Program Publications
Publications Search by Program
Search Results
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 |
How patients view probiotics: findings from a multicenter study of patients with inflammatory bowel disease and irritable bowel syndrome. | Mercer, MaryBeth; Brinich, Margaret A; Geller, Gail; Harrison, Krista; Highland, Janelle; James, Katherine; Marshall, Patricia; McCormick, Jennifer B; Tilburt, Jon; Achkar, Jean-Paul; Farrell, Ruth M; Sharp, Richard R | Journal of clinical gastroenterology | 21716123 | 2012 Feb |
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. | Werner, Jeffrey J; Koren, Omry; Hugenholtz, Philip; DeSantis, Todd Z; Walters, William A; Caporaso, J Gregory; Angenent, Largus T; Knight, Rob; Ley, Ruth E | The ISME journal | 21716311 | 2012 Jan |
DNACLUST: accurate and efficient clustering of phylogenetic marker genes. | Ghodsi, Mohammadreza; Liu, Bo; Pop, Mihai | BMC bioinformatics | 21718538 | 2011 |
Extrapolation of urn models via poissonization: accurate measurements of the microbial unknown. | Lladser, Manuel E; Gouet, Raul; Reeder, Jens | PloS one | 21738613 | 2011 |
Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. | Saulnier, Delphine M; Riehle, Kevin; Mistretta, Toni-Ann; Diaz, Maria-Alejandra; Mandal, Debasmita; Raza, Sabeen; Weidler, Erica M; Qin, Xiang; Coarfa, Cristian; Milosavljevic, Aleksandar; Petrosino, Joseph F; Highlander, Sarah; Gibbs, Richard; Lynch, Sus | Gastroenterology | 21741921 | 2011 Nov |
Microfluidic fluorescence in situ hybridization and flow cytometry (ýýFlowFISH). | Liu, Peng; Meagher, Robert J; Light, Yooli K; Yilmaz, Suzan; Chakraborty, Romy; Arkin, Adam P; Hazen, Terry C; Singh, Anup K | Lab on a chip | 21755095 | 2011 Aug 21 |
Bayesian community-wide culture-independent microbial source tracking. | Knights, Dan; Kuczynski, Justin; Charlson, Emily S; Zaneveld, Jesse; Mozer, Michael C; Collman, Ronald G; Bushman, Frederic D; Knight, Rob; Kelley, Scott T | Nature methods | 21765408 | 2011 Sep |
Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting through the Growing Pains and Moving Forward. | Young, Vincent B; Kahn, Stacy A; Schmidt, Thomas M; Chang, Eugene B | Frontiers in microbiology | 21772835 | 2011 |
Investigating the biological and clinical significance of human dysbioses. | Frank, Daniel N; Zhu, Wei; Sartor, R Balfour; Li, Ellen | Trends in microbiology | 21775143 | 2011 Sep |
The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. | He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong | The ISME journal | 21796217 | 2012 Feb |
The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection. | Reeves, Angela E; Theriot, Casey M; Bergin, Ingrid L; Huffnagle, Gary B; Schloss, Patrick D; Young, Vincent B | Gut microbes | 21804357 | 2011 May-Jun |
Specific sorting of single bacterial cells with microfabricated fluorescence-activated cell sorting and tyramide signal amplification fluorescence in situ hybridization. | Chen, Chun H; Cho, Sung H; Chiang, Hsin-I; Tsai, Frank; Zhang, Kun; Lo, Yu-Hwa | Analytical chemistry | 21809842 | 2011 Oct 1 |
Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison. | Ahn, Jiyoung; Yang, Liying; Paster, Bruce J; Ganly, Ian; Morris, Luc; Pei, Zhiheng; Hayes, Richard B | PloS one | 21829515 | 2011 |
Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. | Zaneveld, Jesse R R; Parfrey, Laura Wegener; Van Treuren, Will; Lozupone, Catherine; Clemente, Jose C; Knights, Dan; Stombaugh, Jesse; Kuczynski, Justin; Knight, Rob | Trends in microbiology | 21872475 | 2011 Oct |
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 | 2012 Jan |
Linking long-term dietary patterns with gut microbial enterotypes. | Wu, Gary D; Chen, Jun; Hoffmann, Christian; Bittinger, Kyle; Chen, Ying-Yu; Keilbaugh, Sue A; Bewtra, Meenakshi; Knights, Dan; Walters, William A; Knight, Rob; Sinha, Rohini; Gilroy, Erin; Gupta, Kernika; Baldassano, Robert; Nessel, Lisa; Li, Hongzhe; Bus | Science (New York, N.Y.) | 21885731 | 2011 Oct 7 |
Genetic basis for in vivo daptomycin resistance in enterococci. | Arias, Cesar A; Panesso, Diana; McGrath, Danielle M; Qin, Xiang; Mojica, Maria F; Miller, Corwin; Diaz, Lorena; Tran, Truc T; Rincon, Sandra; Barbu, E Magda; Reyes, Jinnethe; Roh, Jung H; Lobos, Elizabeth; Sodergren, Erica; Pasqualini, Renata; Arap, Wadih | The New England journal of medicine | 21899450 | 2011 Sep 8 |
WebMGA: a customizable web server for fast metagenomic sequence analysis. | Wu, Sitao; Zhu, Zhengwei; Fu, Liming; Niu, Beifang; Li, Weizhong | BMC genomics | 21899761 | 2011 |
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. | Pirrung, Meg; Kennedy, Ryan; Caporaso, J Gregory; Stombaugh, Jesse; Wendel, Doug; Knight, Rob | Bioinformatics (Oxford, England) | 21903626 | 2011 Nov 1 |
Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). | Youssef, Noha H; Blainey, Paul C; Quake, Stephen R; Elshahed, Mostafa S | Applied and environmental microbiology | 21908640 | 2011 Nov |
Applying an optical space-time coding method to enhance light scattering signals in microfluidic devices. | Mei, Zhe; Wu, Tsung-Feng; Pion-Tonachini, Luca; Qiao, Wen; Zhao, Chao; Liu, Zhiwen; Lo, Yu-Hwa | Biomicrofluidics. | 21915241 | 2011 Sep; |
The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. | Sczesnak, Andrew; Segata, Nicola; Qin, Xiang; Gevers, Dirk; Petrosino, Joseph F; Huttenhower, Curtis; Littman, Dan R; Ivanov, Ivaylo I | Cell host & microbe | 21925113 | 2011 Sep 15 |
Bambus 2: scaffolding metagenomes. | Koren, Sergey; Treangen, Todd J; Pop, Mihai | Bioinformatics (Oxford, England) | 21926123 | 2011 Nov 1 |
Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. | Segata, Nicola; Huttenhower, Curtis | PloS one | 21931822 | 2011 |
Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data. | Liu, Zhenqiu; Hsiao, William; Cantarel, Brandi L; Drabek, Elliott Franco; Fraser-Liggett, Claire | Bioinformatics (Oxford, England) | 21984758 | 2011 Dec 1 |
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. | Liu, Bo; Gibbons, Theodore; Ghodsi, Mohammad; Treangen, Todd; Pop, Mihai | BMC genomics | 21989143 | 2011 |
Fluorescent labeling of antibody fragments using split GFP. | Ferrara, Fortunato; Listwan, Pawel; Waldo, Geoffrey S; Bradbury, Andrew R M | PloS one | 21998685 | 2011 |
Human-associated microbial signatures: examining their predictive value. | Knights, Dan; Parfrey, Laura Wegener; Zaneveld, Jesse; Lozupone, Catherine; Knight, Rob | Cell host & microbe. | 22018228 | 2011 Oct 20; |
Microbiome and malignancy. | Plottel, Claudia S; Blaser, Martin J | Cell host & microbe | 22018233 | 2011 Oct 20 |
Graph accordance of next-generation sequence assemblies. | Yao, Guohui; Ye, Liang; Gao, Hongyu; Minx, Patrick; Warren, Wesley C; Weinstock, George M | Bioinformatics (Oxford, England) | 22025481 | 2012 Jan 1 |
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. | Zhao, Yongan; Tang, Haixu; Ye, Yuzhen | Bioinformatics (Oxford, England) | 22039206 | 2012 Jan 1 |
De minimis risk: a proposal for a new category of research risk. | Rhodes, Rosamond; Azzouni, Jody; Baumrin, Stefan Bernard; Benkov, Keith; Blaser, Martin J; Brenner, Barbara; Dauben, Joseph W; Earle, William J; Frank, Lily; Gligorov, Nada; Goldfarb, Joseph; Hirschhorn, Kurt; Hirschhorn, Rochelle; Holzman, Ian; Indyk, De | The American journal of bioethics : AJOB | 22047112 | 2011 Nov |
Saying privacy, meaning confidentiality. | Schwab, Abraham P; Frank, Lily; Gligorov, Nada | The American journal of bioethics : AJOB | 22047127 | 2011 Nov |
2,2'-Bis(meth-oxy-meth-oxy)-3-methyl-1,1'-binaphth-yl. | Carrilho, Rui M B; Abreu, Artur R; Pereira, Mariette M; Rodrigues, V H | Acta crystallographica. Section E, Structure reports online. | 22058976 | 2011 Sep 01; |
Tetra-?-acetato-?O:O'-bis-[(3,5-di-methyl-1H-pyrazole-?N)-copper(II)]. | van Wyk, Juanita; Omondi, Bernard; Darkwa, James | Acta crystallographica. Section E, Structure reports online. | 22065823 | 2011 Sep 01; |
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. | Basu, Malay K; Selengut, Jeremy D; Haft, Daniel H | BMC bioinformatics | 22070167 | 2011 |
Epigenetic priors for identifying active transcription factor binding sites. | Cuellar-Partida, Gabriel; Buske, Fabian A; McLeay, Robert C; Whitington, Tom; Noble, William Stafford; Bailey, Timothy L | Bioinformatics (Oxford, England) | 22072382 | 2012 Jan 1 |
The intestinal microbiota in health and disease. | Young, Vincent B | Current opinion in gastroenterology | 22080827 | 2012 Jan |
IMG/M: the integrated metagenome data management and comparative analysis system. | Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Pati, Amrita; Huntemann, Marcel; Liolios, Konstantinos; Pagani, Ioanna; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natali | Nucleic acids research | 22086953 | 2012 Jan |
Astrovirus MLB2 viremia in febrile child. | Holtz, Lori R; Wylie, Kristine M; Sodergren, Erica; Jiang, Yanfang; Franz, Carl J; Weinstock, George M; Storch, Gregory A; Wang, David | Emerging infectious diseases | 22099095 | 2011 Nov |
Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment. | Ye, Yuzhen | Proceedings. IEEE International Conference on Bioinformatics and Biomedicine | 22102981 | 2011 Feb 4 |
The Human Microbiome Project: lessons from human genomics. | Lewis Jr, Cecil M; Obregon-Tito, Alexandra; Tito, Raul Y; Foster, Morris W; Spicer, Paul G | Trends in microbiology | 22112388 | 2012 Jan |
An optical-coding method to measure particle distribution in microfluidic devices. | Wu, Tsung-Feng; Mei, Zhe; Pion-Tonachini, Luca; Zhao, Chao; Qiao, Wen; Arianpour, Ashkan; Lo, Yu-Hwa | AIP advances. | 22125760 | 2011 Jun; |
Strategies for metagenomic-guided whole-community proteomics of complex microbial environments. | Cantarel, Brandi L; Erickson, Alison R; VerBerkmoes, Nathan C; Erickson, Brian K; Carey, Patricia A; Pan, Chongle; Shah, Manesh; Mongodin, Emmanuel F; Jansson, Janet K; Fraser-Liggett, Claire M; Hettich, Robert L | PloS one | 22132090 | 2011 |
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. | McDonald, Daniel; Price, Morgan N; Goodrich, Julia; Nawrocki, Eric P; DeSantis, Todd Z; Probst, Alexander; Andersen, Gary L; Knight, Rob; Hugenholtz, Philip | The ISME journal | 22134646 | 2012 Mar |
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. | Pagani, Ioanna; Liolios, Konstantinos; Jansson, Jakob; Chen, I-Min A; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor M; Kyrpides, Nikos C | Nucleic acids research | 22135293 | 2012 Jan |
CharProtDB: a database of experimentally characterized protein annotations. | Madupu, Ramana; Richter, Alexander; Dodson, Robert J; Brinkac, Lauren; Harkins, Derek; Durkin, Scott; Shrivastava, Susmita; Sutton, Granger; Haft, Daniel | Nucleic acids research | 22140108 | 2012 Jan |
GAGE: A critical evaluation of genome assemblies and assembly algorithms. | Salzberg, Steven L; Phillippy, Adam M; Zimin, Aleksey; Puiu, Daniela; Magoc, Tanja; Koren, Sergey; Treangen, Todd J; Schatz, Michael C; Delcher, Arthur L; Roberts, Michael; Marcais, Guillaume; Pop, Mihai; Yorke, James A | Genome research | 22147368 | 2012 Mar |
Characterizing microbial communities through space and time. | Gonzalez, Antonio; King, Andrew; Robeson 2nd, Michael S; Song, Sejin; Shade, Ashley; Metcalf, Jessica L; Knight, Rob | Current opinion in biotechnology | 22154467 | 2012 Jun |
Single cell genome sequencing. | Yilmaz, Suzan; Singh, Anup K | Current opinion in biotechnology | 22154471 | 2012 Jun |
Using QIIME to analyze 16S rRNA gene sequences from microbial communities. | Kuczynski, Justin; Stombaugh, Jesse; Walters, William Anton; Gonzalez, Antonio; Caporaso, J Gregory; Knight, Rob | Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] | 22161565 | 2011 Dec |
Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences. | Wang, Xiaoyu; Cai, Yunpeng; Sun, Yijun; Knight, Rob; Mai, Volker | The ISME journal | 22170430 | 2012 Jul |
SitePainter: a tool for exploring biogeographical patterns. | Gonzalez, Antonio; Stombaugh, Jesse; Lauber, Christian L; Fierer, Noah; Knight, Rob | Bioinformatics (Oxford, England) | 22171330 | 2012 Feb 1 |
Advancing analytical algorithms and pipelines for billions of microbial sequences. | Gonzalez, Antonio; Knight, Rob | Current opinion in biotechnology | 22172529 | 2012 Feb |
Artificial functional difference between microbial communities caused by length difference of sequencing reads. | Zhang, Quan; Doak, Thomas G; Ye, Yuzhen | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 22174281 | 2012 |
Experimental and analytical tools for studying the human microbiome. | Kuczynski, Justin; Lauber, Christian L; Walters, William A; Parfrey, Laura Wegener; Clemente, Jose C; Gevers, Dirk; Knight, Rob | Nature reviews. Genetics | 22179717 | 2012 Jan |
Single-cell protein analysis. | Wu, Meiye; Singh, Anup K | Current opinion in biotechnology | 22189001 | 2012 Feb |
Human microbiome and HIV/AIDS. | Saxena, Deepak; Li, Yihong; Yang, Liying; Pei, Zhiheng; Poles, Michael; Abrams, William R; Malamud, Daniel | Current HIV/AIDS reports | 22193889 | 2012 Mar |
IMG: the Integrated Microbial Genomes database and comparative analysis system. | Markowitz, Victor M; Chen, I-Min A; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos | Nucleic acids research | 22194640 | 2012 Jan |
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. | Schloss, Patrick D; Gevers, Dirk; Westcott, Sarah L | PloS one | 22194782 | 2011 |
GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease. | Haft, Daniel H; Varghese, Neha | PloS one | 22194940 | 2011 |
Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws. | Smajs, David; Norris, Steven J; Weinstock, George M | Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases | 22198325 | 2012 Mar |
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. | Schatz, Michael C; Phillippy, Adam M; Sommer, Daniel D; Delcher, Arthur L; Puiu, Daniela; Narzisi, Giuseppe; Salzberg, Steven L; Pop, Mihai | Briefings in bioinformatics | 22199379 | 2013 Mar |
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. | Soergel, David A W; Dey, Neelendu; Knight, Rob; Brenner, Steven E | The ISME journal | 22237546 | 2012 Jul |
Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments. | Ozok, A R; Persoon, I F; Huse, S M; Keijser, B J F; Wesselink, P R; Crielaard, W; Zaura, E | International endodontic journal | 22251411 | 2012 Jun |
Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis. | Feazel, Leah M; Robertson, Charles E; Ramakrishnan, Vijay R; Frank, Daniel N | The Laryngoscope | 22253013 | 2012 Feb |
Perturbation dynamics of the rumen microbiota in response to exogenous butyrate. | Li, Robert W; Wu, Sitao; Baldwin 6th, Ransom L; Li, Weizhong; Li, Congjun | PloS one | 22253719 | 2012 |
Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine. | Preidis, Geoffrey A; Saulnier, Delphine M; Blutt, Sarah E; Mistretta, Toni-Ann; Riehle, Kevin P; Major, Angela M; Venable, Susan F; Finegold, Milton J; Petrosino, Joseph F; Conner, Margaret E; Versalovic, James | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 22267340 | 2012 May |
The under-recognized dominance of Verrucomicrobia in soil bacterial communities. | Bergmann, Gaddy T; Bates, Scott T; Eilers, Kathryn G; Lauber, Christian L; Caporaso, J Gregory; Walters, William A; Knight, Rob; Fierer, Noah | Soil biology & biochemistry | 22267877 | 2011 Jul |
Significance of the microbiome in obstructive lung disease. | Han, Meilan K; Huang, Yvonne J; Lipuma, John J; Boushey, Homer A; Boucher, Richard C; Cookson, William O; Curtis, Jeffrey L; Erb-Downward, John; Lynch, Susan V; Sethi, Sanjay; Toews, Galen B; Young, Vincent B; Wolfgang, Matthew C; Huffnagle, Gary B; Marti | Thorax | 22318161 | 2012 May |
Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice. | Mei, Junjie; Liu, Yuhong; Dai, Ning; Hoffmann, Christian; Hudock, Kristin M; Zhang, Peggy; Guttentag, Susan H; Kolls, Jay K; Oliver, Paula M; Bushman, Frederic D; Worthen, G Scott | The Journal of clinical investigation | 22326959 | 2012 Mar 1 |
Altered vaginal microbiota are associated with perinatal mother-to-child transmission of HIV in African women from Burkina Faso. | Frank, Daniel N; Manigart, Olivier; Leroy, Valeriane; Meda, Nicolas; Valea, Diane; Zhang, Weiming; Dabis, Francois; Pace, Norman R; Van de Perre, Philippe; Janoff, Edward N | Journal of acquired immune deficiency syndromes (1999) | 22343176 | 2012 Jul 1 |
Host response to probiotics determined by nutritional status of rotavirus-infected neonatal mice. | Preidis, Geoffrey A; Saulnier, Delphine M; Blutt, Sarah E; Mistretta, Toni-Ann; Riehle, Kevin P; Major, Angela M; Venable, Susan F; Barrish, James P; Finegold, Milton J; Petrosino, Joseph F; Guerrant, Richard L; Conner, Margaret E; Versalovic, James | Journal of pediatric gastroenterology and nutrition | 22343914 | 2012 Sep |
Molecular pathways: pathogenesis and clinical implications of microbiome alteration in esophagitis and Barrett esophagus. | Yang, Liying; Francois, Fritz; Pei, Zhiheng | Clinical cancer research : an official journal of the American Association for Cancer Research | 22344232 | 2012 Apr 15 |
Hypervariable loci in the human gut virome. | Minot, Samuel; Grunberg, Stephanie; Wu, Gary D; Lewis, James D; Bushman, Frederic D | Proceedings of the National Academy of Sciences of the United States of America | 22355105 | 2012 Mar 6 |
Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment. | Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta; Pel, Joel; Marziali, Andre | PloS one | 22355378 | 2012 |
Of microbes and meals: the health consequences of dietary endotoxemia. | Kelly, Caleb J; Colgan, Sean P; Frank, Daniel N | Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition. | 22378797 | 2012 Apr; |
A format for phylogenetic placements. | Matsen, Frederick A; Hoffman, Noah G; Gallagher, Aaron; Stamatakis, Alexandros | PloS one | 22383988 | 2012 |
Standard colonic lavage alters the natural state of mucosal-associated microbiota in the human colon. | Harrell, Laura; Wang, Yunwei; Antonopoulos, Dionysios; Young, Vincent; Lichtenstein, Lev; Huang, Yong; Hanauer, Stephen; Chang, Eugene | PloS one | 22389708 | 2012 |
Experiences of patients with chronic gastrointestinal conditions: in their own words. | McCormick, Jennifer B; Hammer, Rachel R; Farrell, Ruth M; Geller, Gail; James, Katherine M; Loftus Jr, Edward V; Mercer, Mary Beth; Tilburt, Jon C; Sharp, Richard R | Health and quality of life outcomes | 22401607 | 2012 |
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. | Caporaso, J Gregory; Lauber, Christian L; Walters, William A; Berg-Lyons, Donna; Huntley, James; Fierer, Noah; Owens, Sarah M; Betley, Jason; Fraser, Louise; Bauer, Markus; Gormley, Niall; Gilbert, Jack A; Smith, Geoff; Knight, Rob | The ISME journal. | 22402401 | 2012 Aug; |
The human microbiome: at the interface of health and disease. | Cho, Ilseung; Blaser, Martin J | Nature reviews. Genetics | 22411464 | 2012 Apr |
Dichlorido{1-[N-(5-chloro-2-oxidophen-yl)carboximido-yl]naphthalen-2-olato-?O,N,O'}(methanol-?O)tin(IV). | Shahverdizadeh, Gholam Hossein; Ng, Seik Weng; Tiekink, Edward R T; Mirtamizdoust, Babak | Acta crystallographica. Section E, Structure reports online. | 22412406 | 2012 Mar 01; |
4,5-Diphen-oxy-benzene-1,2-dicarbo-nitrile. | Foo, Chuan Ching; Tan, Ai Ling; Wimmer, Franz L; Mirza, Aminul Huq; Young, David J; Ng, Seik Weng; Tiekink, Edward R T | Acta crystallographica. Section E, Structure reports online. | 22412514 | 2012 Mar 01; |
The impact of the gut microbiota on human health: an integrative view. | Clemente, Jose C; Ursell, Luke K; Parfrey, Laura Wegener; Knight, Rob | Cell. | 22424233 | 2012 Mar 16; |
Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). | Pamp, Sunje J; Harrington, Eoghan D; Quake, Stephen R; Relman, David A; Blainey, Paul C | Genome research | 22434425 | 2012 Jun |
AntiFam: a tool to help identify spurious ORFs in protein annotation. | Eberhardt, Ruth Y; Haft, Daniel H; Punta, Marco; Martin, Maria; O'Donovan, Claire; Bateman, Alex | Database : the journal of biological databases and curation | 22434837 | 2012 |
Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation. | Hill, David A; Siracusa, Mark C; Abt, Michael C; Kim, Brian S; Kobuley, Dmytro; Kubo, Masato; Kambayashi, Taku; Larosa, David F; Renner, Ellen D; Orange, Jordan S; Bushman, Frederic D; Artis, David | Nature medicine | 22447074 | 2012 Apr |
Decade-long bacterial community dynamics in cystic fibrosis airways. | Zhao, Jiangchao; Schloss, Patrick D; Kalikin, Linda M; Carmody, Lisa A; Foster, Bridget K; Petrosino, Joseph F; Cavalcoli, James D; VanDevanter, Donald R; Murray, Susan; Li, Jun Z; Young, Vincent B; LiPuma, John J | Proceedings of the National Academy of Sciences of the United States of America | 22451929 | 2012 Apr 10 |
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. | Giannoukos, Georgia; Ciulla, Dawn M; Huang, Katherine; Haas, Brian J; Izard, Jacques; Levin, Joshua Z; Livny, Jonathan; Earl, Ashlee M; Gevers, Dirk; Ward, Doyle V; Nusbaum, Chad; Birren, Bruce W; Gnirke, Andreas | Genome biology | 22455878 | 2012 |
Alterations in the porcine colon microbiota induced by the gastrointestinal nematode Trichuris suis. | Li, Robert W; Wu, Sitao; Li, Weizhong; Navarro, Karl; Couch, Robin D; Hill, Dolores; Urban Jr, Joseph F | Infection and immunity | 22493085 | 2012 Jun |
Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism. | Pathak, Darshankumar T; Wei, Xueming; Bucuvalas, Alex; Haft, Daniel H; Gerloff, Dietlind L; Wall, Daniel | PLoS genetics | 22511878 | 2012 |
Worm burden-dependent disruption of the porcine colon microbiota by Trichuris suis infection. | Wu, Sitao; Li, Robert W; Li, Weizhong; Beshah, Ethiopia; Dawson, Harry D; Urban Jr, Joseph F | PloS one | 22532855 | 2012 |
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. | Ursell, Luke K; Clemente, Jose C; Rideout, Jai Ram; Gevers, Dirk; Caporaso, J Gregory; Knight, Rob | The Journal of allergy and clinical immunology | 22541361 | 2012 May |
We are what we eat: how the diet of infants affects their gut microbiome. | Pop, Mihai | Genome biology | 22546514 | 2012 |
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots. | Matsen, Frederick A; Gallagher, Aaron | Algorithms for molecular biology : AMB. | 22549005 | 2012 May 02; |
Temporal dynamics of the human vaginal microbiota. | Gajer, Pawel; Brotman, Rebecca M; Bai, Guoyun; Sakamoto, Joyce; Schutte, Ursel M E; Zhong, Xue; Koenig, Sara S K; Fu, Li; Ma, Zhanshan Sam; Zhou, Xia; Abdo, Zaid; Forney, Larry J; Ravel, Jacques | Science translational medicine | 22553250 | 2012 May 2 |
Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. | Xiong, Xuejian; Frank, Daniel N; Robertson, Charles E; Hung, Stacy S; Markle, Janet; Canty, Angelo J; McCoy, Kathy D; Macpherson, Andrew J; Poussier, Philippe; Danska, Jayne S; Parkinson, John | PloS one | 22558305 | 2012 |
Food and the gut microbiota in inflammatory bowel diseases: a critical connection. | Albenberg, Lindsey G; Lewis, James D; Wu, Gary D | Current opinion in gastroenterology | 22573192 | 2012 Jul |
A new era of the vaginal microbiome: advances using next-generation sequencing. | Fettweis, Jennifer M; Serrano, Myrna G; Girerd, Philippe H; Jefferson, Kimberly K; Buck, Gregory A | Chemistry & biodiversity | 22589096 | 2012 May |
Interaction between the intestinal microbiota and host in Clostridium difficile colonization resistance. | Britton, Robert A; Young, Vincent B | Trends in microbiology | 22595318 | 2012 Jul |
Bacterial communities of the coronal sulcus and distal urethra of adolescent males. | Nelson, David E; Dong, Qunfeng; Van der Pol, Barbara; Toh, Evelyn; Fan, Baochang; Katz, Barry P; Mi, Deming; Rong, Ruichen; Weinstock, George M; Sodergren, Erica; Fortenberry, J Dennis | PloS one | 22606251 | 2012 |
An ileal Crohn's disease gene signature based on whole human genome expression profiles of disease unaffected ileal mucosal biopsies. | Zhang, Tianyi; Song, Bowen; Zhu, Wei; Xu, Xiao; Gong, Qing Qing; Morando, Christopher; Dassopoulos, Themistocles; Newberry, Rodney D; Hunt, Steven R; Li, Ellen | PloS one | 22606341 | 2012 |
Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells. | Wu, Sitao; Li, Robert W; Li, Weizhong; Li, Cong-Jun | PloS one | 22615851 | 2012 |
'Omics' of the mammalian gut--new insights into function. | Lamendella, Regina; VerBerkmoes, Nathan; Jansson, Janet K | Current opinion in biotechnology | 22626866 | 2012 Jun |
RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. | Widmann, Jeremy; Stombaugh, Jesse; McDonald, Daniel; Chocholousova, Jana; Gardner, Paul; Iyer, Matthew K; Liu, Zongzhi; Lozupone, Catherine A; Quinn, John; Smit, Sandra; Wikman, Shandy; Zaneveld, Jesse R R; Knight, Rob | RNA (New York, N.Y.) | 22645380 | 2012 Jul |
Spatial and temporal variability of the human microbiota. | Parfrey, L W; Knight, R | Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases | 22647040 | 2012 Jul |
Quantification of Transcriptome Responses of the Rumen Epithelium to Butyrate Infusion using RNA-seq Technology. | Baldwin 6th, Ransom L; Wu, Sitao; Li, Weizhong; Li, Congjun; Bequette, Brian J; Li, Robert W | Gene regulation and systems biology | 22654504 | 2012 |
Comparison of storage conditions for human vaginal microbiome studies. | Bai, Guoyun; Gajer, Pawel; Nandy, Melissa; Ma, Bing; Yang, Hongqiu; Sakamoto, Joyce; Blanchard, May H; Ravel, Jacques; Brotman, Rebecca M | PloS one | 22655031 | 2012 |
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. | Lozupone, Catherine; Faust, Karoline; Raes, Jeroen; Faith, Jeremiah J; Frank, Daniel N; Zaneveld, Jesse; Gordon, Jeffrey I; Knight, Rob | Genome research | 22665442 | 2012 Oct |
Deep sequencing of the oral microbiome reveals signatures of periodontal disease. | Liu, Bo; Faller, Lina L; Klitgord, Niels; Mazumdar, Varun; Ghodsi, Mohammad; Sommer, Daniel D; Gibbons, Theodore R; Treangen, Todd J; Chang, Yi-Chien; Li, Shan; Stine, O Colin; Hasturk, Hatice; Kasif, Simon; Segre, Daniel; Pop, Mihai; Amar, Salomon | PloS one | 22675498 | 2012 |
High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)). | Earl, Ashlee M; Desjardins, Christopher A; Fitzgerald, Michael G; Arachchi, Harindra M; Zeng, Qiandong; Mehta, Teena; Griggs, Allison; Birren, Bruce W; Toney, Nadege C; Carr, Janice; Posey, James; Butler, W Ray | Standards in genomic sciences. | 22675588 | 2011 Dec 31; |
Unlocking the potential of metagenomics through replicated experimental design. | Knight, Rob; Jansson, Janet; Field, Dawn; Fierer, Noah; Desai, Narayan; Fuhrman, Jed A; Hugenholtz, Phil; van der Lelie, Daniel; Meyer, Folker; Stevens, Rick; Bailey, Mark J; Gordon, Jeffrey I; Kowalchuk, George A; Gilbert, Jack A | Nature biotechnology. | 22678395 | 2012 Jun; |
The microbiome of the lung. | Beck, James M; Young, Vincent B; Huffnagle, Gary B | Translational research : the journal of laboratory and clinical medicine | 22683412 | 2012 Oct |
Understanding vaginal microbiome complexity from an ecological perspective. | Hickey, Roxana J; Zhou, Xia; Pierson, Jacob D; Ravel, Jacques; Forney, Larry J | Translational research : the journal of laboratory and clinical medicine | 22683415 | 2012 Oct |
Emerging view of the human virome. | Wylie, Kristine M; Weinstock, George M; Storch, Gregory A | Translational research : the journal of laboratory and clinical medicine | 22683423 | 2012 Oct |
Metagenomic microbial community profiling using unique clade-specific marker genes. | Segata, Nicola; Waldron, Levi; Ballarini, Annalisa; Narasimhan, Vagheesh; Jousson, Olivier; Huttenhower, Curtis | Nature methods | 22688413 | 2012 Aug |
Stabilization of the murine gut microbiome following weaning. | Schloss, Patrick D; Schubert, Alyxandria M; Zackular, Joseph P; Iverson, Kathryn D; Young, Vincent B; Petrosino, Joseph F | Gut microbes | 22688727 | 2012 Jul-Aug |
mcaGUI: microbial community analysis R-Graphical User Interface (GUI). | Copeland, Wade K; Krishnan, Vandhana; Beck, Daniel; Settles, Matt; Foster, James A; Cho, Kyu-Chul; Day, Mitch; Hickey, Roxana; Schutte, Ursel M E; Zhou, Xia; Williams, Christopher J; Forney, Larry J; Abdo, Zaid | Bioinformatics (Oxford, England) | 22692220 | 2012 Aug 15 |
Host genetic and environmental effects on mouse intestinal microbiota. | Campbell, James H; Foster, Carmen M; Vishnivetskaya, Tatiana; Campbell, Alisha G; Yang, Zamin K; Wymore, Ann; Palumbo, Anthony V; Chesler, Elissa J; Podar, Mircea | The ISME journal | 22695862 | 2012 Nov |
A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community. | Wang, Mingjie; Ye, Yuzhen; Tang, Haixu | Journal of computational biology : a journal of computational molecular cell biology | 22697249 | 2012 Jun |
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. | Segata, Nicola; Haake, Susan Kinder; Mannon, Peter; Lemon, Katherine P; Waldron, Levi; Gevers, Dirk; Huttenhower, Curtis; Izard, Jacques | Genome biology | 22698087 | 2012 |
Structure, function and diversity of the healthy human microbiome. | Human Microbiome Project Consortium | Nature | 22699609 | 2012 Jun 14 |
A framework for human microbiome research. | Human Microbiome Project Consortium | Nature | 22699610 | 2012 Jun 14 |
Associating microbiome composition with environmental covariates using generalized UniFrac distances. | Chen, Jun; Bittinger, Kyle; Charlson, Emily S; Hoffmann, Christian; Lewis, James; Wu, Gary D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe | Bioinformatics (Oxford, England) | 22711789 | 2012 Aug 15 |
Metabolic reconstruction for metagenomic data and its application to the human microbiome. | Abubucker, Sahar; Segata, Nicola; Goll, Johannes; Schubert, Alyxandria M; Izard, Jacques; Cantarel, Brandi L; Rodriguez-Mueller, Beltran; Zucker, Jeremy; Thiagarajan, Mathangi; Henrissat, Bernard; White, Owen; Kelley, Scott T; Methe, Barbara; Schloss, Pat | PLoS computational biology | 22719234 | 2012 |
Diverse CRISPRs evolving in human microbiomes. | Rho, Mina; Wu, Yu-Wei; Tang, Haixu; Doak, Thomas G; Ye, Yuzhen | PLoS genetics | 22719260 | 2012 |
Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. | Li, Ellen; Hamm, Christina M; Gulati, Ajay S; Sartor, R Balfour; Chen, Hongyan; Wu, Xiao; Zhang, Tianyi; Rohlf, F James; Zhu, Wei; Gu, Chi; Robertson, Charles E; Pace, Norman R; Boedeker, Edgar C; Harpaz, Noam; Yuan, Jeffrey; Weinstock, George M; Sodergre | PloS one | 22719818 | 2012 |
Sequence analysis of the human virome in febrile and afebrile children. | Wylie, Kristine M; Mihindukulasuriya, Kathie A; Sodergren, Erica; Weinstock, George M; Storch, Gregory A | PloS one | 22719819 | 2012 |
Complex carbohydrate utilization by the healthy human microbiome. | Cantarel, Brandi L; Lombard, Vincent; Henrissat, Bernard | PloS one | 22719820 | 2012 |
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). | Goll, Johannes; Thiagarajan, Mathangi; Abubucker, Sahar; Huttenhower, Curtis; Yooseph, Shibu; Methe, Barbara A | PloS one | 22719821 | 2012 |
Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition. | Zhang, Tianyi; DeSimone, Robert A; Jiao, Xiangmin; Rohlf, F James; Zhu, Wei; Gong, Qing Qing; Hunt, Steven R; Dassopoulos, Themistocles; Newberry, Rodney D; Sodergren, Erica; Weinstock, George; Robertson, Charles E; Frank, Daniel N; Li, Ellen | PloS one | 22719822 | 2012 |
Analyses of the microbial diversity across the human microbiome. | Li, Kelvin; Bihan, Monika; Yooseph, Shibu; Methe, Barbara A | PloS one | 22719823 | 2012 |
A core human microbiome as viewed through 16S rRNA sequence clusters. | Huse, Susan M; Ye, Yuzhen; Zhou, Yanjiao; Fodor, Anthony A | PloS one | 22719824 | 2012 |
Novel bacterial taxa in the human microbiome. | Wylie, Kristine M; Truty, Rebecca M; Sharpton, Thomas J; Mihindukulasuriya, Kathie A; Zhou, Yanjiao; Gao, Hongyu; Sodergren, Erica; Weinstock, George M; Pollard, Katherine S | PloS one | 22719826 | 2012 |
Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. | Martin, John; Sykes, Sean; Young, Sarah; Kota, Karthik; Sanka, Ravi; Sheth, Nihar; Orvis, Joshua; Sodergren, Erica; Wang, Zhengyuan; Weinstock, George M; Mitreva, Makedonka | PloS one | 22719831 | 2012 |
A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. | Aagaard, Kjersti; Riehle, Kevin; Ma, Jun; Segata, Nicola; Mistretta, Toni-Ann; Coarfa, Cristian; Raza, Sabeen; Rosenbaum, Sean; Van den Veyver, Ignatia; Milosavljevic, Aleksandar; Gevers, Dirk; Huttenhower, Curtis; Petrosino, Joseph; Versalovic, James | PloS one | 22719832 | 2012 |
Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria. | Srinivasan, Sujatha; Hoffman, Noah G; Morgan, Martin T; Matsen, Frederick A; Fiedler, Tina L; Hall, Robert W; Ross, Frederick J; McCoy, Connor O; Bumgarner, Roger; Marrazzo, Jeanne M; Fredricks, David N | PloS one | 22719852 | 2012 |
Alternative splicing regulated by butyrate in bovine epithelial cells. | Wu, Sitao; Li, Congjun; Huang, Wen; Li, Weizhong; Li, Robert W | PloS one | 22720068 | 2012 |
Evaluation of 16S rDNA-based community profiling for human microbiome research. | Jumpstart Consortium Human Microbiome Project Data Generation Working Group | PloS one | 22720093 | 2012 |
Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. | Devkota, Suzanne; Wang, Yunwei; Musch, Mark W; Leone, Vanessa; Fehlner-Peach, Hannah; Nadimpalli, Anuradha; Antonopoulos, Dionysios A; Jabri, Bana; Chang, Eugene B | Nature | 22722865 | 2012 Jul 5 |
The world within: living with our microbial guests and guides. | Janoff, Edward N; Gustafson, Claire; Frank, Daniel N | Translational research : the journal of laboratory and clinical medicine | 22732305 | 2012 Oct |
Vaginal microbiome: rethinking health and disease. | Ma, Bing; Forney, Larry J; Ravel, Jacques | Annual review of microbiology | 22746335 | 2012 |
Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability. | Filkins, L M; Hampton, T H; Gifford, A H; Gross, M J; Hogan, D A; Sogin, M L; Morrison, H G; Paster, B J; O'Toole, G A | Journal of bacteriology | 22753064 | 2012 Sep |
Caring about trees in the forest: incorporating frailty in risk analysis for personalized medicine. | Ma, Zhanshan Sam; Abdo, Zaid; Forney, Larry J | Personalized medicine | 22754581 | 2011 Nov |
A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. | Dollive, Serena; Peterfreund, Gregory L; Sherrill-Mix, Scott; Bittinger, Kyle; Sinha, Rohini; Hoffmann, Christian; Nabel, Christopher S; Hill, David A; Artis, David; Bachman, Michael A; Custers-Allen, Rebecca; Grunberg, Stephanie; Wu, Gary D; Lewis, James D; Bushman, Frederic D | Genome biology. | 22759449 | 2012; |
Diversity of 5S rRNA genes within individual prokaryotic genomes. | Pei, Anna; Li, Hongru; Oberdorf, William E; Alekseyenko, Alexander V; Parsons, Tamasha; Yang, Liying; Gerz, Erika A; Lee, Peng; Xiang, Charlie; Nossa, Carlos W; Pei, Zhiheng | FEMS microbiology letters | 22765222 | 2012 Oct |
Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. | Qin, Xiang; Galloway-Pena, Jessica R; Sillanpaa, Jouko; Roh, Jung Hyeob; Nallapareddy, Sreedhar R; Chowdhury, Shahreen; Bourgogne, Agathe; Choudhury, Tina; Muzny, Donna M; Buhay, Christian J; Ding, Yan; Dugan-Rocha, Shannon; Liu, Wen; Kovar, Christie; Sod | BMC microbiology | 22769602 | 2012 |
Ultrafast clustering algorithms for metagenomic sequence analysis. | Li, Weizhong; Fu, Limin; Niu, Beifang; Wu, Sitao; Wooley, John | Briefings in bioinformatics | 22772836 | 2012 Nov |
Ethical Discourse about the Modification of Food for Therapeutic Purposes: How Patients with Gastrointestinal Diseases View the Good, the Bad, and the Healthy. | Harrison, Krista L; Geller, Gail; Marshall, Patricia; Tilburt, Jon; Mercer, Marybeth; Brinich, Margaret A; Highland, Janelle; Farrell, Ruth M; Sharp, Richard R | AJOB primary research | 22773953 | 2012 Jul 1 |
IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. | Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Jacob, Biju; Ratner, Anna; Liolios, Konstantinos; Pagani, Ioanna; Huntemann, Marcel; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos C | PloS one | 22792232 | 2012 |
Microbial co-occurrence relationships in the human microbiome. | Faust, Karoline; Sathirapongsasuti, J Fah; Izard, Jacques; Segata, Nicola; Gevers, Dirk; Raes, Jeroen; Huttenhower, Curtis | PLoS computational biology | 22807668 | 2012 |
Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma. | Pushalkar, Smruti; Ji, Xiaojie; Li, Yihong; Estilo, Cherry; Yegnanarayana, Ramanathan; Singh, Bhuvanesh; Li, Xin; Saxena, Deepak | BMC microbiology | 22817758 | 2012 |
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. | Trimble, William L; Keegan, Kevin P; D'Souza, Mark; Wilke, Andreas; Wilkening, Jared; Gilbert, Jack; Meyer, Folker | BMC bioinformatics | 22839106 | 2012 |
The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples. | Evans, Steven N; Matsen, Frederick A | Journal of the Royal Statistical Society. Series B, Statistical methodology | 22844205 | 2012 Jun 1 |
The "most wanted" taxa from the human microbiome for whole genome sequencing. | Fodor, Anthony A; DeSantis, Todd Z; Wylie, Kristine M; Badger, Jonathan H; Ye, Yuzhen; Hepburn, Theresa; Hu, Ping; Sodergren, Erica; Liolios, Konstantinos; Huot-Creasy, Heather; Birren, Bruce W; Earl, Ashlee M | PloS one | 22848458 | 2012 |
Perspectives on human microbiome research ethics. | McGuire, Amy L; Achenbaum, Laura S; Whitney, Simon N; Slashinski, Melody J; Versalovic, James; Keitel, Wendy A; McCurdy, Sheryl A | Journal of empirical research on human research ethics : JERHRE | 22850139 | 2012 Jul |
Defining the human microbiome. | Ursell, Luke K; Metcalf, Jessica L; Parfrey, Laura Wegener; Knight, Rob | Nutrition reviews | 22861806 | 2012 Aug |
Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. | Blaser, Martin J; Dominguez-Bello, Maria G; Contreras, Monica; Magris, Magda; Hidalgo, Glida; Estrada, Isidoro; Gao, Zhan; Clemente, Jose C; Costello, Elizabeth K; Knight, Rob | The ISME journal | 22895161 | 2013 Jan |
Conservation of gene cassettes among diverse viruses of the human gut. | Minot, Samuel; Wu, Gary D; Lewis, James D; Bushman, Frederic D | PloS one | 22900013 | 2012 |
The Human Microbiome Project: a community resource for the healthy human microbiome. | Gevers, Dirk; Knight, Rob; Petrosino, Joseph F; Huang, Katherine; McGuire, Amy L; Birren, Bruce W; Nelson, Karen E; White, Owen; Methe, Barbara A; Huttenhower, Curtis | PLoS biology | 22904687 | 2012 |
Analysis of the gut microbiota in the old order Amish and its relation to the metabolic syndrome. | Zupancic, Margaret L; Cantarel, Brandi L; Liu, Zhenqiu; Drabek, Elliott F; Ryan, Kathleen A; Cirimotich, Shana; Jones, Cheron; Knight, Rob; Walters, William A; Knights, Daniel; Mongodin, Emmanuel F; Horenstein, Richard B; Mitchell, Braxton D; Steinle, Nan | PloS one | 22905200 | 2012 |
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, J C; Koestler, D C; Stanton, B A; Davidson, L; Moulton, L A; Housman, M L; Moore, J H; Guill, M F; Morrison, H G; Sogin, M L; Hampton, T H; Karagas, M R; Palumbo, P E; Foster, J A; Hibberd, P L; O'Toole, G A | mBio | 22911969 | 2012 |
Current technology in the diagnosis of developmentally related lung disorders. | Hamvas, Aaron | Neonatology | 22940625 | 2012 |
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. | Wu, Yu-Wei; Rho, Mina; Doak, Thomas G; Ye, Yuzhen | Bioinformatics (Oxford, England) | 22962453 | 2012 Sep 15 |
Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem. | Wendl, Michael C; Kota, Karthik; Weinstock, George M; Mitreva, Makedonka | Journal of mathematical biology | 22965653 | 2013 Nov |
Genomic approaches to studying the human microbiota. | Weinstock, George M | Nature | 22972298 | 2012 Sep 13 |
Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. | Semova, Ivana; Carten, Juliana D; Stombaugh, Jesse; Mackey, Lantz C; Knight, Rob; Farber, Steven A; Rawls, John F | Cell host & microbe | 22980325 | 2012 Sep 13 |
Prevention of virus-induced type 1 diabetes with antibiotic therapy. | Hara, Naoko; Alkanani, Aimon K; Ir, Diana; Robertson, Charles E; Wagner, Brandie D; Frank, Daniel N; Zipris, Danny | Journal of immunology (Baltimore, Md. : 1950) | 22988033 | 2012 Oct 15 |
Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women. | Brotman, Rebecca M; Bradford, L Latey; Conrad, Melissa; Gajer, Pawel; Ault, Kevin; Peralta, Ligia; Forney, Larry J; Carlton, Jane M; Abdo, Zaid; Ravel, Jacques | Sexually transmitted diseases | 23007708 | 2012 Oct |
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. | Morgan, Xochitl C; Tickle, Timothy L; Sokol, Harry; Gevers, Dirk; Devaney, Kathryn L; Ward, Doyle V; Reyes, Joshua A; Shah, Samir A; LeLeiko, Neal; Snapper, Scott B; Bousvaros, Athos; Korzenik, Joshua; Sands, Bruce E; Xavier, Ramnik J; Huttenhower, Curtis | Genome biology | 23013615 | 2012 |
Secondary structure improves OTU assignments of 16S rRNA gene sequences. | Schloss, Patrick D | The ISME journal | 23018771 | 2013 Mar |
Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis. | Blainey, Paul C; Milla, Carlos E; Cornfield, David N; Quake, Stephen R | Science translational medicine | 23019655 | 2012 Sep 26 |
The L1-norm best-fit hyperplane problem. | Brooks, J P; Dula, J H | Applied mathematics letters | 23024460 | 2012 Jan 1 |
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data. | Zhu, Zhengwei; Niu, Beifang; Chen, Jing; Wu, Sitao; Sun, Shulei; Li, Weizhong | Bioinformatics (Oxford, England) | 23044549 | 2013 Jan 1 |
CD-HIT: accelerated for clustering the next-generation sequencing data. | Fu, Limin; Niu, Beifang; Zhu, Zhengwei; Wu, Sitao; Li, Weizhong | Bioinformatics (Oxford, England) | 23060610 | 2012 Dec 1 |
Succession in the gut microbiome following antibiotic and antibody therapies for Clostridium difficile. | Peterfreund, Gregory L; Vandivier, Lee E; Sinha, Rohini; Marozsan, Andre J; Olson, William C; Zhu, Jun; Bushman, Frederic D | PloS one | 23071679 | 2012 |
Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis. | Chen, Jun; Bushman, Frederic D; Lewis, James D; Wu, Gary D; Li, Hongzhe | Biostatistics (Oxford, England) | 23074263 | 2013 Apr |
Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa. | Williams, Tiffany M; Loman, Nicholas J; Ebruke, Chinelo; Musher, Daniel M; Adegbola, Richard A; Pallen, Mark J; Weinstock, George M; Antonio, Martin | PloS one | 23082106 | 2012 |
Dietary issues in recurrent abdominal pain. | Shulman, Robert J | Journal of pediatric gastroenterology and nutrition | 23103654 | 2012 Nov |
Snake-oil, "quack medicine," and "industrially cultured organisms:" biovalue and the commercialization of human microbiome research. | Slashinski, Melody J; McCurdy, Sheryl A; Achenbaum, Laura S; Whitney, Simon N; McGuire, Amy L | BMC medical ethics | 23110633 | 2012 |
Whole-genome analysis of a daptomycin-susceptible enterococcus faecium strain and its daptomycin-resistant variant arising during therapy. | Tran, Truc T; Panesso, Diana; Gao, Hongyu; Roh, Jung H; Munita, Jose M; Reyes, Jinnethe; Diaz, Lorena; Lobos, Elizabeth A; Shamoo, Yousif; Mishra, Nagendra N; Bayer, Arnold S; Murray, Barbara E; Weinstock, George M; Arias, Cesar A | Antimicrobial agents and chemotherapy | 23114757 | 2013 Jan |
Detection of viruses in young children with fever without an apparent source. | Colvin, Joshua M; Muenzer, Jared T; Jaffe, David M; Smason, Avraham; Deych, Elena; Shannon, William D; Arens, Max Q; Buller, Richard S; Lee, Wai-Ming; Weinstock, Erica J Sodergren; Weinstock, George M; Storch, Gregory A | Pediatrics | 23129086 | 2012 Dec |
Estimation of distribution overlap of urn models. | Hampton, Jerrad; Lladser, Manuel E | PloS one | 23139734 | 2012 |
Biodiversity and functional genomics in the human microbiome. | Morgan, Xochitl C; Segata, Nicola; Huttenhower, Curtis | Trends in genetics : TIG | 23140990 | 2013 Jan |
Statistical object data analysis of taxonomic trees from human microbiome data. | La Rosa, Patricio S; Shands, Berkley; Deych, Elena; Zhou, Yanjiao; Sodergren, Erica; Weinstock, George; Shannon, William D | PloS one | 23152838 | 2012 |
The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. | Aagaard, Kjersti; Petrosino, Joseph; Keitel, Wendy; Watson, Mark; Katancik, James; Garcia, Nathalia; Patel, Shital; Cutting, Mary; Madden, Tessa; Hamilton, Holli; Harris, Emily; Gevers, Dirk; Simone, Gina; McInnes, Pamela; Versalovic, James | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 23165986 | 2013 Mar |
Using QIIME to analyze 16S rRNA gene sequences from microbial communities. | Kuczynski, Justin; Stombaugh, Jesse; Walters, William Anton; Gonzalez, Antonio; Caporaso, J Gregory; Knight, Rob | Current protocols in microbiology | 23184592 | 2012 Nov |
TIGRFAMs and Genome Properties in 2013. | Haft, Daniel H; Selengut, Jeremy D; Richter, Roland A; Harkins, Derek; Basu, Malay K; Beck, Erin | Nucleic acids research | 23197656 | 2013 Jan |
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. | Bokulich, Nicholas A; Subramanian, Sathish; Faith, Jeremiah J; Gevers, Dirk; Gordon, Jeffrey I; Knight, Rob; Mills, David A; Caporaso, J Gregory | Nature methods | 23202435 | 2013 Jan |
Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome. | Kontur, Wayne S; Schackwitz, Wendy S; Ivanova, Natalia; Martin, Joel; Labutti, Kurt; Deshpande, Shweta; Tice, Hope N; Pennacchio, Christa; Sodergren, Erica; Weinstock, George M; Noguera, Daniel R; Donohue, Timothy J | Journal of bacteriology | 23209255 | 2012 Dec |
Bioinformatics for the Human Microbiome Project. | Gevers, Dirk; Pop, Mihai; Schloss, Patrick D; Huttenhower, Curtis | PLoS computational biology | 23209389 | 2012 |
Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. | Erickson, Alison R; Cantarel, Brandi L; Lamendella, Regina; Darzi, Youssef; Mongodin, Emmanuel F; Pan, Chongle; Shah, Manesh; Halfvarson, Jonas; Tysk, Curt; Henrissat, Bernard; Raes, Jeroen; Verberkmoes, Nathan C; Fraser, Claire M; Hettich, Robert L; Jans | PloS one | 23209564 | 2012 |
Nestly--a framework for running software with nested parameter choices and aggregating results. | McCoy, Connor O; Gallagher, Aaron; Hoffman, Noah G; Matsen, Frederick A | Bioinformatics (Oxford, England) | 23220574 | 2013 Feb 1 |
Genomic variation landscape of the human gut microbiome. | Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi; Mitreva, Makedonka; Tap, Julien; Zhu, Ana; Waller, Alison; Mende, Daniel R; Kultima, Jens Roat; Martin, John; Kota, Karthik; Sunyaev, Shamil R; Weinstock, George M; Bork, Peer | Nature | 23222524 | 2013 Jan 3 |
Increased prevalence of anellovirus in pediatric patients with fever. | McElvania TeKippe, Erin; Wylie, Kristine M; Deych, Elena; Sodergren, Erica; Weinstock, George; Storch, Gregory A | PloS one | 23226428 | 2012 |
Insights from characterizing extinct human gut microbiomes. | Tito, Raul Y; Knights, Dan; Metcalf, Jessica; Obregon-Tito, Alexandra J; Cleeland, Lauren; Najar, Fares; Roe, Bruce; Reinhard, Karl; Sobolik, Kristin; Belknap, Samuel; Foster, Morris; Spicer, Paul; Knight, Rob; Lewis Jr, Cecil M | PloS one | 23251439 | 2012 |
'Someone should oversee it': patient perspectives on the ethical issues arising with the regulation of probiotics. | Harrison, Krista L; Farrell, Ruth M; Brinich, Margaret A; Highland, Janelle; Mercer, Marybeth; McCormick, Jennifer B; Tilburt, Jon; Geller, Gail; Marshall, Patricia; Sharp, Richard R | Health expectations : an international journal of public participation in health care and health policy | 23279082 | 2012 Dec 28 |
Genomic sequence analysis and characterization of Sneathia amnii sp. nov. | Harwich Jr, Michael D; Serrano, Myrna G; Fettweis, Jennifer M; Alves, Joao M P; Reimers, Mark A; Vaginal Microbiome Consortium (additional members); Buck, Gregory A; Jefferson, Kimberly K | BMC genomics | 23281612 | 2012 |
Species-level classification of the vaginal microbiome. | Fettweis, Jennifer M; Serrano, Myrna G; Sheth, Nihar U; Mayer, Carly M; Glascock, Abigail L; Brooks, J Paul; Jefferson, Kimberly K; Vaginal Microbiome Consortium (additional members); Buck, Gregory A | BMC genomics | 23282177 | 2012 |
