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Human Microbiome Project (558)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
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, RobThe ISME journal.2016 Feb 23;26905627
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 KMicrobiology (Reading, England).2016 Jan 8;26747455
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 JNature genetics.2016 Feb;117-2526691984
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, RobScience (New York, N.Y.).2016 Jan 8;158-6226657285
The microbiome quality control project: baseline study design and future directions.Sinha, Rashmi; Abnet, Christian C; White, Owen; Knight, Rob; Huttenhower, CurtisGenome biology.2015;26653756
Emergence of Rotavirus G12P[8] in St. Louis During the 2012-2013 Rotavirus Season.Wylie, Kristine M; Weinstock, George M; Storch, Gregory AJournal of the Pediatric Infectious Diseases Society.2015 Dec;e84-926513823
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, MakedonkaJournal of data mining in genomics & proteomics.2015 Aug;26500804
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 WLancet (London, England).2016 Jan 9;156-6726490195
The influence of non-steroidal anti-inflammatory drugs on the gut microbiome.Rogers, M A M; Aronoff, D MClinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.2016 Feb;178.e1-926482265
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, NicolaNature methods.2015 Oct;902-326418763
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 GGenome biology.2015 Sep 15;26374288
ConStrains identifies microbial strains in metagenomic datasets.Luo, Chengwei; Knight, Rob; Siljander, Heli; Knip, Mikael; Xavier, Ramnik J; Gevers, DirkNature biotechnology.2015 Oct;1045-5226344404
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, JamesMicrobiome.2015;26306392
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, SubraGastroenterology.2015 Nov;1575-8626278503
The gut microbiota in human energy homeostasis and obesity.Rosenbaum, Michael; Knight, Rob; Leibel, Rudolph LTrends in endocrinology and metabolism: TEM.2015 Sep;493-50126257300
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 GloriaScience advances.2015 Apr 3;26229982
Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile.Schubert, Alyxandria M; Sinani, Hamide; Schloss, Patrick DmBio.2015 Jul 14;e0097426173701
Role of Autophagy in the Maintenance of Intestinal Homeostasis.Baxt, Leigh A; Xavier, Ramnik JGastroenterology.2015 Sep;553-6226170139
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 JNature communications.2015 Jun 30;26123276
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, NunoScientific reports.2015 Jun 26;26113465
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 LPloS one.2015 Jun 25;e013060426110908
Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis.Kang, Dezhi; Shi, Baochen; Erfe, Marie C; Craft, Noah; Li, HuiyingScience translational medicine.2015 Jun 24;293ra10326109103
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 JAlimentary pharmacology & therapeutics.2015 Aug;418-2726104013
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 DThe Journal of clinical investigation.2015 Jul 1;2841-5026098218
Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease.Vital, Marius; Harkema, Jack R; Rizzo, Mike; Tiedje, James; Brandenberger, ChristinaJournal of immunology research.2015 April 16;26090504
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 DInflammatory bowel diseases.2015 Aug;1948-5626083617
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 DmBio.2015 June 16;e0064826081634
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 RPloS one.2015 June 15;e012905526076489
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, DannyDiabetes.2015 Oct;3510-2026068542
Lungs, microbes and the developing neonate.Warner, Barbara B; Hamvas, AaronNeonatology.2015 June;337-4326044101
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, CeciliaAIDS (London, England).2015 Jun 19;F1-826035329
High-throughput sequencing technologies.Reuter, Jason A; Spacek, Damek V; Snyder, Michael PMolecular cell.2015 May 21;586-9726000844
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, PeterJournal of bacteriology.2015 Aug 1;2508-1625986902
An integrative view of microbiome-host interactions in inflammatory bowel diseases.Wlodarska, Marta; Kostic, Aleksandar D; Xavier, Ramnik JCell host & microbe.2015 May 13;577-9125974300
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 DInflammatory bowel diseases.2015 Aug;1786-9325970545
Identifying personal microbiomes using metagenomic codes.Franzosa, Eric A; Huang, Katherine; Meadow, James F; Gevers, Dirk; Lemon, Katherine P; Bohannan, Brendan J M; Huttenhower, CurtisProceedings of the National Academy of Sciences of the United States of America.2015 Jun 2;E2930-825964341
Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis.Segal, Leopoldo N; Blaser, Martin JThe Journal of pediatrics.2015 Jul;16-18.e125934071
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, CurtisNature reviews. Microbiology.2015 Jun;360-7225915636
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 BCell host & microbe.2015 May 13;681-925891358
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, CurtisGenome biology.2015 Apr 8;25887922
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 ABMC microbiology.2015 Mar 21;25880246
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, JiyoungPloS one.2015 Apr 15;e012459925874569
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 NmBio.2015 Apr 14;25873373
