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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
Human Microbiome Project (837)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| "What is the FDA Going to Think?": Negotiating Values through Reflective and Strategic Category Work in Microbiome Science. | Darling, Katherine W; Boyce, Angie M; Cho, Mildred K; Sankar, Pamela L | Science, technology & human values | 2015 Jan | 36119463 | |
| Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression. | Delgado-Diaz, David Jose; Jesaveluk, Brianna; Hayward, Joshua A; Tyssen, David; Alisoltani, Arghavan; Potgieter, Matthys; Bell, Liam; Ross, Elizabeth; Iranzadeh, Arash; Allali, Imane; Dabee, Smritee; Barnabas, Shaun; Gamieldien, Hoyam; Blackburn, Jonathan M; Mulder, Nicola; Smith, Steven B; Edwards, Vonetta L; Burgener, Adam D; Bekker, Linda-Gail; Ravel, Jacques; Passmore, Jo-Ann S; Masson, Lindi; Hearps, Anna C; Tachedjian, Gilda | Microbiome | 2022 08 31 | 36045402 | |
| A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria. | Yao, Lina; D'Agostino, Gabriel D; Park, Jinseok; Hang, Saiyu; Adhikari, Arijit A; Zhang, Yancong; Li, Wei; Avila-Pacheco, Julian; Bae, Sena; Clish, Clary B; Franzosa, Eric A; Huttenhower, Curtis; Huh, Jun R; Devlin, A Sloan | Nature microbiology | 2022 09 | 35982310 | |
| Factors Associated With Incidence and Spontaneous Clearance of Molecular-Bacterial Vaginosis: Results From a Longitudinal Frequent-Sampling Observational Study. | Tamarelle, Jeanne; Shardell, Michelle D; Ravel, Jacques; Brotman, Rebecca M | Sexually transmitted diseases | 2022 Sep 01 | 35969846 | |
| Complete Genome Sequences of Ezakiella coagulans C0061C1 and Fenollaria massiliensis C0061C2. | France, Michael T; Clifford, Jack; Narina, Shilpa; Rutt, Lindsay; Ravel, Jacques | Microbiology resource announcements | 2022 Jul 21 | 35861554 | |
| High-sensitivity pattern discovery in large, paired multiomic datasets. | Ghazi, Andrew R; Sucipto, Kathleen; Rahnavard, Ali; Franzosa, Eric A; McIver, Lauren J; Lloyd-Price, Jason; Schwager, Emma; Weingart, George; Moon, Yo Sup; Morgan, Xochitl C; Waldron, Levi; Huttenhower, Curtis | Bioinformatics (Oxford, England) | 2022 06 24 | 35758795 | |
| Progressive dysbiosis of human orodigestive microbiota along the sequence of gastroesophageal reflux, Barrett's esophagus and esophageal adenocarcinoma. | Hao, Yuhan; Karaoz, Ulas; Yang, Liying; Yachimski, Patrick S; Tseng, Wenzhi; Nossa, Carlos W; Ye, Weimin; Tseng, Mengkao; Poles, Michael; Francois, Fritz; Traube, Morris; Brown, Stuart M; Chen, Yu; Torralba, Manolito; Peek, Richard M; Brodie, Eoin L; Pei, Zhiheng | International journal of cancer | 2022 Jun 24 | 35751398 | |
| Douching cessation and molecular bacterial vaginosis: a reanalysis of archived specimens. | Brown, Sarah Elizabeth; He, Xin; Shardell, Michelle D; Ravel, Jacques; Ghanem, Khalil G; Zenilman, Jonathan M; Brotman, Rebecca M | Sexually transmitted infections | 2022 May 30 | 35636931 | |
| Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants. | Kaelin, Emily A; Rodriguez, Cynthia; Hall-Moore, Carla; Hoffmann, Julie A; Linneman, Laura A; Ndao, I Malick; Warner, Barbara B; Tarr, Phillip I; Holtz, Lori R; Lim, Efrem S | Nature microbiology | 2022 May | 35449461 | |
| Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome. | Li, Yanping; Wang, Fenglei; Li, Jun; Ivey, Kerry L; Wilkinson, Jeremy E; Wang, Dong D; Li, Ruifeng; Liu, Gang; Eliassen, Heather A; Chan, Andrew T; Clish, Clary B; Huttenhower, Curtis; Hu, Frank B; Sun, Qi; Rimm, Eric B | BMC microbiology | 2022 03 29 | 35350985 | |
| Associations Between Vaginal Bacteria and Bacterial Vaginosis Signs and Symptoms: A Comparative Study of Kenyan and American Women. | Carter, Kayla A; Balkus, Jennifer E; Anzala, Omu; Kimani, Joshua; Hoffman, Noah G; Fiedler, Tina L; Mochache, Vernon; Fredricks, David N; McClelland, Raymond Scott; Srinivasan, Sujatha | Frontiers in cellular and infection microbiology | 2022 | 35310847 | |
| Exerkines in health, resilience and disease. | Chow, Lisa S; Gerszten, Robert E; Taylor, Joan M; Pedersen, Bente K; van Praag, Henriette; Trappe, Scott; Febbraio, Mark A; Galis, Zorina S; Gao, Yunling; Haus, Jacob M; Lanza, Ian R; Lavie, Carl J; Lee, Chih-Hao; Lucia, Alejandro; Moro, Cedric; Pandey, Ambarish; Robbins, Jeremy M; Stanford, Kristin I; Thackray, Alice E; Villeda, Saul; Watt, Matthew J; Xia, Ashley; Zierath, Juleen R; Goodpaster, Bret H; Snyder, Michael P | Nature reviews. Endocrinology | 2022 05 | 35304603 | |
| Human gut bacteria produce ΤΗ17-modulating bile acid metabolites. | Paik, Donggi; Yao, Lina; Zhang, Yancong; Bae, Sena; D'Agostino, Gabriel D; Zhang, Minghao; Kim, Eunha; Franzosa, Eric A; Avila-Pacheco, Julian; Bisanz, Jordan E; Rakowski, Christopher K; Vlamakis, Hera; Xavier, Ramnik J; Turnbaugh, Peter J; Longman, Randy S; Krout, Michael R; Clish, Clary B; Rastinejad, Fraydoon; Huttenhower, Curtis; Huh, Jun R; Devlin, A Sloan | Nature | 2022 03 | 35296854 | |
| Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data. | France, Michael T; Fu, Li; Rutt, Lindsay; Yang, Hongqiu; Humphrys, Michael S; Narina, Shilpa; Gajer, Pawel M; Ma, Bing; Forney, Larry J; Ravel, Jacques | Genome biology | 2022 Mar 01 | 35232471 | |
| Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing. | Zuo, Zheng; Chang, Yiming Kenny; Stormo, Gary D | Briefings in functional genomics | 2022 Apr 11 | 34923581 | |
| Unique roles of vaginal Megasphaera phylotypes in reproductive health. | Glascock, Abigail L; Jimenez, Nicole R; Boundy, Sam; Koparde, Vishal N; Brooks, J Paul; Edwards, David J; Strauss Iii, Jerome F; Jefferson, Kimberly K; Serrano, Myrna G; Buck, Gregory A; Fettweis, Jennifer M | Microbial genomics | 2021 12 | 34898422 | |
| The vaginal microbiome in women of reproductive age with healthy weight versus overweight/obesity. | Allen, Natalie G; Edupuganti, Laahirie; Edwards, David J; Jimenez, Nicole R; Buck, Gregory A; Jefferson, Kimberly K; Strauss 3rd, Jerome F; Vaginal Microbiome Consortium; Wickham 3rd, Edmond P; Fettweis, Jennifer M | Obesity (Silver Spring, Md.) | 2022 01 | 34806323 | |
| Multivariable association discovery in population-scale meta-omics studies. | Mallick, Himel; Rahnavard, Ali; McIver, Lauren J; Ma, Siyuan; Zhang, Yancong; Nguyen, Long H; Tickle, Timothy L; Weingart, George; Ren, Boyu; Schwager, Emma H; Chatterjee, Suvo; Thompson, Kelsey N; Wilkinson, Jeremy E; Subramanian, Ayshwarya; Lu, Yiren; Waldron, Levi; Paulson, Joseph N; Franzosa, Eric A; Bravo, Hector Corrada; Huttenhower, Curtis | PLoS computational biology | 2021 11 | 34784344 | |
| Metagenomic profiling of placental tissue suggests DNA virus infection of the placenta is rare. | Witney, Adam A; Aller, Sean; Strang, Blair L | The Journal of general virology | 2021 11 | 34723784 | |
| Complex species and strain ecology of the vaginal microbiome from pregnancy to postpartum and association with preterm birth. | Pace, Ryan M; Chu, Derrick M; Prince, Amanda L; Ma, Jun; Seferovic, Maxim D; Aagaard, Kjersti M | Med (New York, N.Y.) | 2021 Sep 10 | 34617072 | |
| Vaginal microbiome Lactobacillus crispatus is heritable among European American women. | Wright, Michelle L; Fettweis, Jennifer M; Eaves, Lindon J; Silberg, Judy L; Neale, Michael C; Serrano, Myrna G; Jimenez, Nicole R; Prom-Wormley, Elizabeth; Girerd, Philippe H; Borzelleca Jr, Joseph F; Jefferson, Kimberly K; Strauss 3rd, Jerome F; York, Timothy P; Buck, Gregory A | Communications biology | 2021 08 05 | 34354222 | |
| The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men. | Sikavi, Daniel R; Nguyen, Long H; Haruki, Koichiro; Ugai, Tomotaka; Ma, Wenjie; Wang, Dong D; Thompson, Kelsey N; Yan, Yan; Branck, Tobyn; Wilkinson, Jeremy E; Akimoto, Naohiko; Zhong, Rong; Lau, Mai Chan; Mima, Kosuke; Kosumi, Keisuke; Morikawa, Teppei; Rimm, Eric B; Garrett, Wendy S; Izard, Jacques; Cao, Yin; Song, Mingyang; Huttenhower, Curtis; Ogino, Shuji; Chan, Andrew T | Clinical and translational gastroenterology | 2021 08 01 | 34333506 | |
| Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment. | Roodgar, Morteza; Good, Benjamin H; Garud, Nandita R; Martis, Stephen; Avula, Mohan; Zhou, Wenyu; Lancaster, Samuel M; Lee, Hayan; Babveyh, Afshin; Nesamoney, Sophia; Pollard, Katherine S; Snyder, Michael P | Genome research | 2021 08 | 34301627 | |
| Assessing the Concordance Between Urogenital and Vaginal Microbiota: Can Urine Specimens Be Used as a Proxy for Vaginal Samples? | Brown, Sarah E; Robinson, Courtney K; Shardell, Michelle D; Holm, Johanna B; Ravel, Jacques; Ghanem, Khalil G; Brotman, Rebecca M | Frontiers in cellular and infection microbiology | 2021 | 34268137 | |
| Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. | Thänert, Robert; Thänert, Anna; Ou, Jocelyn; Bajinting, Adam; Burnham, Carey-Ann D; Engelstad, Holly J; Tecos, Maria E; Ndao, I Malick; Hall-Moore, Carla; Rouggly-Nickless, Colleen; Carl, Mike A; Rubin, Deborah C; Davidson, Nicholas O; Tarr, Phillip I; Warner, Barbara B; Dantas, Gautam; Warner, Brad W | Gut microbes | 2021 Jan-Dec | 34264786 | |
| Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men. | Ma, Wenjie; Nguyen, Long H; Song, Mingyang; Wang, Dong D; Franzosa, Eric A; Cao, Yin; Joshi, Amit; Drew, David A; Mehta, Raaj; Ivey, Kerry L; Strate, Lisa L; Giovannucci, Edward L; Izard, Jacques; Garrett, Wendy; Rimm, Eric B; Huttenhower, Curtis; Chan, Andrew T | Genome medicine | 2021 06 17 | 34140026 | |
| Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome. | Li, Yanping; Wang, Dong D; Satija, Ambika; Ivey, Kerry L; Li, Jun; Wilkinson, Jeremy E; Li, Ruifeng; Baden, Megu; Chan, Andrew T; Huttenhower, Curtis; Rimm, Eric B; Hu, Frank B; Sun, Qi | The Journal of nutrition | 2021 Jun 10 | 34114015 | |
| Wearable sensors enable personalized predictions of clinical laboratory measurements. | Dunn, Jessilyn; Kidzinski, Lukasz; Runge, Ryan; Witt, Daniel; Hicks, Jennifer L; Schüssler-Fiorenza Rose, Sophia Miryam; Li, Xiao; Bahmani, Amir; Delp, Scott L; Hastie, Trevor; Snyder, Michael P | Nature medicine | 2021 Jun | 34031607 | |
| Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. | Beghini, Francesco; McIver, Lauren J; Blanco-Míguez, Aitor; Dubois, Leonard; Asnicar, Francesco; Maharjan, Sagun; Mailyan, Ana; Manghi, Paolo; Scholz, Matthias; Thomas, Andrew Maltez; Valles-Colomer, Mireia; Weingart, George; Zhang, Yancong; Zolfo, Moreno; Huttenhower, Curtis; Franzosa, Eric A; Segata, Nicola | eLife | 2021 May 04 | 33944776 | |
| Biogenic Amines Increase the Odds of Bacterial Vaginosis and Affect the Growth of and Lactic Acid Production by Vaginal Lactobacillus spp. | Borgogna, Joanna-Lynn C; Shardell, Michelle D; Grace, Savannah G; Santori, Elisa K; Americus, Benjamin; Li, Zhong; Ulanov, Alexander; Forney, Larry; Nelson, Tiffanie M; Brotman, Rebecca M; Ravel, Jacques; Yeoman, Carl J | Applied and environmental microbiology | 2021 04 27 | 33674429 | |
| Megasphaera lornae sp. nov., Megasphaera hutchinsoni sp. nov., and Megasphaera vaginalis sp. nov.: novel bacteria isolated from the female genital tract. | Srinivasan, Sujatha; Beamer, May A; Fiedler, Tina L; Austin, Michele N; Sizova, Maria V; Strenk, Susan M; Agnew, Kathy J; Gowda, G A Nagana; Raftery, Daniel; Epstein, Slava S; Fredricks, David N; Hillier, Sharon L | International journal of systematic and evolutionary microbiology | 2019 Jun | 33616513 | |
| Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease. | Somineni, Hari K; Nagpal, Sini; Venkateswaran, Suresh; Cutler, David J; Okou, David T; Haritunians, Talin; Simpson, Claire L; Begum, Ferdouse; Datta, Lisa W; Quiros, Antonio J; Seminerio, Jenifer; Mengesha, Emebet; Alexander, Jonathan S; Baldassano, Robert N; Dudley-Brown, Sharon; Cross, Raymond K; Dassopoulos, Themistocles; Denson, Lee A; Dhere, Tanvi A; Iskandar, Heba; Dryden, Gerald W; Hou, Jason K; Hussain, Sunny Z; Hyams, Jeffrey S; Isaacs, Kim L; Kader, Howard; Kappelman, Michael D; Katz, Jeffry; Kellermayer, Richard; Kuemmerle, John F; Lazarev, Mark; Li, Ellen; Mannon, Peter; Moulton, Dedrick E; Newberry, Rodney D; Patel, Ashish S; Pekow, Joel; Saeed, Shehzad A; Valentine, John F; Wang, Ming-Hsi; McCauley, Jacob L; Abreu, Maria T; Jester, Traci; Molle-Rios, Zarela; Palle, Sirish; Scherl, Ellen J; Kwon, John; Rioux, John D; Duerr, Richard H; Silverberg, Mark S; Zwick, Michael E; Stevens, Christine; Daly, Mark J; Cho, Judy H; Gibson, Greg; McGovern, Dermot P B; Brant, Steven R; Kugathasan, Subra | American journal of human genetics | 2021 03 04 | 33600772 | |
| The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. | Wang, Dong D; Nguyen, Long H; Li, Yanping; Yan, Yan; Ma, Wenjie; Rinott, Ehud; Ivey, Kerry L; Shai, Iris; Willett, Walter C; Hu, Frank B; Rimm, Eric B; Stampfer, Meir J; Chan, Andrew T; Huttenhower, Curtis | Nature medicine | 2021 02 | 33574608 | |
| Sequence Comparison of Vaginolysin from Different Gardnerella Species. | Garcia, Erin M; Serrano, Myrna G; Edupuganti, Laahirie; Edwards, David J; Buck, Gregory A; Jefferson, Kimberly K | Pathogens (Basel, Switzerland) | 2021 Jan 20 | 33498226 | |
| Fructan-sensitive children with irritable bowel syndrome have distinct gut microbiome signatures. | Chumpitazi, Bruno P; Hoffman, Kristi L; Smith, Daniel P; McMeans, Ann R; Musaad, Salma; Versalovic, James; Petrosino, Joseph F; Shulman, Robert J | Alimentary pharmacology & therapeutics. | 2020 Dec 13; | 33314183 | |
| HMPDACC: a Human Microbiome Project Multi-omic data resource. | Creasy, Heather Huot; Felix, Victor; Aluvathingal, Jain; Crabtree, Jonathan; Ifeonu, Olukemi; Matsumura, James; McCracken, Carrie; Nickel, Lance; Orvis, Joshua; Schor, Mike; Giglio, Michelle; Mahurkar, Anup; White, Owen | Nucleic acids research | 2021 01 08 | 33305317 | |
| VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. | France, Michael T; Ma, Bing; Gajer, Pawel; Brown, Sarah; Humphrys, Michael S; Holm, Johanna B; Waetjen, L Elaine; Brotman, Rebecca M; Ravel, Jacques | Microbiome. | 2020 11 23; | 33228810 | |
| Identification of Natural CRISPR Systems and Targets in the Human Microbiome. | Münch, Philipp C; Franzosa, Eric A; Stecher, Bärbel; McHardy, Alice C; Huttenhower, Curtis | Cell host & microbe. | 2020 Nov 16; | 33217332 | |
| Genetic Variation in Toll-Like Receptor 5 and Colonization with Flagellated Bacterial Vaginosis-Associated Bacteria. | Dela Cruz, Erin J; Fiedler, Tina L; Liu, Congzhou; Munch, Matthew M; Kohler, Christina M; Oot, Antoinette R; Wallis, Jacqueline M; Wang, Junhui; Frishman, Anna; Garcia, Kristina; Wiser, Andrew; Balkus, Jennifer E; Srinivasan, Sujatha; Golob, Jonathan L; Sycuro, Laura K; Marrazzo, Jeanne M; Hawn, Thomas R; Fredricks, David N | Infection and immunity | 2021 Feb 16 | 33199356 | |
| Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. | Nishiyama, Hiroki; Endo, Hisashi; Blanc-Mathieu, Romain; Ogata, Hiroyuki | Microorganisms. | 2020 Oct 27; | 33121006 | |
| Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial 'dark matter'. | Tan, James Y; Wang, Sida; Dick, Gregory J; Young, Vincent B; Sherman, David H; Burns, Mark A; Lin, Xiaoxia N | Integrative biology : quantitative biosciences from nano to macro. | 2020 11 18; | 33089329 | |
| Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California. | Sailani, M Reza; Metwally, Ahmed A; Zhou, Wenyu; Rose, Sophia Miryam Schüssler-Fiorenza; Ahadi, Sara; Contrepois, Kevin; Mishra, Tejaswini; Zhang, Martin Jinye; Kidzi?ski, ?ukasz; Chu, Theodore J; Snyder, Michael P | Nature communications. | 2020 10 01; | 33004787 | |
| Association of diet with circulating trimethylamine-N-oxide concentration. | Hamaya, Rikuta; Ivey, Kerry L; Lee, Dong H; Wang, Molin; Li, Jun; Franke, Adrian; Sun, Qi; Rimm, Eric B | The American journal of clinical nutrition. | 2020 12 10; | 32936862 | |
| Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz. | Wagner, Justin; Kancherla, Jayaram; Braccia, Domenick; Matsumara, James; Felix, Victor; Crabtree, Jonathan; Mahurkar, Anup; Corrada Bravo, Héctor | F1000Research | 2020 | 32742640 | |
| Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. | Karcher, Nicolai; Pasolli, Edoardo; Asnicar, Francesco; Huang, Kun D; Tett, Adrian; Manara, Serena; Armanini, Federica; Bain, Debbie; Duncan, Sylvia H; Louis, Petra; Zolfo, Moreno; Manghi, Paolo; Valles-Colomer, Mireia; Raffaetà, Roberta; Rota-Stabelli, Omar; Collado, Maria Carmen; Zeller, Georg; Falush, Daniel; Maixner, Frank; Walker, Alan W; Huttenhower, Curtis; Segata, Nicola | Genome biology. | 2020 06 08; | 32513234 | |
| PICRUSt2 for prediction of metagenome functions. | Douglas, Gavin M; Maffei, Vincent J; Zaneveld, Jesse R; Yurgel, Svetlana N; Brown, James R; Taylor, Christopher M; Huttenhower, Curtis; Langille, Morgan G I | Nature biotechnology. | 2020 Jun; | 32483366 | |
| Molecular Choreography of Acute Exercise. | Contrepois, Kévin; Wu, Si; Moneghetti, Kegan J; Hornburg, Daniel; Ahadi, Sara; Tsai, Ming-Shian; Metwally, Ahmed A; Wei, Eric; Lee-McMullen, Brittany; Quijada, Jeniffer V; Chen, Songjie; Christle, Jeffrey W; Ellenberger, Mathew; Balliu, Brunilda; Taylor, Shalina; Durrant, Matthew G; Knowles, David A; Choudhry, Hani; Ashland, Melanie; Bahmani, Amir; Enslen, Brooke; Amsallem, Myriam; Kobayashi, Yukari; Avina, Monika; Perelman, Dalia; Schüssler-Fiorenza Rose, Sophia Miryam; Zhou, Wenyu; Ashley, Euan A; Montgomery, Stephen B; Chaib, Hassan; Haddad, Francois; Snyder, Michael P | Cell. | 2020 May 28; | 32470399 | |
| Complete Genome Sequences of Six Lactobacillus iners Strains Isolated from the Human Vagina. | France, Michael T; Rutt, Lindsay; Narina, Shilpa; Arbaugh, Sarah; McComb, Elias; Humphrys, Mike S; Ma, Bing; Hayward, Matthew R; Costello, Elizabeth K; Relman, David A; Kwon, Douglas S; Ravel, Jacques | Microbiology resource announcements. | 2020 May 14; | 32409537 | |
| MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data. | Bangayan, Nathanael J; Shi, Baochen; Trinh, Jerry; Barnard, Emma; Kasimatis, Gabriela; Curd, Emily; Li, Huiying | Microorganisms. | 2020 May 08; | 32397065 | |
| Asymptomatic Bacterial Vaginosis Is Associated With Depletion of Mature Superficial Cells Shed From the Vaginal Epithelium. | O'Hanlon, D Elizabeth; Gajer, Pawel; Brotman, Rebecca M; Ravel, Jacques | Frontiers in cellular and infection microbiology. | 2020; | 32211347 | |
| Associations of Sleep Characteristics With Cognitive Function and Decline Among Older Adults. | McSorley, V Eloesa; Bin, Yu Sun; Lauderdale, Diane S | American journal of epidemiology. | 2019 06 01; | 32181824 | |
| Maternal activation of the EGFR prevents translocation of gut-residing pathogenic Escherichia coli in a model of late-onset neonatal sepsis. | Knoop, Kathryn A; Coughlin, Paige E; Floyd, Alexandria N; Ndao, I Malick; Hall-Moore, Carla; Shaikh, Nurmohammad; Gasparrini, Andrew J; Rusconi, Brigida; Escobedo, Marilyn; Good, Misty; Warner, Barbara B; Tarr, Phillip I; Newberry, Rodney D | Proceedings of the National Academy of Sciences of the United States of America. | 2020 04 07; | 32179676 | |
| Global chemical effects of the microbiome include new bile-acid conjugations. | Quinn, Robert A; Melnik, Alexey V; Vrbanac, Alison; Fu, Ting; Patras, Kathryn A; Christy, Mitchell P; Bodai, Zsolt; Belda-Ferre, Pedro; Tripathi, Anupriya; Chung, Lawton K; Downes, Michael; Welch, Ryan D; Quinn, Melissa; Humphrey, Greg; Panitchpakdi, Morgan; Weldon, Kelly C; Aksenov, Alexander; da Silva, Ricardo; Avila-Pacheco, Julian; Clish, Clary; Bae, Sena; Mallick, Himel; Franzosa, Eric A; Lloyd-Price, Jason; Bussell, Robert; Thron, Taren; Nelson, Andrew T; Wang, Mingxun; Leszczynski, Eric; Vargas, Fernando; Gauglitz, Julia M; Meehan, Michael J; Gentry, Emily; Arthur, Timothy D; Komor, Alexis C; Poulsen, Orit; Boland, Brigid S; Chang, John T; Sandborn, William J; Lim, Meerana; Garg, Neha; Lumeng, Julie C; Xavier, Ramnik J; Kazmierczak, Barbara I; Jain, Ruchi; Egan, Marie; Rhee, Kyung E; Ferguson, David; Raffatellu, Manuela; Vlamakis, Hera; Haddad, Gabriel G; Siegel, Dionicio; Huttenhower, Curtis; Mazmanian, Sarkis K; Evans, Ronald M; Nizet, Victor; Knight, Rob; Dorrestein, Pieter C | Nature. | 2020 03; | 32103176 | |
| Single-Cell Genomics and the Oral Microbiome. | Balachandran, M; Cross, K L; Podar, M | Journal of dental research | 2020 06 | 32091935 | |
| Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. | Nguyen, Long H; Ma, Wenjie; Wang, Dong D; Cao, Yin; Mallick, Himel; Gerbaba, Teklu K; Lloyd-Price, Jason; Abu-Ali, Galeb; Hall, A Brantley; Sikavi, Daniel; Drew, David A; Mehta, Raaj S; Arze, Cesar; Joshi, Amit D; Yan, Yan; Branck, Tobyn; DuLong, Casey; Ivey, Kerry L; Ogino, Shuji; Rimm, Eric B; Song, Mingyang; Garrett, Wendy S; Izard, Jacques; Huttenhower, Curtis; Chan, Andrew T | Gastroenterology. | 2020 04; | 31972239 | |
| Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. | Fornelos, Nadine; Franzosa, Eric A; Bishai, Jason; Annand, John W; Oka, Akihiko; Lloyd-Price, Jason; Arthur, Timothy D; Garner, Ashley; Avila-Pacheco, Julian; Haiser, Henry J; Tolonen, Andrew C; Porter, Jeffrey A; Clish, Clary B; Sartor, R Balfour; Huttenhower, Curtis; Vlamakis, Hera; Xavier, Ramnik J | Nature microbiology. | 2020 03; | 31959971 | |
| Personal aging markers and ageotypes revealed by deep longitudinal profiling. | Ahadi, Sara; Zhou, Wenyu; Schüssler-Fiorenza Rose, Sophia Miryam; Sailani, M Reza; Contrepois, Kévin; Avina, Monika; Ashland, Melanie; Brunet, Anne; Snyder, Michael | Nature medicine. | 2020 01; | 31932806 | |
| Windows Into Human Health Through Wearables Data Analytics. | Witt, Daniel; Kellogg, Ryan; Snyder, Michael; Dunn, Jessilyn | Current opinion in biomedical engineering. | 2019 Mar; | 31832566 | |
| Discordant transmission of bacteria and viruses from mothers to babies at birth. | Maqsood, Rabia; Rodgers, Rachel; Rodriguez, Cynthia; Handley, Scott A; Ndao, I Malick; Tarr, Phillip I; Warner, Barbara B; Lim, Efrem S; Holtz, Lori R | Microbiome | 2019 12 10 | 31823811 | |
| Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains. | Kirmiz, Nina; Galindo, Kadir; Cross, Karissa L; Luna, Estefani; Rhoades, Nicholas; Podar, Mircea; Flores, Gilberto E | Applied and environmental microbiology. | 2020 Jan 21; | 31757822 | |
| The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. | Tett, Adrian; Huang, Kun D; Asnicar, Francesco; Fehlner-Peach, Hannah; Pasolli, Edoardo; Karcher, Nicolai; Armanini, Federica; Manghi, Paolo; Bonham, Kevin; Zolfo, Moreno; De Filippis, Francesca; Magnabosco, Cara; Bonneau, Richard; Lusingu, John; Amuasi, John; Reinhard, Karl; Rattei, Thomas; Boulund, Fredrik; Engstrand, Lars; Zink, Albert; Collado, Maria Carmen; Littman, Dan R; Eibach, Daniel; Ercolini, Danilo; Rota-Stabelli, Omar; Huttenhower, Curtis; Maixner, Frank; Segata, Nicola | Cell host & microbe. | 2019 11 13; | 31607556 | |
| Nonoptimal Vaginal Microbiota After Azithromycin Treatment for Chlamydia trachomatis Infection. | Tamarelle, Jeanne; Ma, Bing; Gajer, Pawel; Humphrys, Mike S; Terplan, Mishka; Mark, Katrina S; Thiébaut, Anne C M; Forney, Larry J; Brotman, Rebecca M; Delarocque-Astagneau, Elisabeth; Bavoil, Patrik M; Ravel, Jacques | The Journal of infectious diseases. | 2020 02 03; | 31573603 | |
| Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly. | Ivey, Kerry L; Chan, Andrew T; Izard, Jacques; Cassidy, Aedin; Rogers, Geraint B; Rimm, Eric B | mBio. | 2019 Sep 24; | 31551328 | |
| The Cervicovaginal Microbiota-Host Interaction Modulates Chlamydia trachomatis Infection. | Edwards, Vonetta L; Smith, Steven B; McComb, Elias J; Tamarelle, Jeanne; Ma, Bing; Humphrys, Michael S; Gajer, Pawel; Gwilliam, Kathleen; Schaefer, Alison M; Lai, Samuel K; Terplan, Mishka; Mark, Katrina S; Brotman, Rebecca M; Forney, Larry J; Bavoil, Patrik M; Ravel, Jacques | mBio. | 2019 Aug 13; | 31409678 | |
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| Genome Sequences of 11 Human Vaginal Actinobacteria Strains. | Lewis, Amanda L; Deitzler, Grace E; Ruiz, Maria J; Weimer, Cory; Park, SoEun; Robinson, Lloyd S; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G | Genome announcements. | 2016 Sep 29; | 27688328 | |
| Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women. | Weimer, Cory M; Deitzler, Grace E; Robinson, Lloyd S; Park, SoEun; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G; Lewis, Amanda L | Genome announcements. | 2016 Sep 29; | 27688327 | |
| Genome Sequences of 15 Gardnerella vaginalis Strains Isolated from the Vaginas of Women with and without Bacterial Vaginosis. | Robinson, Lloyd S; Perry, Justin; Lek, Sai; Wollam, Aye; Sodergren, Erica; Weinstock, George; Lewis, Warren G; Lewis, Amanda L | Genome announcements. | 2016 Sep 29; | 27688326 | |
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| Cutaneous microbiome effects of fluticasone propionate cream and adjunctive bleach baths in childhood atopic dermatitis. | Gonzalez, Mercedes E; Schaffer, Julie V; Orlow, Seth J; Gao, Zhan; Li, Huilin; Alekseyenko, Alexander V; Blaser, Martin J | Journal of the American Academy of Dermatology. | 2016 Sep; | 27543211 | |
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| STOPPING DECEPTIVE HEALTH CLAIMS: THE NEED FOR A PRIVATE RIGHT OF ACTION UNDER FEDERAL LAW. | Hoffmann, Diane; Schwartz, Jack | American journal of law & medicine. | 2016; | 27263263 | |
| Prophages mediate defense against phage infection through diverse mechanisms. | Bondy-Denomy, Joseph; Qian, Jason; Westra, Edze R; Buckling, Angus; Guttman, David S; Davidson, Alan R; Maxwell, Karen L | The ISME journal. | 2016 12; | 27258950 | |
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| Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation. | Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha; Theriot, Casey M; Young, Vincent B; Jansson, Janet K; Fredricks, David N; Borenstein, Elhanan | mSystems. | 2016 Jan-Feb; | 27239563 | |
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| Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. | Blaser, Martin J; Cardon, Zoe G; Cho, Mildred K; Dangl, Jeffrey L; Donohue, Timothy J; Green, Jessica L; Knight, Rob; Maxon, Mary E; Northen, Trent R; Pollard, Katherine S; Brodie, Eoin L | mBio. | 2016 05 13; | 27178263 | |
| Cathelicidin suppresses lipid accumulation and hepatic steatosis by inhibition of the CD36 receptor. | Hoang-Yen Tran, D; Hoang-Ngoc Tran, D; Mattai, S A; Sallam, T; Ortiz, C; Lee, E C; Robbins, L; Ho, S; Lee, J E; Fisseha, E; Shieh, C; Sideri, A; Shih, D Q; Fleshner, P; McGovern, D P B; Vu, M; Hing, T C; Bakirtzi, K; Cheng, M; Su, B; Law, I; Karagiannides, I; Targan, S R; Gallo, R L; Li, Z; Koon, H W | International journal of obesity (2005). | 2016 Sep; | 27163748 | |
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| Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans. | Vatanen, Tommi; Kostic, Aleksandar D; d'Hennezel, Eva; Siljander, Heli; Franzosa, Eric A; Yassour, Moran; Kolde, Raivo; Vlamakis, Hera; Arthur, Timothy D; Hämäläinen, Anu-Maaria; Peet, Aleksandr; Tillmann, Vallo; Uibo, Raivo; Mokurov, Sergei; Dorshakova, Natalya; Ilonen, Jorma; Virtanen, Suvi M; Szabo, Susanne J; Porter, Jeffrey A; Lähdesmäki, Harri; Huttenhower, Curtis; Gevers, Dirk; Cullen, Thomas W; Knip, Mikael; DIABIMMUNE Study Group; Xavier, Ramnik J | Cell. | 2016 May 5; | 27133167 | |
| The interactome of Streptococcus pneumoniae and its bacteriophages show highly specific patterns of interactions among bacteria and their phages. | Mariano, Rachelle; Wuchty, Stefan; Vizoso-Pinto, Maria G; Häuser, Roman; Uetz, Peter | Scientific reports. | 2016 Apr 22; | 27103053 | |
| Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome. | Perez Perez, Guillermo I; Gao, Zhan; Jourdain, Roland; Ramirez, Julia; Gany, Francesca; Clavaud, Cecile; Demaude, Julien; Breton, Lionel; Blaser, Martin J | PloS one. | 2016; | 27088867 | |
| Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility. | Ward, Marc A; Pierre, Joseph F; Leal, Raquel F; Huang, Yong; Shogan, Benjamin; Dalal, Sushila R; Weber, Christopher R; Leone, Vanessa A; Musch, Mark W; An, Gary C; Rao, Mrinalini C; Rubin, David T; Raffals, Laura E; Antonopoulos, Dionysios A; Sogin, Mitch L; Hyman, Neil H; Alverdy, John C; Chang, Eugene B | American journal of physiology. Gastrointestinal and liver physiology. | 2016 06 01; | 27079612 | |
| Papillary urothelial carcinoma with squamous differentiation in association with human papilloma virus: case report and literature review. | Guma, Sergei; Maglantay, Remegio; Lau, Ryan; Wieczorek, Rosemary; Melamed, Jonathan; Deng, Fang-Ming; Zhou, Ming; Makarov, Danil; Lee, Peng; Pincus, Matthew R; Pei, Zhi-Heng | American journal of clinical and experimental urology. | 2016; | 27069958 | |
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| Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation. | Chehoud, Christel; Dryga, Anatoly; Hwang, Young; Nagy-Szakal, Dorottya; Hollister, Emily B; Luna, Ruth Ann; Versalovic, James; Kellermayer, Richard; Bushman, Frederic D | mBio. | 2016 Mar 29; | 27025251 | |
| Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants. | Ward, Doyle V; Scholz, Matthias; Zolfo, Moreno; Taft, Diana H; Schibler, Kurt R; Tett, Adrian; Segata, Nicola; Morrow, Ardythe L | Cell reports. | 2016 Mar 29; | 26997279 | |
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| Erratum to: The first microbial environment of infants born by C-section: the operating room microbes. | Shin, Hakdong; Pei, Zhiheng; Martinez 2nd, Keith A; Rivera-Vinas, Juana I; Mendez, Keimari; Cavallin, Humberto; Dominguez-Bello, Maria G | Microbiome. | 2016 Jan 21; | 26796629 | |
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| Association of Systemic Sclerosis With a Unique Colonic Microbial Consortium. | Volkmann, Elizabeth R; Chang, Yu-Ling; Barroso, Nashla; Furst, Daniel E; Clements, Philip J; Gorn, Alan H; Roth, Bennett E; Conklin, Jeffrey L; Getzug, Terri; Borneman, James; McGovern, Dermot P B; Tong, Maomeng; Jacobs, Jonathan P; Braun, Jonathan | Arthritis & rheumatology (Hoboken, N.J.). | 2016 06; | 26749064 | |
| Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria. | Abdelmaksoud, Abdallah A; Koparde, Vishal N; Sheth, Nihar U; Serrano, Myrna G; Glascock, Abigail L; Fettweis, Jennifer M; Strauss Iii, Jerome F; Buck, Gregory A; Jefferson, Kimberly K | Microbiology (Reading, England). | 2016 Jan 8; | 26747455 | |
| HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria. | Yang, Liying; Poles, Michael A; Fisch, Gene S; Ma, Yingfei; Nossa, Carlos; Phelan, Joan A; Pei, Zhiheng | AIDS (London, England). | 2016 Jan 02; | 26731752 | |
| Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. | Araya, Carlos L; Cenik, Can; Reuter, Jason A; Kiss, Gert; Pande, Vijay S; Snyder, Michael P; Greenleaf, William J | Nature genetics. | 2016 Feb; | 117-25 | 26691984 |
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| Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma. | Sankaranarayanan, Krithivasan; Ozga, Andrew T; Warinner, Christina; Tito, Raul Y; Obregon-Tito, Alexandra J; Xu, Jiawu; Gaffney, Patrick M; Jervis, Lori L; Cox, Derrell; Stephens, Lancer; Foster, Morris; Tallbull, Gloria; Spicer, Paul; Lewis, Cecil M | Current biology : CB. | 2015 Dec 21; | 26671671 | |
| Histamine H2 Receptor-Mediated Suppression of Intestinal Inflammation by Probiotic Lactobacillus reuteri. | Gao, Chunxu; Major, Angela; Rendon, David; Lugo, Monica; Jackson, Vanessa; Shi, Zhongcheng; Mori-Akiyama, Yuko; Versalovic, James | mBio. | 2015 Dec 15; | 26670383 | |
| Microbial community assembly and metabolic function during mammalian corpse decomposition. | Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob | Science (New York, N.Y.). | 2016 Jan 8; | 158-62 | 26657285 |
| Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. | Kuleshov, Volodymyr; Jiang, Chao; Zhou, Wenyu; Jahanbani, Fereshteh; Batzoglou, Serafim; Snyder, Michael | Nature biotechnology. | 2016 Jan; | 26655498 | |
| The microbiome quality control project: baseline study design and future directions. | Sinha, Rashmi; Abnet, Christian C; White, Owen; Knight, Rob; Huttenhower, Curtis | Genome biology. | 2015; | 26653756 | |
| Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens. | Zhou, Yanjiao; Wylie, Kristine M; El Feghaly, Rana E; Mihindukulasuriya, Kathie A; Elward, Alexis; Haslam, David B; Storch, Gregory A; Weinstock, George M | Journal of clinical microbiology. | 2016 Feb; | 26637379 | |
| Engineering Values Into Genetic Engineering: A Proposed Analytic Framework for Scientific Social Responsibility. | Sankar, Pamela L; Cho, Mildred K | The American journal of bioethics : AJOB. | 2015; | 26632356 | |
| Wham: Identifying Structural Variants of Biological Consequence. | Kronenberg, Zev N; Osborne, Edward J; Cone, Kelsey R; Kennedy, Brett J; Domyan, Eric T; Shapiro, Michael D; Elde, Nels C; Yandell, Mark | PLoS computational biology. | 2015 Dec; | 26625158 | |
| The first microbial environment of infants born by C-section: the operating room microbes. | Shin, Hakdong; Pei, Zhiheng; Martinez 2nd, Keith A; Rivera-Vinas, Juana I; Mendez, Keimari; Cavallin, Humberto; Dominguez-Bello, Maria G | Microbiome. | 2015 Dec 01; | 26620712 | |
| Luminal Conversion and Immunoregulation by Probiotics. | Ganesh, Bhanu Priya; Versalovic, James | Frontiers in pharmacology. | 2015; | 26617521 | |
| Nurturing the microbiome field. | Schloss, Patrick | Science (New York, N.Y.) | 2015 Nov 27 | 26612945 | |
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| Microbiome, a new dimension in cancer research. | Neto, Antonio Galvao; Bradshaw, Azore-Dee; Pei, Zhiheng | Annals of translational medicine. | 2015 Sep; | 26539446 | |
| Emergence of Rotavirus G12P[8] in St. Louis During the 2012-2013 Rotavirus Season. | Wylie, Kristine M; Weinstock, George M; Storch, Gregory A | Journal of the Pediatric Infectious Diseases Society. | 2015 Dec; | e84-9 | 26513823 |
| mBLAST: Keeping up with the sequencing explosion for (meta)genome analysis. | Davis, Curtis; Kota, Karthik; Baldhandapani, Venkat; Gong, Wei; Abubucker, Sahar; Becker, Eric; Martin, John; Wylie, Kristine M; Khetani, Radhika; Hudson, Matthew E; Weinstock, George M; Mitreva, Makedonka | Journal of data mining in genomics & proteomics. | 2015 Aug; | 26500804 | |
| High Frequency of Detection by PCR of Viral Nucleic Acid in The Blood of Infants Presenting with Clinical Myocarditis. | Simpson, Kathleen E; Storch, Gregory A; Lee, Caroline K; Ward, Kent E; Danon, Saar; Simon, Catherine M; Delaney, Jeffrey W; Tong, Alan; Canter, Charles E | Pediatric cardiology. | 2016 Feb; | 26499513 | |
| Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study. | Cleynen, Isabelle; Boucher, Gabrielle; Jostins, Luke; Schumm, L Philip; Zeissig, Sebastian; Ahmad, Tariq; Andersen, Vibeke; Andrews, Jane M; Annese, Vito; Brand, Stephan; Brant, Steven R; Cho, Judy H; Daly, Mark J; Dubinsky, Marla; Duerr, Richard H; Ferguson, Lynnette R; Franke, Andre; Gearry, Richard B; Goyette, Philippe; Hakonarson, Hakon; Halfvarson, Jonas; Hov, Johannes R; Huang, Hailang; Kennedy, Nicholas A; Kupcinskas, Limas; Lawrance, Ian C; Lee, James C; Satsangi, Jack; Schreiber, Stephan; Théâtre, Emilie; van der Meulen-de Jong, Andrea E; Weersma, Rinse K; Wilson, David C; International Inflammatory Bowel Disease Genetics Consortium; Parkes, Miles; Vermeire, Severine; Rioux, John D; Mansfield, John; Silverberg, Mark S; Radford-Smith, Graham; McGovern, Dermot P B; Barrett, Jeffrey C; Lees, Charlie W | Lancet (London, England). | 2016 Jan 9; | 156-67 | 26490195 |