Hypothesis testing and power calculations for taxonomic-based human microbiome data. | La Rosa, Patricio S; Brooks, J Paul; Deych, Elena; Boone, Edward L; Edwards, David J; Wang, Qin; Sodergren, Erica; Weinstock, George; Shannon, William D | PloS one | 23284876 | 2012 |
The future is now: single-cell genomics of bacteria and archaea. | Blainey, Paul C | FEMS microbiology reviews | 23298390 | 2013 May |
Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men. | Redel, Henry; Gao, Zhan; Li, Huilin; Alekseyenko, Alexander V; Zhou, Yanjiao; Perez-Perez, Guillermo I; Weinstock, George; Sodergren, Erica; Blaser, Martin J | The Journal of infectious diseases | 23300163 | 2013 Apr |
Chapter 12: Human microbiome analysis. | Morgan, Xochitl C; Huttenhower, Curtis | PLoS computational biology | 23300406 | 2012 |
The Jeremiah Metzger lecture: Global warming redux: the disappearing microbiota and epidemic obesity. | Blaser, Martin J | Transactions of the American Clinical and Climatological Association | 23303990 | 2012 |
An analysis of online messages about probiotics. | Brinich, Margaret A; Mercer, Mary Beth; Sharp, Richard R | BMC gastroenterology | 23311418 | 2013 |
Biogeography of the ecosystems of the healthy human body. | Zhou, Yanjiao; Gao, Hongyu; Mihindukulasuriya, Kathie A; La Rosa, Patricio S; Wylie, Kristine M; Vishnivetskaya, Tatiana; Podar, Mircea; Warner, Barb; Tarr, Phillip I; Nelson, David E; Fortenberry, J Dennis; Holland, Martin J; Burr, Sarah E; Shannon, Will | Genome biology | 23316946 | 2013 Jan 14 |
Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. | Hemarajata, Peera; Versalovic, James | Therapeutic advances in gastroenterology. | 23320049 | 2013 Jan; |
The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences. | Riehle, Kevin; Coarfa, Cristian; Jackson, Andrew; Ma, Jun; Tandon, Arpit; Paithankar, Sameer; Raghuraman, Sriram; Mistretta, Toni-Ann; Saulnier, Delphine; Raza, Sabeen; Diaz, Maria Alejandra; Shulman, Robert; Aagaard, Kjersti; Versalovic, James; Milosavlj | BMC bioinformatics | 23320832 | 2012 |
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. | Treangen, Todd J; Koren, Sergey; Sommer, Daniel D; Liu, Bo; Astrovskaya, Irina; Ondov, Brian; Darling, Aaron E; Phillippy, Adam M; Pop, Mihai | Genome biology. | 23320958 | 2013; |
A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. | Koren, Omry; Knights, Dan; Gonzalez, Antonio; Waldron, Levi; Segata, Nicola; Knight, Rob; Huttenhower, Curtis; Ley, Ruth E | PLoS computational biology | 23326225 | 2013 Jan |
Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. | Markle, Janet G M; Frank, Daniel N; Mortin-Toth, Steven; Robertson, Charles E; Feazel, Leah M; Rolle-Kampczyk, Ulrike; von Bergen, Martin; McCoy, Kathy D; Macpherson, Andrew J; Danska, Jayne S | Science (New York, N.Y.) | 23328391 | 2013 Mar 1 |
Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne. | Fitz-Gibbon, Sorel; Tomida, Shuta; Chiu, Bor-Han; Nguyen, Lin; Du, Christine; Liu, Minghsun; Elashoff, David; Erfe, Marie C; Loncaric, Anya; Kim, Jenny; Modlin, Robert L; Miller, Jeff F; Sodergren, Erica; Craft, Noah; Weinstock, George M; Li, Huiying | The Journal of investigative dermatology | 23337890 | 2013 Jan 21 |
Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. | Ansong, Charles; Ortega, Corrie; Payne, Samuel H; Haft, Daniel H; Chauvigne-Hines, Lacie M; Lewis, Michael P; Ollodart, Anja R; Purvine, Samuel O; Shukla, Anil K; Fortuin, Suereta; Smith, Richard D; Adkins, Joshua N; Grundner, Christoph; Wright, Aaron T | Chemistry & biology | 23352146 | 2013 Jan 24 |
Single cell microRNA analysis using microfluidic flow cytometry. | Wu, Meiye; Piccini, Matthew; Koh, Chung-Yan; Lam, Kit S; Singh, Anup K | PloS one | 23383050 | 2013 |
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. | Shakya, Migun; Quince, Christopher; Campbell, James H; Yang, Zamin K; Schadt, Christopher W; Podar, Mircea | Environmental microbiology | 23387867 | 2013 Jun |
The human gut microbiome and body metabolism: implications for obesity and diabetes. | Devaraj, Sridevi; Hemarajata, Peera; Versalovic, James | Clinical chemistry | 23401286 | 2013 Apr |
Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes. | Ballarini, Annalisa; Segata, Nicola; Huttenhower, Curtis; Jousson, Olivier | PloS one | 23409037 | 2013 |
The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness. | Liolios, Konstantinos; Schriml, Lynn; Hirschman, Lynette; Pagani, Ioanna; Nosrat, Bahador; Sterk, Peter; White, Owen; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Taylor, Chris; Kyrpides, Nikos C; Field, Dawn | Standards in genomic sciences. | 23409217 | 2012 Jul 30; |
Shallow breathing: bacterial life at low O(2). | Morris, Rachel L; Schmidt, Thomas M | Nature reviews. Microbiology | 23411864 | 2013 Mar |
Transcriptome profiling of microRNA by Next-Gen deep sequencing reveals known and novel miRNA species in the lipid fraction of human breast milk. | Munch, Erika M; Harris, R Alan; Mohammad, Mahmoud; Benham, Ashley L; Pejerrey, Sasha M; Showalter, Lori; Hu, Min; Shope, Cynthia D; Maningat, Patricia D; Gunaratne, Preethi H; Haymond, Morey; Aagaard, Kjersti | PloS one | 23418415 | 2013 |
SPA: a short peptide assembler for metagenomic data. | Yang, Youngik; Yooseph, Shibu | Nucleic acids research | 23435317 | 2013 Apr |
Challenges in IBD research: update on progress and prioritization of the CCFA's research agenda. | Denson, Lee A; Long, Millie D; McGovern, Dermot P B; Kugathasan, Subra; Wu, Gary D; Young, Vincent B; Pizarro, Theresa T; de Zoeten, Edwin F; Stappenbeck, Thaddeus S; Plevy, Scott E; Abraham, Clara; Nusrat, Asma; Jobin, Christian; McCole, Declan F; Siegel | Inflammatory bowel diseases | 23448796 | 2013 Mar-Apr |
Effects of different complementary feeding regimens on iron status and enteric microbiota in breastfed infants. | Krebs, Nancy F; Sherlock, Laurie G; Westcott, Jamie; Culbertson, Diana; Hambidge, K Michael; Feazel, Leah M; Robertson, Charles E; Frank, Daniel N | The Journal of pediatrics | 23452586 | 2013 Aug |
Draft Genome Sequence of Enterococcus faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces. | O Cuív, Páraic; Klaassens, Eline S; Smith, Wendy J; Mondot, Stanislas; Durkin, A Scott; Harkins, Derek M; Foster, Les; McCorrison, Jamison; Torralba, Manolito; Nelson, Karen E; Morrison, Mark | Genome announcements. | 23469340 | 2013 Jan; |
Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. | Hettich, Robert L; Pan, Chongle; Chourey, Karuna; Giannone, Richard J | Analytical chemistry | 23469896 | 2013 May 7 |
Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players. | Ursell, Luke K; Knight, Rob | Cell metabolism | 23473028 | 2013 Mar 5 |
Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases. | Leone, Vanessa; Chang, Eugene B; Devkota, Suzanne | Journal of gastroenterology | 23475322 | 2013 Mar |
Comparison of the respiratory microbiome in healthy nonsmokers and smokers. | Morris, Alison; Beck, James M; Schloss, Patrick D; Campbell, Thomas B; Crothers, Kristina; Curtis, Jeffrey L; Flores, Sonia C; Fontenot, Andrew P; Ghedin, Elodie; Huang, Laurence; Jablonski, Kathleen; Kleerup, Eric; Lynch, Susan V; Sodergren, Erica; Twigg | American journal of respiratory and critical care medicine | 23491408 | 2013 May 15 |
Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. | Fitzsimons, Michael S; Novotny, Mark; Lo, Chien-Chi; Dichosa, Armand E K; Yee-Greenbaum, Joyclyn L; Snook, Jeremy P; Gu, Wei; Chertkov, Olga; Davenport, Karen W; McMurry, Kim; Reitenga, Krista G; Daughton, Ashlynn R; He, Jian; Johnson, Shannon L; Gleasner | Genome research | 23493677 | 2013 May |
Comparative analysis of microbiome measurement platforms using latent variable structural equation modeling. | Wu, Xiao; Berkow, Kathryn; Frank, Daniel N; Li, Ellen; Gulati, Ajay S; Zhu, Wei | BMC bioinformatics | 23497007 | 2013 |
Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison. | Matsen 4th, Frederick A; Evans, Steven N | PloS one | 23505415 | 2013 |
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. | Campbell, James H; O'Donoghue, Patrick; Campbell, Alisha G; Schwientek, Patrick; Sczyrba, Alexander; Woyke, Tanja; Soll, Dieter; Podar, Mircea | Proceedings of the National Academy of Sciences of the United States of America | 23509275 | 2013 Apr 2 |
Culture-independent analysis of aerosol microbiology in a metropolitan subway system. | Robertson, Charles E; Baumgartner, Laura K; Harris, J Kirk; Peterson, Kristen L; Stevens, Mark J; Frank, Daniel N; Pace, Norman R | Applied and environmental microbiology | 23542619 | 2013 Jun |
Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences. | Jiao, Dazhi; Ye, Yuzhen; Tang, Haixu | PLoS computational biology | 23555216 | 2013 Mar |
Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity. | Campbell, Alisha G; Campbell, James H; Schwientek, Patrick; Woyke, Tanja; Sczyrba, Alexander; Allman, Steve; Beall, Clifford J; Griffen, Ann; Leys, Eugene; Podar, Mircea | PloS one | 23555659 | 2013 |
Gastrointestinal viruses were not found as an aetiology of culture-negative illness in NICU patients. | Melamed, Rimma; Storch, Gregory A; Warner, Barbara B; Tarr, Phillip I | Archives of disease in childhood. Fetal and neonatal edition | 23563694 | 2013 Jul |
Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. | Koeth, Robert A; Wang, Zeneng; Levison, Bruce S; Buffa, Jennifer A; Org, Elin; Sheehy, Brendan T; Britt, Earl B; Fu, Xiaoming; Wu, Yuping; Li, Lin; Smith, Jonathan D; DiDonato, Joseph A; Chen, Jun; Li, Hongzhe; Wu, Gary D; Lewis, James D; Warrier, Manya; | Nature medicine | 23563705 | 2013 May |
Cohabiting family members share microbiota with one another and with their dogs. | Song, Se Jin; Lauber, Christian; Costello, Elizabeth K; Lozupone, Catherine A; Humphrey, Gregory; Berg-Lyons, Donna; Caporaso, J Gregory; Knights, Dan; Clemente, Jose C; Nakielny, Sara; Gordon, Jeffrey I; Fierer, Noah; Knight, Rob | eLife. | 23599893 | 2013 Apr 16; |
Investigators' perspectives on translating human microbiome research into clinical practice. | Slashinski, M J; Whitney, S N; Achenbaum, L S; Keitel, W A; McCurdy, S A; McGuire, A L | Public health genomics | 23615375 | 2013 |
Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome. | Tomida, Shuta; Nguyen, Lin; Chiu, Bor-Han; Liu, Jared; Sodergren, Erica; Weinstock, George M; Li, Huiying | mBio | 23631911 | 2013 |
Composition of dietary fat source shapes gut microbiota architecture and alters host inflammatory mediators in mouse adipose tissue. | Huang, Edmond Y; Leone, Vanessa A; Devkota, Suzanne; Wang, Yunwei; Brady, Matthew J; Chang, Eugene B | JPEN. Journal of parenteral and enteral nutrition | 23639897 | 2013 Nov |
Analysis of the human gut microbiome and association with disease. | Wu, Gary D; Lewis, James D | Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association | 23643636 | 2013 Jul |
Clarifying Prehistoric Parasitism from a Complementary Morphological and Molecular Approach. | Cleeland, Lauren M; Reichard, Mason V; Tito, Raul Y; Reinhard, Karl J; Lewis Jr, Cecil M | Journal of archaeological science | 23645967 | 2013 Jul 01 |
Butyrate Induced IGF2 Activation Correlated with Distinct Chromatin Signatures Due to Histone Modification. | Shin, Joo Heon; Li, Robert W; Gao, Yuan; Bickhart, Derek M; Liu, George E; Li, Weizhong; Wu, Sitao; Li, Cong-Jun | Gene regulation and systems biology. | 23645985 | 2013; |
Computational meta'omics for microbial community studies. | Segata, Nicola; Boernigen, Daniela; Tickle, Timothy L; Morgan, Xochitl C; Garrett, Wendy S; Huttenhower, Curtis | Molecular systems biology | 23670539 | 2013 |
Analyses of the stability and core taxonomic memberships of the human microbiome. | Li, Kelvin; Bihan, Monika; Methe, Barbara A | PloS one | 23671663 | 2013 |
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, A N; Efimov, B A; Khokhlova, E V; Chaplin, A V; Kafarskaya, L I; Durkin, A S; McCorrison, J; Torralba, M; Gillis, M; Sutton, G; Weibel, D B; Nelson, K E; Smeianov, V V | Genome announcements. | 23682142 | 2013; |
DRISEE overestimates errors in metagenomic sequencing data. | Eren, A Murat; Morrison, Hilary G; Huse, Susan M; Sogin, Mitchell L | Briefings in bioinformatics. | 23698723 | 2014 Sep; |
Colitis-induced Bone Loss is Gender Dependent and Associated with Increased Inflammation. | Irwin, Regina; Lee, Taehyung; Young, Vincent B; Parameswaran, Narayanan; McCabe, Laura R | Inflammatory bowel diseases | 23702805 | 2013 Jul |
Virome genomics: a tool for defining the human virome. | Wylie, Kristine M; Weinstock, George M; Storch, Gregory A | Current opinion in microbiology | 23706900 | 2013 May 23 |
Sequencing viral genomes from a single isolated plaque. | Depew, Jessica; Zhou, Bin; McCorrison, Jamison M; Wentworth, David E; Purushe, Janaki; Koroleva, Galina; Fouts, Derrick E | Virology journal | 23742765 | 2013 |
Analysis of complete genomes of Propionibacterium acnes reveals a novel plasmid and increased pseudogenes in an acne associated strain. | Kasimatis, Gabriela; Fitz-Gibbon, Sorel; Tomida, Shuta; Wong, Marthew; Li, Huiying | BioMed research international | 23762865 | 2013 |
Carrageenan-induced colonic inflammation is reduced in Bcl10 null mice and increased in IL-10-deficient mice. | Bhattacharyya, Sumit; Xue, Liquan; Devkota, Suzanne; Chang, Eugene; Morris, Stephan; Tobacman, Joanne K | Mediators of inflammation | 23766559 | 2013 |
Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. | Kozich, James J; Westcott, Sarah L; Baxter, Nielson T; Highlander, Sarah K; Schloss, Patrick D | Applied and environmental microbiology | 23793624 | 2013 Sep |
Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses. | Smeekens, Sanne P; Huttenhower, Curtis; Riza, Anca; van de Veerdonk, Frank L; Zeeuwen, Patrick L J M; Schalkwijk, Joost; van der Meer, Jos W M; Xavier, Ramnik J; Netea, Mihai G; Gevers, Dirk | Journal of innate immunity. | 23796786 | 2014; |
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. | Hoffmann, Christian; Dollive, Serena; Grunberg, Stephanie; Chen, Jun; Li, Hongzhe; Wu, Gary D; Lewis, James D; Bushman, Frederic D | PloS one | 23799070 | 2013 |
A filtering method to generate high quality short reads using illumina paired-end technology. | Eren, A Murat; Vineis, Joseph H; Morrison, Hilary G; Sogin, Mitchell L | PloS one | 23799126 | 2013 |
Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. | Carmody, Lisa A; Zhao, Jiangchao; Schloss, Patrick D; Petrosino, Joseph F; Murray, Susan; Young, Vincent B; Li, Jun Z; LipPuma, John J | Annals of the American Thoracic Society | 23802813 | 2013 Jun |
Are changes to the common rule necessary to address evolving areas of research? A case study focusing on the human microbiome project. | Hoffmann, Diane E; Fortenberry, J Dennis; Ravel, Jacques | The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics. | 23802897 | 2013; |
Microfluidic platforms for single-cell protein analysis. | Liu, Yanli; Singh, Anup K | Journal of laboratory automation | 23821679 | 2013 Dec |
The mean and variance of phylogenetic diversity under rarefaction. | Nipperess, David A; Matsen 4th, Frederick A | Methods in ecology and evolution / British Ecological Society | 23833701 | 2013 Jun 1 |
Rapid evolution of the human gut virome. | Minot, Samuel; Bryson, Alexandra; Chehoud, Christel; Wu, Gary D; Lewis, James D; Bushman, Frederic D | Proceedings of the National Academy of Sciences of the United States of America | 23836644 | 2013 Jul 23 |
Gene expression profiles in febrile children with defined viral and bacterial infection. | Hu, Xinran; Yu, Jinsheng; Crosby, Seth D; Storch, Gregory A | Proceedings of the National Academy of Sciences of the United States of America | 23858444 | 2013 Jul 30 |
Urethral adenocarcinoma associated with intestinal-type metaplasia, case report and literature review. | Hale, Christopher S; Huang, Hongying; Melamed, Jonathan; Xu, Ruliang; Roberts, Larry; Wieczorek, Rosemary; Pei, Zhiheng; Lee, Peng | International journal of clinical and experimental pathology | 23923086 | 2013 |
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. | Segata, Nicola; Bornigen, Daniela; Morgan, Xochitl C; Huttenhower, Curtis | Nature communications | 23942190 | 2013 Aug 14 |
Two-stage microbial community experimental design. | Tickle, Timothy L; Segata, Nicola; Waldron, Levi; Weingart, Uri; Huttenhower, Curtis | The ISME journal | 23949665 | 2013 Aug 15 |
Association of gut microbiota with post-operative clinical course in Crohn's disease. | Dey, Neelendu; Soergel, David A W; Repo, Susanna; Brenner, Steven E | BMC gastroenterology | 23964800 | 2013 |
De novo likelihood-based measures for comparing genome assemblies. | Ghodsi, Mohammadreza; Hill, Christopher M; Astrovskaya, Irina; Lin, Henry; Sommer, Dan D; Koren, Sergey; Pop, Mihai | BMC research notes | 23965294 | 2013 |
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. | Langille, Morgan G I; Zaneveld, Jesse; Caporaso, J Gregory; McDonald, Daniel; Knights, Dan; Reyes, Joshua A; Clemente, Jose C; Burkepile, Deron E; Vega Thurber, Rebecca L; Knight, Rob; Beiko, Robert G; Huttenhower, Curtis | Nature biotechnology | 23975157 | 2013 Sep |
A Pure L1-norm Principal Component Analysis. | Brooks, Jp; Dula, Jh; Boone, El | Computational statistics & data analysis | 23976807 | 2013 May 1 |
Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. | Dollive, Serena; Chen, Ying-Yu; Grunberg, Stephanie; Bittinger, Kyle; Hoffmann, Christian; Vandivier, Lee; Cuff, Christopher; Lewis, James D; Wu, Gary D; Bushman, Frederic D | PloS one | 23977147 | 2013 |
Microbiomic signatures of psoriasis: feasibility and methodology comparison. | Statnikov, Alexander; Alekseyenko, Alexander V; Li, Zhiguo; Henaff, Mikael; Perez-Perez, Guillermo I; Blaser, Martin J; Aliferis, Constantin F | Scientific reports | 24018484 | 2013 |
Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. | Robertson, Charles E; Harris, J Kirk; Wagner, Brandie D; Granger, David; Browne, Kathy; Tatem, Beth; Feazel, Leah M; Park, Kristin; Pace, Norman R; Frank, Daniel N | Bioinformatics (Oxford, England) | 24021386 | 2013 Dec 1 |
Antibacterial property expressed by a novel calcium phosphate glass. | Liu, Lela; Pushalkar, Smruti; Saxena, Deepak; LeGeros, Racquel Z; Zhang, Yu | Journal of biomedical materials research. Part B, Applied biomaterials. | 24039127 | 2014 Apr; |
Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. | Wang, Qiong; Quensen 3rd, John F; Fish, Jordan A; Lee, Tae Kwon; Sun, Yanni; Tiedje, James M; Cole, James R | mBio | 24045641 | 2013 |
Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis. | Turabelidze, George; Lawrence, Steven J; Gao, Hongyu; Sodergren, Erica; Weinstock, George M; Abubucker, Sahar; Wylie, Todd; Mitreva, Makedonka; Shaikh, Nurmohammad; Gautom, Romesh; Tarr, Phillip I | Journal of clinical microbiology | 24048526 | 2013 Dec |
Optofluidic cell selection from complex microbial communities for single-genome analysis. | Landry, Zachary C; Giovanonni, Stephen J; Quake, Stephen R; Blainey, Paul C | Methods in enzymology | 24060116 | 2013 |
A metagenomics portal for a democratized sequencing world. | Wilke, Andreas; Glass, Elizabeth M; Bartels, Daniela; Bischof, Jared; Braithwaite, Daniel; D'Souza, Mark; Gerlach, Wolfgang; Harrison, Travis; Keegan, Kevin; Matthews, Hunter; Kottmann, Renzo; Paczian, Tobias; Tang, Wei; Trimble, William L; Yilmaz, Pelin; | Methods in enzymology | 24060134 | 2013 |
Differential abundance analysis for microbial marker-gene surveys. | Paulson, Joseph N; Stine, O Colin; Bravo, Hector Corrada; Pop, Mihai | Nature methods | 24076764 | 2013 Dec |
Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy. | Brotman, Rebecca M; Shardell, Michelle D; Gajer, Pawel; Fadrosh, Doug; Chang, Kathryn; Silver, Michelle I; Viscidi, Raphael P; Burke, Anne E; Ravel, Jacques; Gravitt, Patti E | Menopause (New York, N.Y.) | 24080849 | 2013 Oct 21 |
FunGene: the functional gene pipeline and repository. | Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R | Frontiers in microbiology. | 24101916 | 2013; |
Diet, gut enterotypes and health: is there a link? | Bushman, Frederic D; Lewis, James D; Wu, Gary D | Nestle Nutrition Institute workshop series | 24107497 | 2013 |
A single-molecule long-read survey of the human transcriptome. | Sharon, Donald; Tilgner, Hagen; Grubert, Fabian; Snyder, Michael | Nature biotechnology. | 24108091 | 2013 Nov; |
Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota. | Lee, Sunghee; Cantarel, Brandi; Henrissat, Bernard; Gevers, Dirk; Birren, Bruce W; Huttenhower, Curtis; Ko, Gwangpyo | The ISME journal | 24108330 | 2013 Oct 10 |
Lactobacillus reuteri-specific immunoregulatory gene rsiR modulates histamine production and immunomodulation by Lactobacillus reuteri. | Hemarajata, P; Gao, C; Pflughoeft, K J; Thomas, C M; Saulnier, D M; Spinler, J K; Versalovic, J | Journal of bacteriology | 24123819 | 2013 Dec |
Interprovider variation of celiac disease testing in childhood chronic abdominal pain. | Chumpitazi, Bruno Pedro; Mysore, Krupa; Tsai, Cynthia Man-Wai; Shulman, Robert Jay | BMC gastroenterology | 24124697 | 2013 |
Science and regulation. Probiotics: finding the right regulatory balance. | Hoffmann, D E; Fraser, C M; Palumbo, F B; Ravel, J; Rothenberg, K; Rowthorn, V; Schwartz, J | Science (New York, N.Y.) | 24136953 | 2013 Oct 18 |
IMG/M 4 version of the integrated metagenome comparative analysis system. | Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Pagani, Ioanna; Tringe, Susannah; Huntemann, Marcel; Billis, Konstantinos; Varghese, Neha; Tennessen, Kristin; Mavromatis, Kons | Nucleic acids research | 24136997 | 2014 Jan |
Bringing the gut microbiota into focus through microbial culture: recent progress and future perspective. | Allen-Vercoe, Emma | Current opinion in microbiology | 24148301 | 2013 Oct |
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. | Scher, Jose U; Sczesnak, Andrew; Longman, Randy S; Segata, Nicola; Ubeda, Carles; Bielski, Craig; Rostron, Tim; Cerundolo, Vincenzo; Pamer, Eric G; Abramson, Steven B; Huttenhower, Curtis; Littman, Dan R | eLife | 24192039 | 2013 Nov 05 |
The gut microbiome modulates colon tumorigenesis. | Zackular, Joseph P; Baxter, Nielson T; Iverson, Kathryn D; Sadler, William D; Petrosino, Joseph F; Chen, Grace Y; Schloss, Patrick D | mBio | 24194538 | 2013 |
Monodisperse alginate microgel formation in a three-dimensional microfluidic droplet generator. | Lian, Meng; Collier, C Patrick; Doktycz, Mitchel J; Retterer, Scott T | Biomicrofluidics. | 24198865 | 2012; |
MetaRef: a pan-genomic database for comparative and community microbial genomics. | Huang, Katherine; Brady, Arthur; Mahurkar, Anup; White, Owen; Gevers, Dirk; Huttenhower, Curtis; Segata, Nicola | Nucleic acids research | 24203705 | 2014 Jan |
Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. | Gole, Jeff; Gore, Athurva; Richards, Andrew; Chiu, Yu-Jui; Fung, Ho-Lim; Bushman, Diane; Chiang, Hsin-I; Chun, Jerold; Lo, Yu-Hwa; Zhang, Kun | Nature biotechnology | 24213699 | 2013 Dec |
Diversified microbiota of meconium is affected by maternal diabetes status. | Hu, Jianzhong; Nomura, Yoko; Bashir, Ali; Fernandez-Hernandez, Heriberto; Itzkowitz, Steven; Pei, Zhiheng; Stone, Joanne; Loudon, Holly; Peter, Inga | PloS one | 24223144 | 2013 |
A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. | Tong, Maomeng; Li, Xiaoxiao; Wegener Parfrey, Laura; Roth, Bennett; Ippoliti, Andrew; Wei, Bo; Borneman, James; McGovern, Dermot P B; Frank, Daniel N; Li, Ellen; Horvath, Steve; Knight, Rob; Braun, Jonathan | PloS one | 24260458 | 2013 |
Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes. | Close, Devin W; Ferrara, Fortunato; Dichosa, Armand E K; Kumar, Sandeep; Daughton, Ashlynn R; Daligault, Hajnalka E; Reitenga, Krista G; Velappan, Nileena; Sanchez, Timothy C; Iyer, Srinivas; Kiss, Csaba; Han, Cliff S; Bradbury, Andrew R M | BMC microbiology | 24279426 | 2013 |