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 YCell.2015 Apr 9;264-7625860609
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 MGenome research.2015 May;679-8925858952
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, HuiyingThe ISME journal.2015 Sep;2078-9325848871
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 CThe Journal of pediatrics.2015 Jul;138-47.e1-325818499
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 MNature communications.2015 Mar 25;25807110
Personal genomes, quantitative dynamic omics and personalized medicine.Mias, George I; Snyder, MichaelQuantitative biology.2013 Mar;71-9025798291
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, MichaelMolecular & cellular proteomics : MCP.2015 Jun;1684-9525787789
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 EPloS one.2015 Mar 5;e011863225741698
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 BInflammatory bowel diseases.2015 May;963-7225738379
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 CCell host & microbe.2015 Mar 11;385-9125732063
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 DPloS one.2015 Feb 17;e011773825689864
Mitochondrial DNA sequence variation is largely conserved at birth with rare de novo mutations in neonates.Ma, Jun; Purcell, Heidi; Showalter, Lori; Aagaard, Kjersti MAmerican journal of obstetrics and gynecology.2015 Apr;530.e1-825687567
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, FernandoPLoS genetics.2015 Feb;e100485025679959
Impact of allele-specific peptides in proteome quantification.Wu, Linfeng; Snyder, MichaelProteomics. Clinical applications.2015 Apr;432-625676416
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 JCell host & microbe.2015 Feb 11;260-7325662751
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 KAmerican journal of obstetrics and gynecology.2015 Jun;779.e1-779.e1325637842
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 WCell.2015 Jan 29;447-6025619688
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 DGastroenterology.2015 May;1087-10625597840
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 JGenome medicine.2014;25587358
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 JThe Journal of infectious diseases.2015 Jun 15;1895-90425583170
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, FolkerPLoS computational biology.2015 Jan;e100400825569221
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 DNature genetics.2015 Feb;172-925559196
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, KjerstiAmerican journal of obstetrics and gynecology.2015 May;653.e1-1625557210
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, ManfredScientific reports.2014;25519916
Personalized sequencing and the future of medicine: discovery, diagnosis and defeat of disease.Esplin, Edward D; Oei, Ling; Snyder, Michael PPharmacogenomics.2014 Nov;1771-179025493570
Determining microbial products and identifying molecular targets in the human microbiome.Joice, Regina; Yasuda, Koji; Shafquat, Afrah; Morgan, Xochitl C; Huttenhower, CurtisCell metabolism.2014 Nov 4;731-4125440055
The changing landscape of the vaginal microbiome.Huang, Bernice; Fettweis, Jennifer M; Brooks, J Paul; Jefferson, Kimberly K; Buck, Gregory AClinics in laboratory medicine.2014 Dec;747-6125439274
Microbiome, innate immunity, and esophageal adenocarcinoma.Baghdadi, Jonathan; Chaudhary, Noami; Pei, Zhiheng; Yang, LiyingClinics in laboratory medicine.2014 Dec;721-3225439272
The interrelationships of the gut microbiome and inflammation in colorectal carcinogenesis.Cho, Margaret; Carter, Janell; Harari, Saul; Pei, ZhihengClinics in laboratory medicine.2014 Dec;699-71025439270
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 DGut.2014 Nov 26;25431456
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 ABMC bioinformatics.2014;25407910
The gut microbiome in health and in disease.Shreiner, Andrew B; Kao, John Y; Young, Vincent BCurrent opinion in gastroenterology.2015 Jan;69-7525394236
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 MmBio.2014;e0186425370491
Spec-seq: determining protein-DNA-binding specificity by sequencing.Stormo, Gary D; Zuo, Zheng; Chang, Yiming KennyBriefings in functional genomics.2015 Jan;30-825362070
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 DApplied and environmental microbiology.2015 Jan;396-40425362056
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 JG3 (Bethesda, Md.).2014 Dec;2353-6325344410
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 MThe ISME journal.2015 Apr;832-4325343515
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 MThe ISME journal.2015 May;1130-4025343512
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 APloS one.2014;e11094325337710
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, OwenCell.2014 Oct 9;227-3025303518
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 RInternational forum of allergy & rhinology.2015 Jan;25278448
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 RJournal of clinical microbiology.2014 Dec;4260-625275005
The microbiome revolution.Blaser, Martin JThe Journal of clinical investigation.2014 Oct;4162-525271724
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 KLab on a chip.2014 Dec 7;4533-925270338
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 EAIDS research and human retroviruses.2014 Nov;1046-5425265254
MiRNA detection at single-cell resolution using microfluidic LNA flow-FISH.Wu, Meiye; Piccini, Matthew E; Singh, Anup KMethods in molecular biology (Clifton, N.J.).2014;245-6025218391
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 MBMC biology.2014;25212266