| The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. | Rogers, M A M; Aronoff, D M | Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. | 2016 Feb; | 178.e1-9 | 26482265 |
| Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. | Lewis, James D; Chen, Eric Z; Baldassano, Robert N; Otley, Anthony R; Griffiths, Anne M; Lee, Dale; Bittinger, Kyle; Bailey, Aubrey; Friedman, Elliot S; Hoffmann, Christian; Albenberg, Lindsey; Sinha, Rohini; Compher, Charlene; Gilroy, Erin; Nessel, Lisa; Grant, Amy; Chehoud, Christel; Li, Hongzhe; Wu, Gary D; Bushman, Frederic D | Cell host & microbe. | 2015 Oct 14; | 26468751 | |
| MetaPhlAn2 for enhanced metagenomic taxonomic profiling. | Truong, Duy Tin; Franzosa, Eric A; Tickle, Timothy L; Scholz, Matthias; Weingart, George; Pasolli, Edoardo; Tett, Adrian; Huttenhower, Curtis; Segata, Nicola | Nature methods. | 2015 Oct; | 902-3 | 26418763 |
| Host genetic variation impacts microbiome composition across human body sites. | Blekhman, Ran; Goodrich, Julia K; Huang, Katherine; Sun, Qi; Bukowski, Robert; Bell, Jordana T; Spector, Timothy D; Keinan, Alon; Ley, Ruth E; Gevers, Dirk; Clark, Andrew G | Genome biology. | 2015 Sep 15; | 26374288 | |
| Early life dynamics of the human gut virome and bacterial microbiome in infants. | Lim, Efrem S; Zhou, Yanjiao; Zhao, Guoyan; Bauer, Irma K; Droit, Lindsay; Ndao, I Malick; Warner, Barbara B; Tarr, Phillip I; Wang, David; Holtz, Lori R | Nature medicine. | 2015 Oct; | 26366711 | |
| ConStrains identifies microbial strains in metagenomic datasets. | Luo, Chengwei; Knight, Rob; Siljander, Heli; Knip, Mikael; Xavier, Ramnik J; Gevers, Dirk | Nature biotechnology. | 2015 Oct; | 1045-52 | 26344404 |
| Structure and function of the healthy pre-adolescent pediatric gut microbiome. | Hollister, Emily B; Riehle, Kevin; Luna, Ruth Ann; Weidler, Erica M; Rubio-Gonzales, Michelle; Mistretta, Toni-Ann; Raza, Sabeen; Doddapaneni, Harsha V; Metcalf, Ginger A; Muzny, Donna M; Gibbs, Richard A; Petrosino, Joseph F; Shulman, Robert J; Versalovic, James | Microbiome. | 2015; | 26306392 | |
| Alterations of the Subgingival Microbiota in Pediatric Crohn's Disease Studied Longitudinally in Discovery and Validation Cohorts. | Kelsen, Judith; Bittinger, Kyle; Pauly-Hubbard, Helen; Posivak, Leah; Grunberg, Stephanie; Baldassano, Robert; Lewis, James D; Wu, Gary D; Bushman, Frederic D | Inflammatory bowel diseases. | 2015 Dec; | 26288001 | |
| Characterization of genetic loci that affect susceptibility to inflammatory bowel diseases in African Americans. | Huang, Chengrui; Haritunians, Talin; Okou, David T; Cutler, David J; Zwick, Michael E; Taylor, Kent D; Datta, Lisa W; Maranville, Joseph C; Liu, Zhenqiu; Ellis, Shannon; Chopra, Pankaj; Alexander, Jonathan S; Baldassano, Robert N; Cross, Raymond K; Dassopoulos, Themistocles; Dhere, Tanvi A; Duerr, Richard H; Hanson, John S; Hou, Jason K; Hussain, Sunny Z; Isaacs, Kim L; Kachelries, Kelly E; Kader, Howard; Kappelman, Michael D; Katz, Jeffrey; Kellermayer, Richard; Kirschner, Barbara S; Kuemmerle, John F; Kumar, Archana; Kwon, John H; Lazarev, Mark; Mannon, Peter; Moulton, Dedrick E; Osuntokun, Bankole O; Patel, Ashish; Rioux, John D; Rotter, Jerome I; Saeed, Shehzad; Scherl, Ellen J; Silverberg, Mark S; Silverman, Ann; Targan, Stephan R; Valentine, John F; Wang, Ming-Hsi; Simpson, Claire L; Bridges, S Louis; Kimberly, Robert P; Rich, Stephen S; Cho, Judy H; Di Rienzo, Anna; Kao, Linda W H; McGovern, Dermot P B; Brant, Steven R; Kugathasan, Subra | Gastroenterology. | 2015 Nov; | 1575-86 | 26278503 |
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| Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. | Beck, James M; Schloss, Patrick D; Venkataraman, Arvind; Twigg 3rd, Homer; Jablonski, Kathleen A; Bushman, Frederic D; Campbell, Thomas B; Charlson, Emily S; Collman, Ronald G; Crothers, Kristina; Curtis, Jeffrey L; Drews, Kimberly L; Flores, Sonia C; Fontenot, Andrew P; Foulkes, Mary A; Frank, Ian; Ghedin, Elodie; Huang, Laurence; Lynch, Susan V; Morris, Alison; Palmer, Brent E; Schmidt, Thomas M; Sodergren, Erica; Weinstock, George M; Young, Vincent B; Lung HIV Microbiome Project | American journal of respiratory and critical care medicine. | 2015 Dec 01; | 26247840 | |
| The microbiome of uncontacted Amerindians. | Clemente, Jose C; Pehrsson, Erica C; Blaser, Martin J; Sandhu, Kuldip; Gao, Zhan; Wang, Bin; Magris, Magda; Hidalgo, Glida; Contreras, Monica; Noya-Alarcón, Óscar; Lander, Orlana; McDonald, Jeremy; Cox, Mike; Walter, Jens; Oh, Phaik Lyn; Ruiz, Jean F; Rodriguez, Selena; Shen, Nan; Song, Se Jin; Metcalf, Jessica; Knight, Rob; Dantas, Gautam; Dominguez-Bello, M Gloria | Science advances. | 2015 Apr 3; | 26229982 | |
| High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae. | Sizova, Maria V; Chilaka, Amanda; Earl, Ashlee M; Doerfert, Sebastian N; Muller, Paul A; Torralba, Manolito; McCorrison, Jamison M; Durkin, A Scott; Nelson, Karen E; Epstein, Slava S | Standards in genomic sciences. | 2015; | 26221418 | |
| Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile. | Schubert, Alyxandria M; Sinani, Hamide; Schloss, Patrick D | mBio. | 2015 Jul 14; | e00974 | 26173701 |
| Role of Autophagy in the Maintenance of Intestinal Homeostasis. | Baxt, Leigh A; Xavier, Ramnik J | Gastroenterology. | 2015 Sep; | 553-62 | 26170139 |
| Compact graphical representation of phylogenetic data and metadata with GraPhlAn. | Asnicar, Francesco; Weingart, George; Tickle, Timothy L; Huttenhower, Curtis; Segata, Nicola | PeerJ. | 2015; | 26157614 | |
| Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. | Nobel, Yael R; Cox, Laura M; Kirigin, Francis F; Bokulich, Nicholas A; Yamanishi, Shingo; Teitler, Isabel; Chung, Jennifer; Sohn, Jiho; Barber, Cecily M; Goldfarb, David S; Raju, Kartik; Abubucker, Sahar; Zhou, Yanjiao; Ruiz, Victoria E; Li, Huilin; Mitreva, Makedonka; Alekseyenko, Alexander V; Weinstock, George M; Sodergren, Erica; Blaser, Martin J | Nature communications. | 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, Nuno | Scientific 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 L | PloS one. | 2015 Jun 25; | e0130604 | 26110908 |
| Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis. | Kang, Dezhi; Shi, Baochen; Erfe, Marie C; Craft, Noah; Li, Huiying | Science translational medicine. | 2015 Jun 24; | 293ra103 | 26109103 |
| Impact of neonatal intensive care bed configuration on rates of late-onset bacterial sepsis and methicillin-resistant Staphylococcus aureus colonization. | Julian, Samuel; Burnham, Carey-Ann D; Sellenriek, Patricia; Shannon, William D; Hamvas, Aaron; Tarr, Phillip I; Warner, Barbara B | Infection control and hospital epidemiology. | 2015 Oct; | 26108888 | |
| Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome. | Chumpitazi, B P; Cope, J L; Hollister, E B; Tsai, C M; McMeans, A R; Luna, R A; Versalovic, J; Shulman, R J | Alimentary pharmacology & therapeutics. | 2015 Aug; | 418-27 | 26104013 |
| Engineering the gut microbiota to treat hyperammonemia. | Shen, Ting-Chin David; Albenberg, Lindsey; Bittinger, Kyle; Chehoud, Christel; Chen, Ying-Yu; Judge, Colleen A; Chau, Lillian; Ni, Josephine; Sheng, Michael; Lin, Andrew; Wilkins, Benjamin J; Buza, Elizabeth L; Lewis, James D; Daikhin, Yevgeny; Nissim, Ilana; Yudkoff, Marc; Bushman, Frederic D; Wu, Gary D | The Journal of clinical investigation. | 2015 Jul 1; | 2841-50 | 26098218 |
| Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease. | Vital, Marius; Harkema, Jack R; Rizzo, Mike; Tiedje, James; Brandenberger, Christina | Journal of immunology research. | 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 D | Inflammatory bowel diseases. | 2015 Aug; | 1948-56 | 26083617 |
| Effects of Vaccination with 10-Valent Pneumococcal Non-Typeable Haemophilus influenza Protein D Conjugate Vaccine (PHiD-CV) on the Nasopharyngeal Microbiome of Kenyan Toddlers. | Feazel, Leah M; Santorico, Stephanie A; Robertson, Charles E; Bashraheil, Mahfudh; Scott, J Anthony G; Frank, Daniel N; Hammitt, Laura L | PloS one. | 2015; | 26083474 | |
| Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9. | Bryson, Alexandra L; Hwang, Young; Sherrill-Mix, Scott; Wu, Gary D; Lewis, James D; Black, Lindsay; Clark, Tyson A; Bushman, Frederic D | mBio. | 2015 June 16; | e00648 | 26081634 |
| Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett's Esophagus Cohort. | Gall, Alevtina; Fero, Jutta; McCoy, Connor; Claywell, Brian C; Sanchez, Carissa A; Blount, Patricia L; Li, Xiaohong; Vaughan, Thomas L; Matsen, Frederick A; Reid, Brian J; Salama, Nina R | PloS one. | 2015 June 15; | e0129055 | 26076489 |
| Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes. | Alkanani, Aimon K; Hara, Naoko; Gottlieb, Peter A; Ir, Diana; Robertson, Charles E; Wagner, Brandie D; Frank, Daniel N; Zipris, Danny | Diabetes. | 2015 Oct; | 3510-20 | 26068542 |
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| Lungs, microbes and the developing neonate. | Warner, Barbara B; Hamvas, Aaron | Neonatology. | 2015 June; | 337-43 | 26044101 |
| Fast disease progression in simian HIV-infected female macaque is accompanied by a robust local inflammatory innate immune and microbial response. | Ren, Wuze; Ma, Yingfei; Yang, Liying; Gettie, Agegnehu; Salas, January; Russell, Kasi; Blanchard, James; Davidow, Amy; Pei, Zhiheng; Chang, Theresa L; Cheng-Mayer, Cecilia | AIDS (London, England). | 2015 Jun 19; | F1-8 | 26035329 |
| Carcass mass has little influence on the structure of gravesoil microbial communities. | Weiss, Sophie; Carter, David O; Metcalf, Jessica L; Knight, Rob | International journal of legal medicine. | 2016 Jan; | 26024793 | |
| Skin-to-Skin Care and the Development of the Preterm Infant Oral Microbiome. | Hendricks-Muñoz, Karen D; Xu, Jie; Parikh, Hardik I; Xu, Ping; Fettweis, Jennifer M; Kim, Yang; Louie, Moi; Buck, Gregory A; Thacker, Leroy R; Sheth, Nihar U | American journal of perinatology. | 2015 Nov; | 26007311 | |
| High-throughput sequencing technologies. | Reuter, Jason A; Spacek, Damek V; Snyder, Michael P | Molecular cell. | 2015 May 21; | 586-97 | 26000844 |
| The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins. | Mehla, Jitender; Dedrick, Rebekah M; Caufield, J Harry; Siefring, Rachel; Mair, Megan; Johnson, Allison; Hatfull, Graham F; Uetz, Peter | Journal of bacteriology. | 2015 Aug 1; | 2508-16 | 25986902 |
| An integrative view of microbiome-host interactions in inflammatory bowel diseases. | Wlodarska, Marta; Kostic, Aleksandar D; Xavier, Ramnik J | Cell host & microbe. | 2015 May 13; | 577-91 | 25974300 |
| Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease. | Lee, Dale; Baldassano, Robert N; Otley, Anthony R; Albenberg, Lindsey; Griffiths, Anne M; Compher, Charlene; Chen, Eric Z; Li, Hongzhe; Gilroy, Erin; Nessel, Lisa; Grant, Amy; Chehoud, Christel; Bushman, Frederic D; Wu, Gary D; Lewis, James D | Inflammatory bowel diseases. | 2015 Aug; | 1786-93 | 25970545 |
| Identifying personal microbiomes using metagenomic codes. | Franzosa, Eric A; Huang, Katherine; Meadow, James F; Gevers, Dirk; Lemon, Katherine P; Bohannan, Brendan J M; Huttenhower, Curtis | Proceedings of the National Academy of Sciences of the United States of America. | 2015 Jun 2; | E2930-8 | 25964341 |
| Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis. | Segal, Leopoldo N; Blaser, Martin J | The Journal of pediatrics. | 2015 Jul; | 16-18.e1 | 25934071 |
| Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. | Franzosa, Eric A; Hsu, Tiffany; Sirota-Madi, Alexandra; Shafquat, Afrah; Abu-Ali, Galeb; Morgan, Xochitl C; Huttenhower, Curtis | Nature reviews. Microbiology. | 2015 Jun; | 360-72 | 25915636 |
| Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. | Leone, Vanessa; Gibbons, Sean M; Martinez, Kristina; Hutchison, Alan L; Huang, Edmond Y; Cham, Candace M; Pierre, Joseph F; Heneghan, Aaron F; Nadimpalli, Anuradha; Hubert, Nathaniel; Zale, Elizabeth; Wang, Yunwei; Huang, Yong; Theriault, Betty; Dinner, Aaron R; Musch, Mark W; Kudsk, Kenneth A; Prendergast, Brian J; Gilbert, Jack A; Chang, Eugene B | Cell host & microbe. | 2015 May 13; | 681-9 | 25891358 |
| Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. | Morgan, Xochitl C; Kabakchiev, Boyko; Waldron, Levi; Tyler, Andrea D; Tickle, Timothy L; Milgrom, Raquel; Stempak, Joanne M; Gevers, Dirk; Xavier, Ramnik J; Silverberg, Mark S; Huttenhower, Curtis | Genome biology. | 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 A | BMC 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, Jiyoung | PloS one. | 2015 Apr 15; | e0124599 | 25874569 |
| Metabolic signatures of bacterial vaginosis. | Srinivasan, Sujatha; Morgan, Martin T; Fiedler, Tina L; Djukovic, Danijel; Hoffman, Noah G; Raftery, Daniel; Marrazzo, Jeanne M; Fredricks, David N | mBio. | 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 Y | Cell. | 2015 Apr 9; | 264-76 | 25860609 |
| New signaling pathways govern the host response to C. albicans infection in various niches. | Liu, Yaoping; Shetty, Amol C; Schwartz, Jennifer A; Bradford, L Latey; Xu, Wenjie; Phan, Qyunh T; Kumari, Priti; Mahurkar, Anup; Mitchell, Aaron P; Ravel, Jacques; Fraser, Claire M; Filler, Scott G; Bruno, Vincent M | Genome research. | 2015 May; | 679-89 | 25858952 |
| Serial fecal microbiota transplantation alters mucosal gene expression in pediatric ulcerative colitis. | Kellermayer, Richard; Nagy-Szakal, Dorottya; Harris, R Alan; Luna, Ruth Ann; Pitashny, Milena; Schady, Deborah; Mir, Sabina A V; Lopez, Monica E; Gilger, Mark A; Belmont, John; Hollister, Emily B; Versalovic, James | The American journal of gastroenterology. | 2015 Apr; | 25853207 | |
| The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin. | Liu, Jared; Yan, Riceley; Zhong, Qiao; Ngo, Sam; Bangayan, Nathanael J; Nguyen, Lin; Lui, Timothy; Liu, Minghsun; Erfe, Marie C; Craft, Noah; Tomida, Shuta; Li, Huiying | The ISME journal. | 2015 Sep; | 2078-93 | 25848871 |
| Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. | Kelly, Brendan J; Gross, Robert; Bittinger, Kyle; Sherrill-Mix, Scott; Lewis, James D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe | Bioinformatics (Oxford, England). | 2015 Aug 01; | 25819674 | |
| Sinus microbiota varies among chronic rhinosinusitis phenotypes and predicts surgical outcome. | Ramakrishnan, Vijay R; Hauser, Leah J; Feazel, Leah M; Ir, Diana; Robertson, Charles E; Frank, Daniel N | The Journal of allergy and clinical immunology. | 2015 Aug; | 25819063 | |
| Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis. | Hoen, Anne G; Li, Jing; Moulton, Lisa A; O'Toole, George A; Housman, Molly L; Koestler, Devin C; Guill, Margaret F; Moore, Jason H; Hibberd, Patricia L; Morrison, Hilary G; Sogin, Mitchell L; Karagas, Margaret R; Madan, Juliette C | The Journal of pediatrics. | 2015 Jul; | 138-47.e1-3 | 25818499 |
| Subsistence strategies in traditional societies distinguish gut microbiomes. | Obregon-Tito, Alexandra J; Tito, Raul Y; Metcalf, Jessica; Sankaranarayanan, Krithivasan; Clemente, Jose C; Ursell, Luke K; Zech Xu, Zhenjiang; Van Treuren, Will; Knight, Rob; Gaffney, Patrick M; Spicer, Paul; Lawson, Paul; Marin-Reyes, Luis; Trujillo-Villarroel, Omar; Foster, Morris; Guija-Poma, Emilio; Troncoso-Corzo, Luzmila; Warinner, Christina; Ozga, Andrew T; Lewis, Cecil M | Nature communications. | 2015 Mar 25; | 25807110 | |
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| Optimized Analytical Procedures for the Untargeted Metabolomic Profiling of Human Urine and Plasma by Combining Hydrophilic Interaction (HILIC) and Reverse-Phase Liquid Chromatography (RPLC)-Mass Spectrometry. | Contrepois, Kévin; Jiang, Lihua; Snyder, Michael | Molecular & cellular proteomics : MCP. | 2015 Jun; | 1684-95 | 25787789 |
| Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study. | Zhou, Yanjiao; Shan, Gururaj; Sodergren, Erica; Weinstock, George; Walker, W Allan; Gregory, Katherine E | PloS one. | 2015 Mar 5; | e0118632 | 25741698 |
| Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases. | Huang, Edmond Y; Inoue, Takuya; Leone, Vanessa A; Dalal, Sushila; Touw, Ketrija; Wang, Yunwei; Musch, Mark W; Theriault, Betty; Higuchi, Kazuhide; Donovan, Sharon; Gilbert, Jack; Chang, Eugene B | Inflammatory bowel diseases. | 2015 May; | 963-72 | 25738379 |
| Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. | Yasuda, Koji; Oh, Keunyoung; Ren, Boyu; Tickle, Timothy L; Franzosa, Eric A; Wachtman, Lynn M; Miller, Andrew D; Westmoreland, Susan V; Mansfield, Keith G; Vallender, Eric J; Miller, Gregory M; Rowlett, James K; Gevers, Dirk; Huttenhower, Curtis; Morgan, Xochitl C | Cell host & microbe. | 2015 Mar 11; | 385-91 | 25732063 |
| A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification. | Bigdeli, Saharnaz; Dettloff, Roger O; Frank, Curtis W; Davis, Ronald W; Crosby, Laurel D | PloS one. | 2015 Feb 17; | e0117738 | 25689864 |
| Mitochondrial DNA sequence variation is largely conserved at birth with rare de novo mutations in neonates. | Ma, Jun; Purcell, Heidi; Showalter, Lori; Aagaard, Kjersti M | American journal of obstetrics and gynecology. | 2015 Apr; | 530.e1-8 | 25687567 |
| A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2. | Didion, John P; Morgan, Andrew P; Clayshulte, Amelia M-F; Mcmullan, Rachel C; Yadgary, Liran; Petkov, Petko M; Bell, Timothy A; Gatti, Daniel M; Crowley, James J; Hua, Kunjie; Aylor, David L; Bai, Ling; Calaway, Mark; Chesler, Elissa J; French, John E; Geiger, Thomas R; Gooch, Terry J; Garland Jr, Theodore; Harrill, Alison H; Hunter, Kent; McMillan, Leonard; Holt, Matt; Miller, Darla R; O'Brien, Deborah A; Paigen, Kenneth; Pan, Wenqi; Rowe, Lucy B; Shaw, Ginger D; Simecek, Petr; Sullivan, Patrick F; Svenson, Karen L; Weinstock, George M; Threadgill, David W; Pomp, Daniel; Churchill, Gary A; Pardo-Manuel de Villena, Fernando | PLoS genetics. | 2015 Feb; | e1004850 | 25679959 |