Ribosomal Database Project: data and tools for high throughput rRNA analysis. | Cole, James R; Wang, Qiong; Fish, Jordan A; Chai, Benli; McGarrell, Donna M; Sun, Yanni; Brown, C Titus; Porras-Alfaro, Andrea; Kuske, Cheryl R; Tiedje, James M | Nucleic acids research | 24288368 | 2014 Jan |
More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis. | Srinivasan, Sujatha; Morgan, Martin T; Liu, Congzhou; Matsen, Frederick A; Hoffman, Noah G; Fiedler, Tina L; Agnew, Kathy J; Marrazzo, Jeanne M; Fredricks, David N | PloS one | 24302980 | 2013 |
VARIABLE SELECTION FOR SPARSE DIRICHLET-MULTINOMIAL REGRESSION WITH AN APPLICATION TO MICROBIOME DATA ANALYSIS. | Chen, Jun; Li, Hongzhe | The annals of applied statistics. | 24312162 | 2013 Mar 01; |
Inferring developmental stage composition from gene expression in human malaria. | Joice, Regina; Narasimhan, Vagheesh; Montgomery, Jacqui; Sidhu, Amar Bir; Oh, Keunyoung; Meyer, Evan; Pierre-Louis, Willythssa; Seydel, Karl; Milner, Danny; Williamson, Kim; Wiegand, Roger; Ndiaye, Daouda; Daily, Johanna; Wirth, Dyann; Taylor, Terrie; Hut | PLoS computational biology | 24348235 | 2013 Dec |
Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data. | Eren, A Murat; Maignien, Lois; Sul, Woo Jun; Murphy, Leslie G; Grim, Sharon L; Morrison, Hilary G; Sogin, Mitchell L | Methods in ecology and evolution / British Ecological Society | 24358444 | 2013 Dec 1 |
Mathematical modeling of primary succession of murine intestinal microbiota. | Marino, Simeone; Baxter, Nielson T; Huffnagle, Gary B; Petrosino, Joseph F; Schloss, Patrick D | Proceedings of the National Academy of Sciences of the United States of America | 24367073 | 2014 Jan 7 |
The microbiome of the middle meatus in healthy adults. | Ramakrishnan, Vijay R; Feazel, Leah M; Gitomer, Sarah A; Ir, Diana; Robertson, Charles E; Frank, Daniel N | PloS one | 24386477 | 2013 |
A brave new world: the lung microbiota in an era of change. | Segal, Leopoldo N; Blaser, Martin J | Annals of the American Thoracic Society | 24437400 | 2014 Jan |
Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. | Price, Katherine E; Hampton, Thomas H; Gifford, Alex H; Dolben, Emily L; Hogan, Deborah A; Morrison, Hilary G; Sogin, Mitchell L; O'Toole, George A | Microbiome | 24451123 | 2013 |
Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis. | Ravel, Jacques; Brotman, Rebecca M; Gajer, Pawel; Ma, Bing; Nandy, Melissa; Fadrosh, Douglas W; Sakamoto, Joyce; Koenig, Sara Sk; Fu, Li; Zhou, Xia; Hickey, Roxana J; Schwebke, Jane R; Forney, Larry J | Microbiome | 24451163 | 2013 |
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. | Mason, Olivia U; Scott, Nicole M; Gonzalez, Antonio; Robbins-Pianka, Adam; Baelum, Jacob; Kimbrel, Jeffrey; Bouskill, Nicholas J; Prestat, Emmanuel; Borglin, Sharon; Joyner, Dominique C; Fortney, Julian L; Jurelevicius, Diogo; Stringfellow, William T; Alv | The ISME journal | 24451203 | 2014 Jan 23 |
A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. | Vital, Marius; Penton, Christopher R; Wang, Qiong; Young, Vincent B; Antonopoulos, Dion A; Sogin, Mitchell L; Morrison, Hilary G; Raffals, Laura; Chang, Eugene B; Huffnagle, Gary B; Schmidt, Thomas M; Cole, James R; Tiedje, James M | Microbiome | 24451334 | 2013 |
Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. | Young, Vincent B; Raffals, Laura H; Huse, Susan M; Vital, Marius; Dai, Dongjuan; Schloss, Patrick D; Brulc, Jennifer M; Antonopoulos, Dionysios A; Arrieta, Rose L; Kwon, John H; Reddy, K Gautham; Hubert, Nathaniel A; Grim, Sharon L; Vineis, Joseph H; Dala | Microbiome | 24451366 | 2013 |
Compositional and functional features of the gastrointestinal microbiome and their effects on human health. | Hollister, Emily B; Gao, Chunxu; Versalovic, James | Gastroenterology | 24486050 | 2014 May |
Meta'omic analytic techniques for studying the intestinal microbiome. | Morgan, Xochitl C; Huttenhower, Curtis | Gastroenterology | 24486053 | 2014 May |
Identification of a proton-chloride antiporter (EriC) by Himar1 transposon mutagenesis in Lactobacillus reuteri and its role in histamine production. | Hemarajata, P; Spinler, J K; Balderas, M A; Versalovic, J | Antonie van Leeuwenhoek | 24488273 | 2014 Mar |
Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen. | Chen, Zehua; Martinez, Diego A; Gujja, Sharvari; Sykes, Sean M; Zeng, Qiandong; Szaniszlo, Paul J; Wang, Zheng; Cuomo, Christina A | G3 (Bethesda, Md.) | 24496724 | 2014 Apr |
Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. | Rooks, Michelle G; Veiga, Patrick; Wardwell-Scott, Leslie H; Tickle, Timothy; Segata, Nicola; Michaud, Monia; Gallini, Carey Ann; Beal, Chloe; van Hylckama-Vlieg, Johan E T; Ballal, Sonia A; Morgan, Xochitl C; Glickman, Jonathan N; Gevers, Dirk; Huttenhow | The ISME journal | 24500617 | 2014 Jul |
Diet and the intestinal microbiome: associations, functions, and implications for health and disease. | Albenberg, Lindsey G; Wu, Gary D | Gastroenterology | 24503132 | 2014 May |
Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets. | Ma, Yingfei; Madupu, Ramana; Karaoz, Ulas; Nossa, Carlos W; Yang, Liying; Yooseph, Shibu; Yachimski, Patrick S; Brodie, Eoin L; Nelson, Karen E; Pei, Zhiheng | Journal of virology | 24522917 | 2014 May |
Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects. | Huse, Susan M; Young, Vincent B; Morrison, Hilary G; Antonopoulos, Dionysios A; Kwon, John; Dalal, Sushila; Arrieta, Rose; Hubert, Nathaniel A; Shen, Lici; Vineis, Joseph H; Koval, Jason C; Sogin, Mitchell L; Chang, Eugene B; Raffals, Laura E | Microbiome | 24529162 | 2014 |
Early Empiric Antibiotic Use in Preterm Infants Is Associated with Lower Bacterial Diversity and Higher Relative Abundance of Enterobacter. | Greenwood, Corryn; Morrow, Ardythe L; Lagomarcino, Anne J; Altaye, Mekibib; Taft, Diana H; Yu, Zhuoteng; Newburg, David S; Ward, Doyle V; Schibler, Kurt R | The Journal of pediatrics | 24529620 | 2014 Feb 13 |
Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286) and comparison to the closely related pathogen Tannerella forsythia. | Beall, Clifford J; Campbell, Alisha G; Dayeh, Daniel M; Griffen, Ann L; Podar, Mircea; Leys, Eugene J | PloS one | 24551246 | 2014 |
An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. | Fadrosh, Douglas W; Ma, Bing; Gajer, Pawel; Sengamalay, Naomi; Ott, Sandra; Brotman, Rebecca M; Ravel, Jacques | Microbiome. | 24558975 | 2014; |
The microbiome in inflammatory bowel disease: current status and the future ahead. | Kostic, Aleksandar D; Xavier, Ramnik J; Gevers, Dirk | Gastroenterology | 24560869 | 2014 May |
Whole-genome haplotyping using long reads and statistical methods. | Kuleshov, Volodymyr; Xie, Dan; Chen, Rui; Pushkarev, Dmitry; Ma, Zhihai; Blauwkamp, Tim; Kertesz, Michael; Snyder, Michael | Nature biotechnology | 24561555 | 2014 Mar |
Pathogens and host immunity in the ancient human oral cavity. | Warinner, Christina; Rodrigues, Joao F Matias; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y; Tito, Raul Y; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar- | Nature genetics | 24562188 | 2014 Apr |
History and impact of RDP: a legacy from Carl Woese to microbiology. | Cole, James R; Tiedje, James M | RNA biology | 24607969 | 2014 Mar |
Immune and genetic gardening of the intestinal microbiome. | Jacobs, Jonathan P; Braun, Jonathan | FEBS letters | 24613921 | 2014 Mar 5 |
Functional and phylogenetic assembly of microbial communities in the human microbiome. | Shafquat, Afrah; Joice, Regina; Simmons, Sheri L; Huttenhower, Curtis | Trends in microbiology | 24618403 | 2014 Mar 4 |
The treatment-naive microbiome in new-onset Crohn's disease. | Gevers, Dirk; Kugathasan, Subra; Denson, Lee A; Vazquez-Baeza, Yoshiki; Van Treuren, Will; Ren, Boyu; Schwager, Emma; Knights, Dan; Song, Se Jin; Yassour, Moran; Morgan, Xochitl C; Kostic, Aleksandar D; Luo, Chengwei; Gonzalez, Antonio; McDonald, Daniel; | Cell host & microbe | 24629344 | 2014 Mar 12 |
Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome. | Chumpitazi, Bruno P; Hollister, Emily B; Oezguen, Numan; Tsai, Cynthia M; McMeans, Ann R; Luna, Ruth A; Savidge, Tor C; Versalovic, James; Shulman, Robert J | Gut microbes | 24637601 | 2014 Mar-Apr |
Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. | Carl, Mike A; Ndao, I Malick; Springman, A Cody; Manning, Shannon D; Johnson, James R; Johnston, Brian D; Burnham, Carey-Ann D; Weinstock, Erica Sodergren; Weinstock, George M; Wylie, Todd N; Mitreva, Makedonka; Abubucker, Sahar; Zhou, Yanjiao; Stevens, H | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 24647013 | 2014 May |
Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis. | Hyde, Embriette R; Andrade, Fernando; Vaksman, Zalman; Parthasarathy, Kavitha; Jiang, Hong; Parthasarathy, Deepa K; Torregrossa, Ashley C; Tribble, Gena; Kaplan, Heidi B; Petrosino, Joseph F; Bryan, Nathan S | PloS one | 24670812 | 2014 |
Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. | Campbell, Alisha G; Schwientek, Patrick; Vishnivetskaya, Tatiana; Woyke, Tanja; Levy, Shawn; Beall, Clifford J; Griffen, Ann; Leys, Eugene; Podar, Mircea | Environmental microbiology | 24738594 | 2014 Apr 17 |
Transferable vancomycin resistance in a community-associated MRSA lineage. | Rossi, Flavia; Diaz, Lorena; Wollam, Aye; Panesso, Diana; Zhou, Yanjiao; Rincon, Sandra; Narechania, Apurva; Xing, Galen; Di Gioia, Thais S R; Doi, Andre; Tran, Truc T; Reyes, Jinnethe; Munita, Jose M; Carvajal, Lina P; Hernandez-Roldan, Alejandra; Branda | The New England journal of medicine | 24738669 | 2014 Apr 17 |
Dynamics and associations of microbial community types across the human body. | Ding, Tao; Schloss, Patrick D | Nature | 24739969 | 2014 May 15 |
Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. | Swan, Brandon K; Chaffin, Mark D; Martinez-Garcia, Manuel; Morrison, Hilary G; Field, Erin K; Poulton, Nicole J; Masland, E Dashiell P; Harris, Christopher C; Sczyrba, Alexander; Chain, Patrick S G; Koren, Sergey; Woyke, Tanja; Stepanauskas, Ramunas | PloS one | 24743558 | 2014 |
Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. | Vital, Marius; Howe, Adina Chuang; Tiedje, James M | mBio | 24757212 | 2014 |
Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. | Tong, Maomeng; McHardy, Ian; Ruegger, Paul; Goudarzi, Maryam; Kashyap, Purna C; Haritunians, Talin; Li, Xiaoxiao; Graeber, Thomas G; Schwager, Emma; Huttenhower, Curtis; Fornace Jr, Albert J; Sonnenburg, Justin L; McGovern, Dermot Pb; Borneman, James; Bra | The ISME journal | 24781901 | 2014 Apr 29 |
Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. | Schubert, Alyxandria M; Rogers, Mary A M; Ring, Cathrin; Mogle, Jill; Petrosino, Joseph P; Young, Vincent B; Aronoff, David M; Schloss, Patrick D | mBio | 24803517 | 2014 |
Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium. | Sizova, Maria V; Muller, Paul A; Stancyk, David; Panikov, Nicolai S; Mandalakis, Manolis; Hazen, Amanda; Hohmann, Tine; Doerfert, Sebastian N; Fowle, William; Earl, Ashlee M; Nelson, Karen E; Epstein, Slava S | International journal of systematic and evolutionary microbiology. | 24824639 | 2014 Aug; |
The prevalence of species and strains in the human microbiome: a resource for experimental efforts. | Kraal, Laurens; Abubucker, Sahar; Kota, Karthik; Fischbach, Michael A; Mitreva, Makedonka | PloS one | 24827833 | 2014 |
Relating the metatranscriptome and metagenome of the human gut. | Franzosa, Eric A; Morgan, Xochitl C; Segata, Nicola; Waldron, Levi; Reyes, Joshua; Earl, Ashlee M; Giannoukos, Georgia; Boylan, Matthew R; Ciulla, Dawn; Gevers, Dirk; Izard, Jacques; Garrett, Wendy S; Chan, Andrew T; Huttenhower, Curtis | Proceedings of the National Academy of Sciences of the United States of America | 24843156 | 2014 Jun 3 |
The placenta harbors a unique microbiome. | Aagaard, Kjersti; Ma, Jun; Antony, Kathleen M; Ganu, Radhika; Petrosino, Joseph; Versalovic, James | Science translational medicine | 24848255 | 2014 May 21 |
Microbiome in reflux disorders and esophageal adenocarcinoma. | Yang, Liying; Chaudhary, Noami; Baghdadi, Jonathan; Pei, Zhiheng | Cancer journal (Sudbury, Mass.) | 24855009 | 2014 May-Jun |
Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251). | Cuomo, Christina A; Rodriguez-Del Valle, Nuri; Perez-Sanchez, Lizaida; Abouelleil, Amr; Goldberg, Jonathan; Young, Sarah; Zeng, Qiandong; Birren, Bruce W | Genome announcements. | 24855299 | 2014; |
BOTUX: bayesian-like operational taxonomic unit examiner. | Koparde, Vishal N; Adkins, Ricky S; Fettweis, Jennifer M; Serrano, Myrna G; Buck, Gregory A A; Reimers, Mark A; Sheth, Nihar U | International journal of computational biology and drug design. | 24878725 | 2014; |
Exploration of bacterial community classes in major human habitats. | Zhou, Yanjiao; Mihindukulasuriya, Kathie A; Gao, Hongyu; La Rosa, Patricio S; Wylie, Kristine M; Martin, John C; Kota, Karthik; Shannon, William D; Mitreva, Makedonka; Sodergren, Erica; Weinstock, George M | Genome biology | 24887286 | 2014 |
CcpA is important for growth and virulence of Enterococcus faecium. | Somarajan, Sudha R; Roh, Jung H; Singh, Kavindra V; Weinstock, George M; Murray, Barbara E | Infection and immunity. | 24914215 | 2014 Sep; |
Evidence of extensive DNA transfer between bacteroidales species within the human gut. | Coyne, Michael J; Zitomersky, Naamah Levy; McGuire, Abigail Manson; Earl, Ashlee M; Comstock, Laurie E | mBio | 24939888 | 2014 |
Interplay between the temporal dynamics of the vaginal microbiota and human papillomavirus detection. | Brotman, Rebecca M; Shardell, Michelle D; Gajer, Pawel; Tracy, J Kathleen; Zenilman, Jonathan M; Ravel, Jacques; Gravitt, Patti E | The Journal of infectious diseases. | 24943724 | 2014 Dec 1; |
Finding the missing links among metabolites, microbes, and the host. | Dorrestein, Pieter C; Mazmanian, Sarkis K; Knight, Rob | Immunity. | 24950202 | 2014 Jun 19; |
Inflammatory bowel disease as a model for translating the microbiome. | Huttenhower, Curtis; Kostic, Aleksandar D; Xavier, Ramnik J | Immunity | 24950204 | 2014 Jun 19 |
From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions. | Spinler, Jennifer K; Sontakke, Amrita; Hollister, Emily B; Venable, Susan F; Oh, Phaik Lyn; Balderas, Miriam A; Saulnier, Delphine M A; Mistretta, Toni-Ann; Devaraj, Sridevi; Walter, Jens; Versalovic, James; Highlander, Sarah K | Genome biology and evolution | 24951561 | 2014 Jul |
Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips. | Ma, Liang; Datta, Sujit S; Karymov, Mikhail A; Pan, Qichao; Begolo, Stefano; Ismagilov, Rustem F | Integrative biology : quantitative biosciences from nano to macro | 24953827 | 2014 Jun 23 |
Defining a personal, allele-specific, and single-molecule long-read transcriptome. | Tilgner, Hagen; Grubert, Fabian; Sharon, Donald; Snyder, Michael P | Proceedings of the National Academy of Sciences of the United States of America. | 24961374 | 2014 Jul 8; |
Oligotyping analysis of the human oral microbiome. | Eren, A Murat; Borisy, Gary G; Huse, Susan M; Mark Welch, Jessica L | Proceedings of the National Academy of Sciences of the United States of America | 24965363 | 2014 Jul 15 |
Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa. | Ma, Liang; Kim, Jungwoo; Hatzenpichler, Roland; Karymov, Mikhail A; Hubert, Nathaniel; Hanan, Ira M; Chang, Eugene B; Ismagilov, Rustem F | Proceedings of the National Academy of Sciences of the United States of America | 24965364 | 2014 Jul 8 |
Lactobacillus rhamnosus L34 and Lactobacillus casei L39 suppress Clostridium difficile-induced IL-8 production by colonic epithelial cells. | Boonma, Prapaporn; Spinler, Jennifer K; Venable, Susan F; Versalovic, James; Tumwasorn, Somying | BMC microbiology | 24989059 | 2014 |
Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. | Parfrey, Laura Wegener; Walters, William A; Lauber, Christian L; Clemente, Jose C; Berg-Lyons, Donna; Teiling, Clotilde; Kodira, Chinnappa; Mohiuddin, Mohammed; Brunelle, Julie; Driscoll, Mark; Fierer, Noah; Gilbert, Jack A; Knight, Rob | Frontiers in microbiology. | 24995004 | 2014; |
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. | Pop, Mihai; Walker, Alan W; Paulson, Joseph; Lindsay, Brianna; Antonio, Martin; Hossain, M Anowar; Oundo, Joseph; Tamboura, Boubou; Mai, Volker; Astrovskaya, Irina; Corrada Bravo, Hector; Rance, Richard; Stares, Mark; Levine, Myron M; Panchalingam, Sandra | Genome biology | 24995464 | 2014 |
Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. | Haberman, Yael; Tickle, Timothy L; Dexheimer, Phillip J; Kim, Mi-Ok; Tang, Dora; Karns, Rebekah; Baldassano, Robert N; Noe, Joshua D; Rosh, Joel; Markowitz, James; Heyman, Melvin B; Griffiths, Anne M; Crandall, Wallace V; Mack, David R; Baker, Susan S; Huttenhower, Curtis; Keljo, David J; Hyams, Jeffrey S; Kugathasan, Subra; Walters, Thomas D; Aronow, Bruce; Xavier, Ramnik J; Gevers, Dirk; Denson, Lee A | The Journal of clinical investigation. | 25003194 | 2014 Aug; |
Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt. | Lee, Soo Chan; Billmyre, R Blake; Li, Alicia; Carson, Sandra; Sykes, Sean M; Huh, Eun Young; Mieczkowski, Piotr; Ko, Dennis C; Cuomo, Christina A; Heitman, Joseph | mBio | 25006230 | 2014 |
Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays. | VanDussen, Kelli L; Marinshaw, Jeffrey M; Shaikh, Nurmohammad; Miyoshi, Hiroyuki; Moon, Clara; Tarr, Phillip I; Ciorba, Matthew A; Stappenbeck, Thaddeus S | Gut. | 25007816 | 2015 Jun; |
Microfluidic molecular assay platform for the detection of miRNAs, mRNAs, proteins, and posttranslational modifications at single-cell resolution. | Wu, Meiye; Singh, Anup K | Journal of laboratory automation. | 25027027 | 2014 Dec; |
Serum profiling using protein microarrays to identify disease related antigens. | Sharon, Donald; Snyder, Michael | Methods in molecular biology (Clifton, N.J.). | 25030927 | 2014; |
Conducting a microbiome study. | Goodrich, Julia K; Di Rienzi, Sara C; Poole, Angela C; Koren, Omry; Walters, William A; Caporaso, J Gregory; Knight, Rob; Ley, Ruth E | Cell. | 25036628 | 2014 Jul 17; |
Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. | Albenberg, Lindsey; Esipova, Tatiana V; Judge, Colleen P; Bittinger, Kyle; Chen, Jun; Laughlin, Alice; Grunberg, Stephanie; Baldassano, Robert N; Lewis, James D; Li, Hongzhe; Thom, Stephen R; Bushman, Frederic D; Vinogradov, Sergei A; Wu, Gary D | Gastroenterology. | 25046162 | 2014 Nov; |
The dynamics of a family's gut microbiota reveal variations on a theme. | Schloss, Patrick D; Iverson, Kathryn D; Petrosino, Joseph F; Schloss, Sarah J | Microbiome. | 25061514 | 2014; |
The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention. | Hampton, Thomas H; Green, Deanna M; Cutting, Garry R; Morrison, Hilary G; Sogin, Mitchell L; Gifford, Alex H; Stanton, Bruce A; O'Toole, George A | Microbiome | 25071935 | 2014 |
Differences in vaginal microbiome in African American women versus women of European ancestry. | Fettweis, Jennifer M; Brooks, J Paul; Serrano, Myrna G; Sheth, Nihar U; Girerd, Philippe H; Edwards, David J; Strauss, Jerome F; Reimers, Mark A; Rivera, Maria C; Puma, Federico A; Huang, Bernice; Shyu, Conrad; Koparde, Vishal N; Lee, Vladimir; Jefferson, | Microbiology (Reading, England) | 25073854 | 2014 Jul 29 |
Phase variation of poly-N-acetylglucosamine expression in Staphylococcus aureus. | Brooks, Jamie L; Jefferson, Kimberly K | PLoS pathogens. | 25077798 | 2014 Jul; |
Phylogenetics and the human microbiome. | Matsen 4th, Frederick A | Systematic biology. | 25102857 | 2015 Jan; |
The Human Gut Microbiome as a Screening Tool for Colorectal Cancer. | Zackular, Joseph P; Rogers, Mary A M; Ruffin 4th, Mack T; Schloss, Patrick D | Cancer prevention research (Philadelphia, Pa.) | 25104642 | 2014 Aug 7 |
Oral microbiota and host innate immune response in bisphosphonate-related osteonecrosis of the jaw. | Pushalkar, Smruti; Li, Xin; Kurago, Zoya; Ramanathapuram, Lalitha V; Matsumura, Satoko; Fleisher, Kenneth E; Glickman, Robert; Yan, Wenbo; Li, Yihong; Saxena, Deepak | International journal of oral science. | 25105817 | 2014 Dec; |
Patterned progression of bacterial populations in the premature infant gut. | La Rosa, Patricio S; Warner, Barbara B; Zhou, Yanjiao; Weinstock, George M; Sodergren, Erica; Hall-Moore, Carla M; Stevens, Harold J; Bennett Jr, William E; Shaikh, Nurmohammad; Linneman, Laura A; Hoffmann, Julie A; Hamvas, Aaron; Deych, Elena; Shands, Berkley A; Shannon, William D; Tarr, Phillip I | Proceedings of the National Academy of Sciences of the United States of America. | 25114261 | 2014 Aug 26; |
Mini-review: perspective of the microbiome in the pathogenesis of urothelial carcinoma. | Xu, Weisheng; Yang, Liying; Lee, Peng; Huang, William C; Nossa, Carlos; Ma, Yingfei; Deng, Fang-Ming; Zhou, Ming; Melamed, Jonathan; Pei, Zhiheng | American journal of clinical and experimental urology | 25126590 | 2014 Apr 15 |
Probiotics: achieving a better regulatory fit. | Hoffmann, Diane E; Fraser, Claire M; Palumbo, Francis; Ravel, Jacques; Rowthorn, Virginia; Schwartz, Jack | Food and drug law journal | 25163211 | 2014 |
Longitudinal analysis of microbial interaction between humans and the indoor environment. | Lax, Simon; Smith, Daniel P; Hampton-Marcell, Jarrad; Owens, Sarah M; Handley, Kim M; Scott, Nicole M; Gibbons, Sean M; Larsen, Peter; Shogan, Benjamin D; Weiss, Sophie; Metcalf, Jessica L; Ursell, Luke K; Vázquez-Baeza, Yoshiki; Van Treuren, Will; Hasan, Nur A; Gibson, Molly K; Colwell, Rita; Dantas, Gautam; Knight, Rob; Gilbert, Jack A | Science (New York, N.Y.). | 25170151 | 2014 Aug 29; |
From deep sequencing to actual clones. | D'Angelo, Sara; Kumar, Sandeep; Naranjo, Leslie; Ferrara, Fortunato; Kiss, Csaba; Bradbury, Andrew R M | Protein engineering, design & selection : PEDS. | 25183780 | 2014 Oct; |
Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35. | Boonma, Prapaporn; Spinler, Jennifer K; Qin, Xiang; Jittaprasatsin, Chutima; Muzny, Donna M; Doddapaneni, Harsha; Gibbs, Richard; Petrosino, Joe; Tumwasorn, Somying; Versalovic, James | Standards in genomic sciences. | 25197459 | 2014 Jun 15; |
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding. | Zuo, Zheng; Stormo, Gary D | Genetics. | 25209146 | 2014 Nov; |
The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. | Integrative HMP (iHMP) Research Network Consortium | Cell host & microbe. | 25211071 | 2014 Sep 10; |
Metagenomic analysis of double-stranded DNA viruses in healthy adults. | Wylie, Kristine M; Mihindukulasuriya, Kathie A; Zhou, Yanjiao; Sodergren, Erica; Storch, Gregory A; Weinstock, George M | BMC biology. | 25212266 | 2014; |
MiRNA detection at single-cell resolution using microfluidic LNA flow-FISH. | Wu, Meiye; Piccini, Matthew E; Singh, Anup K | Methods in molecular biology (Clifton, N.J.). | 25218391 | 2014; |
An effective intervention to reduce intravaginal practices among HIV-1 uninfected Kenyan women. | Sivapalasingam, Sumathi; McClelland, R Scott; Ravel, Jacques; Ahmed, Aabid; Cleland, Charles M; Gajer, Pawel; Mwamzaka, Musa; Marshed, Fatma; Shafi, Juma; Masese, Linnet; Fajans, Mark; Anderson, Molly E; Jaoko, Walter; Kurth, Ann E | AIDS research and human retroviruses. | 25265254 | 2014 Nov; |
Pressure stabilizer for reproducible picoinjection in droplet microfluidic systems. | Rhee, Minsoung; Light, Yooli K; Yilmaz, Suzan; Adams, Paul D; Saxena, Deepak; Meagher, Robert J; Singh, Anup K | Lab on a chip. | 25270338 | 2014 Dec 7; |
The microbiome revolution. | Blaser, Martin J | The Journal of clinical investigation. | 25271724 | 2014 Oct; |
Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study. | Zhou, Yanjiao; Burnham, Carey-Ann D; Hink, Tiffany; Chen, Lei; Shaikh, Nurmohammad; Wollam, Aye; Sodergren, Erica; Weinstock, George M; Tarr, Phillip I; Dubberke, Erik R | Journal of clinical microbiology. | 25275005 | 2014 Dec; |
Sinus culture poorly predicts resident microbiota. | Hauser, Leah J; Feazel, Leah M; Ir, Diana; Fang, Rui; Wagner, Brandie D; Robertson, Charles E; Frank, Daniel N; Ramakrishnan, Vijay R | International forum of allergy & rhinology. | 25278448 | 2015 Jan; |