The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease.Integrative HMP (iHMP) Research Network ConsortiumCell host & microbe.2014 Sep 10;276-8925211071
High-resolution specificity from DNA sequencing highlights alternative modes of Lac repressor binding.Zuo, Zheng; Stormo, Gary DGenetics.2014 Nov;1329-4325209146
From deep sequencing to actual clones.D'Angelo, Sara; Kumar, Sandeep; Naranjo, Leslie; Ferrara, Fortunato; Kiss, Csaba; Bradbury, Andrew R MProtein engineering, design & selection : PEDS.2014 Oct;301-725183780
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 AScience (New York, N.Y.).2014 Aug 29;1048-5225170151
Probiotics: achieving a better regulatory fit.Hoffmann, Diane E; Fraser, Claire M; Palumbo, Francis; Ravel, Jacques; Rowthorn, Virginia; Schwartz, JackFood and drug law journal2014237-72, ii25163211
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, ZhihengAmerican journal of clinical and experimental urology2014 Apr 1557-6125126590
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 IProceedings of the National Academy of Sciences of the United States of America.2014 Aug 26;12522-725114261
The Human Gut Microbiome as a Screening Tool for Colorectal Cancer.Zackular, Joseph P; Rogers, Mary A M; Ruffin 4th, Mack T; Schloss, Patrick DCancer prevention research (Philadelphia, Pa.)2014 Aug 7NULL25104642
Phylogenetics and the human microbiome.Matsen 4th, Frederick ASystematic biology.2015 Jan;e26-4125102857
Phase variation of poly-N-acetylglucosamine expression in Staphylococcus aureus.Brooks, Jamie L; Jefferson, Kimberly KPLoS pathogens.2014 Jul;e100429225077798
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)2014 Jul 29NULL25073854
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 AMicrobiome20141425071935
The dynamics of a family's gut microbiota reveal variations on a theme.Schloss, Patrick D; Iverson, Kathryn D; Petrosino, Joseph F; Schloss, Sarah JMicrobiome.2014;25061514
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 DGastroenterology.2014 Nov;1055-63.e825046162
Serum profiling using protein microarrays to identify disease related antigens.Sharon, Donald; Snyder, MichaelMethods in molecular biology (Clifton, N.J.).2014;169-7825030927
Microfluidic molecular assay platform for the detection of miRNAs, mRNAs, proteins, and posttranslational modifications at single-cell resolution.Wu, Meiye; Singh, Anup KJournal of laboratory automation.2014 Dec;587-9225027027
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 SGut.2015 Jun;911-2025007816
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, JosephmBio2014e01390-1425006230
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 AThe Journal of clinical investigation.2014 Aug;3617-3325003194
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, SandraGenome biology2014R7624995464
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, SomyingBMC microbiology201417724989059
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 FProceedings of the National Academy of Sciences of the United States of America2014 Jul 89768-7324965364
Oligotyping analysis of the human oral microbiome.Eren, A Murat; Borisy, Gary G; Huse, Susan M; Mark Welch, Jessica LProceedings of the National Academy of Sciences of the United States of America2014 Jul 15E2875-8424965363
Defining a personal, allele-specific, and single-molecule long-read transcriptome.Tilgner, Hagen; Grubert, Fabian; Sharon, Donald; Snyder, Michael PProceedings of the National Academy of Sciences of the United States of America.2014 Jul 8;9869-7424961374
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 FIntegrative biology : quantitative biosciences from nano to macro2014 Jun 23NULL24953827
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 KGenome biology and evolution2014 Jul1772-8924951561
Inflammatory bowel disease as a model for translating the microbiome.Huttenhower, Curtis; Kostic, Aleksandar D; Xavier, Ramnik JImmunity2014 Jun 19843-5424950204
Finding the missing links among metabolites, microbes, and the host.Dorrestein, Pieter C; Mazmanian, Sarkis K; Knight, RobImmunity.2014 Jun 19;824-3224950202
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 EThe Journal of infectious diseases.2014 Dec 1;1723-3324943724
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 EmBio2014e01305-1424939888
CcpA is important for growth and virulence of Enterococcus faecium.Somarajan, Sudha R; Roh, Jung H; Singh, Kavindra V; Weinstock, George M; Murray, Barbara EInfection and immunity.2014 Sep;3580-724914215
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 MGenome biology2014R6624887286
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 UInternational journal of computational biology and drug design.2014;130-4524878725
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 WGenome announcements.2014;24855299
Microbiome in reflux disorders and esophageal adenocarcinoma.Yang, Liying; Chaudhary, Noami; Baghdadi, Jonathan; Pei, ZhihengCancer journal (Sudbury, Mass.)2014 May-Jun207-1024855009
The placenta harbors a unique microbiome.Aagaard, Kjersti; Ma, Jun; Antony, Kathleen M; Ganu, Radhika; Petrosino, Joseph; Versalovic, JamesScience translational medicine2014 May 21237ra6524848255
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, CurtisProceedings of the National Academy of Sciences of the United States of America2014 Jun 3E2329-3824843156
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, MakedonkaPloS one2014e9727924827833
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 SInternational journal of systematic and evolutionary microbiology.2014 Aug;2642-924824639