| Impact of allele-specific peptides in proteome quantification. | Wu, Linfeng; Snyder, Michael | Proteomics. Clinical applications. | 2015 Apr; | 432-6 | 25676416 |
| The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. | Kostic, Aleksandar D; Gevers, Dirk; Siljander, Heli; Vatanen, Tommi; Hyötyläinen, Tuulia; Hämäläinen, Anu-Maaria; Peet, Aleksandr; Tillmann, Vallo; Pöhö, Päivi; Mattila, Ismo; Lähdesmäki, Harri; Franzosa, Eric A; Vaarala, Outi; de Goffau, Marcus; Harmsen, Hermie; Ilonen, Jorma; Virtanen, Suvi M; Clish, Clary B; Ore?i?, Matej; Huttenhower, Curtis; Knip, Mikael; DIABIMMUNE Study Group; Xavier, Ramnik J | Cell host & microbe. | 2015 Feb 11; | 260-73 | 25662751 |
| Identification of a gene in Mycoplasma hominis associated with preterm birth and microbial burden in intraamniotic infection. | Allen-Daniels, Matthew Josiah; Serrano, Myrna G; Pflugner, Lindsey P; Fettweis, Jennifer M; Prestosa, Melissa A; Koparde, Vishal N; Brooks, J Paul; Strauss 3rd, Jerome F; Romero, Roberto; Chaiworapongsa, Tinnakorn; Eschenbach, David A; Buck, Gregory A; Jefferson, Kimberly K | American journal of obstetrics and gynecology. | 2015 Jun; | 779.e1-779.e13 | 25637842 |
| Disease-specific alterations in the enteric virome in inflammatory bowel disease. | Norman, Jason M; Handley, Scott A; Baldridge, Megan T; Droit, Lindsay; Liu, Catherine Y; Keller, Brian C; Kambal, Amal; Monaco, Cynthia L; Zhao, Guoyan; Fleshner, Phillip; Stappenbeck, Thaddeus S; McGovern, Dermot P B; Keshavarzian, Ali; Mutlu, Ece A; Sauk, Jenny; Gevers, Dirk; Xavier, Ramnik J; Wang, David; Parkes, Miles; Virgin, Herbert W | Cell. | 2015 Jan 29; | 447-60 | 25619688 |
| De novo large cell neuroendocrine carcinoma of the prostate, case report and literature review. | Acosta-Gonzalez, Gabriel; Qin, Jia; Wieczorek, Rosemary; Melamed, Jonathan; Deng, Fang-Ming; Zhou, Ming; Makarov, Danil; Ye, Fei; Pei, Zhiheng; Pincus, Matthew R; Lee, Peng | American journal of clinical and experimental urology. | 2014; | 25606580 | |
| Diet in the pathogenesis and treatment of inflammatory bowel diseases. | Lee, Dale; Albenberg, Lindsey; Compher, Charlene; Baldassano, Robert; Piccoli, David; Lewis, James D; Wu, Gary D | Gastroenterology. | 2015 May; | 1087-106 | 25597840 |
| Asynchronous Magnetic Bead Rotation (AMBR) Microviscometer for Label-Free DNA Analysis. | Li, Yunzi; Burke, David T; Kopelman, Raoul; Burns, Mark A | Biosensors | 2014 Mar | 25587411 | |
| Complex host genetics influence the microbiome in inflammatory bowel disease. | Knights, Dan; Silverberg, Mark S; Weersma, Rinse K; Gevers, Dirk; Dijkstra, Gerard; Huang, Hailiang; Tyler, Andrea D; van Sommeren, Suzanne; Imhann, Floris; Stempak, Joanne M; Huang, Hu; Vangay, Pajau; Al-Ghalith, Gabriel A; Russell, Caitlin; Sauk, Jenny; Knight, Jo; Daly, Mark J; Huttenhower, Curtis; Xavier, Ramnik J | Genome medicine. | 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 J | The Journal of infectious diseases. | 2015 Jun 15; | 1895-904 | 25583170 |
| A RESTful API for accessing microbial community data for MG-RAST. | Wilke, Andreas; Bischof, Jared; Harrison, Travis; Brettin, Tom; D'Souza, Mark; Gerlach, Wolfgang; Matthews, Hunter; Paczian, Tobias; Wilkening, Jared; Glass, Elizabeth M; Desai, Narayan; Meyer, Folker | PLoS computational biology. | 2015 Jan; | e1004008 | 25569221 |
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| The preterm placental microbiome varies in association with excess maternal gestational weight gain. | Antony, Kathleen M; Ma, Jun; Mitchell, Kristen B; Racusin, Diana A; Versalovic, James; Aagaard, Kjersti | American journal of obstetrics and gynecology. | 2015 May; | 653.e1-16 | 25557210 |
| The EHEC-host interactome reveals novel targets for the translocated intimin receptor. | Blasche, Sonja; Arens, Stefan; Ceol, Arnaud; Siszler, Gabriella; Schmidt, M Alexander; Hauser, Roman; Schwarz, Frank; Wuchty, Stefan; Aloy, Patrick; Uetz, Peter; Stradal, Theresia; Koegl, Manfred | Scientific reports. | 2014; | 25519916 | |
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| The conjunctival microbiome in health and trachomatous disease: a case control study. | Zhou, Yanjiao; Holland, Martin J; Makalo, Pateh; Joof, Hassan; Roberts, Chrissy H; Mabey, David Cw; Bailey, Robin L; Burton, Matthew J; Weinstock, George M; Burr, Sarah E | Genome medicine | 2014 | 25484919 | |
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| The changing landscape of the vaginal microbiome. | Huang, Bernice; Fettweis, Jennifer M; Brooks, J Paul; Jefferson, Kimberly K; Buck, Gregory A | Clinics in laboratory medicine. | 2014 Dec; | 747-61 | 25439274 |
| Microbiome, innate immunity, and esophageal adenocarcinoma. | Baghdadi, Jonathan; Chaudhary, Noami; Pei, Zhiheng; Yang, Liying | Clinics in laboratory medicine. | 2014 Dec; | 721-32 | 25439272 |
| The interrelationships of the gut microbiome and inflammation in colorectal carcinogenesis. | Cho, Margaret; Carter, Janell; Harari, Saul; Pei, Zhiheng | Clinics in laboratory medicine. | 2014 Dec; | 699-710 | 25439270 |
| Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. | Wu, Gary D; Compher, Charlene; Chen, Eric Z; Smith, Sarah A; Shah, Rachana D; Bittinger, Kyle; Chehoud, Christel; Albenberg, Lindsey G; Nessel, Lisa; Gilroy, Erin; Star, Julie; Weljie, Aalim M; Flint, Harry J; Metz, David C; Bennett, Michael J; Li, Hongzhe; Bushman, Frederic D; Lewis, James D | Gut. | 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 A | BMC bioinformatics. | 2014; | 25407910 | |
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| Spec-seq: determining protein-DNA-binding specificity by sequencing. | Stormo, Gary D; Zuo, Zheng; Chang, Yiming Kenny | Briefings in functional genomics. | 2015 Jan; | 30-8 | 25362070 |
| Intra- and interindividual variations mask interspecies variation in the microbiota of sympatric peromyscus populations. | Baxter, Nielson T; Wan, Judy J; Schubert, Alyxandria M; Jenior, Matthew L; Myers, Philip; Schloss, Patrick D | Applied and environmental microbiology. | 2015 Jan; | 396-404 | 25362056 |
| High-resolution genetic mapping in the diversity outbred mouse population identifies Apobec1 as a candidate gene for atherosclerosis. | Smallwood, Tangi L; Gatti, Daniel M; Quizon, Pamela; Weinstock, George M; Jung, Kuo-Chen; Zhao, Liyang; Hua, Kunjie; Pomp, Daniel; Bennett, Brian J | G3 (Bethesda, Md.). | 2014 Dec; | 2353-63 | 25344410 |
| Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia. | Vital, Marius; Gao, Jiarong; Rizzo, Mike; Harrison, Tara; Tiedje, James M | The ISME journal. | 2015 Apr; | 832-43 | 25343515 |
| Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification. | Vital, Marius; Chai, Benli; Ostman, Bjorn; Cole, James; Konstantinidis, Konstantinos T; Tiedje, James M | The ISME journal. | 2015 May; | 1130-40 | 25343512 |
| An emerging mycoplasma associated with trichomoniasis, vaginal infection and disease. | Fettweis, Jennifer M; Serrano, Myrna G; Huang, Bernice; Brooks, J Paul; Glascock, Abigail L; Sheth, Nihar U; Vaginal Microbiome Consortium; Strauss 3rd, Jerome F; Jefferson, Kimberly K; Buck, Gregory A | PloS one. | 2014; | e110943 | 25337710 |
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| Microbiology: An integrated view of the skin microbiome. | Schloss, Patrick D | Nature | 2014 Oct 02 | 25279916 | |
| Sinus culture poorly predicts resident microbiota. | Hauser, Leah J; Feazel, Leah M; Ir, Diana; Fang, Rui; Wagner, Brandie D; Robertson, Charles E; Frank, Daniel N; Ramakrishnan, Vijay R | International forum of allergy & rhinology. | 2015 Jan; | 25278448 | |
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| An effective intervention to reduce intravaginal practices among HIV-1 uninfected Kenyan women. | Sivapalasingam, Sumathi; McClelland, R Scott; Ravel, Jacques; Ahmed, Aabid; Cleland, Charles M; Gajer, Pawel; Mwamzaka, Musa; Marshed, Fatma; Shafi, Juma; Masese, Linnet; Fajans, Mark; Anderson, Molly E; Jaoko, Walter; Kurth, Ann E | AIDS research and human retroviruses. | 2014 Nov; | 1046-54 | 25265254 |
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| Mini-review: perspective of the microbiome in the pathogenesis of urothelial carcinoma. | Xu, Weisheng; Yang, Liying; Lee, Peng; Huang, William C; Nossa, Carlos; Ma, Yingfei; Deng, Fang-Ming; Zhou, Ming; Melamed, Jonathan; Pei, Zhiheng | American journal of clinical and experimental urology | 2014 Apr 15 | 57-61 | 25126590 |
| Patterned progression of bacterial populations in the premature infant gut. | La Rosa, Patricio S; Warner, Barbara B; Zhou, Yanjiao; Weinstock, George M; Sodergren, Erica; Hall-Moore, Carla M; Stevens, Harold J; Bennett Jr, William E; Shaikh, Nurmohammad; Linneman, Laura A; Hoffmann, Julie A; Hamvas, Aaron; Deych, Elena; Shands, Berkley A; Shannon, William D; Tarr, Phillip I | Proceedings of the National Academy of Sciences of the United States of America. | 2014 Aug 26; | 12522-7 | 25114261 |
| Oral microbiota and host innate immune response in bisphosphonate-related osteonecrosis of the jaw. | Pushalkar, Smruti; Li, Xin; Kurago, Zoya; Ramanathapuram, Lalitha V; Matsumura, Satoko; Fleisher, Kenneth E; Glickman, Robert; Yan, Wenbo; Li, Yihong; Saxena, Deepak | International journal of oral science. | 2014 Dec; | 25105817 | |
| The Human Gut Microbiome as a Screening Tool for Colorectal Cancer. | Zackular, Joseph P; Rogers, Mary A M; Ruffin 4th, Mack T; Schloss, Patrick D | Cancer prevention research (Philadelphia, Pa.) | 2014 Aug 7 | NULL | 25104642 |
| Phylogenetics and the human microbiome. | Matsen 4th, Frederick A | Systematic biology. | 2015 Jan; | e26-41 | 25102857 |
| Phase variation of poly-N-acetylglucosamine expression in Staphylococcus aureus. | Brooks, Jamie L; Jefferson, Kimberly K | PLoS pathogens. | 2014 Jul; | e1004292 | 25077798 |
| 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 29 | NULL | 25073854 |
| The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention. | Hampton, Thomas H; Green, Deanna M; Cutting, Garry R; Morrison, Hilary G; Sogin, Mitchell L; Gifford, Alex H; Stanton, Bruce A; O'Toole, George A | Microbiome | 2014 | 14 | 25071935 |
| The dynamics of a family's gut microbiota reveal variations on a theme. | Schloss, Patrick D; Iverson, Kathryn D; Petrosino, Joseph F; Schloss, Sarah J | Microbiome. | 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 D | Gastroenterology. | 2014 Nov; | 1055-63.e8 | 25046162 |
| Conducting a microbiome study. | Goodrich, Julia K; Di Rienzi, Sara C; Poole, Angela C; Koren, Omry; Walters, William A; Caporaso, J Gregory; Knight, Rob; Ley, Ruth E | Cell. | 2014 Jul 17; | 25036628 | |
| Serum profiling using protein microarrays to identify disease related antigens. | Sharon, Donald; Snyder, Michael | Methods in molecular biology (Clifton, N.J.). | 2014; | 169-78 | 25030927 |
| Microfluidic molecular assay platform for the detection of miRNAs, mRNAs, proteins, and posttranslational modifications at single-cell resolution. | Wu, Meiye; Singh, Anup K | Journal of laboratory automation. | 2014 Dec; | 587-92 | 25027027 |
| Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays. | VanDussen, Kelli L; Marinshaw, Jeffrey M; Shaikh, Nurmohammad; Miyoshi, Hiroyuki; Moon, Clara; Tarr, Phillip I; Ciorba, Matthew A; Stappenbeck, Thaddeus S | Gut. | 2015 Jun; | 911-20 | 25007816 |
| Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt. | Lee, Soo Chan; Billmyre, R Blake; Li, Alicia; Carson, Sandra; Sykes, Sean M; Huh, Eun Young; Mieczkowski, Piotr; Ko, Dennis C; Cuomo, Christina A; Heitman, Joseph | mBio | 2014 | e01390-14 | 25006230 |
| Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. | Haberman, Yael; Tickle, Timothy L; Dexheimer, Phillip J; Kim, Mi-Ok; Tang, Dora; Karns, Rebekah; Baldassano, Robert N; Noe, Joshua D; Rosh, Joel; Markowitz, James; Heyman, Melvin B; Griffiths, Anne M; Crandall, Wallace V; Mack, David R; Baker, Susan S; Huttenhower, Curtis; Keljo, David J; Hyams, Jeffrey S; Kugathasan, Subra; Walters, Thomas D; Aronow, Bruce; Xavier, Ramnik J; Gevers, Dirk; Denson, Lee A | The Journal of clinical investigation. | 2014 Aug; | 3617-33 | 25003194 |
| Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. | Pop, Mihai; Walker, Alan W; Paulson, Joseph; Lindsay, Brianna; Antonio, Martin; Hossain, M Anowar; Oundo, Joseph; Tamboura, Boubou; Mai, Volker; Astrovskaya, Irina; Corrada Bravo, Hector; Rance, Richard; Stares, Mark; Levine, Myron M; Panchalingam, Sandra | Genome biology | 2014 | R76 | 24995464 |
| Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. | Parfrey, Laura Wegener; Walters, William A; Lauber, Christian L; Clemente, Jose C; Berg-Lyons, Donna; Teiling, Clotilde; Kodira, Chinnappa; Mohiuddin, Mohammed; Brunelle, Julie; Driscoll, Mark; Fierer, Noah; Gilbert, Jack A; Knight, Rob | Frontiers in microbiology. | 2014; | 24995004 | |
| Lactobacillus rhamnosus L34 and Lactobacillus casei L39 suppress Clostridium difficile-induced IL-8 production by colonic epithelial cells. | Boonma, Prapaporn; Spinler, Jennifer K; Venable, Susan F; Versalovic, James; Tumwasorn, Somying | BMC microbiology | 2014 | 177 | 24989059 |
| Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa. | Ma, Liang; Kim, Jungwoo; Hatzenpichler, Roland; Karymov, Mikhail A; Hubert, Nathaniel; Hanan, Ira M; Chang, Eugene B; Ismagilov, Rustem F | Proceedings of the National Academy of Sciences of the United States of America | 2014 Jul 8 | 9768-73 | 24965364 |
| Oligotyping analysis of the human oral microbiome. | Eren, A Murat; Borisy, Gary G; Huse, Susan M; Mark Welch, Jessica L | Proceedings of the National Academy of Sciences of the United States of America | 2014 Jul 15 | E2875-84 | 24965363 |
| Defining a personal, allele-specific, and single-molecule long-read transcriptome. | Tilgner, Hagen; Grubert, Fabian; Sharon, Donald; Snyder, Michael P | Proceedings of the National Academy of Sciences of the United States of America. | 2014 Jul 8; | 9869-74 | 24961374 |
| Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips. | Ma, Liang; Datta, Sujit S; Karymov, Mikhail A; Pan, Qichao; Begolo, Stefano; Ismagilov, Rustem F | Integrative biology : quantitative biosciences from nano to macro | 2014 Jun 23 | NULL | 24953827 |
| From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions. | Spinler, Jennifer K; Sontakke, Amrita; Hollister, Emily B; Venable, Susan F; Oh, Phaik Lyn; Balderas, Miriam A; Saulnier, Delphine M A; Mistretta, Toni-Ann; Devaraj, Sridevi; Walter, Jens; Versalovic, James; Highlander, Sarah K | Genome biology and evolution | 2014 Jul | 1772-89 | 24951561 |
| Inflammatory bowel disease as a model for translating the microbiome. | Huttenhower, Curtis; Kostic, Aleksandar D; Xavier, Ramnik J | Immunity | 2014 Jun 19 | 843-54 | 24950204 |
| Finding the missing links among metabolites, microbes, and the host. | Dorrestein, Pieter C; Mazmanian, Sarkis K; Knight, Rob | Immunity. | 2014 Jun 19; | 824-32 | 24950202 |
| Interplay between the temporal dynamics of the vaginal microbiota and human papillomavirus detection. | Brotman, Rebecca M; Shardell, Michelle D; Gajer, Pawel; Tracy, J Kathleen; Zenilman, Jonathan M; Ravel, Jacques; Gravitt, Patti E | The Journal of infectious diseases. | 2014 Dec 1; | 1723-33 | 24943724 |
| Evidence of extensive DNA transfer between bacteroidales species within the human gut. | Coyne, Michael J; Zitomersky, Naamah Levy; McGuire, Abigail Manson; Earl, Ashlee M; Comstock, Laurie E | mBio | 2014 | e01305-14 | 24939888 |
| CcpA is important for growth and virulence of Enterococcus faecium. | Somarajan, Sudha R; Roh, Jung H; Singh, Kavindra V; Weinstock, George M; Murray, Barbara E | Infection and immunity. | 2014 Sep; | 3580-7 | 24914215 |
| Exploration of bacterial community classes in major human habitats. | Zhou, Yanjiao; Mihindukulasuriya, Kathie A; Gao, Hongyu; La Rosa, Patricio S; Wylie, Kristine M; Martin, John C; Kota, Karthik; Shannon, William D; Mitreva, Makedonka; Sodergren, Erica; Weinstock, George M | Genome biology | 2014 | R66 | 24887286 |
| BOTUX: bayesian-like operational taxonomic unit examiner. | Koparde, Vishal N; Adkins, Ricky S; Fettweis, Jennifer M; Serrano, Myrna G; Buck, Gregory A A; Reimers, Mark A; Sheth, Nihar U | International journal of computational biology and drug design. | 2014; | 130-45 | 24878725 |
| Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251). | Cuomo, Christina A; Rodriguez-Del Valle, Nuri; Perez-Sanchez, Lizaida; Abouelleil, Amr; Goldberg, Jonathan; Young, Sarah; Zeng, Qiandong; Birren, Bruce W | Genome announcements. | 2014; | 24855299 | |
| Microbiome in reflux disorders and esophageal adenocarcinoma. | Yang, Liying; Chaudhary, Noami; Baghdadi, Jonathan; Pei, Zhiheng | Cancer journal (Sudbury, Mass.) | 2014 May-Jun | 207-10 | 24855009 |
| The placenta harbors a unique microbiome. | Aagaard, Kjersti; Ma, Jun; Antony, Kathleen M; Ganu, Radhika; Petrosino, Joseph; Versalovic, James | Science translational medicine | 2014 May 21 | 237ra65 | 24848255 |
| Relating the metatranscriptome and metagenome of the human gut. | Franzosa, Eric A; Morgan, Xochitl C; Segata, Nicola; Waldron, Levi; Reyes, Joshua; Earl, Ashlee M; Giannoukos, Georgia; Boylan, Matthew R; Ciulla, Dawn; Gevers, Dirk; Izard, Jacques; Garrett, Wendy S; Chan, Andrew T; Huttenhower, Curtis | Proceedings of the National Academy of Sciences of the United States of America | 2014 Jun 3 | E2329-38 | 24843156 |