Microbiology: An integrated view of the skin microbiome. | Schloss, Patrick D | Nature | 25279916 | 2014 Oct 02 |
Advancing the microbiome research community. | Huttenhower, Curtis; Knight, Rob; Brown, C Titus; Caporaso, J Gregory; Clemente, Jose C; Gevers, Dirk; Franzosa, Eric A; Kelley, Scott T; Knights, Dan; Ley, Ruth E; Mahurkar, Anup; Ravel, Jacques; Scientists for Advancement of Microbiome Research; White, Owen | Cell. | 25303518 | 2014 Oct 9; |
Meta-analyses of human gut microbes associated with obesity and IBD. | Walters, William A; Xu, Zech; Knight, Rob | FEBS letters. | 25307765 | 2014 Nov 17; |
Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. | Eren, A Murat; Morrison, Hilary G; Lescault, Pamela J; Reveillaud, Julie; Vineis, Joseph H; Sogin, Mitchell L | The ISME journal. | 25325381 | 2015 Mar 17; |
An emerging mycoplasma associated with trichomoniasis, vaginal infection and disease. | Fettweis, Jennifer M; Serrano, Myrna G; Huang, Bernice; Brooks, J Paul; Glascock, Abigail L; Sheth, Nihar U; Vaginal Microbiome Consortium; Strauss 3rd, Jerome F; Jefferson, Kimberly K; Buck, Gregory A | PloS one. | 25337710 | 2014; |
Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification. | Vital, Marius; Chai, Benli; Ostman, Bjorn; Cole, James; Konstantinidis, Konstantinos T; Tiedje, James M | The ISME journal. | 25343512 | 2015 May; |
Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia. | Vital, Marius; Gao, Jiarong; Rizzo, Mike; Harrison, Tara; Tiedje, James M | The ISME journal. | 25343515 | 2015 Apr; |
High-resolution genetic mapping in the diversity outbred mouse population identifies Apobec1 as a candidate gene for atherosclerosis. | Smallwood, Tangi L; Gatti, Daniel M; Quizon, Pamela; Weinstock, George M; Jung, Kuo-Chen; Zhao, Liyang; Hua, Kunjie; Pomp, Daniel; Bennett, Brian J | G3 (Bethesda, Md.). | 25344410 | 2014 Dec; |
Intra- and interindividual variations mask interspecies variation in the microbiota of sympatric peromyscus populations. | Baxter, Nielson T; Wan, Judy J; Schubert, Alyxandria M; Jenior, Matthew L; Myers, Philip; Schloss, Patrick D | Applied and environmental microbiology. | 25362056 | 2015 Jan; |
Spec-seq: determining protein-DNA-binding specificity by sequencing. | Stormo, Gary D; Zuo, Zheng; Chang, Yiming Kenny | Briefings in functional genomics. | 25362070 | 2015 Jan; |
Evolution of invasion in a diverse set of Fusobacterium species. | Manson McGuire, Abigail; Cochrane, Kyla; Griggs, Allison D; Haas, Brian J; Abeel, Thomas; Zeng, Qiandong; Nice, Justin B; MacDonald, Hanlon; Birren, Bruce W; Berger, Bryan W; Allen-Vercoe, Emma; Earl, Ashlee M | mBio. | 25370491 | 2014; |
Versatile on-demand droplet generation for controlled encapsulation. | Rhee, Minsoung; Liu, Peng; Meagher, Robert J; Light, Yooli K; Singh, Anup K | Biomicrofluidics. | 25379072 | 2014 May; |
The gut microbiome in health and in disease. | Shreiner, Andrew B; Kao, John Y; Young, Vincent B | Current opinion in gastroenterology. | 25394236 | 2015 Jan; |
Fetal exposures and perinatal influences on the stool microbiota of premature infants. | Chernikova, Diana A; Koestler, Devin C; Hoen, Anne Gatewood; Housman, Molly L; Hibberd, Patricia L; Moore, Jason H; Morrison, Hilary G; Sogin, Mitchell L; Zain-Ul-Abideen, Muhammad; Madan, Juliette C | 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 | 2016; |
NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly. | McCorrison, Jamison M; Venepally, Pratap; Singh, Indresh; Fouts, Derrick E; Lasken, Roger S; Methé, Barbara A | BMC bioinformatics. | 25407910 | 2014; |
Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. | Wu, Gary D; Compher, Charlene; Chen, Eric Z; Smith, Sarah A; Shah, Rachana D; Bittinger, Kyle; Chehoud, Christel; Albenberg, Lindsey G; Nessel, Lisa; Gilroy, Erin; Star, Julie; Weljie, Aalim M; Flint, Harry J; Metz, David C; Bennett, Michael J; Li, Hongzhe; Bushman, Frederic D; Lewis, James D | Gut. | 25431456 | 2014 Nov 26; |
The interrelationships of the gut microbiome and inflammation in colorectal carcinogenesis. | Cho, Margaret; Carter, Janell; Harari, Saul; Pei, Zhiheng | Clinics in laboratory medicine. | 25439270 | 2014 Dec; |
Microbiome, innate immunity, and esophageal adenocarcinoma. | Baghdadi, Jonathan; Chaudhary, Noami; Pei, Zhiheng; Yang, Liying | Clinics in laboratory medicine. | 25439272 | 2014 Dec; |
The changing landscape of the vaginal microbiome. | Huang, Bernice; Fettweis, Jennifer M; Brooks, J Paul; Jefferson, Kimberly K; Buck, Gregory A | Clinics in laboratory medicine. | 25439274 | 2014 Dec; |
Beyond infectious disease: welcome to the era of population microbiology. | Pincus, Matthew R; Pei, Zhiheng | Clinics in laboratory medicine. | 25439278 | 2014 Dec; |
Determining microbial products and identifying molecular targets in the human microbiome. | Joice, Regina; Yasuda, Koji; Shafquat, Afrah; Morgan, Xochitl C; Huttenhower, Curtis | Cell metabolism. | 25440055 | 2014 Nov 4; |
The conjunctival microbiome in health and trachomatous disease: a case control study. | Zhou, Yanjiao; Holland, Martin J; Makalo, Pateh; Joof, Hassan; Roberts, Chrissy H; Mabey, David Cw; Bailey, Robin L; Burton, Matthew J; Weinstock, George M; Burr, Sarah E | Genome medicine | 25484919 | 2014 |
Personalized sequencing and the future of medicine: discovery, diagnosis and defeat of disease. | Esplin, Edward D; Oei, Ling; Snyder, Michael P | Pharmacogenomics. | 25493570 | 2014 Nov; |
The EHEC-host interactome reveals novel targets for the translocated intimin receptor. | Blasche, Sonja; Arens, Stefan; Ceol, Arnaud; Siszler, Gabriella; Schmidt, M Alexander; Hauser, Roman; Schwarz, Frank; Wuchty, Stefan; Aloy, Patrick; Uetz, Peter; Stradal, Theresia; Koegl, Manfred | Scientific reports. | 25519916 | 2014; |
The preterm placental microbiome varies in association with excess maternal gestational weight gain. | Antony, Kathleen M; Ma, Jun; Mitchell, Kristen B; Racusin, Diana A; Versalovic, James; Aagaard, Kjersti | American journal of obstetrics and gynecology. | 25557210 | 2015 May; |
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, Philippe; Boucher, Gabrielle; Mallon, Dermot; Ellinghaus, Eva; Jostins, Luke; Huang, Hailiang; Ripke, Stephan; Gusareva, Elena S; Annese, Vito; Hauser, Stephen L; Oksenberg, Jorge R; Thomsen, Ingo; Leslie, Stephen; 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, Mark J; Van Steen, Kristel; Duerr, Richard H; Barrett, Jeffrey C; McGovern, Dermot P B; Schumm, L Philip; Traherne, James A; Carrington, Mary N; Kosmoliaptsis, Vasilis; Karlsen, Tom H; Franke, Andre; Rioux, John D | Nature genetics. | 25559196 | 2015 Feb; |
A RESTful API for accessing microbial community data for MG-RAST. | Wilke, Andreas; Bischof, Jared; Harrison, Travis; Brettin, Tom; D'Souza, Mark; Gerlach, Wolfgang; Matthews, Hunter; Paczian, Tobias; Wilkening, Jared; Glass, Elizabeth M; Desai, Narayan; Meyer, Folker | PLoS computational biology. | 25569221 | 2015 Jan; |
The cutaneous microbiome in outpatients presenting with acute skin abscesses. | Horton, James M; Gao, Zhan; Sullivan, D Matthew; Shopsin, Bo; Perez-Perez, Guillermo I; Blaser, Martin J | The Journal of infectious diseases. | 25583170 | 2015 Jun 15; |
Complex host genetics influence the microbiome in inflammatory bowel disease. | Knights, Dan; Silverberg, Mark S; Weersma, Rinse K; Gevers, Dirk; Dijkstra, Gerard; Huang, Hailiang; Tyler, Andrea D; van Sommeren, Suzanne; Imhann, Floris; Stempak, Joanne M; Huang, Hu; Vangay, Pajau; Al-Ghalith, Gabriel A; Russell, Caitlin; Sauk, Jenny; Knight, Jo; Daly, Mark J; Huttenhower, Curtis; Xavier, Ramnik J | Genome medicine. | 25587358 | 2014; |
Asynchronous Magnetic Bead Rotation (AMBR) Microviscometer for Label-Free DNA Analysis. | Li, Yunzi; Burke, David T; Kopelman, Raoul; Burns, Mark A | Biosensors | 25587411 | 2014 Mar |
Diet in the pathogenesis and treatment of inflammatory bowel diseases. | Lee, Dale; Albenberg, Lindsey; Compher, Charlene; Baldassano, Robert; Piccoli, David; Lewis, James D; Wu, Gary D | Gastroenterology. | 25597840 | 2015 May; |
De novo large cell neuroendocrine carcinoma of the prostate, case report and literature review. | Acosta-Gonzalez, Gabriel; Qin, Jia; Wieczorek, Rosemary; Melamed, Jonathan; Deng, Fang-Ming; Zhou, Ming; Makarov, Danil; Ye, Fei; Pei, Zhiheng; Pincus, Matthew R; Lee, Peng | American journal of clinical and experimental urology. | 25606580 | 2014; |
Disease-specific alterations in the enteric virome in inflammatory bowel disease. | Norman, Jason M; Handley, Scott A; Baldridge, Megan T; Droit, Lindsay; Liu, Catherine Y; Keller, Brian C; Kambal, Amal; Monaco, Cynthia L; Zhao, Guoyan; Fleshner, Phillip; Stappenbeck, Thaddeus S; McGovern, Dermot P B; Keshavarzian, Ali; Mutlu, Ece A; Sauk, Jenny; Gevers, Dirk; Xavier, Ramnik J; Wang, David; Parkes, Miles; Virgin, Herbert W | Cell. | 25619688 | 2015 Jan 29; |
Identification of a gene in Mycoplasma hominis associated with preterm birth and microbial burden in intraamniotic infection. | Allen-Daniels, Matthew Josiah; Serrano, Myrna G; Pflugner, Lindsey P; Fettweis, Jennifer M; Prestosa, Melissa A; Koparde, Vishal N; Brooks, J Paul; Strauss 3rd, Jerome F; Romero, Roberto; Chaiworapongsa, Tinnakorn; Eschenbach, David A; Buck, Gregory A; Jefferson, Kimberly K | American journal of obstetrics and gynecology. | 25637842 | 2015 Jun; |
The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. | Kostic, Aleksandar D; Gevers, Dirk; Siljander, Heli; Vatanen, Tommi; Hyötyläinen, Tuulia; Hämäläinen, Anu-Maaria; Peet, Aleksandr; Tillmann, Vallo; Pöhö, Päivi; Mattila, Ismo; Lähdesmäki, Harri; Franzosa, Eric A; Vaarala, Outi; de Goffau, Marcus; Harmsen, Hermie; Ilonen, Jorma; Virtanen, Suvi M; Clish, Clary B; Ore?i?, Matej; Huttenhower, Curtis; Knip, Mikael; DIABIMMUNE Study Group; Xavier, Ramnik J | Cell host & microbe. | 25662751 | 2015 Feb 11; |
Impact of allele-specific peptides in proteome quantification. | Wu, Linfeng; Snyder, Michael | Proteomics. Clinical applications. | 25676416 | 2015 Apr; |
A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2. | Didion, John P; Morgan, Andrew P; Clayshulte, Amelia M-F; Mcmullan, Rachel C; Yadgary, Liran; Petkov, Petko M; Bell, Timothy A; Gatti, Daniel M; Crowley, James J; Hua, Kunjie; Aylor, David L; Bai, Ling; Calaway, Mark; Chesler, Elissa J; French, John E; Geiger, Thomas R; Gooch, Terry J; Garland Jr, Theodore; Harrill, Alison H; Hunter, Kent; McMillan, Leonard; Holt, Matt; Miller, Darla R; O'Brien, Deborah A; Paigen, Kenneth; Pan, Wenqi; Rowe, Lucy B; Shaw, Ginger D; Simecek, Petr; Sullivan, Patrick F; Svenson, Karen L; Weinstock, George M; Threadgill, David W; Pomp, Daniel; Churchill, Gary A; Pardo-Manuel de Villena, Fernando | PLoS genetics. | 25679959 | 2015 Feb; |
Mitochondrial DNA sequence variation is largely conserved at birth with rare de novo mutations in neonates. | Ma, Jun; Purcell, Heidi; Showalter, Lori; Aagaard, Kjersti M | American journal of obstetrics and gynecology. | 25687567 | 2015 Apr; |
A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification. | Bigdeli, Saharnaz; Dettloff, Roger O; Frank, Curtis W; Davis, Ronald W; Crosby, Laurel D | PloS one. | 25689864 | 2015 Feb 17; |
Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. | Yasuda, Koji; Oh, Keunyoung; Ren, Boyu; Tickle, Timothy L; Franzosa, Eric A; Wachtman, Lynn M; Miller, Andrew D; Westmoreland, Susan V; Mansfield, Keith G; Vallender, Eric J; Miller, Gregory M; Rowlett, James K; Gevers, Dirk; Huttenhower, Curtis; Morgan, Xochitl C | Cell host & microbe. | 25732063 | 2015 Mar 11; |
Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases. | Huang, Edmond Y; Inoue, Takuya; Leone, Vanessa A; Dalal, Sushila; Touw, Ketrija; Wang, Yunwei; Musch, Mark W; Theriault, Betty; Higuchi, Kazuhide; Donovan, Sharon; Gilbert, Jack; Chang, Eugene B | Inflammatory bowel diseases. | 25738379 | 2015 May; |
Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study. | Zhou, Yanjiao; Shan, Gururaj; Sodergren, Erica; Weinstock, George; Walker, W Allan; Gregory, Katherine E | PloS one. | 25741698 | 2015 Mar 5; |
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, Kévin; Jiang, Lihua; Snyder, Michael | Molecular & cellular proteomics : MCP. | 25787789 | 2015 Jun; |
Personal genomes, quantitative dynamic omics and personalized medicine. | Mias, George I; Snyder, Michael | Quantitative biology. | 25798291 | 2013 Mar; |
Subsistence strategies in traditional societies distinguish gut microbiomes. | Obregon-Tito, Alexandra J; Tito, Raul Y; Metcalf, Jessica; Sankaranarayanan, Krithivasan; Clemente, Jose C; Ursell, Luke K; Zech Xu, Zhenjiang; Van Treuren, Will; Knight, Rob; Gaffney, Patrick M; Spicer, Paul; Lawson, Paul; Marin-Reyes, Luis; Trujillo-Villarroel, Omar; Foster, Morris; Guija-Poma, Emilio; Troncoso-Corzo, Luzmila; Warinner, Christina; Ozga, Andrew T; Lewis, Cecil M | Nature communications. | 25807110 | 2015 Mar 25; |
Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis. | Hoen, Anne G; Li, Jing; Moulton, Lisa A; O'Toole, George A; Housman, Molly L; Koestler, Devin C; Guill, Margaret F; Moore, Jason H; Hibberd, Patricia L; Morrison, Hilary G; Sogin, Mitchell L; Karagas, Margaret R; Madan, Juliette C | The Journal of pediatrics. | 25818499 | 2015 Jul; |
Sinus microbiota varies among chronic rhinosinusitis phenotypes and predicts surgical outcome. | Ramakrishnan, Vijay R; Hauser, Leah J; Feazel, Leah M; Ir, Diana; Robertson, Charles E; Frank, Daniel N | The Journal of allergy and clinical immunology. | 25819063 | 2015 Aug; |
Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. | Kelly, Brendan J; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe | Bioinformatics (Oxford, England). | 25819674 | 2015 Aug 01; |
The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin. | Liu, Jared; Yan, Riceley; Zhong, Qiao; Ngo, Sam; Bangayan, Nathanael J; Nguyen, Lin; Lui, Timothy; Liu, Minghsun; Erfe, Marie C; Craft, Noah; Tomida, Shuta; Li, Huiying | The ISME journal. | 25848871 | 2015 Sep; |
Serial fecal microbiota transplantation alters mucosal gene expression in pediatric ulcerative colitis. | Kellermayer, Richard; Nagy-Szakal, Dorottya; Harris, R Alan; Luna, Ruth Ann; Pitashny, Milena; Schady, Deborah; Mir, Sabina A V; Lopez, Monica E; Gilger, Mark A; Belmont, John; Hollister, Emily B; Versalovic, James | The American journal of gastroenterology. | 25853207 | 2015 Apr; |
New signaling pathways govern the host response to C. albicans infection in various niches. | Liu, Yaoping; Shetty, Amol C; Schwartz, Jennifer A; Bradford, L Latey; Xu, Wenjie; Phan, Qyunh T; Kumari, Priti; Mahurkar, Anup; Mitchell, Aaron P; Ravel, Jacques; Fraser, Claire M; Filler, Scott G; Bruno, Vincent M | Genome research. | 25858952 | 2015 May; |
Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. | Yano, Jessica M; Yu, Kristie; Donaldson, Gregory P; Shastri, Gauri G; Ann, Phoebe; Ma, Liang; Nagler, Cathryn R; Ismagilov, Rustem F; Mazmanian, Sarkis K; Hsiao, Elaine Y | Cell. | 25860609 | 2015 Apr 9; |
Metabolic signatures of bacterial vaginosis. | Srinivasan, Sujatha; Morgan, Martin T; Fiedler, Tina L; Djukovic, Danijel; Hoffman, Noah G; Raftery, Daniel; Marrazzo, Jeanne M; Fredricks, David N | mBio. | 25873373 | 2015 Apr 14; |
Sex, body mass index, and dietary fiber intake influence the human gut microbiome. | Dominianni, Christine; Sinha, Rashmi; Goedert, James J; Pei, Zhiheng; Yang, Liying; Hayes, Richard B; Ahn, Jiyoung | PloS one. | 25874569 | 2015 Apr 15; |
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. | Brooks, J Paul; Edwards, David J; Harwich Jr, Michael D; Rivera, Maria C; Fettweis, Jennifer M; Serrano, Myrna G; Reris, Robert A; Sheth, Nihar U; Huang, Bernice; Girerd, Philippe; Vaginal Microbiome Consortium; Strauss 3rd, Jerome F; Jefferson, Kimberly K; Buck, Gregory A | BMC microbiology. | 25880246 | 2015 Mar 21; |
Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. | Morgan, Xochitl C; Kabakchiev, Boyko; Waldron, Levi; Tyler, Andrea D; Tickle, Timothy L; Milgrom, Raquel; Stempak, Joanne M; Gevers, Dirk; Xavier, Ramnik J; Silverberg, Mark S; Huttenhower, Curtis | Genome biology. | 25887922 | 2015 Apr 8; |
Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. | Leone, Vanessa; Gibbons, Sean M; Martinez, Kristina; Hutchison, Alan L; Huang, Edmond Y; Cham, Candace M; Pierre, Joseph F; Heneghan, Aaron F; Nadimpalli, Anuradha; Hubert, Nathaniel; Zale, Elizabeth; Wang, Yunwei; Huang, Yong; Theriault, Betty; Dinner, Aaron R; Musch, Mark W; Kudsk, Kenneth A; Prendergast, Brian J; Gilbert, Jack A; Chang, Eugene B | Cell host & microbe. | 25891358 | 2015 May 13; |
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. | Franzosa, Eric A; Hsu, Tiffany; Sirota-Madi, Alexandra; Shafquat, Afrah; Abu-Ali, Galeb; Morgan, Xochitl C; Huttenhower, Curtis | Nature reviews. Microbiology. | 25915636 | 2015 Jun; |
Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis. | Segal, Leopoldo N; Blaser, Martin J | The Journal of pediatrics. | 25934071 | 2015 Jul; |
Identifying personal microbiomes using metagenomic codes. | Franzosa, Eric A; Huang, Katherine; Meadow, James F; Gevers, Dirk; Lemon, Katherine P; Bohannan, Brendan J M; Huttenhower, Curtis | Proceedings of the National Academy of Sciences of the United States of America. | 25964341 | 2015 Jun 2; |
Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease. | Lee, Dale; Baldassano, Robert N; Otley, Anthony R; Albenberg, Lindsey; Griffiths, Anne M; Compher, Charlene; Chen, Eric Z; Li, Hongzhe; Gilroy, Erin; Nessel, Lisa; Grant, Amy; Chehoud, Christel; Bushman, Frederic D; Wu, Gary D; Lewis, James D | Inflammatory bowel diseases. | 25970545 | 2015 Aug; |
An integrative view of microbiome-host interactions in inflammatory bowel diseases. | Wlodarska, Marta; Kostic, Aleksandar D; Xavier, Ramnik J | Cell host & microbe. | 25974300 | 2015 May 13; |
The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins. | Mehla, Jitender; Dedrick, Rebekah M; Caufield, J Harry; Siefring, Rachel; Mair, Megan; Johnson, Allison; Hatfull, Graham F; Uetz, Peter | Journal of bacteriology. | 25986902 | 2015 Aug 1; |
High-throughput sequencing technologies. | Reuter, Jason A; Spacek, Damek V; Snyder, Michael P | Molecular cell. | 26000844 | 2015 May 21; |
Skin-to-Skin Care and the Development of the Preterm Infant Oral Microbiome. | Hendricks-Muñoz, Karen D; Xu, Jie; Parikh, Hardik I; Xu, Ping; Fettweis, Jennifer M; Kim, Yang; Louie, Moi; Buck, Gregory A; Thacker, Leroy R; Sheth, Nihar U | American journal of perinatology. | 26007311 | 2015 Nov; |
Carcass mass has little influence on the structure of gravesoil microbial communities. | Weiss, Sophie; Carter, David O; Metcalf, Jessica L; Knight, Rob | International journal of legal medicine. | 26024793 | 2016 Jan; |
Inflammation-associated microbiota in pediatric eosinophilic esophagitis. | Benitez, Alain J; Hoffmann, Christian; Muir, Amanda B; Dods, Kara K; Spergel, Jonathan M; Bushman, Frederic D; Wang, Mei-Lun | Microbiome | 26034601 | 2015 |
Fast disease progression in simian HIV-infected female macaque is accompanied by a robust local inflammatory innate immune and microbial response. | Ren, Wuze; Ma, Yingfei; Yang, Liying; Gettie, Agegnehu; Salas, January; Russell, Kasi; Blanchard, James; Davidow, Amy; Pei, Zhiheng; Chang, Theresa L; Cheng-Mayer, Cecilia | AIDS (London, England). | 26035329 | 2015 Jun 19; |
Lungs, microbes and the developing neonate. | Warner, Barbara B; Hamvas, Aaron | Neonatology. | 26044101 | 2015 June; |
The Fecal Microbiome in Pediatric Patients With Short Bowel Syndrome. | Davidovics, Zev H; Carter, Beth A; Luna, Ruth Ann; Hollister, Emily B; Shulman, Robert J; Versalovic, James | JPEN. Journal of parenteral and enteral nutrition. | 26059898 | 2016 11; |
Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes. | Alkanani, Aimon K; Hara, Naoko; Gottlieb, Peter A; Ir, Diana; Robertson, Charles E; Wagner, Brandie D; Frank, Daniel N; Zipris, Danny | Diabetes. | 26068542 | 2015 Oct; |
Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett's Esophagus Cohort. | Gall, Alevtina; Fero, Jutta; McCoy, Connor; Claywell, Brian C; Sanchez, Carissa A; Blount, Patricia L; Li, Xiaohong; Vaughan, Thomas L; Matsen, Frederick A; Reid, Brian J; Salama, Nina R | PloS one. | 26076489 | 2015 June 15; |
Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9. | Bryson, Alexandra L; Hwang, Young; Sherrill-Mix, Scott; Wu, Gary D; Lewis, James D; Black, Lindsay; Clark, Tyson A; Bushman, Frederic D | mBio. | 26081634 | 2015 June 16; |
Effects of Vaccination with 10-Valent Pneumococcal Non-Typeable Haemophilus influenza Protein D Conjugate Vaccine (PHiD-CV) on the Nasopharyngeal Microbiome of Kenyan Toddlers. | Feazel, Leah M; Santorico, Stephanie A; Robertson, Charles E; Bashraheil, Mahfudh; Scott, J Anthony G; Frank, Daniel N; Hammitt, Laura L | PloS one. | 26083474 | 2015; |
Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease. | Chehoud, Christel; Albenberg, Lindsey G; Judge, Colleen; Hoffmann, Christian; Grunberg, Stephanie; Bittinger, Kyle; Baldassano, Robert N; Lewis, James D; Bushman, Frederic D; Wu, Gary D | Inflammatory bowel diseases. | 26083617 | 2015 Aug; |
Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease. | Vital, Marius; Harkema, Jack R; Rizzo, Mike; Tiedje, James; Brandenberger, Christina | Journal of immunology research. | 26090504 | 2015 April 16; |
Engineering the gut microbiota to treat hyperammonemia. | Shen, Ting-Chin David; Albenberg, Lindsey; Bittinger, Kyle; Chehoud, Christel; Chen, Ying-Yu; Judge, Colleen A; Chau, Lillian; Ni, Josephine; Sheng, Michael; Lin, Andrew; Wilkins, Benjamin J; Buza, Elizabeth L; Lewis, James D; Daikhin, Yevgeny; Nissim, Ilana; Yudkoff, Marc; Bushman, Frederic D; Wu, Gary D | The Journal of clinical investigation. | 26098218 | 2015 Jul 1; |
Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome. | Chumpitazi, B P; Cope, J L; Hollister, E B; Tsai, C M; McMeans, A R; Luna, R A; Versalovic, J; Shulman, R J | Alimentary pharmacology & therapeutics. | 26104013 | 2015 Aug; |
Impact of neonatal intensive care bed configuration on rates of late-onset bacterial sepsis and methicillin-resistant Staphylococcus aureus colonization. | Julian, Samuel; Burnham, Carey-Ann D; Sellenriek, Patricia; Shannon, William D; Hamvas, Aaron; Tarr, Phillip I; Warner, Barbara B | Infection control and hospital epidemiology. | 26108888 | 2015 Oct; |
Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis. | Kang, Dezhi; Shi, Baochen; Erfe, Marie C; Craft, Noah; Li, Huiying | Science translational medicine. | 26109103 | 2015 Jun 24; |
Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants. | Taft, Diana H; Ambalavanan, Namasivayam; Schibler, Kurt R; Yu, Zhuoteng; Newburg, David S; Deshmukh, Hitesh; Ward, Doyle V; Morrow, Ardythe L | PloS one. | 26110908 | 2015 Jun 25; |
Using an in-vitro biofilm model to assess the virulence potential of bacterial vaginosis or non-bacterial vaginosis Gardnerella vaginalis isolates. | Castro, Joana; Alves, Patrícia; Sousa, Cármen; Cereija, Tatiana; França, Ângela; Jefferson, Kimberly K; Cerca, Nuno | Scientific reports. | 26113465 | 2015 Jun 26; |
Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. | Nobel, Yael R; Cox, Laura M; Kirigin, Francis F; Bokulich, Nicholas A; Yamanishi, Shingo; Teitler, Isabel; Chung, Jennifer; Sohn, Jiho; Barber, Cecily M; Goldfarb, David S; Raju, Kartik; Abubucker, Sahar; Zhou, Yanjiao; Ruiz, Victoria E; Li, Huilin; Mitreva, Makedonka; Alekseyenko, Alexander V; Weinstock, George M; Sodergren, Erica; Blaser, Martin J | Nature communications. | 26123276 | 2015 Jun 30; |
Compact graphical representation of phylogenetic data and metadata with GraPhlAn. | Asnicar, Francesco; Weingart, George; Tickle, Timothy L; Huttenhower, Curtis; Segata, Nicola | PeerJ. | 26157614 | 2015; |
Role of Autophagy in the Maintenance of Intestinal Homeostasis. | Baxt, Leigh A; Xavier, Ramnik J | Gastroenterology. | 26170139 | 2015 Sep; |
Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile. | Schubert, Alyxandria M; Sinani, Hamide; Schloss, Patrick D | mBio. | 26173701 | 2015 Jul 14; |
High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae. | Sizova, Maria V; Chilaka, Amanda; Earl, Ashlee M; Doerfert, Sebastian N; Muller, Paul A; Torralba, Manolito; McCorrison, Jamison M; Durkin, A Scott; Nelson, Karen E; Epstein, Slava S | Standards in genomic sciences. | 26221418 | 2015; |
The microbiome of uncontacted Amerindians. | Clemente, Jose C; Pehrsson, Erica C; Blaser, Martin J; Sandhu, Kuldip; Gao, Zhan; Wang, Bin; Magris, Magda; Hidalgo, Glida; Contreras, Monica; Noya-Alarcón, Óscar; Lander, Orlana; McDonald, Jeremy; Cox, Mike; Walter, Jens; Oh, Phaik Lyn; Ruiz, Jean F; Rodriguez, Selena; Shen, Nan; Song, Se Jin; Metcalf, Jessica; Knight, Rob; Dantas, Gautam; Dominguez-Bello, M Gloria | Science advances. | 26229982 | 2015 Apr 3; |
Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. | Beck, James M; Schloss, Patrick D; Venkataraman, Arvind; Twigg 3rd, Homer; Jablonski, Kathleen A; Bushman, Frederic D; Campbell, Thomas B; Charlson, Emily S; Collman, Ronald G; Crothers, Kristina; Curtis, Jeffrey L; Drews, Kimberly L; Flores, Sonia C; Fontenot, Andrew P; Foulkes, Mary A; Frank, Ian; Ghedin, Elodie; Huang, Laurence; Lynch, Susan V; Morris, Alison; Palmer, Brent E; Schmidt, Thomas M; Sodergren, Erica; Weinstock, George M; Young, Vincent B; Lung HIV Microbiome Project | American journal of respiratory and critical care medicine. | 26247840 | 2015 Dec 01; |
The gut microbiota in human energy homeostasis and obesity. | Rosenbaum, Michael; Knight, Rob; Leibel, Rudolph L | Trends in endocrinology and metabolism: TEM. | 26257300 | 2015 Sep; |
Characterization of genetic loci that affect susceptibility to inflammatory bowel diseases in African Americans. | Huang, Chengrui; Haritunians, Talin; Okou, David T; Cutler, David J; Zwick, Michael E; Taylor, Kent D; Datta, Lisa W; Maranville, Joseph C; Liu, Zhenqiu; Ellis, Shannon; Chopra, Pankaj; Alexander, Jonathan S; Baldassano, Robert N; Cross, Raymond K; Dassopoulos, Themistocles; Dhere, Tanvi A; Duerr, Richard H; Hanson, John S; Hou, Jason K; Hussain, Sunny Z; Isaacs, Kim L; Kachelries, Kelly E; Kader, Howard; Kappelman, Michael D; Katz, Jeffrey; Kellermayer, Richard; Kirschner, Barbara S; Kuemmerle, John F; Kumar, Archana; Kwon, John H; Lazarev, Mark; Mannon, Peter; Moulton, Dedrick E; Osuntokun, Bankole O; Patel, Ashish; Rioux, John D; Rotter, Jerome I; Saeed, Shehzad; Scherl, Ellen J; Silverberg, Mark S; Silverman, Ann; Targan, Stephan R; Valentine, John F; Wang, Ming-Hsi; Simpson, Claire L; Bridges, S Louis; Kimberly, Robert P; Rich, Stephen S; Cho, Judy H; Di Rienzo, Anna; Kao, Linda W H; McGovern, Dermot P B; Brant, Steven R; Kugathasan, Subra | Gastroenterology. | 26278503 | 2015 Nov; |
Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts. | Kelsen, Judith; Bittinger, Kyle; Pauly-Hubbard, Helen; Posivak, Leah; Grunberg, Stephanie; Baldassano, Robert; Lewis, James D; Wu, Gary D; Bushman, Frederic D | Inflammatory bowel diseases. | 26288001 | 2015 Dec; |
Structure and function of the healthy pre-adolescent pediatric gut microbiome. | Hollister, Emily B; Riehle, Kevin; Luna, Ruth Ann; Weidler, Erica M; Rubio-Gonzales, Michelle; Mistretta, Toni-Ann; Raza, Sabeen; Doddapaneni, Harsha V; Metcalf, Ginger A; Muzny, Donna M; Gibbs, Richard A; Petrosino, Joseph F; Shulman, Robert J; Versalovic, James | Microbiome. | 26306392 | 2015; |
ConStrains identifies microbial strains in metagenomic datasets. | Luo, Chengwei; Knight, Rob; Siljander, Heli; Knip, Mikael; Xavier, Ramnik J; Gevers, Dirk | Nature biotechnology. | 26344404 | 2015 Oct; |
Early life dynamics of the human gut virome and bacterial microbiome in infants. | Lim, Efrem S; Zhou, Yanjiao; Zhao, Guoyan; Bauer, Irma K; Droit, Lindsay; Ndao, I Malick; Warner, Barbara B; Tarr, Phillip I; Wang, David; Holtz, Lori R | Nature medicine. | 26366711 | 2015 Oct; |
Host genetic variation impacts microbiome composition across human body sites. | Blekhman, Ran; Goodrich, Julia K; Huang, Katherine; Sun, Qi; Bukowski, Robert; Bell, Jordana T; Spector, Timothy D; Keinan, Alon; Ley, Ruth E; Gevers, Dirk; Clark, Andrew G | Genome biology. | 26374288 | 2015 Sep 15; |
MetaPhlAn2 for enhanced metagenomic taxonomic profiling. | Truong, Duy Tin; Franzosa, Eric A; Tickle, Timothy L; Scholz, Matthias; Weingart, George; Pasolli, Edoardo; Tett, Adrian; Huttenhower, Curtis; Segata, Nicola | Nature methods. | 26418763 | 2015 Oct; |
Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. | Lewis, James D; Chen, Eric Z; Baldassano, Robert N; Otley, Anthony R; Griffiths, Anne M; Lee, Dale; Bittinger, Kyle; Bailey, Aubrey; Friedman, Elliot S; Hoffmann, Christian; Albenberg, Lindsey; Sinha, Rohini; Compher, Charlene; Gilroy, Erin; Nessel, Lisa; Grant, Amy; Chehoud, Christel; Li, Hongzhe; Wu, Gary D; Bushman, Frederic D | Cell host & microbe. | 26468751 | 2015 Oct 14; |
The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. | Rogers, M A M; Aronoff, D M | Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. | 26482265 | 2016 Feb; |
Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study. | Cleynen, Isabelle; Boucher, Gabrielle; Jostins, Luke; Schumm, L Philip; Zeissig, Sebastian; Ahmad, Tariq; Andersen, Vibeke; Andrews, Jane M; Annese, Vito; Brand, Stephan; Brant, Steven R; Cho, Judy H; Daly, Mark J; Dubinsky, Marla; Duerr, Richard H; Ferguson, Lynnette R; Franke, Andre; Gearry, Richard B; Goyette, Philippe; Hakonarson, Hakon; Halfvarson, Jonas; Hov, Johannes R; Huang, Hailang; Kennedy, Nicholas A; Kupcinskas, Limas; Lawrance, Ian C; Lee, James C; Satsangi, Jack; Schreiber, Stephan; Théâtre, Emilie; van der Meulen-de Jong, Andrea E; Weersma, Rinse K; Wilson, David C; International Inflammatory Bowel Disease Genetics Consortium; Parkes, Miles; Vermeire, Severine; Rioux, John D; Mansfield, John; Silverberg, Mark S; Radford-Smith, Graham; McGovern, Dermot P B; Barrett, Jeffrey C; Lees, Charlie W | Lancet (London, England). | 26490195 | 2016 Jan 9; |
High Frequency of Detection by PCR of Viral Nucleic Acid in The Blood of Infants Presenting with Clinical Myocarditis. | Simpson, Kathleen E; Storch, Gregory A; Lee, Caroline K; Ward, Kent E; Danon, Saar; Simon, Catherine M; Delaney, Jeffrey W; Tong, Alan; Canter, Charles E | Pediatric cardiology. | 26499513 | 2016 Feb; |
mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. | Davis, Curtis; Kota, Karthik; Baldhandapani, Venkat; Gong, Wei; Abubucker, Sahar; Becker, Eric; Martin, John; Wylie, Kristine M; Khetani, Radhika; Hudson, Matthew E; Weinstock, George M; Mitreva, Makedonka | Journal of data mining in genomics & proteomics. | 26500804 | 2015 Aug; |
Emergence of Rotavirus G12P[8] in St. Louis During the 2012-2013 Rotavirus Season. | Wylie, Kristine M; Weinstock, George M; Storch, Gregory A | Journal of the Pediatric Infectious Diseases Society. | 26513823 | 2015 Dec; |
Microbiome, a new dimension in cancer research. | Neto, Antonio Galvao; Bradshaw, Azore-Dee; Pei, Zhiheng | Annals of translational medicine. | 26539446 | 2015 Sep; |
Microfluidic Flow Cytometry for Single-Cell Protein Analysis. | Wu, Meiye; Singh, Anup K | Methods in molecular biology (Clifton, N.J.). | 26542716 | 2015; |
Global prevalence and distribution of genes and microorganisms involved in mercury methylation. | Podar, Mircea; Gilmour, Cynthia C; Brandt, Craig C; Soren, Allyson; Brown, Steven D; Crable, Bryan R; Palumbo, Anthony V; Somenahally, Anil C; Elias, Dwayne A | Science advances | 26601305 | 2015 Oct |
Nurturing the microbiome field. | Schloss, Patrick | Science (New York, N.Y.) | 26612945 | 2015 Nov 27 |
Luminal Conversion and Immunoregulation by Probiotics. | Ganesh, Bhanu Priya; Versalovic, James | Frontiers in pharmacology. | 26617521 | 2015; |
The first microbial environment of infants born by C-section: the operating room microbes. | Shin, Hakdong; Pei, Zhiheng; Martinez 2nd, Keith A; Rivera-Vinas, Juana I; Mendez, Keimari; Cavallin, Humberto; Dominguez-Bello, Maria G | Microbiome. | 26620712 | 2015 Dec 01; |
Wham: Identifying Structural Variants of Biological Consequence. | Kronenberg, Zev N; Osborne, Edward J; Cone, Kelsey R; Kennedy, Brett J; Domyan, Eric T; Shapiro, Michael D; Elde, Nels C; Yandell, Mark | PLoS computational biology. | 26625158 | 2015 Dec; |
Engineering Values Into Genetic Engineering: A Proposed Analytic Framework for Scientific Social Responsibility. | Sankar, Pamela L; Cho, Mildred K | The American journal of bioethics : AJOB. | 26632356 | 2015; |
Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens. | Zhou, Yanjiao; Wylie, Kristine M; El Feghaly, Rana E; Mihindukulasuriya, Kathie A; Elward, Alexis; Haslam, David B; Storch, Gregory A; Weinstock, George M | Journal of clinical microbiology. | 26637379 | 2016 Feb; |
The microbiome quality control project: baseline study design and future directions. | Sinha, Rashmi; Abnet, Christian C; White, Owen; Knight, Rob; Huttenhower, Curtis | Genome biology. | 26653756 | 2015; |
Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. | Kuleshov, Volodymyr; Jiang, Chao; Zhou, Wenyu; Jahanbani, Fereshteh; Batzoglou, Serafim; Snyder, Michael | Nature biotechnology | 26655498 | 2016 Jan |
Microbial community assembly and metabolic function during mammalian corpse decomposition. | Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob | Science (New York, N.Y.). | 26657285 | 2016 Jan 8; |
Histamine H2 Receptor-Mediated Suppression of Intestinal Inflammation by Probiotic Lactobacillus reuteri. | Gao, Chunxu; Major, Angela; Rendon, David; Lugo, Monica; Jackson, Vanessa; Shi, Zhongcheng; Mori-Akiyama, Yuko; Versalovic, James | mBio. | 26670383 | 2015 Dec 15; |
Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma. | Sankaranarayanan, Krithivasan; Ozga, Andrew T; Warinner, Christina; Tito, Raul Y; Obregon-Tito, Alexandra J; Xu, Jiawu; Gaffney, Patrick M; Jervis, Lori L; Cox, Derrell; Stephens, Lancer; Foster, Morris; Tallbull, Gloria; Spicer, Paul; Lewis, Cecil M | Current biology : CB. | 26671671 | 2015 Dec 21; |
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. | Kaminski, James; Gibson, Molly K; Franzosa, Eric A; Segata, Nicola; Dantas, Gautam; Huttenhower, Curtis | PLoS computational biology | 26682918 | 2015 Dec |
Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. | Araya, Carlos L; Cenik, Can; Reuter, Jason A; Kiss, Gert; Pande, Vijay S; Snyder, Michael P; Greenleaf, William J | Nature genetics. | 26691984 | 2016 Feb; |
HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria. | Yang, Liying; Poles, Michael A; Fisch, Gene S; Ma, Yingfei; Nossa, Carlos; Phelan, Joan A; Pei, Zhiheng | AIDS (London, England). | 26731752 | 2016 Jan 02; |
Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria. | Abdelmaksoud, Abdallah A; Koparde, Vishal N; Sheth, Nihar U; Serrano, Myrna G; Glascock, Abigail L; Fettweis, Jennifer M; Strauss Iii, Jerome F; Buck, Gregory A; Jefferson, Kimberly K | Microbiology (Reading, England). | 26747455 | 2016 Jan 8; |
Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium. | Volkmann, Elizabeth R; Chang, Yu-Ling; Barroso, Nashla; Furst, Daniel E; Clements, Philip J; Gorn, Alan H; Roth, Bennett E; Conklin, Jeffrey L; Getzug, Terri; Borneman, James; McGovern, Dermot P B; Tong, Maomeng; Jacobs, Jonathan P; Braun, Jonathan | Arthritis & rheumatology (Hoboken, N.J.). | 26749064 | 2016 06; |
A quantitative understanding of lac repressor's binding specificity and flexibility. | Zuo, Zheng; Chang, Yiming; Stormo, Gary D | Quantitative biology (Beijing, China). | 26752632 | 2015 Jun 01; |
Erratum to: The first microbial environment of infants born by C-section: the operating room microbes. | Shin, Hakdong; Pei, Zhiheng; Martinez 2nd, Keith A; Rivera-Vinas, Juana I; Mendez, Keimari; Cavallin, Humberto; Dominguez-Bello, Maria G | Microbiome. | 26796629 | 2016 Jan 21; |
Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes. | Yassour, Moran; Lim, Mi Young; Yun, Hyun Sun; Tickle, Timothy L; Sung, Joohon; Song, Yun-Mi; Lee, Kayoung; Franzosa, Eric A; Morgan, Xochitl C; Gevers, Dirk; Lander, Eric S; Xavier, Ramnik J; Birren, Bruce W; Ko, GwangPyo; Huttenhower, Curtis | Genome medicine | 26884067 | 2016 Feb 17 |
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. | Weiss, Sophie; Van Treuren, Will; Lozupone, Catherine; Faust, Karoline; Friedman, Jonathan; Deng, Ye; Xia, Li Charlie; Xu, Zhenjiang Zech; Ursell, Luke; Alm, Eric J; Birmingham, Amanda; Cram, Jacob A; Fuhrman, Jed A; Raes, Jeroen; Sun, Fengzhu; Zhou, Jizhong; Knight, Rob | The ISME journal. | 26905627 | 2016 Feb 23; |
Can Metabolic Profiles Be Used as a Phenotypic Readout of the Genome to Enhance Precision Medicine? | Contrepois, Kévin; Liang, Liang; Snyder, Michael | Clinical chemistry. | 26960666 | 2016 May; |
Gut bacteria dysbiosis and necrotising enterocolitis in very low birthweight infants: a prospective case-control study. | Warner, Barbara B; Deych, Elena; Zhou, Yanjiao; Hall-Moore, Carla; Weinstock, George M; Sodergren, Erica; Shaikh, Nurmohammad; Hoffmann, Julie A; Linneman, Laura A; Hamvas, Aaron; Khanna, Geetika; Rouggly-Nickless, Lucina C; Ndao, I Malick; Shands, Berkley A; Escobedo, Marilyn; Sullivan, Janice E; Radmacher, Paula G; Shannon, William D; Tarr, Phillip I | Lancet (London, England). | 26969089 | 2016 May 07; |
Microbiome and potential targets for chemoprevention of esophageal adenocarcinoma. | Neto, Antonio Galvao; Whitaker, April; Pei, Zhiheng | Seminars in oncology. | 26970127 | 2016 Feb; |
Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants. | Ward, Doyle V; Scholz, Matthias; Zolfo, Moreno; Taft, Diana H; Schibler, Kurt R; Tett, Adrian; Segata, Nicola; Morrow, Ardythe L | Cell reports. | 26997279 | 2016 Mar 29; |
Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation. | Chehoud, Christel; Dryga, Anatoly; Hwang, Young; Nagy-Szakal, Dorottya; Hollister, Emily B; Luna, Ruth Ann; Versalovic, James; Kellermayer, Richard; Bushman, Frederic D | mBio. | 27025251 | 2016 Mar 29; |
Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. | Schloss, Patrick D; Jenior, Matthew L; Koumpouras, Charles C; Westcott, Sarah L; Highlander, Sarah K | PeerJ. | 27069806 | 2016; |
Papillary urothelial carcinoma with squamous differentiation in association with human papilloma virus: case report and literature review. | Guma, Sergei; Maglantay, Remegio; Lau, Ryan; Wieczorek, Rosemary; Melamed, Jonathan; Deng, Fang-Ming; Zhou, Ming; Makarov, Danil; Lee, Peng; Pincus, Matthew R; Pei, Zhi-Heng | American journal of clinical and experimental urology. | 27069958 | 2016; |
Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility. | Ward, Marc A; Pierre, Joseph F; Leal, Raquel F; Huang, Yong; Shogan, Benjamin; Dalal, Sushila R; Weber, Christopher R; Leone, Vanessa A; Musch, Mark W; An, Gary C; Rao, Mrinalini C; Rubin, David T; Raffals, Laura E; Antonopoulos, Dionysios A; Sogin, Mitch L; Hyman, Neil H; Alverdy, John C; Chang, Eugene B | American journal of physiology. Gastrointestinal and liver physiology. | 27079612 | 2016 06 01; |
Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome. | Perez Perez, Guillermo I; Gao, Zhan; Jourdain, Roland; Ramirez, Julia; Gany, Francesca; Clavaud, Cecile; Demaude, Julien; Breton, Lionel; Blaser, Martin J | PloS one. | 27088867 | 2016; |
The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages. | Mariano, Rachelle; Wuchty, Stefan; Vizoso-Pinto, Maria G; Häuser, Roman; Uetz, Peter | Scientific reports. | 27103053 | 2016 Apr 22; |
Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. | Vatanen, Tommi; Kostic, Aleksandar D; d'Hennezel, Eva; Siljander, Heli; Franzosa, Eric A; Yassour, Moran; Kolde, Raivo; Vlamakis, Hera; Arthur, Timothy D; Hämäläinen, Anu-Maaria; Peet, Aleksandr; Tillmann, Vallo; Uibo, Raivo; Mokurov, Sergei; Dorshakova, Natalya; Ilonen, Jorma; Virtanen, Suvi M; Szabo, Susanne J; Porter, Jeffrey A; Lähdesmäki, Harri; Huttenhower, Curtis; Gevers, Dirk; Cullen, Thomas W; Knip, Mikael; DIABIMMUNE Study Group; Xavier, Ramnik J | Cell. | 27133167 | 2016 May 5; |
Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples. | Rhee, Minsoung; Light, Yooli K; Meagher, Robert J; Singh, Anup K | PloS one. | 27144304 | 2016; |
Cathelicidin suppresses lipid accumulation and hepatic steatosis by inhibition of the CD36 receptor. | Hoang-Yen Tran, D; Hoang-Ngoc Tran, D; Mattai, S A; Sallam, T; Ortiz, C; Lee, E C; Robbins, L; Ho, S; Lee, J E; Fisseha, E; Shieh, C; Sideri, A; Shih, D Q; Fleshner, P; McGovern, D P B; Vu, M; Hing, T C; Bakirtzi, K; Cheng, M; Su, B; Law, I; Karagiannides, I; Targan, S R; Gallo, R L; Li, Z; Koon, H W | International journal of obesity (2005). | 27163748 | 2016 Sep; |
Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. | Blaser, Martin J; Cardon, Zoe G; Cho, Mildred K; Dangl, Jeffrey L; Donohue, Timothy J; Green, Jessica L; Knight, Rob; Maxon, Mary E; Northen, Trent R; Pollard, Katherine S; Brodie, Eoin L | mBio. | 27178263 | 2016 05 13; |
Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. | Chu, Hiutung; Khosravi, Arya; Kusumawardhani, Indah P; Kwon, Alice H K; Vasconcelos, Anilton C; Cunha, Larissa D; Mayer, Anne E; Shen, Yue; Wu, Wei-Li; Kambal, Amal; Targan, Stephan R; Xavier, Ramnik J; Ernst, Peter B; Green, Douglas R; McGovern, Dermot P B; Virgin, Herbert W; Mazmanian, Sarkis K | Science (New York, N.Y.). | 27230380 | 2016 May 27; |
Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation. | Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha; Theriot, Casey M; Young, Vincent B; Jansson, Janet K; Fredricks, David N; Borenstein, Elhanan | mSystems | 27239563 | 2016 |
Challenges for case-control studies with microbiome data. | Brooks, J Paul | Annals of epidemiology. | 27255739 | 2016 05; |
Prophages mediate defense against phage infection through diverse mechanisms. | Bondy-Denomy, Joseph; Qian, Jason; Westra, Edze R; Buckling, Angus; Guttman, David S; Davidson, Alan R; Maxwell, Karen L | The ISME journal. | 27258950 | 2016 12; |
STOPPING DECEPTIVE HEALTH CLAIMS: THE NEED FOR A PRIVATE RIGHT OF ACTION UNDER FEDERAL LAW. | Hoffmann, Diane; Schwartz, Jack | American journal of law & medicine. | 27263263 | 2016; |
Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis. | Zackular, Joseph P; Baxter, Nielson T; Chen, Grace Y; Schloss, Patrick D | mSphere. | 27303681 | 2016 Jan-Feb; |
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; |
Necrotizing enterocolitis and preterm infant gut bacteria. | Warner, Barbara B; Tarr, Phillip I | Seminars in fetal & neonatal medicine. | 27343151 | 2016 12; |
Gut bacteria and late-onset neonatal bloodstream infections in preterm infants. | Tarr, Phillip I; Warner, Barbara B | Seminars in fetal & neonatal medicine. | 27345372 | 2016 12; |
Oral microbiome diversity among Cheyenne and Arapaho individuals from Oklahoma. | Ozga, Andrew T; Sankaranarayanan, Krithivasan; Tito, Raúl Y; Obregon-Tito, Alexandra J; Foster, Morris W; Tallbull, Gloria; Spicer, Paul; Warinner, Christina G; Lewis Jr, Cecil M | American journal of physical anthropology. | 27357925 | 2016 Oct; |
Mobile genes in the human microbiome are structured from global to individual scales. | Brito, I L; Yilmaz, S; Huang, K; Xu, L; Jupiter, S D; Jenkins, A P; Naisilisili, W; Tamminen, M; Smillie, C S; Wortman, J R; Birren, B W; Xavier, R J; Blainey, P C; Singh, A K; Gevers, D; Alm, E J | Nature. | 27409808 | 2016 07 21; |
More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria. | Srinivasan, Sujatha; Munch, Matthew M; Sizova, Maria V; Fiedler, Tina L; Kohler, Christina M; Hoffman, Noah G; Liu, Congzhou; Agnew, Kathy J; Marrazzo, Jeanne M; Epstein, Slava S; Fredricks, David N | The Journal of infectious diseases. | 27449870 | 2016 Aug 15; |
GABA-producing Bifidobacterium dentium modulates visceral sensitivity in the intestine. | Pokusaeva, K; Johnson, C; Luk, B; Uribe, G; Fu, Y; Oezguen, N; Matsunami, R K; Lugo, M; Major, A; Mori-Akiyama, Y; Hollister, E B; Dann, S M; Shi, X Z; Engler, D A; Savidge, T; Versalovic, J | Neurogastroenterology and motility : the official journal of the European Gastrointestinal Motility Society. | 27458085 | 2017 Jan; |
Antibiotic perturbation of the preterm infant gut microbiome and resistome. | Gasparrini, Andrew J; Crofts, Terence S; Gibson, Molly K; Tarr, Phillip I; Warner, Barbara B; Dantas, Gautam | Gut microbes. | 27472377 | 2016 09 02; |
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; |
A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis. | Rivas, Manuel A; Graham, Daniel; Sulem, Patrick; Stevens, Christine; Desch, A Nicole; Goyette, Philippe; Gudbjartsson, Daniel; Jonsdottir, Ingileif; Thorsteinsdottir, Unnur; Degenhardt, Frauke; Mucha, Sören; Kurki, Mitja I; Li, Dalin; D'Amato, Mauro; Annese, Vito; Vermeire, Severine; Weersma, Rinse K; Halfvarson, Jonas; Paavola-Sakki, Paulina; Lappalainen, Maarit; Lek, Monkol; Cummings, Beryl; Tukiainen, Taru; Haritunians, Talin; Halme, Leena; Koskinen, Lotta L E; Ananthakrishnan, Ashwin N; Luo, Yang; Heap, Graham A; Visschedijk, Marijn C; UK IBD Genetics Consortium; NIDDK IBD Genetics Consortium; MacArthur, Daniel G; Neale, Benjamin M; Ahmad, Tariq; Anderson, Carl A; Brant, Steven R; Duerr, Richard H; Silverberg, Mark S; Cho, Judy H; Palotie, Aarno; Saavalainen, Päivi; Kontula, Kimmo; Färkkilä, Martti; McGovern, Dermot P B; Franke, Andre; Stefansson, Kari; Rioux, John D; Xavier, Ramnik J; Daly, Mark J; 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, J P; Bitton, A; Boucher, G; Croitoru, K; Fleshner, P; Glas, J; Kugathasan, S; Limbergen, J V; Milgrom, R; Proctor, D; Regueiro, M; Schumm, P L; Sharma, Y; Stempak, J M; Targan, S R; Wang, M H | Nature communications. | 27503255 | 2016 Aug 09; |
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; |
Butyrate and bioactive proteolytic form of Wnt-5a regulate colonic epithelial proliferation and spatial development. | Uchiyama, Kazuhiko; Sakiyama, Toshio; Hasebe, Takumu; Musch, Mark W; Miyoshi, Hiroyuki; Nakagawa, Yasushi; He, Tong-Chuan; Lichtenstein, Lev; Naito, Yuji; Itoh, Yoshito; Yoshikawa, Toshikazu; Jabri, Bana; Stappenbeck, Thaddeus; Chang, Eugene B | Scientific reports. | 27561676 | 2016 Aug 26; |
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; |
Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers. | Davison, Michelle; Treangen, Todd J; Koren, Sergey; Pop, Mihai; Bhaya, Devaki | PloS one. | 27611571 | 2016; |
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; |
The balance of metagenomic elements shapes the skin microbiome in acne and health. | Barnard, Emma; Shi, Baochen; Kang, Dezhi; Craft, Noah; Li, Huiying | Scientific reports. | 28000755 | 2016 12 21; |
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; |
Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. | Chu, Derrick M; Ma, Jun; Prince, Amanda L; Antony, Kathleen M; Seferovic, Maxim D; Aagaard, Kjersti M | Nature medicine. | 28112736 | 2017 Mar; |
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; |
Microbial strain-level population structure and genetic diversity from metagenomes. | Truong, Duy Tin; Tett, Adrian; Pasolli, Edoardo; Huttenhower, Curtis; Segata, Nicola | Genome research. | 28167665 | 2017 Apr; |
A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-l-proline. | Levin, B J; Huang, Y Y; Peck, S C; Wei, Y; Martínez-Del Campo, A; Marks, J A; Franzosa, E A; Huttenhower, C; Balskus, E P | Science (New York, N.Y.). | 28183913 | 2017 02 10; |
Dynamics of the human gut microbiome in inflammatory bowel disease. | Halfvarson, Jonas; Brislawn, Colin J; Lamendella, Regina; Vázquez-Baeza, Yoshiki; Walters, William A; Bramer, Lisa M; D'Amato, Mauro; Bonfiglio, Ferdinando; McDonald, Daniel; Gonzalez, Antonio; McClure, Erin E; Dunklebarger, Mitchell F; Knight, Rob; Jansson, Janet K | Nature microbiology. | 28191884 | 2017 Feb 13; |
Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. | Huang, Yong; Dalal, Sushila; Antonopoulos, Dionysios; Hubert, Nathaniel; Raffals, Laura H; Dolan, Kyle; Weber, Christopher; Messer, Jeannette S; Jabri, Bana; Bendelac, Albert; Eren, A Murat; Rubin, David T; Sogin, Mitch; Chang, Eugene B | Inflammatory bowel diseases. | 28221248 | 2017 03; |
Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. | Huang, Yong; Dalal, Sushila; Antonopoulos, Dionysios; Hubert, Nathaniel; Raffals, Laura H; Dolan, Kyle; Weber, Christopher; Messer, Jeannette S; Jabri, Bana; Bendelac, Albert; Eren, A Murat; Rubin, David T; Sogin, Mitch; Chang, Eugene B | Inflammatory bowel diseases. | 28248733 | 2017 Feb 13; |
Normalization and microbial differential abundance strategies depend upon data characteristics. | Weiss, Sophie; Xu, Zhenjiang Zech; Peddada, Shyamal; Amir, Amnon; Bittinger, Kyle; Gonzalez, Antonio; Lozupone, Catherine; Zaneveld, Jesse R; Vázquez-Baeza, Yoshiki; Birmingham, Amanda; Hyde, Embriette R; Knight, Rob | Microbiome. | 28253908 | 2017 03 03; |
Intestinal dysbiosis in preterm infants preceding necrotizing enterocolitis: a systematic review and meta-analysis. | Pammi, Mohan; Cope, Julia; Tarr, Phillip I; Warner, Barbara B; Morrow, Ardythe L; Mai, Volker; Gregory, Katherine E; Kroll, J Simon; McMurtry, Valerie; Ferris, Michael J; Engstrand, Lars; Lilja, Helene Engstrand; Hollister, Emily B; Versalovic, James; Neu, Josef | Microbiome. | 28274256 | 2017 03 09; |
Bead mediated separation of microparticles in droplets. | Wang, Sida; Sung, Ki-Joo; Lin, Xiaoxia Nina; Burns, Mark A | PloS one | 28282412 | 2017 |
Antibacterial and bioactive coatings on titanium implant surfaces. | Kulkarni Aranya, Anupama; Pushalkar, Smruti; Zhao, Minglei; LeGeros, Racquel Z; Zhang, Yu; Saxena, Deepak | Journal of biomedical materials research. Part A. | 28380669 | 2017 Aug; |
The protection role of Atg16l1 in CD11c+dendritic cells in murine colitis. | Zhang, Hong; Zheng, Libo; Chen, Jeremy; Fukata, Masayuki; Ichikawa, Ryan; Shih, David Q; Zhang, Xiaolan | Immunobiology. | 28390705 | 2017 Jul; |
Independence of gut bacterial content and neonatal necrotizing enterocolitis severity. | Barron, Lauren K; Warner, Barbara B; Tarr, Phillip I; Shannon, William D; Deych, Elena; Warner, Brad W | Journal of pediatric surgery. | 28410788 | 2017 Jun; |
Re: Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. | Misra, Ravi; Arebi, Naila | Gastroenterology. | 28478146 | 2017 06; |
Early pregnancy vaginal microbiome trends and preterm birth. | Stout, Molly J; Zhou, Yanjiao; Wylie, Kristine M; Tarr, Phillip I; Macones, George A; Tuuli, Methodius G | American journal of obstetrics and gynecology. | 28549981 | 2017 09; |
Isolated Congenital Anosmia and CNGA2 Mutation. | Sailani, M Reza; Jingga, Inlora; MirMazlomi, Seyed Hashem; Bitarafan, Fatemeh; Bernstein, Jonathan A; Snyder, Michael P; Garshasbi, Masoud | Scientific reports. | 28572688 | 2017 06 01; |
Pigs, Unlike Mice, Have Two Distinct Colonic Stem Cell Populations Similar to Humans That Respond to High-Calorie Diet prior to Insulin Resistance. | Charepalli, Venkata; Reddivari, Lavanya; Radhakrishnan, Sridhar; Eriksson, Elisabeth; Xiao, Xia; Kim, Sung Woo; Shen, Frank; Vijay-Kumar, Matam; Li, Qunhua; Bhat, Vadiraja B; Knight, Rob; Vanamala, Jairam K P | Cancer prevention research (Philadelphia, Pa.). | 28576788 | 2017 Aug; |
Vaginal Candida spp. genomes from women with vulvovaginal candidiasis. | Bradford, L Latéy; Chibucos, Marcus C; Ma, Bing; Bruno, Vincent; Ravel, Jacques | Pathogens and disease. | 28582496 | 2017 08 31; |
Dissecting the human microbiome with single-cell genomics. | Tolonen, Andrew C; Xavier, Ramnik J | Genome medicine. | 28615076 | 2017 Jun 14; |
A rare case of anal carcinosarcoma with human papilloma virus infection in both biphasic tumor elements: An immunohistochemical, molecular and ultrastructural study. | Hickman, Richard A; Bradshaw, Azore-Dee; Cassai, Nicholas; Neto, Antonio Galvao; Zhou, David; Fu, Tinghao; Lee, Peng; Pei, Zhiheng; Wieczorek, Rosemary | Papillomavirus research (Amsterdam, Netherlands). | 28616595 | 2016 Dec; |
Fine-mapping inflammatory bowel disease loci to single-variant resolution. | Huang, Hailiang; Fang, Ming; Jostins, Luke; Umi?evi? Mirkov, Ma?a; Boucher, Gabrielle; Anderson, Carl A; Andersen, Vibeke; Cleynen, Isabelle; Cortes, Adrian; Crins, François; D'Amato, Mauro; Deffontaine, Valérie; Dmitrieva, Julia; Docampo, Elisa; Elansary, Mahmoud; Farh, Kyle Kai-How; Franke, Andre; Gori, Ann-Stephan; Goyette, Philippe; Halfvarson, Jonas; Haritunians, Talin; Knight, Jo; Lawrance, Ian C; Lees, Charlie W; Louis, Edouard; Mariman, Rob; Meuwissen, Theo; Mni, Myriam; Momozawa, Yukihide; Parkes, Miles; Spain, Sarah L; Théâtre, Emilie; Trynka, Gosia; Satsangi, Jack; van Sommeren, Suzanne; Vermeire, Severine; Xavier, Ramnik J; International Inflammatory Bowel Disease Genetics Consortium; Weersma, Rinse K; Duerr, Richard H; Mathew, Christopher G; Rioux, John D; McGovern, Dermot P B; Cho, Judy H; Georges, Michel; Daly, Mark J; Barrett, Jeffrey C | Nature. | 28658209 | 2017 Jul 13; |
The Microbiome and Biomarkers for Necrotizing Enterocolitis: Are We Any Closer to Prediction? | Rusconi, Brigida; Good, Misty; Warner, Barbara B | The Journal of pediatrics. | 28669607 | 2017 Oct; |
Diacylglycerol kinase synthesized by commensal Lactobacillus reuteri diminishes protein kinase C phosphorylation and histamine-mediated signaling in the mammalian intestinal epithelium. | Ganesh, B P; Hall, A; Ayyaswamy, S; Nelson, J W; Fultz, R; Major, A; Haag, A; Esparza, M; Lugo, M; Venable, S; Whary, M; Fox, J G; Versalovic, J | Mucosal immunology. | 28745328 | 2018 03; |
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. | Bowers, Robert M; Kyrpides, Nikos C; Stepanauskas, Ramunas; Harmon-Smith, Miranda; Doud, Devin; Reddy, T B K; Schulz, Frederik; Jarett, Jessica; Rivers, Adam R; Eloe-Fadrosh, Emiley A; Tringe, Susannah G; Ivanova, Natalia N; Copeland, Alex; Clum, Alicia; Becraft, Eric D; Malmstrom, Rex R; Birren, Bruce; Podar, Mircea; Bork, Peer; Weinstock, George M; Garrity, George M; Dodsworth, Jeremy A; Yooseph, Shibu; Sutton, Granger; Glöckner, Frank O; Gilbert, Jack A; Nelson, William C; Hallam, Steven J; Jungbluth, Sean P; Ettema, Thijs J G; Tighe, Scott; Konstantinidis, Konstantinos T; Liu, Wen-Tso; Baker, Brett J; Rattei, Thomas; Eisen, Jonathan A; Hedlund, Brian; McMahon, Katherine D; Fierer, Noah; Knight, Rob; Finn, Rob; Cochrane, Guy; Karsch-Mizrachi, Ilene; Tyson, Gene W; Rinke, Christian; Genome Standards Consortium; Lapidus, Alla; Meyer, Folker; Yilmaz, Pelin; Parks, Donovan H; Eren, A M; Schriml, Lynn; Banfield, Jillian F; Hugenholtz, Philip; Woyke, Tanja | Nature biotechnology | 28787424 | 2017 Aug 08 |
Community characteristics of the gut microbiomes of competitive cyclists. | Petersen, Lauren M; Bautista, Eddy J; Nguyen, Hoan; Hanson, Blake M; Chen, Lei; Lek, Sai H; Sodergren, Erica; Weinstock, George M | Microbiome. | 28797298 | 2017 Aug 10; |
Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice. | Yasuda, Koji; Hsu, Tiffany; Gallini, Carey A; Mclver, Lauren J; Schwager, Emma; Shi, Andy; DuLong, Casey R; Schwager, Randall N; Abu-Ali, Galeb S; Franzosa, Eric A; Garrett, Wendy S; Huttenhower, Curtis; Morgan, Xochitl C | mSystems | 28808691 | 2017 |
Human genetic variation and the gut microbiome in disease. | Hall, Andrew Brantley; Tolonen, Andrew C; Xavier, Ramnik J | Nature reviews. Genetics. | 28824167 | 2017 11; |
Association between statin use, the vaginal microbiome, and Gardnerella vaginalis vaginolysin-mediated cytotoxicity. | Abdelmaksoud, Abdallah A; Girerd, Philippe H; Garcia, Erin M; Brooks, J Paul; Leftwich, Lauren M; Sheth, Nihar U; Bradley, Steven P; Serrano, Myrna G; Fettweis, Jennifer M; Huang, Bernice; Strauss 3rd, Jerome F; Buck, Gregory A; Jefferson, Kimberly K | PloS one. | 28846702 | 2017; |
Strains, functions and dynamics in the expanded Human Microbiome Project. | Lloyd-Price, Jason; Mahurkar, Anup; Rahnavard, Gholamali; Crabtree, Jonathan; Orvis, Joshua; Hall, A Brantley; Brady, Arthur; Creasy, Heather H; McCracken, Carrie; Giglio, Michelle G; McDonald, Daniel; Franzosa, Eric A; Knight, Rob; White, Owen; Huttenhower, Curtis | Nature. | 28953883 | 2017 10 05; |
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. | Sinha, Rashmi; Abu-Ali, Galeb; Vogtmann, Emily; Fodor, Anthony A; Ren, Boyu; Amir, Amnon; Schwager, Emma; Crabtree, Jonathan; Ma, Siyuan; Microbiome Quality Control Project Consortium; Abnet, Christian C; Knight, Rob; White, Owen; Huttenhower, Curtis | Nature biotechnology. | 28967885 | 2017 Nov; |
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. | Olson, Nathan D; Treangen, Todd J; Hill, Christopher M; Cepeda-Espinoza, Victoria; Ghurye, Jay; Koren, Sergey; Pop, Mihai | Briefings in bioinformatics. | 28968737 | 2019 Jul 19; |
Cultivation of Peptidiphaga gingivicola from subgingival plaque: The first representative of a novel genus of Actinomycetaceae. | Beall, C J; Mokrzan, E M; Griffen, A L; Leys, E J | Molecular oral microbiology | 29105370 | 2018 02 |
Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation. | Harmon, Brooke; Chylek, Lily A; Liu, Yanli; Mitra, Eshan D; Mahajan, Avanika; Saada, Edwin A; Schudel, Benjamin R; Holowka, David A; Baird, Barbara A; Wilson, Bridget S; Hlavacek, William S; Singh, Anup K | Scientific reports. | 29138425 | 2017 Nov 14; |
A Bayesian method for detecting pairwise associations in compositional data. | Schwager, Emma; Mallick, Himel; Ventz, Steffen; Huttenhower, Curtis | PLoS computational biology. | 29140991 | 2017 Nov; |
A role for bacterial urease in gut dysbiosis and Crohn's disease. | Ni, Josephine; Shen, Ting-Chin David; Chen, Eric Z; Bittinger, Kyle; Bailey, Aubrey; Roggiani, Manuela; Sirota-Madi, Alexandra; Friedman, Elliot S; Chau, Lillian; Lin, Andrew; Nissim, Ilana; Scott, Justin; Lauder, Abigail; Hoffmann, Christopher; Rivas, Gloriany; Albenberg, Lindsey; Baldassano, Robert N; Braun, Jonathan; Xavier, Ramnik J; Clish, Clary B; Yudkoff, Marc; Li, Hongzhe; Goulian, Mark; Bushman, Frederic D; Lewis, James D; Wu, Gary D | Science translational medicine. | 29141885 | 2017 Nov 15; |
CSA13 inhibits colitis-associated intestinal fibrosis via a formyl peptide receptor like-1 mediated HMG-CoA reductase pathway. | Xu, Chunlan; Ghali, Sally; Wang, Jiani; Shih, David Q; Ortiz, Christina; Mussatto, Caroline C; Lee, Elaine C; Tran, Diana H; Jacobs, Jonathan P; Lagishetty, Venu; Fleshner, Phillip; Robbins, Lori; Vu, Michelle; Hing, Tressia C; McGovern, Dermot P B; Koon, Hon Wai | Scientific reports. | 29180648 | 2017 Nov 27; |
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. | Hall, Andrew Brantley; Yassour, Moran; Sauk, Jenny; Garner, Ashley; Jiang, Xiaofang; Arthur, Timothy; Lagoudas, Georgia K; Vatanen, Tommi; Fornelos, Nadine; Wilson, Robin; Bertha, Madeline; Cohen, Melissa; Garber, John; Khalili, Hamed; Gevers, Dirk; Ananthakrishnan, Ashwin N; Kugathasan, Subra; Lander, Eric S; Blainey, Paul; Vlamakis, Hera; Xavier, Ramnik J; Huttenhower, Curtis | Genome medicine. | 29183332 | 2017 Nov 28; |
Experimental design and quantitative analysis of microbial community multiomics. | Mallick, Himel; Ma, Siyuan; Franzosa, Eric A; Vatanen, Tommi; Morgan, Xochitl C; Huttenhower, Curtis | Genome biology. | 29187204 | 2017 Nov 30; |
bioBakery: a meta'omic analysis environment. | McIver, Lauren J; Abu-Ali, Galeb; Franzosa, Eric A; Schwager, Randall; Morgan, Xochitl C; Waldron, Levi; Segata, Nicola; Huttenhower, Curtis | Bioinformatics (Oxford, England). | 29194469 | 2018 Apr 01; |
Optimizing Selection of Biologics in Inflammatory Bowel Disease: Development of an Online Patient Decision Aid Using Conjoint Analysis. | Almario, Christopher V; Keller, Michelle S; Chen, Michelle; Lasch, Karen; Ursos, Lyann; Shklovskaya, Julia; Melmed, Gil Y; Spiegel, Brennan M R | The American journal of gastroenterology. | 29206816 | 2018 01; |
Enterotypes in the landscape of gut microbial community composition. | Costea, Paul I; Hildebrand, Falk; Arumugam, Manimozhiyan; Bäckhed, Fredrik; Blaser, Martin J; Bushman, Frederic D; de Vos, Willem M; Ehrlich, S Dusko; Fraser, Claire M; Hattori, Masahira; Huttenhower, Curtis; Jeffery, Ian B; Knights, Dan; Lewis, James D; Ley, Ruth E; Ochman, Howard; O'Toole, Paul W; Quince, Christopher; Relman, David A; Shanahan, Fergus; Sunagawa, Shinichi; Wang, Jun; Weinstock, George M; Wu, Gary D; Zeller, Georg; Zhao, Liping; Raes, Jeroen; Knight, Rob; Bork, Peer | Nature microbiology. | 29255284 | 2018 Jan; |
Quinones are growth factors for the human gut microbiota. | Fenn, Kathrin; Strandwitz, Philip; Stewart, Eric J; Dimise, Eric; Rubin, Sarah; Gurubacharya, Shreya; Clardy, Jon; Lewis, Kim | Microbiome | 29262868 | 2017 Dec 20 |
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. | Schirmer, Melanie; Franzosa, Eric A; Lloyd-Price, Jason; McIver, Lauren J; Schwager, Randall; Poon, Tiffany W; Ananthakrishnan, Ashwin N; Andrews, Elizabeth; Barron, Gildardo; Lake, Kathleen; Prasad, Mahadev; Sauk, Jenny; Stevens, Betsy; Wilson, Robin G; Braun, Jonathan; Denson, Lee A; Kugathasan, Subra; McGovern, Dermot P B; Vlamakis, Hera; Xavier, Ramnik J; Huttenhower, Curtis | Nature microbiology. | 29311644 | 2018 03; |
Stability of the human faecal microbiome in a cohort of adult men. | Mehta, Raaj S; Abu-Ali, Galeb S; Drew, David A; Lloyd-Price, Jason; Subramanian, Ayshwarya; Lochhead, Paul; Joshi, Amit D; Ivey, Kerry L; Khalili, Hamed; Brown, Gordon T; DuLong, Casey; Song, Mingyang; Nguyen, Long H; Mallick, Himel; Rimm, Eric B; Izard, Jacques; Huttenhower, Curtis; Chan, Andrew T | Nature microbiology. | 29335554 | 2018 03; |
Metatranscriptome of human faecal microbial communities in a cohort of adult men. | Abu-Ali, Galeb S; Mehta, Raaj S; Lloyd-Price, Jason; Mallick, Himel; Branck, Tobyn; Ivey, Kerry L; Drew, David A; DuLong, Casey; Rimm, Eric; Izard, Jacques; Chan, Andrew T; Huttenhower, Curtis | Nature microbiology. | 29335555 | 2018 03; |
Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. | Piening, Brian D; Zhou, Wenyu; Contrepois, Kévin; Röst, Hannes; Gu Urban, Gucci Jijuan; Mishra, Tejaswini; Hanson, Blake M; Bautista, Eddy J; Leopold, Shana; Yeh, Christine Y; Spakowicz, Daniel; Banerjee, Imon; Chen, Cynthia; Kukurba, Kimberly; Perelman, Dalia; Craig, Colleen; Colbert, Elizabeth; Salins, Denis; Rego, Shannon; Lee, Sunjae; Zhang, Cheng; Wheeler, Jessica; Sailani, M Reza; Liang, Liang; Abbott, Charles; Gerstein, Mark; Mardinoglu, Adil; Smith, Ulf; Rubin, Daniel L; Pitteri, Sharon; Sodergren, Erica; McLaughlin, Tracey L; Weinstock, George M; Snyder, Michael P | Cell systems. | 29361466 | 2018 Feb 28; |
Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis. | Noyes, Noelle; Cho, Kyu-Chul; Ravel, Jacques; Forney, Larry J; Abdo, Zaid | PloS one. | 29364944 | 2018; |
One-Way Particle Transport Using Oscillatory Flow in Asymmetric Traps. | Lee, Jaesung; Burns, Mark A | Small (Weinheim an der Bergstrasse, Germany). | 29377529 | 2018 03; |
Host genetic variation and its microbiome interactions within the Human Microbiome Project. | Kolde, Raivo; Franzosa, Eric A; Rahnavard, Gholamali; Hall, Andrew Brantley; Vlamakis, Hera; Stevens, Christine; Daly, Mark J; Xavier, Ramnik J; Huttenhower, Curtis | Genome medicine. | 29378630 | 2018 Jan 29; |
Carriage of Cronobacter sakazakii in the Very Preterm Infant Gut. | Chandrasekaran, Sukantha; Burnham, Carey-Ann D; Warner, Barbara B; Tarr, Phillip I; Wylie, Todd N | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. | 29394356 | 2018 07 02; |
Leveraging a relationship-based sexual health framework for sexual risk prevention in adolescent men in the United States. | Hensel, Devon J; Bales, Casey L; Taylor, Julia F; Fortenberry, J Dennis | Sexual health | 29506642 | 2018 06 |
In situ cultivation of previously uncultivable microorganisms using the ichip. | Berdy, Brittany; Spoering, Amy L; Ling, Losee L; Epstein, Slava S | Nature protocols | 29532802 | 2017 10 |
Personal Omics for Precision Health. | Kellogg, Ryan A; Dunn, Jessilyn; Snyder, Michael P | Circulation research. | 29700064 | 2018 04 27; |
Microbial Metabolism in the Mammalian Gut: Molecular Mechanisms and Clinical Implications. | Hall, Anne; Versalovic, James | Journal of pediatric gastroenterology and nutrition. | 29762384 | 2018 06; |
Prevalence and Associations of Avascular Necrosis of the Hip in a Large Well-characterized Cohort of Patients With Inflammatory Bowel Disease. | Rolston, Vineet S; Patel, Anish V; Learch, Thomas J; Li, Dalin; Karayev, Dmitry; Williams, Chadwick; Siddanthi, Madhavi L; Targan, Stephan R; Weisman, Michael H; McGovern, Dermot P B | Journal of clinical rheumatology : practical reports on rheumatic & musculoskeletal diseases. | 29794876 | 2019 Jan; |
The premature infant gut microbiome during the first 6 weeks of life differs based on gestational maturity at birth. | Chernikova, Diana A; Madan, Juliette C; Housman, Molly L; Zain-Ul-Abideen, Muhammad; Lundgren, Sara N; Morrison, Hilary G; Sogin, Mitchell L; Williams, Scott M; Moore, Jason H; Karagas, Margaret R; Hoen, Anne G | Pediatric research. | 29795209 | 2018 07; |
Neurotransmitter modulation by the gut microbiota. | Strandwitz, Philip | Brain research. | 29903615 | 2018 08 15; |
PERFect: PERmutation Filtering test for microbiome data. | Smirnova, Ekaterina; Huzurbazar, Snehalata; Jafari, Farhad | Biostatistics (Oxford, England). | 29917060 | 2019 10 01; |
Are microbiome studies ready for hypothesis-driven research? | Tripathi, Anupriya; Marotz, Clarisse; Gonzalez, Antonio; Vázquez-Baeza, Yoshiki; Song, Se Jin; Bouslimani, Amina; McDonald, Daniel; Zhu, Qiyun; Sanders, Jon G; Smarr, Larry; Dorrestein, Pieter C; Knight, Rob | Current opinion in microbiology. | 30059804 | 2018 08; |
Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions. | Liu, Chaoyue; Wright, Benjamin; Allen-Vercoe, Emma; Gu, Hong; Beiko, Robert | Genome biology and evolution. | 30137329 | 2018 09 01; |
Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring. | Jiang, Chao; Wang, Xin; Li, Xiyan; Inlora, Jingga; Wang, Ting; Liu, Qing; Snyder, Michael | Cell. | 30241608 | 2018 09 20; |
Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota. | Vital, Marius; Howe, Adina; Bergeron, Nathalie; Krauss, Ronald M; Jansson, Janet K; Tiedje, James M | Applied and environmental microbiology. | 30266729 | 2018 12 01; |
Qiita: rapid, web-enabled microbiome meta-analysis. | Gonzalez, Antonio; Navas-Molina, Jose A; Kosciolek, Tomasz; McDonald, Daniel; Vázquez-Baeza, Yoshiki; Ackermann, Gail; DeReus, Jeff; Janssen, Stefan; Swafford, Austin D; Orchanian, Stephanie B; Sanders, Jon G; Shorenstein, Joshua; Holste, Hannes; Petrus, Semar; Robbins-Pianka, Adam; Brislawn, Colin J; Wang, Mingxun; Rideout, Jai Ram; Bolyen, Evan; Dillon, Matthew; Caporaso, J Gregory; Dorrestein, Pieter C; Knight, Rob | Nature methods. | 30275573 | 2018 10; |
Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course. | Schirmer, Melanie; Denson, Lee; Vlamakis, Hera; Franzosa, Eric A; Thomas, Sonia; Gotman, Nathan M; Rufo, Paul; Baker, Susan S; Sauer, Cary; Markowitz, James; Pfefferkorn, Marian; Oliva-Hemker, Maria; Rosh, Joel; Otley, Anthony; Boyle, Brendan; Mack, David; Baldassano, Robert; Keljo, David; LeLeiko, Neal; Heyman, Melvin; Griffiths, Anne; Patel, Ashish S; Noe, Joshua; Kugathasan, Subra; Walters, Thomas; Huttenhower, Curtis; Hyams, Jeffrey; Xavier, Ramnik J | Cell host & microbe. | 30308161 | 2018 10 10; |
Association of plasma nitrite levels with obesity and metabolic syndrome in the Old Order Amish. | Akram, F; Fuchs, D; Daue, M; Nijjar, G; Ryan, A; Benros, M E; Okusaga, O; Baca-Garcia, E; Brenner, L A; Lowry, C A; Ryan, K A; Pavlovich, M; Mitchell, B D; Snitker, S; Postolache, T T | Obesity science & practice | 30338117 | 2018 Oct |
The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. | Vatanen, Tommi; Franzosa, Eric A; Schwager, Randall; Tripathi, Surya; Arthur, Timothy D; Vehik, Kendra; Lernmark, Åke; Hagopian, William A; Rewers, Marian J; She, Jin-Xiong; Toppari, Jorma; Ziegler, Anette-G; Akolkar, Beena; Krischer, Jeffrey P; Stewart, Christopher J; Ajami, Nadim J; Petrosino, Joseph F; Gevers, Dirk; Lähdesmäki, Harri; Vlamakis, Hera; Huttenhower, Curtis; Xavier, Ramnik J | Nature. | 30356183 | 2018 10; |
Species-level functional profiling of metagenomes and metatranscriptomes. | Franzosa, Eric A; McIver, Lauren J; Rahnavard, Gholamali; Thompson, Luke R; Schirmer, Melanie; Weingart, George; Lipson, Karen Schwarzberg; Knight, Rob; Caporaso, J Gregory; Segata, Nicola; Huttenhower, Curtis | Nature methods. | 30377376 | 2018 11; |
GABA-modulating bacteria of the human gut microbiota. | Strandwitz, Philip; Kim, Ki Hyun; Terekhova, Darya; Liu, Joanne K; Sharma, Anukriti; Levering, Jennifer; McDonald, Daniel; Dietrich, David; Ramadhar, Timothy R; Lekbua, Asama; Mroue, Nader; Liston, Conor; Stewart, Eric J; Dubin, Marc J; Zengler, Karsten; Knight, Rob; Gilbert, Jack A; Clardy, Jon; Lewis, Kim | Nature microbiology. | 30531975 | 2019 03; |
Gut microbiome structure and metabolic activity in inflammatory bowel disease. | Franzosa, Eric A; Sirota-Madi, Alexandra; Avila-Pacheco, Julian; Fornelos, Nadine; Haiser, Henry J; Reinker, Stefan; Vatanen, Tommi; Hall, A Brantley; Mallick, Himel; McIver, Lauren J; Sauk, Jenny S; Wilson, Robin G; Stevens, Betsy W; Scott, Justin M; Pierce, Kerry; Deik, Amy A; Bullock, Kevin; Imhann, Floris; Porter, Jeffrey A; Zhernakova, Alexandra; Fu, Jingyuan; Weersma, Rinse K; Wijmenga, Cisca; Clish, Clary B; Vlamakis, Hera; Huttenhower, Curtis; Xavier, Ramnik J | Nature microbiology. | 30531976 | 2019 Feb; |
Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis. | Haberman, Yael; Schirmer, Melanie; Dexheimer, Phillip J; Karns, Rebekah; Braun, Tzipi; Kim, Mi-Ok; Walters, Thomas D; Baldassano, Robert N; Noe, Joshua D; Rosh, Joel; Markowitz, James; Crandall, Wallace V; Mack, David R; Griffiths, Anne M; Heyman, Melvin B; Baker, Susan S; Kellermayer, Richard; Moulton, Dedrick; Patel, Ashish S; Gulati, Ajay S; Steiner, Steven J; LeLeiko, Neal; Otley, Anthony; Oliva-Hemker, Maria; Ziring, David; Kirschner, Barbara S; Keljo, David J; Guthery, Stephen L; Cohen, Stanley A; Snapper, Scott; Evans, Jonathan; Dubinsky, Marla; Aronow, Bruce; Hyams, Jeffrey S; Kugathasan, Subra; Huttenhower, Curtis; Xavier, Ramnik J; Denson, Lee A | Mucosal immunology. | 30542108 | 2019 03; |
HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor. | Schiffer, Lucas; Azhar, Rimsha; Shepherd, Lori; Ramos, Marcel; Geistlinger, Ludwig; Huttenhower, Curtis; Dowd, Jennifer B; Segata, Nicola; Waldron, Levi | American journal of epidemiology. | 30649166 | 2019 Jun 01; |
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. | Pasolli, Edoardo; Asnicar, Francesco; Manara, Serena; Zolfo, Moreno; Karcher, Nicolai; Armanini, Federica; Beghini, Francesco; Manghi, Paolo; Tett, Adrian; Ghensi, Paolo; Collado, Maria Carmen; Rice, Benjamin L; DuLong, Casey; Morgan, Xochitl C; Golden, Christopher D; Quince, Christopher; Huttenhower, Curtis; Segata, Nicola | Cell. | 30661755 | 2019 Jan 24; |
Toward unrestricted use of public genomic data. | Amann, Rudolf I; Baichoo, Shakuntala; Blencowe, Benjamin J; Bork, Peer; Borodovsky, Mark; Brooksbank, Cath; Chain, Patrick S G; Colwell, Rita R; Daffonchio, Daniele G; Danchin, Antoine; de Lorenzo, Victor; Dorrestein, Pieter C; Finn, Robert D; Fraser, Claire M; Gilbert, Jack A; Hallam, Steven J; Hugenholtz, Philip; Ioannidis, John P A; Jansson, Janet K; Kim, Jihyun F; Klenk, Hans-Peter; Klotz, Martin G; Knight, Rob; Konstantinidis, Konstantinos T; Kyrpides, Nikos C; Mason, Christopher E; McHardy, Alice C; Meyer, Folker; Ouzounis, Christos A; Patrinos, Aristides A N; Podar, Mircea; Pollard, Katherine S; Ravel, Jacques; Muñoz, Alejandro Reyes; Roberts, Richard J; Rosselló-Móra, Ramon; Sansone, Susanna-Assunta; Schloss, Patrick D; Schriml, Lynn M; Setubal, João C; Sorek, Rotem; Stevens, Rick L; Tiedje, James M; Turjanski, Adrian; Tyson, Gene W; Ussery, David W; Weinstock, George M; White, Owen; Whitman, William B; Xenarios, Ioannis | Science (New York, N.Y.) | 30679363 | 2019 01 25 |