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 DmBio2014e01021-1424803517
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; BraThe ISME journal2014 Apr 29NULL24781901
Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data.Vital, Marius; Howe, Adina Chuang; Tiedje, James MmBio2014e0088924757212
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, RamunasPloS one2014e9538024743558
Dynamics and associations of microbial community types across the human body.Ding, Tao; Schloss, Patrick DNature2014 May 15357-6024739969
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; BrandaThe New England journal of medicine2014 Apr 171524-3124738669
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, MirceaEnvironmental microbiology2014 Apr 17NULL24738594
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 SPloS one2014e8864524670812
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, HClinical infectious diseases : an official publication of the Infectious Diseases Society of America2014 May1211-824647013
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 JGut microbes2014 Mar-Apr165-7524637601
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 & microbe2014 Mar 12382-9224629344
Functional and phylogenetic assembly of microbial communities in the human microbiome.Shafquat, Afrah; Joice, Regina; Simmons, Sheri L; Huttenhower, CurtisTrends in microbiology2014 Mar 4NULL24618403
Immune and genetic gardening of the intestinal microbiome.Jacobs, Jonathan P; Braun, JonathanFEBS letters2014 Mar 5NULL24613921
History and impact of RDP: a legacy from Carl Woese to microbiology.Cole, James R; Tiedje, James MRNA biology2014 Mar239-4324607969
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 genetics2014 Apr336-4424562188
Whole-genome haplotyping using long reads and statistical methods.Kuleshov, Volodymyr; Xie, Dan; Chen, Rui; Pushkarev, Dmitry; Ma, Zhihai; Blauwkamp, Tim; Kertesz, Michael; Snyder, MichaelNature biotechnology2014 Mar261-624561555
The microbiome in inflammatory bowel disease: current status and the future ahead.Kostic, Aleksandar D; Xavier, Ramnik J; Gevers, DirkGastroenterology2014 May1489-9924560869
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, JacquesMicrobiome.2014;24558975
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 JPloS one2014e8939824551246
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 RThe Journal of pediatrics2014 Feb 13NULL24529620
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 EMicrobiome2014524529162
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, ZhihengJournal of virology2014 May4786-9724522917
Diet and the intestinal microbiome: associations, functions, and implications for health and disease.Albenberg, Lindsey G; Wu, Gary DGastroenterology2014 May1564-7224503132
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; HuttenhowThe ISME journal2014 Jul1403-1724500617
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 AG3 (Bethesda, Md.)2014 Apr561-7824496724
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, JAntonie van Leeuwenhoek2014 Mar579-9224488273
Meta'omic analytic techniques for studying the intestinal microbiome.Morgan, Xochitl C; Huttenhower, CurtisGastroenterology2014 May1437-1448.e124486053
Compositional and functional features of the gastrointestinal microbiome and their effects on human health.Hollister, Emily B; Gao, Chunxu; Versalovic, JamesGastroenterology2014 May1449-5824486050
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; DalaMicrobiome2013924451366
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 MMicrobiome2013824451334
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; AlvThe ISME journal2014 Jan 23NULL24451203
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 JMicrobiome20132924451163
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 AMicrobiome20132724451123
A brave new world: the lung microbiota in an era of change.Segal, Leopoldo N; Blaser, Martin JAnnals of the American Thoracic Society2014 JanS21-724437400
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 NPloS one2013e8550724386477
Mathematical modeling of primary succession of murine intestinal microbiota.Marino, Simeone; Baxter, Nielson T; Huffnagle, Gary B; Petrosino, Joseph F; Schloss, Patrick DProceedings of the National Academy of Sciences of the United States of America2014 Jan 7439-4424367073
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 LMethods in ecology and evolution / British Ecological Society2013 Dec 1NULL24358444
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; HutPLoS computational biology2013 Dece100339224348235
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 NPloS one2013e7863324302980
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 MNucleic acids research2014 JanD633-4224288368
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 MBMC microbiology201327024279426
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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, MirceaPloS one2013e5936123555659
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Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases.Leone, Vanessa; Chang, Eugene B; Devkota, SuzanneJournal of gastroenterology2013 Mar315-2123475322
Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players.Ursell, Luke K; Knight, RobCell metabolism2013 Mar 5317-823473028
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 JAnalytical chemistry2013 May 74203-1423469896
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 NThe Journal of pediatrics2013 Aug416-2323452586