| The prevalence of species and strains in the human microbiome: a resource for experimental efforts. | Kraal, Laurens; Abubucker, Sahar; Kota, Karthik; Fischbach, Michael A; Mitreva, Makedonka | PloS one | 2014 | e97279 | 24827833 |
| Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium. | Sizova, Maria V; Muller, Paul A; Stancyk, David; Panikov, Nicolai S; Mandalakis, Manolis; Hazen, Amanda; Hohmann, Tine; Doerfert, Sebastian N; Fowle, William; Earl, Ashlee M; Nelson, Karen E; Epstein, Slava S | International journal of systematic and evolutionary microbiology. | 2014 Aug; | 2642-9 | 24824639 |
| Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. | Schubert, Alyxandria M; Rogers, Mary A M; Ring, Cathrin; Mogle, Jill; Petrosino, Joseph P; Young, Vincent B; Aronoff, David M; Schloss, Patrick D | mBio | 2014 | e01021-14 | 24803517 |
| Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism. | Tong, Maomeng; McHardy, Ian; Ruegger, Paul; Goudarzi, Maryam; Kashyap, Purna C; Haritunians, Talin; Li, Xiaoxiao; Graeber, Thomas G; Schwager, Emma; Huttenhower, Curtis; Fornace Jr, Albert J; Sonnenburg, Justin L; McGovern, Dermot Pb; Borneman, James; Bra | The ISME journal | 2014 Apr 29 | NULL | 24781901 |
| Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. | Vital, Marius; Howe, Adina Chuang; Tiedje, James M | mBio | 2014 | e00889 | 24757212 |
| Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. | Swan, Brandon K; Chaffin, Mark D; Martinez-Garcia, Manuel; Morrison, Hilary G; Field, Erin K; Poulton, Nicole J; Masland, E Dashiell P; Harris, Christopher C; Sczyrba, Alexander; Chain, Patrick S G; Koren, Sergey; Woyke, Tanja; Stepanauskas, Ramunas | PloS one | 2014 | e95380 | 24743558 |
| Dynamics and associations of microbial community types across the human body. | Ding, Tao; Schloss, Patrick D | Nature | 2014 May 15 | 357-60 | 24739969 |
| Transferable vancomycin resistance in a community-associated MRSA lineage. | Rossi, Flavia; Diaz, Lorena; Wollam, Aye; Panesso, Diana; Zhou, Yanjiao; Rincon, Sandra; Narechania, Apurva; Xing, Galen; Di Gioia, Thais S R; Doi, Andre; Tran, Truc T; Reyes, Jinnethe; Munita, Jose M; Carvajal, Lina P; Hernandez-Roldan, Alejandra; Branda | The New England journal of medicine | 2014 Apr 17 | 1524-31 | 24738669 |
| Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. | Campbell, Alisha G; Schwientek, Patrick; Vishnivetskaya, Tatiana; Woyke, Tanja; Levy, Shawn; Beall, Clifford J; Griffen, Ann; Leys, Eugene; Podar, Mircea | Environmental microbiology | 2014 Apr 17 | NULL | 24738594 |
| Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis. | Hyde, Embriette R; Andrade, Fernando; Vaksman, Zalman; Parthasarathy, Kavitha; Jiang, Hong; Parthasarathy, Deepa K; Torregrossa, Ashley C; Tribble, Gena; Kaplan, Heidi B; Petrosino, Joseph F; Bryan, Nathan S | PloS one | 2014 | e88645 | 24670812 |
| Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. | Carl, Mike A; Ndao, I Malick; Springman, A Cody; Manning, Shannon D; Johnson, James R; Johnston, Brian D; Burnham, Carey-Ann D; Weinstock, Erica Sodergren; Weinstock, George M; Wylie, Todd N; Mitreva, Makedonka; Abubucker, Sahar; Zhou, Yanjiao; Stevens, H | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 2014 May | 1211-8 | 24647013 |
| Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome. | Chumpitazi, Bruno P; Hollister, Emily B; Oezguen, Numan; Tsai, Cynthia M; McMeans, Ann R; Luna, Ruth A; Savidge, Tor C; Versalovic, James; Shulman, Robert J | Gut microbes | 2014 Mar-Apr | 165-75 | 24637601 |
| The treatment-naive microbiome in new-onset Crohn's disease. | Gevers, Dirk; Kugathasan, Subra; Denson, Lee A; Vazquez-Baeza, Yoshiki; Van Treuren, Will; Ren, Boyu; Schwager, Emma; Knights, Dan; Song, Se Jin; Yassour, Moran; Morgan, Xochitl C; Kostic, Aleksandar D; Luo, Chengwei; Gonzalez, Antonio; McDonald, Daniel; | Cell host & microbe | 2014 Mar 12 | 382-92 | 24629344 |
| Functional and phylogenetic assembly of microbial communities in the human microbiome. | Shafquat, Afrah; Joice, Regina; Simmons, Sheri L; Huttenhower, Curtis | Trends in microbiology | 2014 Mar 4 | NULL | 24618403 |
| Immune and genetic gardening of the intestinal microbiome. | Jacobs, Jonathan P; Braun, Jonathan | FEBS letters | 2014 Mar 5 | NULL | 24613921 |
| History and impact of RDP: a legacy from Carl Woese to microbiology. | Cole, James R; Tiedje, James M | RNA biology | 2014 Mar | 239-43 | 24607969 |
| Pathogens and host immunity in the ancient human oral cavity. | Warinner, Christina; Rodrigues, Joao F Matias; Vyas, Rounak; Trachsel, Christian; Shved, Natallia; Grossmann, Jonas; Radini, Anita; Hancock, Y; Tito, Raul Y; Fiddyment, Sarah; Speller, Camilla; Hendy, Jessica; Charlton, Sophy; Luder, Hans Ulrich; Salazar- | Nature genetics | 2014 Apr | 336-44 | 24562188 |
| Whole-genome haplotyping using long reads and statistical methods. | Kuleshov, Volodymyr; Xie, Dan; Chen, Rui; Pushkarev, Dmitry; Ma, Zhihai; Blauwkamp, Tim; Kertesz, Michael; Snyder, Michael | Nature biotechnology | 2014 Mar | 261-6 | 24561555 |
| The microbiome in inflammatory bowel disease: current status and the future ahead. | Kostic, Aleksandar D; Xavier, Ramnik J; Gevers, Dirk | Gastroenterology | 2014 May | 1489-99 | 24560869 |
| An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. | Fadrosh, Douglas W; Ma, Bing; Gajer, Pawel; Sengamalay, Naomi; Ott, Sandra; Brotman, Rebecca M; Ravel, Jacques | Microbiome. | 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 J | PloS one | 2014 | e89398 | 24551246 |
| Early Empiric Antibiotic Use in Preterm Infants Is Associated with Lower Bacterial Diversity and Higher Relative Abundance of Enterobacter. | Greenwood, Corryn; Morrow, Ardythe L; Lagomarcino, Anne J; Altaye, Mekibib; Taft, Diana H; Yu, Zhuoteng; Newburg, David S; Ward, Doyle V; Schibler, Kurt R | The Journal of pediatrics | 2014 Feb 13 | NULL | 24529620 |
| Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects. | Huse, Susan M; Young, Vincent B; Morrison, Hilary G; Antonopoulos, Dionysios A; Kwon, John; Dalal, Sushila; Arrieta, Rose; Hubert, Nathaniel A; Shen, Lici; Vineis, Joseph H; Koval, Jason C; Sogin, Mitchell L; Chang, Eugene B; Raffals, Laura E | Microbiome | 2014 | 5 | 24529162 |
| Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets. | Ma, Yingfei; Madupu, Ramana; Karaoz, Ulas; Nossa, Carlos W; Yang, Liying; Yooseph, Shibu; Yachimski, Patrick S; Brodie, Eoin L; Nelson, Karen E; Pei, Zhiheng | Journal of virology | 2014 May | 4786-97 | 24522917 |
| Diet and the intestinal microbiome: associations, functions, and implications for health and disease. | Albenberg, Lindsey G; Wu, Gary D | Gastroenterology | 2014 May | 1564-72 | 24503132 |
| Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. | Rooks, Michelle G; Veiga, Patrick; Wardwell-Scott, Leslie H; Tickle, Timothy; Segata, Nicola; Michaud, Monia; Gallini, Carey Ann; Beal, Chloe; van Hylckama-Vlieg, Johan E T; Ballal, Sonia A; Morgan, Xochitl C; Glickman, Jonathan N; Gevers, Dirk; Huttenhow | The ISME journal | 2014 Jul | 1403-17 | 24500617 |
| Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen. | Chen, Zehua; Martinez, Diego A; Gujja, Sharvari; Sykes, Sean M; Zeng, Qiandong; Szaniszlo, Paul J; Wang, Zheng; Cuomo, Christina A | G3 (Bethesda, Md.) | 2014 Apr | 561-78 | 24496724 |
| Identification of a proton-chloride antiporter (EriC) by Himar1 transposon mutagenesis in Lactobacillus reuteri and its role in histamine production. | Hemarajata, P; Spinler, J K; Balderas, M A; Versalovic, J | Antonie van Leeuwenhoek | 2014 Mar | 579-92 | 24488273 |
| Meta'omic analytic techniques for studying the intestinal microbiome. | Morgan, Xochitl C; Huttenhower, Curtis | Gastroenterology | 2014 May | 1437-1448.e1 | 24486053 |
| Compositional and functional features of the gastrointestinal microbiome and their effects on human health. | Hollister, Emily B; Gao, Chunxu; Versalovic, James | Gastroenterology | 2014 May | 1449-58 | 24486050 |
| Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. | Young, Vincent B; Raffals, Laura H; Huse, Susan M; Vital, Marius; Dai, Dongjuan; Schloss, Patrick D; Brulc, Jennifer M; Antonopoulos, Dionysios A; Arrieta, Rose L; Kwon, John H; Reddy, K Gautham; Hubert, Nathaniel A; Grim, Sharon L; Vineis, Joseph H; Dala | Microbiome | 2013 | 9 | 24451366 |
| A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. | Vital, Marius; Penton, Christopher R; Wang, Qiong; Young, Vincent B; Antonopoulos, Dion A; Sogin, Mitchell L; Morrison, Hilary G; Raffals, Laura; Chang, Eugene B; Huffnagle, Gary B; Schmidt, Thomas M; Cole, James R; Tiedje, James M | Microbiome | 2013 | 8 | 24451334 |
| Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. | Mason, Olivia U; Scott, Nicole M; Gonzalez, Antonio; Robbins-Pianka, Adam; Baelum, Jacob; Kimbrel, Jeffrey; Bouskill, Nicholas J; Prestat, Emmanuel; Borglin, Sharon; Joyner, Dominique C; Fortney, Julian L; Jurelevicius, Diogo; Stringfellow, William T; Alv | The ISME journal | 2014 Jan 23 | NULL | 24451203 |
| Daily temporal dynamics of vaginal microbiota before, during and after episodes of bacterial vaginosis. | Ravel, Jacques; Brotman, Rebecca M; Gajer, Pawel; Ma, Bing; Nandy, Melissa; Fadrosh, Douglas W; Sakamoto, Joyce; Koenig, Sara Sk; Fu, Li; Zhou, Xia; Hickey, Roxana J; Schwebke, Jane R; Forney, Larry J | Microbiome | 2013 | 29 | 24451163 |
| Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation. | Price, Katherine E; Hampton, Thomas H; Gifford, Alex H; Dolben, Emily L; Hogan, Deborah A; Morrison, Hilary G; Sogin, Mitchell L; O'Toole, George A | Microbiome | 2013 | 27 | 24451123 |
| A brave new world: the lung microbiota in an era of change. | Segal, Leopoldo N; Blaser, Martin J | Annals of the American Thoracic Society | 2014 Jan | S21-7 | 24437400 |
| The microbiome of the middle meatus in healthy adults. | Ramakrishnan, Vijay R; Feazel, Leah M; Gitomer, Sarah A; Ir, Diana; Robertson, Charles E; Frank, Daniel N | PloS one | 2013 | e85507 | 24386477 |
| Mathematical modeling of primary succession of murine intestinal microbiota. | Marino, Simeone; Baxter, Nielson T; Huffnagle, Gary B; Petrosino, Joseph F; Schloss, Patrick D | Proceedings of the National Academy of Sciences of the United States of America | 2014 Jan 7 | 439-44 | 24367073 |
| Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data. | Eren, A Murat; Maignien, Lois; Sul, Woo Jun; Murphy, Leslie G; Grim, Sharon L; Morrison, Hilary G; Sogin, Mitchell L | Methods in ecology and evolution / British Ecological Society | 2013 Dec 1 | NULL | 24358444 |
| Inferring developmental stage composition from gene expression in human malaria. | Joice, Regina; Narasimhan, Vagheesh; Montgomery, Jacqui; Sidhu, Amar Bir; Oh, Keunyoung; Meyer, Evan; Pierre-Louis, Willythssa; Seydel, Karl; Milner, Danny; Williamson, Kim; Wiegand, Roger; Ndiaye, Daouda; Daily, Johanna; Wirth, Dyann; Taylor, Terrie; Hut | PLoS computational biology | 2013 Dec | e1003392 | 24348235 |
| VARIABLE SELECTION FOR SPARSE DIRICHLET-MULTINOMIAL REGRESSION WITH AN APPLICATION TO MICROBIOME DATA ANALYSIS. | Chen, Jun; Li, Hongzhe | The annals of applied statistics. | 2013 Mar 01; | 24312162 | |
| More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis. | Srinivasan, Sujatha; Morgan, Martin T; Liu, Congzhou; Matsen, Frederick A; Hoffman, Noah G; Fiedler, Tina L; Agnew, Kathy J; Marrazzo, Jeanne M; Fredricks, David N | PloS one | 2013 | e78633 | 24302980 |
| Ribosomal Database Project: data and tools for high throughput rRNA analysis. | Cole, James R; Wang, Qiong; Fish, Jordan A; Chai, Benli; McGarrell, Donna M; Sun, Yanni; Brown, C Titus; Porras-Alfaro, Andrea; Kuske, Cheryl R; Tiedje, James M | Nucleic acids research | 2014 Jan | D633-42 | 24288368 |
| Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes. | Close, Devin W; Ferrara, Fortunato; Dichosa, Armand E K; Kumar, Sandeep; Daughton, Ashlynn R; Daligault, Hajnalka E; Reitenga, Krista G; Velappan, Nileena; Sanchez, Timothy C; Iyer, Srinivas; Kiss, Csaba; Han, Cliff S; Bradbury, Andrew R M | BMC microbiology | 2013 | 270 | 24279426 |
| A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease. | Tong, Maomeng; Li, Xiaoxiao; Wegener Parfrey, Laura; Roth, Bennett; Ippoliti, Andrew; Wei, Bo; Borneman, James; McGovern, Dermot P B; Frank, Daniel N; Li, Ellen; Horvath, Steve; Knight, Rob; Braun, Jonathan | PloS one | 2013 | e80702 | 24260458 |
| Diversified microbiota of meconium is affected by maternal diabetes status. | Hu, Jianzhong; Nomura, Yoko; Bashir, Ali; Fernandez-Hernandez, Heriberto; Itzkowitz, Steven; Pei, Zhiheng; Stone, Joanne; Loudon, Holly; Peter, Inga | PloS one | 2013 | e78257 | 24223144 |
| Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. | Gole, Jeff; Gore, Athurva; Richards, Andrew; Chiu, Yu-Jui; Fung, Ho-Lim; Bushman, Diane; Chiang, Hsin-I; Chun, Jerold; Lo, Yu-Hwa; Zhang, Kun | Nature biotechnology | 2013 Dec | 1126-32 | 24213699 |
| MetaRef: a pan-genomic database for comparative and community microbial genomics. | Huang, Katherine; Brady, Arthur; Mahurkar, Anup; White, Owen; Gevers, Dirk; Huttenhower, Curtis; Segata, Nicola | Nucleic acids research | 2014 Jan | D617-24 | 24203705 |
| Monodisperse alginate microgel formation in a three-dimensional microfluidic droplet generator. | Lian, Meng; Collier, C Patrick; Doktycz, Mitchel J; Retterer, Scott T | Biomicrofluidics. | 2012; | 24198865 | |
| The gut microbiome modulates colon tumorigenesis. | Zackular, Joseph P; Baxter, Nielson T; Iverson, Kathryn D; Sadler, William D; Petrosino, Joseph F; Chen, Grace Y; Schloss, Patrick D | mBio | 2013 | e00692-13 | 24194538 |
| Bringing the gut microbiota into focus through microbial culture: recent progress and future perspective. | Allen-Vercoe, Emma | Current opinion in microbiology | 2013 Oct | 625-9 | 24148301 |
| IMG/M 4 version of the integrated metagenome comparative analysis system. | Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Pagani, Ioanna; Tringe, Susannah; Huntemann, Marcel; Billis, Konstantinos; Varghese, Neha; Tennessen, Kristin; Mavromatis, Kons | Nucleic acids research | 2014 Jan | D568-73 | 24136997 |
| Science and regulation. Probiotics: finding the right regulatory balance. | Hoffmann, D E; Fraser, C M; Palumbo, F B; Ravel, J; Rothenberg, K; Rowthorn, V; Schwartz, J | Science (New York, N.Y.) | 2013 Oct 18 | 314-5 | 24136953 |
| Interprovider variation of celiac disease testing in childhood chronic abdominal pain. | Chumpitazi, Bruno Pedro; Mysore, Krupa; Tsai, Cynthia Man-Wai; Shulman, Robert Jay | BMC gastroenterology | 2013 | 150 | 24124697 |
| Lactobacillus reuteri-specific immunoregulatory gene rsiR modulates histamine production and immunomodulation by Lactobacillus reuteri. | Hemarajata, P; Gao, C; Pflughoeft, K J; Thomas, C M; Saulnier, D M; Spinler, J K; Versalovic, J | Journal of bacteriology | 2013 Dec | 5567-76 | 24123819 |
| Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota. | Lee, Sunghee; Cantarel, Brandi; Henrissat, Bernard; Gevers, Dirk; Birren, Bruce W; Huttenhower, Curtis; Ko, Gwangpyo | The ISME journal | 2013 Oct 10 | NULL | 24108330 |
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| Association between the vaginal microbiota, menopause status, and signs of vulvovaginal atrophy. | Brotman, Rebecca M; Shardell, Michelle D; Gajer, Pawel; Fadrosh, Doug; Chang, Kathryn; Silver, Michelle I; Viscidi, Raphael P; Burke, Anne E; Ravel, Jacques; Gravitt, Patti E | Menopause (New York, N.Y.) | 2013 Oct 21 | NULL | 24080849 |
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| A metagenomics portal for a democratized sequencing world. | Wilke, Andreas; Glass, Elizabeth M; Bartels, Daniela; Bischof, Jared; Braithwaite, Daniel; D'Souza, Mark; Gerlach, Wolfgang; Harrison, Travis; Keegan, Kevin; Matthews, Hunter; Kottmann, Renzo; Paczian, Tobias; Tang, Wei; Trimble, William L; Yilmaz, Pelin; | Methods in enzymology | 2013 | 487-523 | 24060134 |
| Optofluidic cell selection from complex microbial communities for single-genome analysis. | Landry, Zachary C; Giovanonni, Stephen J; Quake, Stephen R; Blainey, Paul C | Methods in enzymology | 2013 | 61-90 | 24060116 |
| Precise dissection of an Escherichia coli O157:H7 outbreak by single nucleotide polymorphism analysis. | Turabelidze, George; Lawrence, Steven J; Gao, Hongyu; Sodergren, Erica; Weinstock, George M; Abubucker, Sahar; Wylie, Todd; Mitreva, Makedonka; Shaikh, Nurmohammad; Gautom, Romesh; Tarr, Phillip I | Journal of clinical microbiology | 2013 Dec | 3950-4 | 24048526 |
| Ecological patterns of nifH genes in four terrestrial climatic zones explored with targeted metagenomics using FrameBot, a new informatics tool. | Wang, Qiong; Quensen 3rd, John F; Fish, Jordan A; Lee, Tae Kwon; Sun, Yanni; Tiedje, James M; Cole, James R | mBio | 2013 | e00592-13 | 24045641 |
| Antibacterial property expressed by a novel calcium phosphate glass. | Liu, Lela; Pushalkar, Smruti; Saxena, Deepak; LeGeros, Racquel Z; Zhang, Yu | Journal of biomedical materials research. Part B, Applied biomaterials. | 2014 Apr; | 423-9 | 24039127 |
| Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. | Robertson, Charles E; Harris, J Kirk; Wagner, Brandie D; Granger, David; Browne, Kathy; Tatem, Beth; Feazel, Leah M; Park, Kristin; Pace, Norman R; Frank, Daniel N | Bioinformatics (Oxford, England) | 2013 Dec 1 | 3100-1 | 24021386 |
| Microbiomic signatures of psoriasis: feasibility and methodology comparison. | Statnikov, Alexander; Alekseyenko, Alexander V; Li, Zhiguo; Henaff, Mikael; Perez-Perez, Guillermo I; Blaser, Martin J; Aliferis, Constantin F | Scientific reports | 2013 | 2620 | 24018484 |
| Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. | Dollive, Serena; Chen, Ying-Yu; Grunberg, Stephanie; Bittinger, Kyle; Hoffmann, Christian; Vandivier, Lee; Cuff, Christopher; Lewis, James D; Wu, Gary D; Bushman, Frederic D | PloS one | 2013 | e71806 | 23977147 |
| A Pure L1-norm Principal Component Analysis. | Brooks, Jp; Dula, Jh; Boone, El | Computational statistics & data analysis | 2013 May 1 | 83-98 | 23976807 |
| Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. | Langille, Morgan G I; Zaneveld, Jesse; Caporaso, J Gregory; McDonald, Daniel; Knights, Dan; Reyes, Joshua A; Clemente, Jose C; Burkepile, Deron E; Vega Thurber, Rebecca L; Knight, Rob; Beiko, Robert G; Huttenhower, Curtis | Nature biotechnology | 2013 Sep | 814-21 | 23975157 |
| De novo likelihood-based measures for comparing genome assemblies. | Ghodsi, Mohammadreza; Hill, Christopher M; Astrovskaya, Irina; Lin, Henry; Sommer, Dan D; Koren, Sergey; Pop, Mihai | BMC research notes | 2013 | 334 | 23965294 |
| Association of gut microbiota with post-operative clinical course in Crohn's disease. | Dey, Neelendu; Soergel, David A W; Repo, Susanna; Brenner, Steven E | BMC gastroenterology | 2013 | 131 | 23964800 |
| Two-stage microbial community experimental design. | Tickle, Timothy L; Segata, Nicola; Waldron, Levi; Weingart, Uri; Huttenhower, Curtis | The ISME journal | 2013 Aug 15 | NULL | 23949665 |
| PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. | Segata, Nicola; Bornigen, Daniela; Morgan, Xochitl C; Huttenhower, Curtis | Nature communications | 2013 Aug 14 | 2304 | 23942190 |
| Urethral adenocarcinoma associated with intestinal-type metaplasia, case report and literature review. | Hale, Christopher S; Huang, Hongying; Melamed, Jonathan; Xu, Ruliang; Roberts, Larry; Wieczorek, Rosemary; Pei, Zhiheng; Lee, Peng | International journal of clinical and experimental pathology | 2013 | 1665-70 | 23923086 |
| Gene expression profiles in febrile children with defined viral and bacterial infection. | Hu, Xinran; Yu, Jinsheng; Crosby, Seth D; Storch, Gregory A | Proceedings of the National Academy of Sciences of the United States of America | 2013 Jul 30 | 12792-7 | 23858444 |
| Rapid evolution of the human gut virome. | Minot, Samuel; Bryson, Alexandra; Chehoud, Christel; Wu, Gary D; Lewis, James D; Bushman, Frederic D | Proceedings of the National Academy of Sciences of the United States of America | 2013 Jul 23 | 12450-5 | 23836644 |
| The mean and variance of phylogenetic diversity under rarefaction. | Nipperess, David A; Matsen 4th, Frederick A | Methods in ecology and evolution / British Ecological Society | 2013 Jun 1 | 566-572 | 23833701 |
| Microfluidic platforms for single-cell protein analysis. | Liu, Yanli; Singh, Anup K | Journal of laboratory automation | 2013 Dec | 446-54 | 23821679 |
| Are changes to the common rule necessary to address evolving areas of research? A case study focusing on the human microbiome project. | Hoffmann, Diane E; Fortenberry, J Dennis; Ravel, Jacques | The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics. | 2013; | 23802897 | |
| Changes in cystic fibrosis airway microbiota at pulmonary exacerbation. | Carmody, Lisa A; Zhao, Jiangchao; Schloss, Patrick D; Petrosino, Joseph F; Murray, Susan; Young, Vincent B; Li, Jun Z; LipPuma, John J | Annals of the American Thoracic Society | 2013 Jun | 179-87 | 23802813 |
| A filtering method to generate high quality short reads using illumina paired-end technology. | Eren, A Murat; Vineis, Joseph H; Morrison, Hilary G; Sogin, Mitchell L | PloS one | 2013 | e66643 | 23799126 |
| Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. | Hoffmann, Christian; Dollive, Serena; Grunberg, Stephanie; Chen, Jun; Li, Hongzhe; Wu, Gary D; Lewis, James D; Bushman, Frederic D | PloS one | 2013 | e66019 | 23799070 |
| Skin microbiome imbalance in patients with STAT1/STAT3 defects impairs innate host defense responses. | Smeekens, Sanne P; Huttenhower, Curtis; Riza, Anca; van de Veerdonk, Frank L; Zeeuwen, Patrick L J M; Schalkwijk, Joost; van der Meer, Jos W M; Xavier, Ramnik J; Netea, Mihai G; Gevers, Dirk | Journal of innate immunity. | 2014; | 253-62 | 23796786 |
| Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. | Kozich, James J; Westcott, Sarah L; Baxter, Nielson T; Highlander, Sarah K; Schloss, Patrick D | Applied and environmental microbiology | 2013 Sep | 5112-20 | 23793624 |
| Carrageenan-induced colonic inflammation is reduced in Bcl10 null mice and increased in IL-10-deficient mice. | Bhattacharyya, Sumit; Xue, Liquan; Devkota, Suzanne; Chang, Eugene; Morris, Stephan; Tobacman, Joanne K | Mediators of inflammation | 2013 | 397642 | 23766559 |
| Analysis of complete genomes of Propionibacterium acnes reveals a novel plasmid and increased pseudogenes in an acne associated strain. | Kasimatis, Gabriela; Fitz-Gibbon, Sorel; Tomida, Shuta; Wong, Marthew; Li, Huiying | BioMed research international | 2013 | 918320 | 23762865 |
| Sequencing viral genomes from a single isolated plaque. | Depew, Jessica; Zhou, Bin; McCorrison, Jamison M; Wentworth, David E; Purushe, Janaki; Koroleva, Galina; Fouts, Derrick E | Virology journal | 2013 | 181 | 23742765 |
| Virome genomics: a tool for defining the human virome. | Wylie, Kristine M; Weinstock, George M; Storch, Gregory A | Current opinion in microbiology | 2013 May 23 | 23706900 | |
| Colitis-induced Bone Loss is Gender Dependent and Associated with Increased Inflammation. | Irwin, Regina; Lee, Taehyung; Young, Vincent B; Parameswaran, Narayanan; McCabe, Laura R | Inflammatory bowel diseases | 2013 Jul | 1586-1597 | 23702805 |
| DRISEE overestimates errors in metagenomic sequencing data. | Eren, A Murat; Morrison, Hilary G; Huse, Susan M; Sogin, Mitchell L | Briefings in bioinformatics. | 2014 Sep; | 783-7 | 23698723 |
| Draft Genome Sequences of Two Pairs of Human Intestinal Bifidobacterium longum subsp. longum Strains, 44B and 1-6B and 35B and 2-2B, Consecutively Isolated from Two Children after a 5-Year Time Period. | Shkoporov, A N; Efimov, B A; Khokhlova, E V; Chaplin, A V; Kafarskaya, L I; Durkin, A S; McCorrison, J; Torralba, M; Gillis, M; Sutton, G; Weibel, D B; Nelson, K E; Smeianov, V V | Genome announcements. | 2013; | 23682142 | |
| Analyses of the stability and core taxonomic memberships of the human microbiome. | Li, Kelvin; Bihan, Monika; Methe, Barbara A | PloS one | 2013 | e63139 | 23671663 |
| Computational meta'omics for microbial community studies. | Segata, Nicola; Boernigen, Daniela; Tickle, Timothy L; Morgan, Xochitl C; Garrett, Wendy S; Huttenhower, Curtis | Molecular systems biology | 2013 | 666 | 23670539 |
| Butyrate Induced IGF2 Activation Correlated with Distinct Chromatin Signatures Due to Histone Modification. | Shin, Joo Heon; Li, Robert W; Gao, Yuan; Bickhart, Derek M; Liu, George E; Li, Weizhong; Wu, Sitao; Li, Cong-Jun | Gene regulation and systems biology. | 2013; | 23645985 | |
| Analysis of the human gut microbiome and association with disease. | Wu, Gary D; Lewis, James D | Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association | 2013 Jul | 774-7 | 23643636 |
| Composition of dietary fat source shapes gut microbiota architecture and alters host inflammatory mediators in mouse adipose tissue. | Huang, Edmond Y; Leone, Vanessa A; Devkota, Suzanne; Wang, Yunwei; Brady, Matthew J; Chang, Eugene B | JPEN. Journal of parenteral and enteral nutrition | 2013 Nov | 746-54 | 23639897 |
| Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome. | Tomida, Shuta; Nguyen, Lin; Chiu, Bor-Han; Liu, Jared; Sodergren, Erica; Weinstock, George M; Li, Huiying | mBio | 2013 | e00003-13 | 23631911 |
| Investigators' perspectives on translating human microbiome research into clinical practice. | Slashinski, M J; Whitney, S N; Achenbaum, L S; Keitel, W A; McCurdy, S A; McGuire, A L | Public health genomics | 2013 | 127-33 | 23615375 |
| Cohabiting family members share microbiota with one another and with their dogs. | Song, Se Jin; Lauber, Christian; Costello, Elizabeth K; Lozupone, Catherine A; Humphrey, Gregory; Berg-Lyons, Donna; Caporaso, J Gregory; Knights, Dan; Clemente, Jose C; Nakielny, Sara; Gordon, Jeffrey I; Fierer, Noah; Knight, Rob | eLife. | 2013 Apr 16; | 23599893 | |
| Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. | Koeth, Robert A; Wang, Zeneng; Levison, Bruce S; Buffa, Jennifer A; Org, Elin; Sheehy, Brendan T; Britt, Earl B; Fu, Xiaoming; Wu, Yuping; Li, Lin; Smith, Jonathan D; DiDonato, Joseph A; Chen, Jun; Li, Hongzhe; Wu, Gary D; Lewis, James D; Warrier, Manya; | Nature medicine | 2013 May | 576-85 | 23563705 |
| Gastrointestinal viruses were not found as an aetiology of culture-negative illness in NICU patients. | Melamed, Rimma; Storch, Gregory A; Warner, Barbara B; Tarr, Phillip I | Archives of disease in childhood. Fetal and neonatal edition | 2013 Jul | F374-5 | 23563694 |
| Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity. | Campbell, Alisha G; Campbell, James H; Schwientek, Patrick; Woyke, Tanja; Sczyrba, Alexander; Allman, Steve; Beall, Clifford J; Griffen, Ann; Leys, Eugene; Podar, Mircea | PloS one | 2013 | e59361 | 23555659 |
| Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences. | Jiao, Dazhi; Ye, Yuzhen; Tang, Haixu | PLoS computational biology | 2013 Mar | e1002981 | 23555216 |
| Culture-independent analysis of aerosol microbiology in a metropolitan subway system. | Robertson, Charles E; Baumgartner, Laura K; Harris, J Kirk; Peterson, Kristen L; Stevens, Mark J; Frank, Daniel N; Pace, Norman R | Applied and environmental microbiology | 2013 Jun | 3485-93 | 23542619 |
| UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. | Campbell, James H; O'Donoghue, Patrick; Campbell, Alisha G; Schwientek, Patrick; Sczyrba, Alexander; Woyke, Tanja; Soll, Dieter; Podar, Mircea | Proceedings of the National Academy of Sciences of the United States of America | 2013 Apr 2 | 5540-5 | 23509275 |
| Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison. | Matsen 4th, Frederick A; Evans, Steven N | PloS one | 2013 | e56859 | 23505415 |
| Comparative analysis of microbiome measurement platforms using latent variable structural equation modeling. | Wu, Xiao; Berkow, Kathryn; Frank, Daniel N; Li, Ellen; Gulati, Ajay S; Zhu, Wei | BMC bioinformatics | 2013 | 79 | 23497007 |
| Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. | Fitzsimons, Michael S; Novotny, Mark; Lo, Chien-Chi; Dichosa, Armand E K; Yee-Greenbaum, Joyclyn L; Snook, Jeremy P; Gu, Wei; Chertkov, Olga; Davenport, Karen W; McMurry, Kim; Reitenga, Krista G; Daughton, Ashlynn R; He, Jian; Johnson, Shannon L; Gleasner | Genome research | 2013 May | 878-88 | 23493677 |
| Comparison of the respiratory microbiome in healthy nonsmokers and smokers. | Morris, Alison; Beck, James M; Schloss, Patrick D; Campbell, Thomas B; Crothers, Kristina; Curtis, Jeffrey L; Flores, Sonia C; Fontenot, Andrew P; Ghedin, Elodie; Huang, Laurence; Jablonski, Kathleen; Kleerup, Eric; Lynch, Susan V; Sodergren, Erica; Twigg | American journal of respiratory and critical care medicine | 2013 May 15 | 1067-75 | 23491408 |
| Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases. | Leone, Vanessa; Chang, Eugene B; Devkota, Suzanne | Journal of gastroenterology | 2013 Mar | 315-21 | 23475322 |
| Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players. | Ursell, Luke K; Knight, Rob | Cell metabolism | 2013 Mar 5 | 317-8 | 23473028 |
| Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. | Hettich, Robert L; Pan, Chongle; Chourey, Karuna; Giannone, Richard J | Analytical chemistry | 2013 May 7 | 4203-14 | 23469896 |
| Draft Genome Sequence of Enterococcus faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces. | O Cuív, Páraic; Klaassens, Eline S; Smith, Wendy J; Mondot, Stanislas; Durkin, A Scott; Harkins, Derek M; Foster, Les; McCorrison, Jamison; Torralba, Manolito; Nelson, Karen E; Morrison, Mark | Genome announcements. | 2013 Jan; | 23469340 | |
| Effects of different complementary feeding regimens on iron status and enteric microbiota in breastfed infants. | Krebs, Nancy F; Sherlock, Laurie G; Westcott, Jamie; Culbertson, Diana; Hambidge, K Michael; Feazel, Leah M; Robertson, Charles E; Frank, Daniel N | The Journal of pediatrics | 2013 Aug | 416-23 | 23452586 |
| Challenges in IBD research: update on progress and prioritization of the CCFA's research agenda. | Denson, Lee A; Long, Millie D; McGovern, Dermot P B; Kugathasan, Subra; Wu, Gary D; Young, Vincent B; Pizarro, Theresa T; de Zoeten, Edwin F; Stappenbeck, Thaddeus S; Plevy, Scott E; Abraham, Clara; Nusrat, Asma; Jobin, Christian; McCole, Declan F; Siegel | Inflammatory bowel diseases | 2013 Mar-Apr | 677-82 | 23448796 |
| SPA: a short peptide assembler for metagenomic data. | Yang, Youngik; Yooseph, Shibu | Nucleic acids research | 2013 Apr | e91 | 23435317 |
| Transcriptome profiling of microRNA by Next-Gen deep sequencing reveals known and novel miRNA species in the lipid fraction of human breast milk. | Munch, Erika M; Harris, R Alan; Mohammad, Mahmoud; Benham, Ashley L; Pejerrey, Sasha M; Showalter, Lori; Hu, Min; Shope, Cynthia D; Maningat, Patricia D; Gunaratne, Preethi H; Haymond, Morey; Aagaard, Kjersti | PloS one | 2013 | e50564 | 23418415 |
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| The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness. | Liolios, Konstantinos; Schriml, Lynn; Hirschman, Lynette; Pagani, Ioanna; Nosrat, Bahador; Sterk, Peter; White, Owen; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Taylor, Chris; Kyrpides, Nikos C; Field, Dawn | Standards in genomic sciences. | 2012 Jul 30; | 23409217 | |
| Simultaneous quantification of multiple bacteria by the BactoChip microarray designed to target species-specific marker genes. | Ballarini, Annalisa; Segata, Nicola; Huttenhower, Curtis; Jousson, Olivier | PloS one | 2013 | e55764 | 23409037 |
| The human gut microbiome and body metabolism: implications for obesity and diabetes. | Devaraj, Sridevi; Hemarajata, Peera; Versalovic, James | Clinical chemistry | 2013 Apr | 617-28 | 23401286 |
| Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. | Shakya, Migun; Quince, Christopher; Campbell, James H; Yang, Zamin K; Schadt, Christopher W; Podar, Mircea | Environmental microbiology | 2013 Jun | 1882-99 | 23387867 |
| Single cell microRNA analysis using microfluidic flow cytometry. | Wu, Meiye; Piccini, Matthew; Koh, Chung-Yan; Lam, Kit S; Singh, Anup K | PloS one | 2013 | e55044 | 23383050 |
| Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis. | Ansong, Charles; Ortega, Corrie; Payne, Samuel H; Haft, Daniel H; Chauvigne-Hines, Lacie M; Lewis, Michael P; Ollodart, Anja R; Purvine, Samuel O; Shukla, Anil K; Fortuin, Suereta; Smith, Richard D; Adkins, Joshua N; Grundner, Christoph; Wright, Aaron T | Chemistry & biology | 2013 Jan 24 | 123-33 | 23352146 |
| Propionibacterium acnes Strain Populations in the Human Skin Microbiome Associated with Acne. | Fitz-Gibbon, Sorel; Tomida, Shuta; Chiu, Bor-Han; Nguyen, Lin; Du, Christine; Liu, Minghsun; Elashoff, David; Erfe, Marie C; Loncaric, Anya; Kim, Jenny; Modlin, Robert L; Miller, Jeff F; Sodergren, Erica; Craft, Noah; Weinstock, George M; Li, Huiying | The Journal of investigative dermatology | 2013 Jan 21 | 23337890 | |
| Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. | Markle, Janet G M; Frank, Daniel N; Mortin-Toth, Steven; Robertson, Charles E; Feazel, Leah M; Rolle-Kampczyk, Ulrike; von Bergen, Martin; McCoy, Kathy D; Macpherson, Andrew J; Danska, Jayne S | Science (New York, N.Y.) | 2013 Mar 1 | 1084-8 | 23328391 |
| A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. | Koren, Omry; Knights, Dan; Gonzalez, Antonio; Waldron, Levi; Segata, Nicola; Knight, Rob; Huttenhower, Curtis; Ley, Ruth E | PLoS computational biology | 2013 Jan | e1002863 | 23326225 |
| MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. | Treangen, Todd J; Koren, Sergey; Sommer, Daniel D; Liu, Bo; Astrovskaya, Irina; Ondov, Brian; Darling, Aaron E; Phillippy, Adam M; Pop, Mihai | Genome biology. | 2013; | R2 | 23320958 |
| The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences. | Riehle, Kevin; Coarfa, Cristian; Jackson, Andrew; Ma, Jun; Tandon, Arpit; Paithankar, Sameer; Raghuraman, Sriram; Mistretta, Toni-Ann; Saulnier, Delphine; Raza, Sabeen; Diaz, Maria Alejandra; Shulman, Robert; Aagaard, Kjersti; Versalovic, James; Milosavlj | BMC bioinformatics | 2012 | S11 | 23320832 |
| Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. | Hemarajata, Peera; Versalovic, James | Therapeutic advances in gastroenterology. | 2013 Jan; | 23320049 | |
| Biogeography of the ecosystems of the healthy human body. | Zhou, Yanjiao; Gao, Hongyu; Mihindukulasuriya, Kathie A; La Rosa, Patricio S; Wylie, Kristine M; Vishnivetskaya, Tatiana; Podar, Mircea; Warner, Barb; Tarr, Phillip I; Nelson, David E; Fortenberry, J Dennis; Holland, Martin J; Burr, Sarah E; Shannon, Will | Genome biology | 2013 Jan 14 | R1 | 23316946 |
| An analysis of online messages about probiotics. | Brinich, Margaret A; Mercer, Mary Beth; Sharp, Richard R | BMC gastroenterology | 2013 | 5 | 23311418 |
| The Jeremiah Metzger lecture: Global warming redux: the disappearing microbiota and epidemic obesity. | Blaser, Martin J | Transactions of the American Clinical and Climatological Association | 2012 | 230-8; discussion 239-41 | 23303990 |
| Chapter 12: Human microbiome analysis. | Morgan, Xochitl C; Huttenhower, Curtis | PLoS computational biology | 2012 | e1002808 | 23300406 |
| Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men. | Redel, Henry; Gao, Zhan; Li, Huilin; Alekseyenko, Alexander V; Zhou, Yanjiao; Perez-Perez, Guillermo I; Weinstock, George; Sodergren, Erica; Blaser, Martin J | The Journal of infectious diseases | 2013 Apr | 1105-14 | 23300163 |
| The future is now: single-cell genomics of bacteria and archaea. | Blainey, Paul C | FEMS microbiology reviews | 2013 May | 407-27 | 23298390 |
| Hypothesis testing and power calculations for taxonomic-based human microbiome data. | La Rosa, Patricio S; Brooks, J Paul; Deych, Elena; Boone, Edward L; Edwards, David J; Wang, Qin; Sodergren, Erica; Weinstock, George; Shannon, William D | PloS one | 2012 | e52078 | 23284876 |
| Species-level classification of the vaginal microbiome. | Fettweis, Jennifer M; Serrano, Myrna G; Sheth, Nihar U; Mayer, Carly M; Glascock, Abigail L; Brooks, J Paul; Jefferson, Kimberly K; Vaginal Microbiome Consortium (additional members); Buck, Gregory A | BMC genomics | 2012 | S17 | 23282177 |
| Genomic sequence analysis and characterization of Sneathia amnii sp. nov. | Harwich Jr, Michael D; Serrano, Myrna G; Fettweis, Jennifer M; Alves, Joao M P; Reimers, Mark A; Vaginal Microbiome Consortium (additional members); Buck, Gregory A; Jefferson, Kimberly K | BMC genomics | 2012 | S4 | 23281612 |
| 'Someone should oversee it': patient perspectives on the ethical issues arising with the regulation of probiotics. | Harrison, Krista L; Farrell, Ruth M; Brinich, Margaret A; Highland, Janelle; Mercer, Marybeth; McCormick, Jennifer B; Tilburt, Jon; Geller, Gail; Marshall, Patricia; Sharp, Richard R | Health expectations : an international journal of public participation in health care and health policy | 2012 Dec 28 | 23279082 | |
| Insights from characterizing extinct human gut microbiomes. | Tito, Raul Y; Knights, Dan; Metcalf, Jessica; Obregon-Tito, Alexandra J; Cleeland, Lauren; Najar, Fares; Roe, Bruce; Reinhard, Karl; Sobolik, Kristin; Belknap, Samuel; Foster, Morris; Spicer, Paul; Knight, Rob; Lewis Jr, Cecil M | PloS one | 2012 | e51146 | 23251439 |
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| Whole-genome analysis of a daptomycin-susceptible enterococcus faecium strain and its daptomycin-resistant variant arising during therapy. | Tran, Truc T; Panesso, Diana; Gao, Hongyu; Roh, Jung H; Munita, Jose M; Reyes, Jinnethe; Diaz, Lorena; Lobos, Elizabeth A; Shamoo, Yousif; Mishra, Nagendra N; Bayer, Arnold S; Murray, Barbara E; Weinstock, George M; Arias, Cesar A | Antimicrobial agents and chemotherapy | 2013 Jan | 261-8 | 23114757 |
| "Snake-oil," "quack medicine," and "industrially cultured organisms:" biovalue and the commercialization of human microbiome research. | Slashinski, Melody J; McCurdy, Sheryl A; Achenbaum, Laura S; Whitney, Simon N; McGuire, Amy L | BMC medical ethics | 2012 | 28 | 23110633 |
| Dietary issues in recurrent abdominal pain. | Shulman, Robert J | Journal of pediatric gastroenterology and nutrition | 2012 Nov | S40-2 | 23103654 |
| Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa. | Williams, Tiffany M; Loman, Nicholas J; Ebruke, Chinelo; Musher, Daniel M; Adegbola, Richard A; Pallen, Mark J; Weinstock, George M; Antonio, Martin | PloS one | 2012 | e26742 | 23082106 |
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| Succession in the gut microbiome following antibiotic and antibody therapies for Clostridium difficile. | Peterfreund, Gregory L; Vandivier, Lee E; Sinha, Rohini; Marozsan, Andre J; Olson, William C; Zhu, Jun; Bushman, Frederic D | PloS one | 2012 | e46966 | 23071679 |
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| Quantitative analysis of the human airway microbial ecology reveals a pervasive signature for cystic fibrosis. | Blainey, Paul C; Milla, Carlos E; Cornfield, David N; Quake, Stephen R | Science translational medicine | 2012 Sep 26 | 153ra130 | 23019655 |
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| Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. | Morgan, Xochitl C; Tickle, Timothy L; Sokol, Harry; Gevers, Dirk; Devaney, Kathryn L; Ward, Doyle V; Reyes, Joshua A; Shah, Samir A; LeLeiko, Neal; Snapper, Scott B; Bousvaros, Athos; Korzenik, Joshua; Sands, Bruce E; Xavier, Ramnik J; Huttenhower, Curtis | Genome biology | 2012 | R79 | 23013615 |
| Association between Trichomonas vaginalis and vaginal bacterial community composition among reproductive-age women. | Brotman, Rebecca M; Bradford, L Latey; Conrad, Melissa; Gajer, Pawel; Ault, Kevin; Peralta, Ligia; Forney, Larry J; Carlton, Jane M; Abdo, Zaid; Ravel, Jacques | Sexually transmitted diseases | 2012 Oct | 807-12 | 23007708 |
| Prevention of virus-induced type 1 diabetes with antibiotic therapy. | Hara, Naoko; Alkanani, Aimon K; Ir, Diana; Robertson, Charles E; Wagner, Brandie D; Frank, Daniel N; Zipris, Danny | Journal of immunology (Baltimore, Md. : 1950) | 2012 Oct 15 | 3805-14 | 22988033 |
| Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. | Semova, Ivana; Carten, Juliana D; Stombaugh, Jesse; Mackey, Lantz C; Knight, Rob; Farber, Steven A; Rawls, John F | Cell host & microbe | 2012 Sep 13 | 277-88 | 22980325 |
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| Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. | Wu, Yu-Wei; Rho, Mina; Doak, Thomas G; Ye, Yuzhen | Bioinformatics (Oxford, England) | 2012 Sep 15 | i363-i369 | 22962453 |
| Current technology in the diagnosis of developmentally related lung disorders. | Hamvas, Aaron | Neonatology | 2012 | 353-9 | 22940625 |
| Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures. | Madan, J C; Koestler, D C; Stanton, B A; Davidson, L; Moulton, L A; Housman, M L; Moore, J H; Guill, M F; Morrison, H G; Sogin, M L; Hampton, T H; Karagas, M R; Palumbo, P E; Foster, J A; Hibberd, P L; O'Toole, G A | mBio | 2012 | 22911969 | |
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| The Human Microbiome Project: a community resource for the healthy human microbiome. | Gevers, Dirk; Knight, Rob; Petrosino, Joseph F; Huang, Katherine; McGuire, Amy L; Birren, Bruce W; Nelson, Karen E; White, Owen; Methe, Barbara A; Huttenhower, Curtis | PLoS biology | 2012 | e1001377 | 22904687 |
| Conservation of gene cassettes among diverse viruses of the human gut. | Minot, Samuel; Wu, Gary D; Lewis, James D; Bushman, Frederic D | PloS one | 2012 | e42342 | 22900013 |
| Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. | Blaser, Martin J; Dominguez-Bello, Maria G; Contreras, Monica; Magris, Magda; Hidalgo, Glida; Estrada, Isidoro; Gao, Zhan; Clemente, Jose C; Costello, Elizabeth K; Knight, Rob | The ISME journal | 2013 Jan | 85-95 | 22895161 |
| Defining the human microbiome. | Ursell, Luke K; Metcalf, Jessica L; Parfrey, Laura Wegener; Knight, Rob | Nutrition reviews | 2012 Aug | S38-44 | 22861806 |
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| The "most wanted" taxa from the human microbiome for whole genome sequencing. | Fodor, Anthony A; DeSantis, Todd Z; Wylie, Kristine M; Badger, Jonathan H; Ye, Yuzhen; Hepburn, Theresa; Hu, Ping; Sodergren, Erica; Liolios, Konstantinos; Huot-Creasy, Heather; Birren, Bruce W; Earl, Ashlee M | PloS one | 2012 | e41294 | 22848458 |
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| Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma. | Pushalkar, Smruti; Ji, Xiaojie; Li, Yihong; Estilo, Cherry; Yegnanarayana, Ramanathan; Singh, Bhuvanesh; Li, Xin; Saxena, Deepak | BMC microbiology | 2012 | 144 | 22817758 |
| Microbial co-occurrence relationships in the human microbiome. | Faust, Karoline; Sathirapongsasuti, J Fah; Izard, Jacques; Segata, Nicola; Gevers, Dirk; Raes, Jeroen; Huttenhower, Curtis | PLoS computational biology | 2012 | e1002606 | 22807668 |
| IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. | Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Jacob, Biju; Ratner, Anna; Liolios, Konstantinos; Pagani, Ioanna; Huntemann, Marcel; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos C | PloS one | 2012 | e40151 | 22792232 |
| Ethical Discourse about the Modification of Food for Therapeutic Purposes: How Patients with Gastrointestinal Diseases View the Good, the Bad, and the Healthy. | Harrison, Krista L; Geller, Gail; Marshall, Patricia; Tilburt, Jon; Mercer, Marybeth; Brinich, Margaret A; Highland, Janelle; Farrell, Ruth M; Sharp, Richard R | AJOB primary research | 2012 Jul 1 | 12-20 | 22773953 |
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| Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. | Qin, Xiang; Galloway-Pena, Jessica R; Sillanpaa, Jouko; Roh, Jung Hyeob; Nallapareddy, Sreedhar R; Chowdhury, Shahreen; Bourgogne, Agathe; Choudhury, Tina; Muzny, Donna M; Buhay, Christian J; Ding, Yan; Dugan-Rocha, Shannon; Liu, Wen; Kovar, Christie; Sod | BMC microbiology | 2012 | 135 | 22769602 |
| Diversity of 5S rRNA genes within individual prokaryotic genomes. | Pei, Anna; Li, Hongru; Oberdorf, William E; Alekseyenko, Alexander V; Parsons, Tamasha; Yang, Liying; Gerz, Erika A; Lee, Peng; Xiang, Charlie; Nossa, Carlos W; Pei, Zhiheng | FEMS microbiology letters | 2012 Oct | 11-8 | 22765222 |
| A tool kit for quantifying eukaryotic rRNA gene sequences from human microbiome samples. | Dollive, Serena; Peterfreund, Gregory L; Sherrill-Mix, Scott; Bittinger, Kyle; Sinha, Rohini; Hoffmann, Christian; Nabel, Christopher S; Hill, David A; Artis, David; Bachman, Michael A; Custers-Allen, Rebecca; Grunberg, Stephanie; Wu, Gary D; Lewis, James D; Bushman, Frederic D | Genome biology. | 2012; | R60 | 22759449 |
| Caring about trees in the forest: incorporating frailty in risk analysis for personalized medicine. | Ma, Zhanshan Sam; Abdo, Zaid; Forney, Larry J | Personalized medicine | 2011 Nov | 681-688 | 22754581 |
| Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability. | Filkins, L M; Hampton, T H; Gifford, A H; Gross, M J; Hogan, D A; Sogin, M L; Morrison, H G; Paster, B J; O'Toole, G A | Journal of bacteriology | 2012 Sep | 4709-17 | 22753064 |
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| Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10-/- mice. | Devkota, Suzanne; Wang, Yunwei; Musch, Mark W; Leone, Vanessa; Fehlner-Peach, Hannah; Nadimpalli, Anuradha; Antonopoulos, Dionysios A; Jabri, Bana; Chang, Eugene B | Nature | 2012 Jul 5 | 104-8 | 22722865 |
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| A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. | Aagaard, Kjersti; Riehle, Kevin; Ma, Jun; Segata, Nicola; Mistretta, Toni-Ann; Coarfa, Cristian; Raza, Sabeen; Rosenbaum, Sean; Van den Veyver, Ignatia; Milosavljevic, Aleksandar; Gevers, Dirk; Huttenhower, Curtis; Petrosino, Joseph; Versalovic, James | PloS one | 2012 | e36466 | 22719832 |
| Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities. | Martin, John; Sykes, Sean; Young, Sarah; Kota, Karthik; Sanka, Ravi; Sheth, Nihar; Orvis, Joshua; Sodergren, Erica; Wang, Zhengyuan; Weinstock, George M; Mitreva, Makedonka | PloS one | 2012 | e36427 | 22719831 |
| Novel bacterial taxa in the human microbiome. | Wylie, Kristine M; Truty, Rebecca M; Sharpton, Thomas J; Mihindukulasuriya, Kathie A; Zhou, Yanjiao; Gao, Hongyu; Sodergren, Erica; Weinstock, George M; Pollard, Katherine S | PloS one | 2012 | e35294 | 22719826 |
| A core human microbiome as viewed through 16S rRNA sequence clusters. | Huse, Susan M; Ye, Yuzhen; Zhou, Yanjiao; Fodor, Anthony A | PloS one | 2012 | e34242 | 22719824 |
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| Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition. | Zhang, Tianyi; DeSimone, Robert A; Jiao, Xiangmin; Rohlf, F James; Zhu, Wei; Gong, Qing Qing; Hunt, Steven R; Dassopoulos, Themistocles; Newberry, Rodney D; Sodergren, Erica; Weinstock, George; Robertson, Charles E; Frank, Daniel N; Li, Ellen | PloS one | 2012 | e30044 | 22719822 |
| A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). | Goll, Johannes; Thiagarajan, Mathangi; Abubucker, Sahar; Huttenhower, Curtis; Yooseph, Shibu; Methe, Barbara A | PloS one | 2012 | e29044 | 22719821 |
| Complex carbohydrate utilization by the healthy human microbiome. | Cantarel, Brandi L; Lombard, Vincent; Henrissat, Bernard | PloS one | 2012 | e28742 | 22719820 |
| Sequence analysis of the human virome in febrile and afebrile children. | Wylie, Kristine M; Mihindukulasuriya, Kathie A; Sodergren, Erica; Weinstock, George M; Storch, Gregory A | PloS one | 2012 | e27735 | 22719819 |
| Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. | Li, Ellen; Hamm, Christina M; Gulati, Ajay S; Sartor, R Balfour; Chen, Hongyan; Wu, Xiao; Zhang, Tianyi; Rohlf, F James; Zhu, Wei; Gu, Chi; Robertson, Charles E; Pace, Norman R; Boedeker, Edgar C; Harpaz, Noam; Yuan, Jeffrey; Weinstock, George M; Sodergre | PloS one | 2012 | e26284 | 22719818 |
| Diverse CRISPRs evolving in human microbiomes. | Rho, Mina; Wu, Yu-Wei; Tang, Haixu; Doak, Thomas G; Ye, Yuzhen | PLoS genetics | 2012 | e1002441 | 22719260 |
| Metabolic reconstruction for metagenomic data and its application to the human microbiome. | Abubucker, Sahar; Segata, Nicola; Goll, Johannes; Schubert, Alyxandria M; Izard, Jacques; Cantarel, Brandi L; Rodriguez-Mueller, Beltran; Zucker, Jeremy; Thiagarajan, Mathangi; Henrissat, Bernard; White, Owen; Kelley, Scott T; Methe, Barbara; Schloss, Pat | PLoS computational biology | 2012 | e1002358 | 22719234 |
| Associating microbiome composition with environmental covariates using generalized UniFrac distances. | Chen, Jun; Bittinger, Kyle; Charlson, Emily S; Hoffmann, Christian; Lewis, James; Wu, Gary D; Collman, Ronald G; Bushman, Frederic D; Li, Hongzhe | Bioinformatics (Oxford, England) | 2012 Aug 15 | 2106-13 | 22711789 |
| A framework for human microbiome research. | Human Microbiome Project Consortium | Nature | 2012 Jun 14 | 215-21 | 22699610 |
| Structure, function and diversity of the healthy human microbiome. | Human Microbiome Project Consortium | Nature | 2012 Jun 14 | 207-14 | 22699609 |
| Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. | Segata, Nicola; Haake, Susan Kinder; Mannon, Peter; Lemon, Katherine P; Waldron, Levi; Gevers, Dirk; Huttenhower, Curtis; Izard, Jacques | Genome biology | 2012 | R42 | 22698087 |
| A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community. | Wang, Mingjie; Ye, Yuzhen; Tang, Haixu | Journal of computational biology : a journal of computational molecular cell biology | 2012 Jun | 814-25 | 22697249 |
| Host genetic and environmental effects on mouse intestinal microbiota. | Campbell, James H; Foster, Carmen M; Vishnivetskaya, Tatiana; Campbell, Alisha G; Yang, Zamin K; Wymore, Ann; Palumbo, Anthony V; Chesler, Elissa J; Podar, Mircea | The ISME journal | 2012 Nov | 2033-44 | 22695862 |
| mcaGUI: microbial community analysis R-Graphical User Interface (GUI). | Copeland, Wade K; Krishnan, Vandhana; Beck, Daniel; Settles, Matt; Foster, James A; Cho, Kyu-Chul; Day, Mitch; Hickey, Roxana; Schutte, Ursel M E; Zhou, Xia; Williams, Christopher J; Forney, Larry J; Abdo, Zaid | Bioinformatics (Oxford, England) | 2012 Aug 15 | 2198-9 | 22692220 |
| Stabilization of the murine gut microbiome following weaning. | Schloss, Patrick D; Schubert, Alyxandria M; Zackular, Joseph P; Iverson, Kathryn D; Young, Vincent B; Petrosino, Joseph F | Gut microbes | 2012 Jul-Aug | 383-93 | 22688727 |
| Metagenomic microbial community profiling using unique clade-specific marker genes. | Segata, Nicola; Waldron, Levi; Ballarini, Annalisa; Narasimhan, Vagheesh; Jousson, Olivier; Huttenhower, Curtis | Nature methods | 2012 Aug | 811-4 | 22688413 |
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| Understanding vaginal microbiome complexity from an ecological perspective. | Hickey, Roxana J; Zhou, Xia; Pierson, Jacob D; Ravel, Jacques; Forney, Larry J | Translational research : the journal of laboratory and clinical medicine | 2012 Oct | 267-82 | 22683415 |
| The microbiome of the lung. | Beck, James M; Young, Vincent B; Huffnagle, Gary B | Translational research : the journal of laboratory and clinical medicine | 2012 Oct | 258-66 | 22683412 |
| Unlocking the potential of metagenomics through replicated experimental design. | Knight, Rob; Jansson, Janet; Field, Dawn; Fierer, Noah; Desai, Narayan; Fuhrman, Jed A; Hugenholtz, Phil; van der Lelie, Daniel; Meyer, Folker; Stevens, Rick; Bailey, Mark J; Gordon, Jeffrey I; Kowalchuk, George A; Gilbert, Jack A | Nature biotechnology. | 2012 Jun; | 22678395 | |
| High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)). | Earl, Ashlee M; Desjardins, Christopher A; Fitzgerald, Michael G; Arachchi, Harindra M; Zeng, Qiandong; Mehta, Teena; Griggs, Allison; Birren, Bruce W; Toney, Nadege C; Carr, Janice; Posey, James; Butler, W Ray | Standards in genomic sciences. | 2011 Dec 31; | 22675588 | |
| Deep sequencing of the oral microbiome reveals signatures of periodontal disease. | Liu, Bo; Faller, Lina L; Klitgord, Niels; Mazumdar, Varun; Ghodsi, Mohammad; Sommer, Daniel D; Gibbons, Theodore R; Treangen, Todd J; Chang, Yi-Chien; Li, Shan; Stine, O Colin; Hasturk, Hatice; Kasif, Simon; Segre, Daniel; Pop, Mihai; Amar, Salomon | PloS one | 2012 | e37919 | 22675498 |
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| Comparison of storage conditions for human vaginal microbiome studies. | Bai, Guoyun; Gajer, Pawel; Nandy, Melissa; Ma, Bing; Yang, Hongqiu; Sakamoto, Joyce; Blanchard, May H; Ravel, Jacques; Brotman, Rebecca M | PloS one | 2012 | e36934 | 22655031 |
| Quantification of Transcriptome Responses of the Rumen Epithelium to Butyrate Infusion using RNA-seq Technology. | Baldwin 6th, Ransom L; Wu, Sitao; Li, Weizhong; Li, Congjun; Bequette, Brian J; Li, Robert W | Gene regulation and systems biology | 2012 | 67-80 | 22654504 |
