshua A; Tyssen, David; Alisoltani, Arghavan; Potgieter, Matthys; Bell, Liam; Ross, Elizabeth; Iranzadeh, Arash; Allali, Imane; Dabee, Smritee; Barnabas, Shaun; Gamieldien, Hoyam; Blackburn, Jonathan M; Mulder, Nicola; Smith, Steven B; Edwards, Vonetta L; Burgener, Adam D; Bekker, Linda-Gail; Ravel, Jacques; Passmore, Jo-Ann S; Masson, Lindi; Hearps, Anna C; Tachedjian, Gilda Microbiome 36045402 2022 08 31
What is the FDA Going to Think?: Negotiating Values through Reflective and Strategic Category Work in Microbiome Science. Darling, Katherine W; Boyce, Angie M; Cho, Mildred K; Sankar, Pamela L Science, technology & human values 36119463 2015 Jan
Differential co-expression networks of the gut microbiota are associated with depression and anxiety treatment resistance among psychiatric inpatients. Thompson, Dominique S; Fu, Chenlian; Gandhi, Tanmay; Fowler, J Christopher; Frueh, B Christopher; Weinstein, Benjamin L; Petrosino, Joseph; Hadden, Julia K; Carlson, Marianne; Coarfa, Cristian; Madan, Alok Progress in neuro-psychopharmacology & biological psychiatry 36122838 2023 Jan 10
Roles of the Microbiota of the Female Reproductive Tract in Gynecological and Reproductive Health. Zhu, Bin; Tao, Zhi; Edupuganti, Laahirie; Serrano, Myrna G; Buck, Gregory A Microbiology and molecular biology reviews : MMBR 36222685 2022 Dec 21
Persistence and In Vivo Evolution of Vaginal Bacterial Strains over a Multiyear Time Period. France, Michael; Ma, Bing; Ravel, Jacques mSystems 36413016 2022 Dec 20
Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth. Liao, Jingqiu; Shenhav, Liat; Urban, Julia A; Serrano, Myrna; Zhu, Bin; Buck, Gregory A; Korem, Tal bioRxiv : the preprint server for biology 36711990 2023 Jun 17
Does the Vaginal Microbiome Operate Differently by Race to Influence Risk of Precervical Cancer? Tossas, Katherine Y; Zhu, Bin; Perera, Robert A; Serrano, Myrna G; Sullivan, Stephanie; Sayeed, Sadia; Strauss 3rd, Jerome F; Winn, Robert A; Buck, Gregory A; Seewaldt, Victoria L Journal of women's health (2002) 36897755 2023 May
History of childhood physical abuse is associated with gut microbiota diversity among adult psychiatric inpatients. Rohr, Jessica C; Bourassa, Katelynn A; Thompson, Dominique S; Fowler, J Christopher; Frueh, B Christopher; Weinstein, Benjamin L; Petrosino, Joseph; Madan, Alok Journal of affective disorders 36933668 2023 Jun 15
The Microbiome and Big Data. Navas-Molina, Jose A; Hyde, Embriette R; Sanders, Jon; Knight, Rob Current opinion in systems biology 36937228 2017 Aug
High-resolution functional description of vaginal microbiomes in health and disease. Holm, Johanna B; France, Michael T; Gajer, Pawel; Ma, Bing; Brotman, Rebecca M; Shardell, Michelle; Forney, Larry; Ravel, Jacques bioRxiv : the preprint server for biology 36993583 2023 Mar 24
Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit. Schwartz, Drew J; Shalon, Nitan; Wardenburg, Kate; DeVeaux, Anna; Wallace, Meghan A; Hall-Moore, Carla; Ndao, I Malick; Sullivan, Janice E; Radmacher, Paula; Escobedo, Marilyn; Burnham, Carey-Ann D; Warner, Barbara B; Tarr, Phillip I; Dantas, Gautam Science translational medicine 37134153 2023 May 03
Investigating the impact of condomless vaginal intercourse and lubricant use on the vaginal metabolome: a pre-post observational study. Borgogna, Joanna-Lynn C; Grace, Savannah G; Holm, Johanna B; Aviles Zuniga, Tadeo; Kadriu, Herlin; He, Xin; McCoski, Sarah R; Ravel, Jacques; Brotman, Rebecca M; Yeoman, Carl J Sexually transmitted infections 37258272 2023 Nov
Evaluation of vaginal microbiome equilibrium states identifies microbial parameters linked to resilience after menses and antibiotic therapy. Lee, Christina Y; Diegel, Jenna; France, Michael T; Ravel, Jacques; Arnold, Kelly B PLoS computational biology 37566641 2023 Aug
Microdiversity of the vaginal microbiome is associated with preterm birth. Liao, Jingqiu; Shenhav, Liat; Urban, Julia A; Serrano, Myrna; Zhu, Bin; Buck, Gregory A; Korem, Tal Nature communications 37591872 2023 Aug 17
Profiling novel lateral gene transfer events in the human microbiome. Hsu, Tiffany Y; Nzabarushimana, Etienne; Wong, Dennis; Luo, Chengwei; Beiko, Robert G; Langille, Morgan; Huttenhower, Curtis; Nguyen, Long H; Franzosa, Eric A bioRxiv : the preprint server for biology 37609252 2023 Aug 14
Integrating compositional and functional content to describe vaginal microbiomes in health and disease. Holm, Johanna B; France, Michael T; Gajer, Pawel; Ma, Bing; Brotman, Rebecca M; Shardell, Michelle; Forney, Larry; Ravel, Jacques Microbiome 38031142 2023 Nov 30
Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Zhou, Xin; Shen, Xiaotao; Johnson, Jethro S; Spakowicz, Daniel J; Agnello, Melissa; Zhou, Wenyu; Avina, Monica; Honkala, Alexander; Chleilat, Faye; Chen, Shirley Jingyi; Cha, Kexin; Leopold, Shana; Zhu, Chenchen; Chen, Lei; Lyu, Lin; Hornburg, Daniel; Wu, Si; Zhang, Xinyue; Jiang, Chao; Jiang, Liuyiqi; Jiang, Lihua; Jian, Ruiqi; Brooks, Andrew W; Wang, Meng; Contrepois, Kévin; Gao, Peng; Rose, Sophia Miryam Schüssler-Fiorenza; Tran, Thi Dong Binh; Nguyen, Hoan; Celli, Alessandra; Hong, Bo-Young; Bautista, Eddy J; Dorsett, Yair; Kavathas, Paula B; Zhou, Yanjiao; Sodergren, Erica; Weinstock, George M; Snyder, Michael P Cell host & microbe 38479397 2024 Apr 10
MetaCompass: Reference-guided Assembly of Metagenomes. Luan, Tu; Cepeda, Victoria; Liu, Bo; Bowen, Zac; Ayyangar, Ujjwal; Almeida, Mathieu; Hill, Christopher M; Koren, Sergey; Treangen, Todd J; Porter, Adam; Pop, Mihai ArXiv 38903742 2024 Mar 03
Antibody Response to the Sneathia vaginalis Cytopathogenic Toxin A during Pregnancy. McCoy, Zion T; Serrano, Myrna G; Edupuganti, Laahirie; Spaine, Katherine M; Edwards, David J; Buck, Gregory A; Jefferson, Kimberly K ImmunoHorizons 38276916 2024 Jan 01
The association of maternal factors with the neonatal microbiota and health. Zhu, Bin; Edwards, David J; Spaine, Katherine M; Edupuganti, Laahirie; Matveyev, Andrey; Serrano, Myrna G; Buck, Gregory A Nature communications 38898021 2024 Jun 19

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