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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, KjerstiPloS one2013e5056423418415
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Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes.Ballarini, Annalisa; Segata, Nicola; Huttenhower, Curtis; Jousson, OlivierPloS one2013e5576423409037
The human gut microbiome and body metabolism: implications for obesity and diabetes.Devaraj, Sridevi; Hemarajata, Peera; Versalovic, JamesClinical chemistry2013 Apr617-2823401286
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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, HuiyingThe Journal of investigative dermatology2013 Jan 2123337890
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 SScience (New York, N.Y.)2013 Mar 11084-823328391
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 EPLoS computational biology2013 Jane100286323326225
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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; MilosavljBMC bioinformatics2012S1123320832
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, WillGenome biology2013 Jan 14R123316946
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The Jeremiah Metzger lecture: Global warming redux: the disappearing microbiota and epidemic obesity.Blaser, Martin JTransactions of the American Clinical and Climatological Association2012230-8; discussion 239-4123303990
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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 JThe Journal of infectious diseases2013 Apr1105-1423300163
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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 DPloS one2012e5207823284876
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 ABMC genomics2012S1723282177
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'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 RHealth expectations : an international journal of public participation in health care and health policy2012 Dec 2823279082
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 MPloS one2012e5114623251439
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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; JansPloS one2012e4913823209564
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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 APloS one2012e2904422719821
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Diverse CRISPRs evolving in human microbiomes.Rho, Mina; Wu, Yu-Wei; Tang, Haixu; Doak, Thomas G; Ye, YuzhenPLoS genetics2012e100244122719260
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, PatPLoS computational biology2012e100235822719234
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, HongzheBioinformatics (Oxford, England)2012 Aug 152106-1322711789
A framework for human microbiome research.Human Microbiome Project ConsortiumNature2012 Jun 14215-2122699610
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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, JacquesGenome biology2012R4222698087
A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community.Wang, Mingjie; Ye, Yuzhen; Tang, HaixuJournal of computational biology : a journal of computational molecular cell biology2012 Jun814-2522697249
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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 FGut microbes2012 Jul-Aug383-9322688727
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Understanding vaginal microbiome complexity from an ecological perspective.Hickey, Roxana J; Zhou, Xia; Pierson, Jacob D; Ravel, Jacques; Forney, Larry JTranslational research : the journal of laboratory and clinical medicine2012 Oct267-8222683415
The microbiome of the lung.Beck, James M; Young, Vincent B; Huffnagle, Gary BTranslational research : the journal of laboratory and clinical medicine2012 Oct258-6622683412
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, SalomonPloS one2012e3791922675498
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, RobGenome research2012 Oct1974-8422665442
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 MPloS one2012e3693422655031
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 WGene regulation and systems biology201267-8022654504
Spatial and temporal variability of the human microbiota.Parfrey, L W; Knight, RClinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases2012 Jul8-1122647040
'Omics' of the mammalian gut--new insights into function.Lamendella, Regina; VerBerkmoes, Nathan; Jansson, Janet KCurrent opinion in biotechnology2012 Jun491-50022626866
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-JunPloS one2012e3694022615851
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, EllenPloS one2012e3713922606341
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 DennisPloS one2012e3629822606251
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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 AChemistry & biodiversity2012 May965-7622589096
Food and the gut microbiota in inflammatory bowel diseases: a critical connection.Albenberg, Lindsey G; Lewis, James D; Wu, Gary DCurrent opinion in gastroenterology2012 Jul314-2022573192
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, JohnPloS one2012e3600922558305
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, JacquesScience translational medicine2012 May 2132ra5222553250
We are what we eat: how the diet of infants affects their gut microbiome.Pop, MihaiGenome biology201215222546514
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, RobThe Journal of allergy and clinical immunology2012 May1204-822541361