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, J Alfredo; Erickson, Alison R; Cantarel, Brandi L; Xiong, Weili; Adams, Rachel; Jansson, Janet K; Fraser, Claire M; Hettich, Robert L | Microbiome. | 30744677 | 2019 02 11; |
2017 NIH-wide workshop report on ''The Human Microbiome: Emerging Themes at the Horizon of the 21st Century''. | 2017 NIH-wide microbiome workshop writing team | Microbiome. | 30808401 | 2019 02 26; |
Influence of Crohn's disease related polymorphisms in innate immune function on ileal microbiome. | Li, Ellen; Zhang, Yuanhao; Tian, Xinyu; Wang, Xuefeng; Gathungu, Grace; Wolber, Ashley; Shiekh, Shehzad S; Sartor, R Balfour; Davidson, Nicholas O; Ciorba, Matthew A; Zhu, Wei; Nelson, Leah M; Robertson, Charles E; Frank, Daniel N | PloS one. | 30818349 | 2019; |
Does the human placenta delivered at term have a microbiota? Results of cultivation, quantitative real-time PCR, 16S rRNA gene sequencing, and metagenomics. | Theis, Kevin R; Romero, Roberto; Winters, Andrew D; Greenberg, Jonathan M; Gomez-Lopez, Nardhy; Alhousseini, Ali; Bieda, Janine; Maymon, Eli; Pacora, Percy; Fettweis, Jennifer M; Buck, Gregory A; Jefferson, Kimberly K; Strauss 3rd, Jerome F; Erez, Offer; Hassan, Sonia S | American journal of obstetrics and gynecology. | 30832984 | 2019 Mar; |
Much ado about nothing: A qualitative study of the experiences of an average-risk population receiving results of exome sequencing. | Rego, Shannon; Dagan-Rosenfeld, Orit; Bivona, Stephanie A; Snyder, Michael P; Ormond, Kelly E | Journal of genetic counseling. | 30835913 | 2019 Apr; |
Relationship between vitamin D status and the vaginal microbiome during pregnancy. | Jefferson, Kimberly K; Parikh, Hardik I; Garcia, Erin M; Edwards, David J; Serrano, Myrna G; Hewison, Martin; Shary, Judith R; Powell, Anna M; Hollis, Bruce W; Fettweis, Jennifer M; Strauss Iii, Jerome F; Buck, Gregory A; Wagner, Carol L | Journal of perinatology : official journal of the California Perinatal Association. | 30858609 | 2019 Jun; |
Gene-Environment Interaction in the Era of Precision Medicine. | Li, Jingjing; Li, Xiao; Zhang, Sai; Snyder, Michael | Cell. | 30901546 | 2019 03 21; |
MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs. | Brown, Stuart M; Chen, Hao; Hao, Yuhan; Laungani, Bobby P; Ali, Thahmina A; Dong, Changsu; Lijeron, Carlos; Kim, Baekdoo; Wultsch, Claudia; Pei, Zhiheng; Krampis, Konstantinos | GigaScience. | 30942867 | 2019 04 01; |
Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. | Hollister, Emily B; Oezguen, Numan; Chumpitazi, Bruno P; Luna, Ruth Ann; Weidler, Erica M; Rubio-Gonzales, Michelle; Dahdouli, Mahmoud; Cope, Julia L; Mistretta, Toni-Ann; Raza, Sabeen; Metcalf, Ginger A; Muzny, Donna M; Gibbs, Richard A; Petrosino, Josep | The Journal of molecular diagnostics : JMD | 31005411 | 2019 May |
A longitudinal big data approach for precision health. | Schüssler-Fiorenza Rose, Sophia Miryam; Contrepois, Kévin; Moneghetti, Kegan J; Zhou, Wenyu; Mishra, Tejaswini; Mataraso, Samson; Dagan-Rosenfeld, Orit; Ganz, Ariel B; Dunn, Jessilyn; Hornburg, Daniel; Rego, Shannon; Perelman, Dalia; Ahadi, Sara; Sailani, M Reza; Zhou, Yanjiao; Leopold, Shana R; Chen, Jieming; Ashland, Melanie; Christle, Jeffrey W; Avina, Monika; Limcaoco, Patricia; Ruiz, Camilo; Tan, Marilyn; Butte, Atul J; Weinstock, George M; Slavich, George M; Sodergren, Erica; McLaughlin, Tracey L; Haddad, Francois; Snyder, Michael P | Nature medicine. | 31068711 | 2019 05; |
Identifying Hospital Antimicrobial Resistance Targets via Robust Ranking. | Brooks, J Paul; Dulá, José H; Pakyz, Amy L; Polk, Ronald E | IISE transactions on healthcare systems engineering. | 31098436 | 2017; |
Impact of Herpes Simplex Virus Type 2 and Human Immunodeficiency Virus Dual Infection on Female Genital Tract Mucosal Immunity and the Vaginal Microbiome. | Keller, Marla J; Huber, Ashley; Espinoza, Lilia; Serrano, Myrna G; Parikh, Hardik I; Buck, Gregory A; Gold, Jeremy A; Wu, Yiqun; Wang, Tao; Herold, Betsy C | The Journal of infectious diseases | 31111902 | 2019 07 31 |
The vaginal microbiome and preterm birth. | Fettweis, Jennifer M; Serrano, Myrna G; Brooks, J Paul; Edwards, David J; Girerd, Philippe H; Parikh, Hardik I; Huang, Bernice; Arodz, Tom J; Edupuganti, Laahirie; Glascock, Abigail L; Xu, Jie; Jimenez, Nicole R; Vivadelli, Stephany C; Fong, Stephen S; Sheth, Nihar U; Jean, Sophonie; Lee, Vladimir; Bokhari, Yahya A; Lara, Ana M; Mistry, Shreni D; Duckworth 3rd, Robert A; Bradley, Steven P; Koparde, Vishal N; Orenda, X Valentine; Milton, Sarah H; Rozycki, Sarah K; Matveyev, Andrey V; Wright, Michelle L; Huzurbazar, Snehalata V; Jackson, Eugenie M; Smirnova, Ekaterina; Korlach, Jonas; Tsai, Yu-Chih; Dickinson, Molly R; Brooks, Jamie L; Drake, Jennifer I; Chaffin, Donald O; Sexton, Amber L; Gravett, Michael G; Rubens, Craig E; Wijesooriya, N Romesh; Hendricks-Muñoz, Karen D; Jefferson, Kimberly K; Strauss 3rd, Jerome F; Buck, Gregory A | Nature medicine. | 31142849 | 2019 06; |
Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy. | Serrano, Myrna G; Parikh, Hardik I; Brooks, J Paul; Edwards, David J; Arodz, Tom J; Edupuganti, Laahirie; Huang, Bernice; Girerd, Philippe H; Bokhari, Yahya A; Bradley, Steven P; Brooks, Jamie L; Dickinson, Molly R; Drake, Jennifer I; Duckworth 3rd, Robert A; Fong, Stephen S; Glascock, Abigail L; Jean, Sophonie; Jimenez, Nicole R; Khoury, Joseph; Koparde, Vishal N; Lara, Ana M; Lee, Vladimir; Matveyev, Andrey V; Milton, Sarah H; Mistry, Shreni D; Rozycki, Sarah K; Sheth, Nihar U; Smirnova, Ekaterina; Vivadelli, Stephany C; Wijesooriya, N Romesh; Xu, Jie; Xu, Ping; Chaffin, Donald O; Sexton, Amber L; Gravett, Michael G; Rubens, Craig E; Hendricks-Muñoz, Karen D; Jefferson, Kimberly K; Strauss 3rd, Jerome F; Fettweis, Jennifer M; Buck, Gregory A | Nature medicine. | 31142850 | 2019 06; |
The Integrative Human Microbiome Project. | Integrative HMP (iHMP) Research Network Consortium | Nature. | 31142853 | 2019 May; |
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. | Lloyd-Price, Jason; Arze, Cesar; Ananthakrishnan, Ashwin N; Schirmer, Melanie; Avila-Pacheco, Julian; Poon, Tiffany W; Andrews, Elizabeth; Ajami, Nadim J; Bonham, Kevin S; Brislawn, Colin J; Casero, David; Courtney, Holly; Gonzalez, Antonio; Graeber, Thomas G; Hall, A Brantley; Lake, Kathleen; Landers, Carol J; Mallick, Himel; Plichta, Damian R; Prasad, Mahadev; Rahnavard, Gholamali; Sauk, Jenny; Shungin, Dmitry; Vázquez-Baeza, Yoshiki; White 3rd, Richard A; IBDMDB Investigators; Braun, Jonathan; Denson, Lee A; Jansson, Janet K; Knight, Rob; Kugathasan, Subra; McGovern, Dermot P B; Petrosino, Joseph F; Stappenbeck, Thaddeus S; Winter, Harland S; Clish, Clary B; Franzosa, Eric A; Vlamakis, Hera; Xavier, Ramnik J; Huttenhower, Curtis | Nature. | 31142855 | 2019 May; |
Longitudinal multi-omics of host-microbe dynamics in prediabetes. | Zhou, Wenyu; Sailani, M Reza; Contrepois, Kévin; Zhou, Yanjiao; Ahadi, Sara; Leopold, Shana R; Zhang, Martin J; Rao, Varsha; Avina, Monika; Mishra, Tejaswini; Johnson, Jethro; Lee-McMullen, Brittany; Chen, Songjie; Metwally, Ahmed A; Tran, Thi Dong Binh; Nguyen, Hoan; Zhou, Xin; Albright, Brandon; Hong, Bo-Young; Petersen, Lauren; Bautista, Eddy; Hanson, Blake; Chen, Lei; Spakowicz, Daniel; Bahmani, Amir; Salins, Denis; Leopold, Benjamin; Ashland, Melanie; Dagan-Rosenfeld, Orit; Rego, Shannon; Limcaoco, Patricia; Colbert, Elizabeth; Allister, Candice; Perelman, Dalia; Craig, Colleen; Wei, Eric; Chaib, Hassan; Hornburg, Daniel; Dunn, Jessilyn; Liang, Liang; Rose, Sophia Miryam Schüssler-Fiorenza; Kukurba, Kim; Piening, Brian; Rost, Hannes; Tse, David; McLaughlin, Tracey; Sodergren, Erica; Weinstock, George M; Snyder, Michael | Nature. | 31142858 | 2019 May; |
The Cervicovaginal Microbiota-Host Interaction Modulates Chlamydia trachomatis Infection. | Edwards, Vonetta L; Smith, Steven B; McComb, Elias J; Tamarelle, Jeanne; Ma, Bing; Humphrys, Michael S; Gajer, Pawel; Gwilliam, Kathleen; Schaefer, Alison M; Lai, Samuel K; Terplan, Mishka; Mark, Katrina S; Brotman, Rebecca M; Forney, Larry J; Bavoil, Patrik M; Ravel, Jacques | mBio. | 31409678 | 2019 Aug 13; |
Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly. | Ivey, Kerry L; Chan, Andrew T; Izard, Jacques; Cassidy, Aedin; Rogers, Geraint B; Rimm, Eric B | mBio. | 31551328 | 2019 Sep 24; |
Nonoptimal Vaginal Microbiota After Azithromycin Treatment for Chlamydia trachomatis Infection. | Tamarelle, Jeanne; Ma, Bing; Gajer, Pawel; Humphrys, Mike S; Terplan, Mishka; Mark, Katrina S; Thiébaut, Anne C M; Forney, Larry J; Brotman, Rebecca M; Delarocque-Astagneau, Elisabeth; Bavoil, Patrik M; Ravel, Jacques | The Journal of infectious diseases. | 31573603 | 2020 02 03; |
The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. | Tett, Adrian; Huang, Kun D; Asnicar, Francesco; Fehlner-Peach, Hannah; Pasolli, Edoardo; Karcher, Nicolai; Armanini, Federica; Manghi, Paolo; Bonham, Kevin; Zolfo, Moreno; De Filippis, Francesca; Magnabosco, Cara; Bonneau, Richard; Lusingu, John; Amuasi, John; Reinhard, Karl; Rattei, Thomas; Boulund, Fredrik; Engstrand, Lars; Zink, Albert; Collado, Maria Carmen; Littman, Dan R; Eibach, Daniel; Ercolini, Danilo; Rota-Stabelli, Omar; Huttenhower, Curtis; Maixner, Frank; Segata, Nicola | Cell host & microbe. | 31607556 | 2019 11 13; |
Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains. | Kirmiz, Nina; Galindo, Kadir; Cross, Karissa L; Luna, Estefani; Rhoades, Nicholas; Podar, Mircea; Flores, Gilberto E | Applied and environmental microbiology. | 31757822 | 2020 Jan 21; |
Discordant transmission of bacteria and viruses from mothers to babies at birth. | Maqsood, Rabia; Rodgers, Rachel; Rodriguez, Cynthia; Handley, Scott A; Ndao, I Malick; Tarr, Phillip I; Warner, Barbara B; Lim, Efrem S; Holtz, Lori R | Microbiome | 31823811 | 2019 12 10 |
Windows Into Human Health Through Wearables Data Analytics. | Witt, Daniel; Kellogg, Ryan; Snyder, Michael; Dunn, Jessilyn | Current opinion in biomedical engineering. | 31832566 | 2019 Mar; |
Personal aging markers and ageotypes revealed by deep longitudinal profiling. | Ahadi, Sara; Zhou, Wenyu; Schüssler-Fiorenza Rose, Sophia Miryam; Sailani, M Reza; Contrepois, Kévin; Avina, Monika; Ashland, Melanie; Brunet, Anne; Snyder, Michael | Nature medicine. | 31932806 | 2020 01; |
Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. | Fornelos, Nadine; Franzosa, Eric A; Bishai, Jason; Annand, John W; Oka, Akihiko; Lloyd-Price, Jason; Arthur, Timothy D; Garner, Ashley; Avila-Pacheco, Julian; Haiser, Henry J; Tolonen, Andrew C; Porter, Jeffrey A; Clish, Clary B; Sartor, R Balfour; Huttenhower, Curtis; Vlamakis, Hera; Xavier, Ramnik J | Nature microbiology. | 31959971 | 2020 03; |
Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. | Nguyen, Long H; Ma, Wenjie; Wang, Dong D; Cao, Yin; Mallick, Himel; Gerbaba, Teklu K; Lloyd-Price, Jason; Abu-Ali, Galeb; Hall, A Brantley; Sikavi, Daniel; Drew, David A; Mehta, Raaj S; Arze, Cesar; Joshi, Amit D; Yan, Yan; Branck, Tobyn; DuLong, Casey; Ivey, Kerry L; Ogino, Shuji; Rimm, Eric B; Song, Mingyang; Garrett, Wendy S; Izard, Jacques; Huttenhower, Curtis; Chan, Andrew T | Gastroenterology. | 31972239 | 2020 04; |
Single-Cell Genomics and the Oral Microbiome. | Balachandran, M; Cross, K L; Podar, M | Journal of dental research | 32091935 | 2020 06 |
Global chemical effects of the microbiome include new bile-acid conjugations. | Quinn, Robert A; Melnik, Alexey V; Vrbanac, Alison; Fu, Ting; Patras, Kathryn A; Christy, Mitchell P; Bodai, Zsolt; Belda-Ferre, Pedro; Tripathi, Anupriya; Chung, Lawton K; Downes, Michael; Welch, Ryan D; Quinn, Melissa; Humphrey, Greg; Panitchpakdi, Morgan; Weldon, Kelly C; Aksenov, Alexander; da Silva, Ricardo; Avila-Pacheco, Julian; Clish, Clary; Bae, Sena; Mallick, Himel; Franzosa, Eric A; Lloyd-Price, Jason; Bussell, Robert; Thron, Taren; Nelson, Andrew T; Wang, Mingxun; Leszczynski, Eric; Vargas, Fernando; Gauglitz, Julia M; Meehan, Michael J; Gentry, Emily; Arthur, Timothy D; Komor, Alexis C; Poulsen, Orit; Boland, Brigid S; Chang, John T; Sandborn, William J; Lim, Meerana; Garg, Neha; Lumeng, Julie C; Xavier, Ramnik J; Kazmierczak, Barbara I; Jain, Ruchi; Egan, Marie; Rhee, Kyung E; Ferguson, David; Raffatellu, Manuela; Vlamakis, Hera; Haddad, Gabriel G; Siegel, Dionicio; Huttenhower, Curtis; Mazmanian, Sarkis K; Evans, Ronald M; Nizet, Victor; Knight, Rob; Dorrestein, Pieter C | Nature. | 32103176 | 2020 03; |
Maternal activation of the EGFR prevents translocation of gut-residing pathogenic Escherichia coli in a model of late-onset neonatal sepsis. | Knoop, Kathryn A; Coughlin, Paige E; Floyd, Alexandria N; Ndao, I Malick; Hall-Moore, Carla; Shaikh, Nurmohammad; Gasparrini, Andrew J; Rusconi, Brigida; Escobedo, Marilyn; Good, Misty; Warner, Barbara B; Tarr, Phillip I; Newberry, Rodney D | Proceedings of the National Academy of Sciences of the United States of America. | 32179676 | 2020 04 07; |
Associations of Sleep Characteristics With Cognitive Function and Decline Among Older Adults. | McSorley, V Eloesa; Bin, Yu Sun; Lauderdale, Diane S | American journal of epidemiology. | 32181824 | 2019 06 01; |
Asymptomatic Bacterial Vaginosis Is Associated With Depletion of Mature Superficial Cells Shed From the Vaginal Epithelium. | O'Hanlon, D Elizabeth; Gajer, Pawel; Brotman, Rebecca M; Ravel, Jacques | Frontiers in cellular and infection microbiology. | 32211347 | 2020; |
MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data. | Bangayan, Nathanael J; Shi, Baochen; Trinh, Jerry; Barnard, Emma; Kasimatis, Gabriela; Curd, Emily; Li, Huiying | Microorganisms. | 32397065 | 2020 May 08; |
Complete Genome Sequences of Six Lactobacillus iners Strains Isolated from the Human Vagina. | France, Michael T; Rutt, Lindsay; Narina, Shilpa; Arbaugh, Sarah; McComb, Elias; Humphrys, Mike S; Ma, Bing; Hayward, Matthew R; Costello, Elizabeth K; Relman, David A; Kwon, Douglas S; Ravel, Jacques | Microbiology resource announcements. | 32409537 | 2020 May 14; |
Molecular Choreography of Acute Exercise. | Contrepois, Kévin; Wu, Si; Moneghetti, Kegan J; Hornburg, Daniel; Ahadi, Sara; Tsai, Ming-Shian; Metwally, Ahmed A; Wei, Eric; Lee-McMullen, Brittany; Quijada, Jeniffer V; Chen, Songjie; Christle, Jeffrey W; Ellenberger, Mathew; Balliu, Brunilda; Taylor, Shalina; Durrant, Matthew G; Knowles, David A; Choudhry, Hani; Ashland, Melanie; Bahmani, Amir; Enslen, Brooke; Amsallem, Myriam; Kobayashi, Yukari; Avina, Monika; Perelman, Dalia; Schüssler-Fiorenza Rose, Sophia Miryam; Zhou, Wenyu; Ashley, Euan A; Montgomery, Stephen B; Chaib, Hassan; Haddad, Francois; Snyder, Michael P | Cell. | 32470399 | 2020 May 28; |
PICRUSt2 for prediction of metagenome functions. | Douglas, Gavin M; Maffei, Vincent J; Zaneveld, Jesse R; Yurgel, Svetlana N; Brown, James R; Taylor, Christopher M; Huttenhower, Curtis; Langille, Morgan G I | Nature biotechnology. | 32483366 | 2020 Jun; |
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. | Karcher, Nicolai; Pasolli, Edoardo; Asnicar, Francesco; Huang, Kun D; Tett, Adrian; Manara, Serena; Armanini, Federica; Bain, Debbie; Duncan, Sylvia H; Louis, Petra; Zolfo, Moreno; Manghi, Paolo; Valles-Colomer, Mireia; Raffaetà, Roberta; Rota-Stabelli, Omar; Collado, Maria Carmen; Zeller, Georg; Falush, Daniel; Maixner, Frank; Walker, Alan W; Huttenhower, Curtis; Segata, Nicola | Genome biology. | 32513234 | 2020 06 08; |
Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz. | Wagner, Justin; Kancherla, Jayaram; Braccia, Domenick; Matsumara, James; Felix, Victor; Crabtree, Jonathan; Mahurkar, Anup; Corrada Bravo, Héctor | F1000Research | 32742640 | 2020 |
Association of diet with circulating trimethylamine-N-oxide concentration. | Hamaya, Rikuta; Ivey, Kerry L; Lee, Dong H; Wang, Molin; Li, Jun; Franke, Adrian; Sun, Qi; Rimm, Eric B | The American journal of clinical nutrition. | 32936862 | 2020 12 10; |
Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California. | Sailani, M Reza; Metwally, Ahmed A; Zhou, Wenyu; Rose, Sophia Miryam Schüssler-Fiorenza; Ahadi, Sara; Contrepois, Kevin; Mishra, Tejaswini; Zhang, Martin Jinye; Kidzi?ski, ?ukasz; Chu, Theodore J; Snyder, Michael P | Nature communications. | 33004787 | 2020 10 01; |
Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial 'dark matter'. | Tan, James Y; Wang, Sida; Dick, Gregory J; Young, Vincent B; Sherman, David H; Burns, Mark A; Lin, Xiaoxia N | Integrative biology : quantitative biosciences from nano to macro. | 33089329 | 2020 11 18; |
Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. | Nishiyama, Hiroki; Endo, Hisashi; Blanc-Mathieu, Romain; Ogata, Hiroyuki | Microorganisms. | 33121006 | 2020 Oct 27; |
Genetic Variation in Toll-Like Receptor 5 and Colonization with Flagellated Bacterial Vaginosis-Associated Bacteria. | Dela Cruz, Erin J; Fiedler, Tina L; Liu, Congzhou; Munch, Matthew M; Kohler, Christina M; Oot, Antoinette R; Wallis, Jacqueline M; Wang, Junhui; Frishman, Anna; Garcia, Kristina; Wiser, Andrew; Balkus, Jennifer E; Srinivasan, Sujatha; Golob, Jonathan L; Sycuro, Laura K; Marrazzo, Jeanne M; Hawn, Thomas R; Fredricks, David N | Infection and immunity | 33199356 | 2021 Feb 16 |
Identification of Natural CRISPR Systems and Targets in the Human Microbiome. | Münch, Philipp C; Franzosa, Eric A; Stecher, Bärbel; McHardy, Alice C; Huttenhower, Curtis | Cell host & microbe. | 33217332 | 2020 Nov 16; |
VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. | France, Michael T; Ma, Bing; Gajer, Pawel; Brown, Sarah; Humphrys, Michael S; Holm, Johanna B; Waetjen, L Elaine; Brotman, Rebecca M; Ravel, Jacques | Microbiome. | 33228810 | 2020 11 23; |
Quantitative modeling predicts mechanistic links between pre-treatment microbiome composition and metronidazole efficacy in bacterial vaginosis. | Lee, Christina Y; Cheu, Ryan K; Lemke, Melissa M; Gustin, Andrew T; France, Michael T; Hampel, Benjamin; Thurman, Andrea R; Doncel, Gustavo F; Ravel, Jacques; Klatt, Nichole R; Arnold, Kelly B | Nature communications | 33262350 | 2020 Dec 01 |
HMPDACC: a Human Microbiome Project Multi-omic data resource. | Creasy, Heather Huot; Felix, Victor; Aluvathingal, Jain; Crabtree, Jonathan; Ifeonu, Olukemi; Matsumura, James; McCracken, Carrie; Nickel, Lance; Orvis, Joshua; Schor, Mike; Giglio, Michelle; Mahurkar, Anup; White, Owen | Nucleic acids research | 33305317 | 2021 01 08 |
Fructan-sensitive children with irritable bowel syndrome have distinct gut microbiome signatures. | Chumpitazi, Bruno P; Hoffman, Kristi L; Smith, Daniel P; McMeans, Ann R; Musaad, Salma; Versalovic, James; Petrosino, Joseph F; Shulman, Robert J | Alimentary pharmacology & therapeutics. | 33314183 | 2020 Dec 13; |
Sequence Comparison of Vaginolysin from Different Gardnerella Species. | Garcia, Erin M; Serrano, Myrna G; Edupuganti, Laahirie; Edwards, David J; Buck, Gregory A; Jefferson, Kimberly K | Pathogens (Basel, Switzerland) | 33498226 | 2021 Jan 20 |
The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. | Wang, Dong D; Nguyen, Long H; Li, Yanping; Yan, Yan; Ma, Wenjie; Rinott, Ehud; Ivey, Kerry L; Shai, Iris; Willett, Walter C; Hu, Frank B; Rimm, Eric B; Stampfer, Meir J; Chan, Andrew T; Huttenhower, Curtis | Nature medicine | 33574608 | 2021 02 |
Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease. | Somineni, Hari K; Nagpal, Sini; Venkateswaran, Suresh; Cutler, David J; Okou, David T; Haritunians, Talin; Simpson, Claire L; Begum, Ferdouse; Datta, Lisa W; Quiros, Antonio J; Seminerio, Jenifer; Mengesha, Emebet; Alexander, Jonathan S; Baldassano, Robert N; Dudley-Brown, Sharon; Cross, Raymond K; Dassopoulos, Themistocles; Denson, Lee A; Dhere, Tanvi A; Iskandar, Heba; Dryden, Gerald W; Hou, Jason K; Hussain, Sunny Z; Hyams, Jeffrey S; Isaacs, Kim L; Kader, Howard; Kappelman, Michael D; Katz, Jeffry; Kellermayer, Richard; Kuemmerle, John F; Lazarev, Mark; Li, Ellen; Mannon, Peter; Moulton, Dedrick E; Newberry, Rodney D; Patel, Ashish S; Pekow, Joel; Saeed, Shehzad A; Valentine, John F; Wang, Ming-Hsi; McCauley, Jacob L; Abreu, Maria T; Jester, Traci; Molle-Rios, Zarela; Palle, Sirish; Scherl, Ellen J; Kwon, John; Rioux, John D; Duerr, Richard H; Silverberg, Mark S; Zwick, Michael E; Stevens, Christine; Daly, Mark J; Cho, Judy H; Gibson, Greg; McGovern, Dermot P B; Brant, Steven R; Kugathasan, Subra | American journal of human genetics | 33600772 | 2021 03 04 |
Megasphaera lornae sp. nov., Megasphaera hutchinsoni sp. nov., and Megasphaera vaginalis sp. nov.: novel bacteria isolated from the female genital tract. | Srinivasan, Sujatha; Beamer, May A; Fiedler, Tina L; Austin, Michele N; Sizova, Maria V; Strenk, Susan M; Agnew, Kathy J; Gowda, G A Nagana; Raftery, Daniel; Epstein, Slava S; Fredricks, David N; Hillier, Sharon L | International journal of systematic and evolutionary microbiology | 33616513 | 2019 Jun |
Biogenic Amines Increase the Odds of Bacterial Vaginosis and Affect the Growth of and Lactic Acid Production by Vaginal Lactobacillus spp. | Borgogna, Joanna-Lynn C; Shardell, Michelle D; Grace, Savannah G; Santori, Elisa K; Americus, Benjamin; Li, Zhong; Ulanov, Alexander; Forney, Larry; Nelson, Tiffanie M; Brotman, Rebecca M; Ravel, Jacques; Yeoman, Carl J | Applied and environmental microbiology | 33674429 | 2021 04 27 |
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. | Beghini, Francesco; McIver, Lauren J; Blanco-Míguez, Aitor; Dubois, Leonard; Asnicar, Francesco; Maharjan, Sagun; Mailyan, Ana; Manghi, Paolo; Scholz, Matthias; Thomas, Andrew Maltez; Valles-Colomer, Mireia; Weingart, George; Zhang, Yancong; Zolfo, Moreno; Huttenhower, Curtis; Franzosa, Eric A; Segata, Nicola | eLife | 33944776 | 2021 May 04 |
Wearable sensors enable personalized predictions of clinical laboratory measurements. | Dunn, Jessilyn; Kidzinski, Lukasz; Runge, Ryan; Witt, Daniel; Hicks, Jennifer L; Schüssler-Fiorenza Rose, Sophia Miryam; Li, Xiao; Bahmani, Amir; Delp, Scott L; Hastie, Trevor; Snyder, Michael P | Nature medicine | 34031607 | 2021 Jun |
Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome. | Li, Yanping; Wang, Dong D; Satija, Ambika; Ivey, Kerry L; Li, Jun; Wilkinson, Jeremy E; Li, Ruifeng; Baden, Megu; Chan, Andrew T; Huttenhower, Curtis; Rimm, Eric B; Hu, Frank B; Sun, Qi | The Journal of nutrition | 34114015 | 2021 Jun 10 |
Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men. | Ma, Wenjie; Nguyen, Long H; Song, Mingyang; Wang, Dong D; Franzosa, Eric A; Cao, Yin; Joshi, Amit; Drew, David A; Mehta, Raaj; Ivey, Kerry L; Strate, Lisa L; Giovannucci, Edward L; Izard, Jacques; Garrett, Wendy; Rimm, Eric B; Huttenhower, Curtis; Chan, Andrew T | Genome medicine | 34140026 | 2021 06 17 |
Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. | Thänert, Robert; Thänert, Anna; Ou, Jocelyn; Bajinting, Adam; Burnham, Carey-Ann D; Engelstad, Holly J; Tecos, Maria E; Ndao, I Malick; Hall-Moore, Carla; Rouggly-Nickless, Colleen; Carl, Mike A; Rubin, Deborah C; Davidson, Nicholas O; Tarr, Phillip I; Warner, Barbara B; Dantas, Gautam; Warner, Brad W | Gut microbes | 34264786 | 2021 Jan-Dec |
Assessing the Concordance Between Urogenital and Vaginal Microbiota: Can Urine Specimens Be Used as a Proxy for Vaginal Samples? | Brown, Sarah E; Robinson, Courtney K; Shardell, Michelle D; Holm, Johanna B; Ravel, Jacques; Ghanem, Khalil G; Brotman, Rebecca M | Frontiers in cellular and infection microbiology | 34268137 | 2021 |
Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment. | Roodgar, Morteza; Good, Benjamin H; Garud, Nandita R; Martis, Stephen; Avula, Mohan; Zhou, Wenyu; Lancaster, Samuel M; Lee, Hayan; Babveyh, Afshin; Nesamoney, Sophia; Pollard, Katherine S; Snyder, Michael P | Genome research | 34301627 | 2021 08 |
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 |
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 |
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 Mar 12 |