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 FPloS one2012e3547022532855
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, DanielPLoS genetics2012e100262622511878
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 FInfection and immunity2012 Jun2150-722493085
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, AndreasGenome biology2012R2322455878
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 JProceedings of the National Academy of Sciences of the United States of America2012 Apr 105809-1422451929
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, DavidNature medicine2012 Apr538-4622447074
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, AlexDatabase : the journal of biological databases and curation2012bas00322434837
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 CGenome research2012 Jun1107-1922434425
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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, RobThe ISME journal.2012 Aug;1621-422402401
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 RHealth and quality of life outcomes20122522401607
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, EugenePloS one2012e3254522389708
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Molecular pathways: pathogenesis and clinical implications of microbiome alteration in esophagitis and Barrett esophagus.Yang, Liying; Francois, Fritz; Pei, ZhihengClinical cancer research : an official journal of the American Association for Cancer Research2012 Apr 152138-4422344232
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, JamesJournal of pediatric gastroenterology and nutrition2012 Sep299-30722343914
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 NJournal of acquired immune deficiency syndromes (1999)2012 Jul 1299-30622343176
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 ScottThe Journal of clinical investigation2012 Mar 1974-8622326959
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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, JamesFASEB journal : official publication of the Federation of American Societies for Experimental Biology2012 May1960-922267340
Perturbation dynamics of the rumen microbiota in response to exogenous butyrate.Li, Robert W; Wu, Sitao; Baldwin 6th, Ransom L; Li, Weizhong; Li, CongjunPloS one2012e2939222253719
Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis.Feazel, Leah M; Robertson, Charles E; Ramakrishnan, Vijay R; Frank, Daniel NThe Laryngoscope2012 Feb467-7222253013
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, EInternational endodontic journal2012 Jun530-4122251411
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences.Soergel, David A W; Dey, Neelendu; Knight, Rob; Brenner, Steven EThe ISME journal2012 Jul1440-422237546
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Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws.Smajs, David; Norris, Steven J; Weinstock, George MInfection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases2012 Mar191-20222198325
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, NehaPloS one2011e2888622194940
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.Schloss, Patrick D; Gevers, Dirk; Westcott, Sarah LPloS one2011e2731022194782
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SitePainter: a tool for exploring biogeographical patterns.Gonzalez, Antonio; Stombaugh, Jesse; Lauber, Christian L; Fierer, Noah; Knight, RobBioinformatics (Oxford, England)2012 Feb 1436-822171330
Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences.Wang, Xiaoyu; Cai, Yunpeng; Sun, Yijun; Knight, Rob; Mai, VolkerThe ISME journal2012 Jul1277-8022170430
Using QIIME to analyze 16S rRNA gene sequences from microbial communities.Kuczynski, Justin; Stombaugh, Jesse; Walters, William Anton; Gonzalez, Antonio; Caporaso, J Gregory; Knight, RobCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]2011 DecUnit 10.7.22161565
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Characterizing microbial communities through space and time.Gonzalez, Antonio; King, Andrew; Robeson 2nd, Michael S; Song, Sejin; Shade, Ashley; Metcalf, Jessica L; Knight, RobCurrent opinion in biotechnology2012 Jun431-622154467
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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, DanielNucleic acids research2012 JanD237-4122140108
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 CNucleic acids research2012 JanD571-922135293
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, PhilipThe ISME journal2012 Mar610-822134646
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 LPloS one2011e2717322132090
The Human Microbiome Project: lessons from human genomics.Lewis Jr, Cecil M; Obregon-Tito, Alexandra; Tito, Raul Y; Foster, Morris W; Spicer, Paul GTrends in microbiology2012 Jan1-422112388
Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment.Ye, YuzhenProceedings. IEEE International Conference on Bioinformatics and Biomedicine2011 Feb 4153-15722102981
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The intestinal microbiota in health and disease.Young, Vincent BCurrent opinion in gastroenterology2012 Jan63-922080827
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 LBioinformatics (Oxford, England)2012 Jan 156-6222072382
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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, DeThe American journal of bioethics : AJOB2011 Nov1-722047112
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data.Zhao, Yongan; Tang, Haixu; Ye, YuzhenBioinformatics (Oxford, England)2012 Jan 1125-622039206
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Microbiome and malignancy.Plottel, Claudia S; Blaser, Martin JCell host & microbe2011 Oct 20324-3522018233
Fluorescent labeling of antibody fragments using split GFP.Ferrara, Fortunato; Listwan, Pawel; Waldo, Geoffrey S; Bradbury, Andrew R MPloS one2011e2572721998685
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Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies.Segata, Nicola; Huttenhower, CurtisPloS one2011e2470421931822
Bambus 2: scaffolding metagenomes.Koren, Sergey; Treangen, Todd J; Pop, MihaiBioinformatics (Oxford, England)2011 Nov 12964-7121926123
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 ICell host & microbe2011 Sep 15260-7221925113
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 SApplied and environmental microbiology2011 Nov7804-1421908640
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.Pirrung, Meg; Kennedy, Ryan; Caporaso, J Gregory; Stombaugh, Jesse; Wendel, Doug; Knight, RobBioinformatics (Oxford, England)2011 Nov 13067-921903626
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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, WadihThe New England journal of medicine2011 Sep 8892-90021899450
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; BusScience (New York, N.Y.)2011 Oct 7105-821885731
Antibiotic effects on bacterial profile in osteonecrosis of the jaw.Ji, X; Pushalkar, S; Li, Y; Glickman, R; Fleisher, K; Saxena, DOral diseases2012 Jan85-9521883710
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, RobTrends in microbiology2011 Oct472-8221872475
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 BPloS one2011e2278821829515
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-HwaAnalytical chemistry2011 Oct 17269-7521809842
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 BGut microbes2011 May-Jun145-5821804357
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, JizhongThe ISME journal2012 Feb259-7221796217
Investigating the biological and clinical significance of human dysbioses.Frank, Daniel N; Zhu, Wei; Sartor, R Balfour; Li, EllenTrends in microbiology2011 Sep427-3421775143
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 BFrontiers in microbiology201114421772835
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 TNature methods2011 Sep761-321765408
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 KLab on a chip2011 Aug 212673-921755095
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, SusGastroenterology2011 Nov1782-9121741921
Extrapolation of urn models via poissonization: accurate measurements of the microbial unknown.Lladser, Manuel E; Gouet, Raul; Reeder, JensPloS one2011e2110521738613
DNACLUST: accurate and efficient clustering of phylogenetic marker genes.Ghodsi, Mohammadreza; Liu, Bo; Pop, MihaiBMC bioinformatics201127121718538
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 EThe ISME journal2012 Jan94-10321716311
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 RJournal of clinical gastroenterology2012 Feb138-4421716123
Metagenomic biomarker discovery and explanation.Segata, Nicola; Izard, Jacques; Waldron, Levi; Gevers, Dirk; Miropolsky, Larisa; Garrett, Wendy S; Huttenhower, CurtisGenome biology2011R6021702898
UCHIME improves sensitivity and speed of chimera detection.Edgar, Robert C; Haas, Brian J; Clemente, Jose C; Quince, Christopher; Knight, RobBioinformatics (Oxford, England)2011 Aug 152194-20021700674
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 WJournal of pediatric surgery2011 Jun1029-3321683193
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 TGut2012 Mar373-8421646247
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, RobGenome biology2011R5021624126
Mammalian Cell Sorting using ýýFACS.Cho, Sung Hwan; Chen, Chun Hao; Tsai, Frank S; Godin, Jessica; Lo, Yu-HwaConference on Lasers and Electro-optics : (CLEO). Conference on Lasers and Electro-optics2010 May 16CTuD121614147
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, BarbaraPloS one2011e1970921603636
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 LObesity (Silver Spring, Md.)2012 Apr738-4721593810
RAPSearch: a fast protein similarity search tool for short reads.Ye, Yuzhen; Choi, Jeong-Hyeon; Tang, HaixuBMC bioinformatics201115921575167
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 VNature reviews. Microbiology2011 Jun467-7721552286
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-SerrNature biotechnology2011 May415-2021552244
Boulder ALignment Editor (ALE): a web-based RNA alignment tool.Stombaugh, Jesse; Widmann, Jeremy; McDonald, Daniel; Knight, RobBioinformatics (Oxford, England)2011 Jun 151706-721546392
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 MAmerican journal of physical anthropology2011 Aug653-721541929
Development of the human gastrointestinal microbiota and insights from high-throughput sequencing.Dominguez-Bello, Maria Gloria; Blaser, Martin J; Ley, Ruth E; Knight, RobGastroenterology2011 May1713-921530737
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, VolkerBriefings in bioinformatics2012 Jan107-2121525143
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, NielsBMC ecology20111121524302
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes.Niu, Beifang; Zhu, Zhengwei; Fu, Limin; Wu, Sitao; Li, WeizhongBioinformatics (Oxford, England)2011 Jun 151704-521505035
Reliability and validity of a modified Bristol Stool Form Scale for children.Lane, Mariella M; Czyzewski, Danita I; Chumpitazi, Bruno P; Shulman, Robert JThe Journal of pediatrics2011 Sep437-441.e121489557
The mind-body-microbial continuum.Gonzalez, Antonio; Stombaugh, Jesse; Lozupone, Catherine; Turnbaugh, Peter J; Gordon, Jeffrey I; Knight, RobDialogues in clinical neuroscience201155-6221485746
Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification.Haft, Daniel H; Basu, Malay KumarJournal of bacteriology2011 Jun2745-5521478363
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, ChangyiWorld journal of surgery2011 Aug1693-921424870
Unravelling the effects of the environment and host genotype on the gut microbiome.Spor, Ayme; Koren, Omry; Ley, RuthNature reviews. Microbiology2011 Apr279-9021407244
Next generation sequence assembly with AMOS.Treangen, Todd J; Sommer, Dan D; Angly, Florent E; Koren, Sergey; Pop, MihaiCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]2011 MarUnit 11.821400694
Beyond natural antibodies: the power of in vitro display technologies.Bradbury, Andrew R M; Sidhu, Sachdev; Dubel, Stefan; McCafferty, JohnNature biotechnology2011 Mar245-5421390033
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.Wu, Yu-Wei; Ye, YuzhenJournal of computational biology : a journal of computational molecular cell biology2011 Mar523-3421385052
Host-associated and free-living phage communities differ profoundly in phylogenetic composition.Caporaso, J Gregory; Knight, Rob; Kelley, Scott TPloS one2011e1690021383980
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 RPloS one2011e1662621364937
Microdroplet-enabled highly parallel co-cultivation of microbial communities.Park, Jihyang; Kerner, Alissa; Burns, Mark A; Lin, Xiaoxia NinaPloS one2011e1701921364881
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 RGut2011 Aug1043-921317176
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 SCellular microbiology2011 Apr508-1721314883
Current concepts of the intestinal microbiota and the pathogenesis of infection.Wardwell, Leslie H; Huttenhower, Curtis; Garrett, Wendy SCurrent infectious disease reports2011 Feb28-3421308452
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 BPloS one2011e1622121283757
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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 BJournal of perinatology : official journal of the California Perinatal Association2011 Aug519-2321273988
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 WayneFASEB journal : official publication of the Federation of American Societies for Experimental Biology2011 May1449-6021228220
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 AWorld journal of surgery2011 Aug1746-5021225260
Dielectrophoresis of Caenorhabditis elegans.Chuang, Han-Sheng; Raizen, David M; Lamb, Annesia; Dabbish, Nooreen; Bau, Haim HLab on a chip2011 Feb 21599-60421225036
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners.Haft, Daniel HBMC genomics20112121223593
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 AWorld journal of surgery2011 Aug1732-721221581
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; KnigGenome research2011 Mar494-50421212162
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, DeepakFEMS immunology and medical microbiology2011 Apr269-7721205002
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 JInfectious diseases in obstetrics and gynecology201073742521197076
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Probiotics, enteric and diarrheal diseases, and global health.Preidis, Geoffrey A; Hill, Colin; Guerrant, Richard L; Ramakrishna, B S; Tannock, Gerald W; Versalovic, JamesGastroenterology2011 Jan8-1421075108
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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 BPloS one2010e1360721042588
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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 HBiochemistry2010 Nov 3010117-3020961038
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, FredrikProceedings of the National Academy of Sciences of the United States of America2011 Mar 154592-820937873
Growth and Development Symposium: promoting healthier humans through healthier livestock: animal agriculture enters the metagenomics era.Frank, D NJournal of animal science2011 Mar835-4420935136
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 BApplied microbiology and biotechnology2010 Dec1333-4220931185
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 one2010e1241120865041
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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 LAmerican journal of medical genetics. Part A2010 Jul1774-8020583190
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, RobProceedings of the National Academy of Sciences of the United States of America2010 Jun 2911971-520566857
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, NoahEnvironmental microbiology2010 Nov2885-9320545741
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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, NoahFEMS microbiology letters2010 Jun80-620412303
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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-HwaLab on a chip2010 Jun 211567-7320379604
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Hepatitis C virus transmission bottlenecks analyzed by deep sequencing.Wang, Gary P; Sherrill-Mix, Scott A; Chang, Kyong-Mi; Quince, Chris; Bushman, Frederic DJournal of virology2010 Jun6218-2820375170
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Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era.Preidis, Geoffrey A; Versalovic, JamesGastroenterology2009 May2015-3119462507
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