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| RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. | Widmann, Jeremy; Stombaugh, Jesse; McDonald, Daniel; Chocholousova, Jana; Gardner, Paul; Iyer, Matthew K; Liu, Zongzhi; Lozupone, Catherine A; Quinn, John; Smit, Sandra; Wikman, Shandy; Zaneveld, Jesse R R; Knight, Rob | RNA (New York, N.Y.) | 2012 Jul | 22645380 | |
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| Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells. | Wu, Sitao; Li, Robert W; Li, Weizhong; Li, Cong-Jun | PloS one | 2012 | e36940 | 22615851 |
| An ileal Crohn's disease gene signature based on whole human genome expression profiles of disease unaffected ileal mucosal biopsies. | Zhang, Tianyi; Song, Bowen; Zhu, Wei; Xu, Xiao; Gong, Qing Qing; Morando, Christopher; Dassopoulos, Themistocles; Newberry, Rodney D; Hunt, Steven R; Li, Ellen | PloS one | 2012 | e37139 | 22606341 |
| Bacterial communities of the coronal sulcus and distal urethra of adolescent males. | Nelson, David E; Dong, Qunfeng; Van der Pol, Barbara; Toh, Evelyn; Fan, Baochang; Katz, Barry P; Mi, Deming; Rong, Ruichen; Weinstock, George M; Sodergren, Erica; Fortenberry, J Dennis | PloS one | 2012 | e36298 | 22606251 |
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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 A | Chemistry & biodiversity | 2012 May | 965-76 | 22589096 |
| Food and the gut microbiota in inflammatory bowel diseases: a critical connection. | Albenberg, Lindsey G; Lewis, James D; Wu, Gary D | Current opinion in gastroenterology | 2012 Jul | 314-20 | 22573192 |
| Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing. | Xiong, Xuejian; Frank, Daniel N; Robertson, Charles E; Hung, Stacy S; Markle, Janet; Canty, Angelo J; McCoy, Kathy D; Macpherson, Andrew J; Poussier, Philippe; Danska, Jayne S; Parkinson, John | PloS one | 2012 | e36009 | 22558305 |
| Temporal dynamics of the human vaginal microbiota. | Gajer, Pawel; Brotman, Rebecca M; Bai, Guoyun; Sakamoto, Joyce; Schutte, Ursel M E; Zhong, Xue; Koenig, Sara S K; Fu, Li; Ma, Zhanshan Sam; Zhou, Xia; Abdo, Zaid; Forney, Larry J; Ravel, Jacques | Science translational medicine | 2012 May 2 | 132ra52 | 22553250 |
| Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots. | Matsen, Frederick A; Gallagher, Aaron | Algorithms for molecular biology : AMB. | 2012 May 02; | 22549005 | |
| We are what we eat: how the diet of infants affects their gut microbiome. | Pop, Mihai | Genome biology | 2012 | 152 | 22546514 |
| The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. | Ursell, Luke K; Clemente, Jose C; Rideout, Jai Ram; Gevers, Dirk; Caporaso, J Gregory; Knight, Rob | The Journal of allergy and clinical immunology | 2012 May | 1204-8 | 22541361 |
| Worm burden-dependent disruption of the porcine colon microbiota by Trichuris suis infection. | Wu, Sitao; Li, Robert W; Li, Weizhong; Beshah, Ethiopia; Dawson, Harry D; Urban Jr, Joseph F | PloS one | 2012 | e35470 | 22532855 |
| Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism. | Pathak, Darshankumar T; Wei, Xueming; Bucuvalas, Alex; Haft, Daniel H; Gerloff, Dietlind L; Wall, Daniel | PLoS genetics | 2012 | e1002626 | 22511878 |
| Alterations in the porcine colon microbiota induced by the gastrointestinal nematode Trichuris suis. | Li, Robert W; Wu, Sitao; Li, Weizhong; Navarro, Karl; Couch, Robin D; Hill, Dolores; Urban Jr, Joseph F | Infection and immunity | 2012 Jun | 2150-7 | 22493085 |
| Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes. | Giannoukos, Georgia; Ciulla, Dawn M; Huang, Katherine; Haas, Brian J; Izard, Jacques; Levin, Joshua Z; Livny, Jonathan; Earl, Ashlee M; Gevers, Dirk; Ward, Doyle V; Nusbaum, Chad; Birren, Bruce W; Gnirke, Andreas | Genome biology | 2012 | R23 | 22455878 |
| Decade-long bacterial community dynamics in cystic fibrosis airways. | Zhao, Jiangchao; Schloss, Patrick D; Kalikin, Linda M; Carmody, Lisa A; Foster, Bridget K; Petrosino, Joseph F; Cavalcoli, James D; VanDevanter, Donald R; Murray, Susan; Li, Jun Z; Young, Vincent B; LiPuma, John J | Proceedings of the National Academy of Sciences of the United States of America | 2012 Apr 10 | 5809-14 | 22451929 |
| Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation. | Hill, David A; Siracusa, Mark C; Abt, Michael C; Kim, Brian S; Kobuley, Dmytro; Kubo, Masato; Kambayashi, Taku; Larosa, David F; Renner, Ellen D; Orange, Jordan S; Bushman, Frederic D; Artis, David | Nature medicine | 2012 Apr | 538-46 | 22447074 |
| AntiFam: a tool to help identify spurious ORFs in protein annotation. | Eberhardt, Ruth Y; Haft, Daniel H; Punta, Marco; Martin, Maria; O'Donovan, Claire; Bateman, Alex | Database : the journal of biological databases and curation | 2012 | bas003 | 22434837 |
| Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). | Pamp, Sunje J; Harrington, Eoghan D; Quake, Stephen R; Relman, David A; Blainey, Paul C | Genome research | 2012 Jun | 1107-19 | 22434425 |
| The impact of the gut microbiota on human health: an integrative view. | Clemente, Jose C; Ursell, Luke K; Parfrey, Laura Wegener; Knight, Rob | Cell. | 2012 Mar 16; | 22424233 | |
| 4,5-Diphen-oxy-benzene-1,2-dicarbo-nitrile. | Foo, Chuan Ching; Tan, Ai Ling; Wimmer, Franz L; Mirza, Aminul Huq; Young, David J; Ng, Seik Weng; Tiekink, Edward R T | Acta crystallographica. Section E, Structure reports online. | 2012 Mar 01; | 22412514 | |
| Dichlorido{1-[N-(5-chloro-2-oxidophen-yl)carboximido-yl]naphthalen-2-olato-?O,N,O'}(methanol-?O)tin(IV). | Shahverdizadeh, Gholam Hossein; Ng, Seik Weng; Tiekink, Edward R T; Mirtamizdoust, Babak | Acta crystallographica. Section E, Structure reports online. | 2012 Mar 01; | 22412406 | |
| The human microbiome: at the interface of health and disease. | Cho, Ilseung; Blaser, Martin J | Nature reviews. Genetics | 2012 Apr | 260-70 | 22411464 |
| Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. | Caporaso, J Gregory; Lauber, Christian L; Walters, William A; Berg-Lyons, Donna; Huntley, James; Fierer, Noah; Owens, Sarah M; Betley, Jason; Fraser, Louise; Bauer, Markus; Gormley, Niall; Gilbert, Jack A; Smith, Geoff; Knight, Rob | The ISME journal. | 2012 Aug; | 1621-4 | 22402401 |
| Experiences of patients with chronic gastrointestinal conditions: in their own words. | McCormick, Jennifer B; Hammer, Rachel R; Farrell, Ruth M; Geller, Gail; James, Katherine M; Loftus Jr, Edward V; Mercer, Mary Beth; Tilburt, Jon C; Sharp, Richard R | Health and quality of life outcomes | 2012 | 25 | 22401607 |
| Standard colonic lavage alters the natural state of mucosal-associated microbiota in the human colon. | Harrell, Laura; Wang, Yunwei; Antonopoulos, Dionysios; Young, Vincent; Lichtenstein, Lev; Huang, Yong; Hanauer, Stephen; Chang, Eugene | PloS one | 2012 | e32545 | 22389708 |
| A format for phylogenetic placements. | Matsen, Frederick A; Hoffman, Noah G; Gallagher, Aaron; Stamatakis, Alexandros | PloS one | 2012 | e31009 | 22383988 |
| Of microbes and meals: the health consequences of dietary endotoxemia. | Kelly, Caleb J; Colgan, Sean P; Frank, Daniel N | Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition. | 2012 Apr; | 22378797 | |
| Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment. | Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta; Pel, Joel; Marziali, Andre | PloS one | 2012 | e31597 | 22355378 |
| Hypervariable loci in the human gut virome. | Minot, Samuel; Grunberg, Stephanie; Wu, Gary D; Lewis, James D; Bushman, Frederic D | Proceedings of the National Academy of Sciences of the United States of America | 2012 Mar 6 | 3962-6 | 22355105 |
| Molecular pathways: pathogenesis and clinical implications of microbiome alteration in esophagitis and Barrett esophagus. | Yang, Liying; Francois, Fritz; Pei, Zhiheng | Clinical cancer research : an official journal of the American Association for Cancer Research | 2012 Apr 15 | 2138-44 | 22344232 |
| Host response to probiotics determined by nutritional status of rotavirus-infected neonatal mice. | Preidis, Geoffrey A; Saulnier, Delphine M; Blutt, Sarah E; Mistretta, Toni-Ann; Riehle, Kevin P; Major, Angela M; Venable, Susan F; Barrish, James P; Finegold, Milton J; Petrosino, Joseph F; Guerrant, Richard L; Conner, Margaret E; Versalovic, James | Journal of pediatric gastroenterology and nutrition | 2012 Sep | 299-307 | 22343914 |
| Altered vaginal microbiota are associated with perinatal mother-to-child transmission of HIV in African women from Burkina Faso. | Frank, Daniel N; Manigart, Olivier; Leroy, Valeriane; Meda, Nicolas; Valea, Diane; Zhang, Weiming; Dabis, Francois; Pace, Norman R; Van de Perre, Philippe; Janoff, Edward N | Journal of acquired immune deficiency syndromes (1999) | 2012 Jul 1 | 299-306 | 22343176 |
| Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice. | Mei, Junjie; Liu, Yuhong; Dai, Ning; Hoffmann, Christian; Hudock, Kristin M; Zhang, Peggy; Guttentag, Susan H; Kolls, Jay K; Oliver, Paula M; Bushman, Frederic D; Worthen, G Scott | The Journal of clinical investigation | 2012 Mar 1 | 974-86 | 22326959 |
| Significance of the microbiome in obstructive lung disease. | Han, Meilan K; Huang, Yvonne J; Lipuma, John J; Boushey, Homer A; Boucher, Richard C; Cookson, William O; Curtis, Jeffrey L; Erb-Downward, John; Lynch, Susan V; Sethi, Sanjay; Toews, Galen B; Young, Vincent B; Wolfgang, Matthew C; Huffnagle, Gary B; Marti | Thorax | 2012 May | 456-63 | 22318161 |
| The under-recognized dominance of Verrucomicrobia in soil bacterial communities. | Bergmann, Gaddy T; Bates, Scott T; Eilers, Kathryn G; Lauber, Christian L; Caporaso, J Gregory; Walters, William A; Knight, Rob; Fierer, Noah | Soil biology & biochemistry | 2011 Jul | 1450-1455 | 22267877 |
| Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine. | Preidis, Geoffrey A; Saulnier, Delphine M; Blutt, Sarah E; Mistretta, Toni-Ann; Riehle, Kevin P; Major, Angela M; Venable, Susan F; Finegold, Milton J; Petrosino, Joseph F; Conner, Margaret E; Versalovic, James | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 2012 May | 1960-9 | 22267340 |
| Perturbation dynamics of the rumen microbiota in response to exogenous butyrate. | Li, Robert W; Wu, Sitao; Baldwin 6th, Ransom L; Li, Weizhong; Li, Congjun | PloS one | 2012 | e29392 | 22253719 |
| Microbiome complexity and Staphylococcus aureus in chronic rhinosinusitis. | Feazel, Leah M; Robertson, Charles E; Ramakrishnan, Vijay R; Frank, Daniel N | The Laryngoscope | 2012 Feb | 467-72 | 22253013 |
| Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments. | Ozok, A R; Persoon, I F; Huse, S M; Keijser, B J F; Wesselink, P R; Crielaard, W; Zaura, E | International endodontic journal | 2012 Jun | 530-41 | 22251411 |
| Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences. | Soergel, David A W; Dey, Neelendu; Knight, Rob; Brenner, Steven E | The ISME journal | 2012 Jul | 1440-4 | 22237546 |
| Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. | Schatz, Michael C; Phillippy, Adam M; Sommer, Daniel D; Delcher, Arthur L; Puiu, Daniela; Narzisi, Giuseppe; Salzberg, Steven L; Pop, Mihai | Briefings in bioinformatics | 2013 Mar | 213-24 | 22199379 |
| Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws. | Smajs, David; Norris, Steven J; Weinstock, George M | Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases | 2012 Mar | 191-202 | 22198325 |
| GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease. | Haft, Daniel H; Varghese, Neha | PloS one | 2011 | e28886 | 22194940 |
| Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. | Schloss, Patrick D; Gevers, Dirk; Westcott, Sarah L | PloS one | 2011 | e27310 | 22194782 |
| IMG: the Integrated Microbial Genomes database and comparative analysis system. | Markowitz, Victor M; Chen, I-Min A; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos | Nucleic acids research | 2012 Jan | D115-22 | 22194640 |
| Human microbiome and HIV/AIDS. | Saxena, Deepak; Li, Yihong; Yang, Liying; Pei, Zhiheng; Poles, Michael; Abrams, William R; Malamud, Daniel | Current HIV/AIDS reports | 2012 Mar | 44-51 | 22193889 |
| Single-cell protein analysis. | Wu, Meiye; Singh, Anup K | Current opinion in biotechnology | 2012 Feb | 83-8 | 22189001 |
| Experimental and analytical tools for studying the human microbiome. | Kuczynski, Justin; Lauber, Christian L; Walters, William A; Parfrey, Laura Wegener; Clemente, Jose C; Gevers, Dirk; Knight, Rob | Nature reviews. Genetics | 2012 Jan | 47-58 | 22179717 |
| Artificial functional difference between microbial communities caused by length difference of sequencing reads. | Zhang, Quan; Doak, Thomas G; Ye, Yuzhen | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 2012 | 259-70 | 22174281 |
| Advancing analytical algorithms and pipelines for billions of microbial sequences. | Gonzalez, Antonio; Knight, Rob | Current opinion in biotechnology | 2012 Feb | 64-71 | 22172529 |
| SitePainter: a tool for exploring biogeographical patterns. | Gonzalez, Antonio; Stombaugh, Jesse; Lauber, Christian L; Fierer, Noah; Knight, Rob | Bioinformatics (Oxford, England) | 2012 Feb 1 | 436-8 | 22171330 |
| Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences. | Wang, Xiaoyu; Cai, Yunpeng; Sun, Yijun; Knight, Rob; Mai, Volker | The ISME journal | 2012 Jul | 1277-80 | 22170430 |
| Using QIIME to analyze 16S rRNA gene sequences from microbial communities. | Kuczynski, Justin; Stombaugh, Jesse; Walters, William Anton; Gonzalez, Antonio; Caporaso, J Gregory; Knight, Rob | Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] | 2011 Dec | Unit 10.7. | 22161565 |
| Single cell genome sequencing. | Yilmaz, Suzan; Singh, Anup K | Current opinion in biotechnology | 2012 Jun | 437-43 | 22154471 |
| Characterizing microbial communities through space and time. | Gonzalez, Antonio; King, Andrew; Robeson 2nd, Michael S; Song, Sejin; Shade, Ashley; Metcalf, Jessica L; Knight, Rob | Current opinion in biotechnology | 2012 Jun | 431-6 | 22154467 |
| GAGE: A critical evaluation of genome assemblies and assembly algorithms. | Salzberg, Steven L; Phillippy, Adam M; Zimin, Aleksey; Puiu, Daniela; Magoc, Tanja; Koren, Sergey; Treangen, Todd J; Schatz, Michael C; Delcher, Arthur L; Roberts, Michael; Marcais, Guillaume; Pop, Mihai; Yorke, James A | Genome research | 2012 Mar | 557-67 | 22147368 |
| CharProtDB: a database of experimentally characterized protein annotations. | Madupu, Ramana; Richter, Alexander; Dodson, Robert J; Brinkac, Lauren; Harkins, Derek; Durkin, Scott; Shrivastava, Susmita; Sutton, Granger; Haft, Daniel | Nucleic acids research | 2012 Jan | D237-41 | 22140108 |
| The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. | Pagani, Ioanna; Liolios, Konstantinos; Jansson, Jakob; Chen, I-Min A; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor M; Kyrpides, Nikos C | Nucleic acids research | 2012 Jan | D571-9 | 22135293 |
| An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. | McDonald, Daniel; Price, Morgan N; Goodrich, Julia; Nawrocki, Eric P; DeSantis, Todd Z; Probst, Alexander; Andersen, Gary L; Knight, Rob; Hugenholtz, Philip | The ISME journal | 2012 Mar | 610-8 | 22134646 |
| Strategies for metagenomic-guided whole-community proteomics of complex microbial environments. | Cantarel, Brandi L; Erickson, Alison R; VerBerkmoes, Nathan C; Erickson, Brian K; Carey, Patricia A; Pan, Chongle; Shah, Manesh; Mongodin, Emmanuel F; Jansson, Janet K; Fraser-Liggett, Claire M; Hettich, Robert L | PloS one | 2011 | e27173 | 22132090 |
| An optical-coding method to measure particle distribution in microfluidic devices. | Wu, Tsung-Feng; Mei, Zhe; Pion-Tonachini, Luca; Zhao, Chao; Qiao, Wen; Arianpour, Ashkan; Lo, Yu-Hwa | AIP advances. | 2011 Jun; | 22125760 | |
| The Human Microbiome Project: lessons from human genomics. | Lewis Jr, Cecil M; Obregon-Tito, Alexandra; Tito, Raul Y; Foster, Morris W; Spicer, Paul G | Trends in microbiology | 2012 Jan | 1-4 | 22112388 |
| Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment. | Ye, Yuzhen | Proceedings. IEEE International Conference on Bioinformatics and Biomedicine | 2011 Feb 4 | 153-157 | 22102981 |
| Astrovirus MLB2 viremia in febrile child. | Holtz, Lori R; Wylie, Kristine M; Sodergren, Erica; Jiang, Yanfang; Franz, Carl J; Weinstock, George M; Storch, Gregory A; Wang, David | Emerging infectious diseases | 2011 Nov | 2050-2 | 22099095 |
| IMG/M: the integrated metagenome data management and comparative analysis system. | Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Pati, Amrita; Huntemann, Marcel; Liolios, Konstantinos; Pagani, Ioanna; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natali | Nucleic acids research | 2012 Jan | D123-9 | 22086953 |
| The intestinal microbiota in health and disease. | Young, Vincent B | Current opinion in gastroenterology | 2012 Jan | 63-9 | 22080827 |
| Epigenetic priors for identifying active transcription factor binding sites. | Cuellar-Partida, Gabriel; Buske, Fabian A; McLeay, Robert C; Whitington, Tom; Noble, William Stafford; Bailey, Timothy L | Bioinformatics (Oxford, England) | 2012 Jan 1 | 56-62 | 22072382 |
| ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. | Basu, Malay K; Selengut, Jeremy D; Haft, Daniel H | BMC bioinformatics | 2011 | 434 | 22070167 |
| Tetra-?-acetato-?O:O'-bis-[(3,5-di-methyl-1H-pyrazole-?N)-copper(II)]. | van Wyk, Juanita; Omondi, Bernard; Darkwa, James | Acta crystallographica. Section E, Structure reports online. | 2011 Sep 01; | 22065823 | |
| 2,2'-Bis(meth-oxy-meth-oxy)-3-methyl-1,1'-binaphth-yl. | Carrilho, Rui M B; Abreu, Artur R; Pereira, Mariette M; Rodrigues, V H | Acta crystallographica. Section E, Structure reports online. | 2011 Sep 01; | 22058976 | |
| Saying privacy, meaning confidentiality. | Schwab, Abraham P; Frank, Lily; Gligorov, Nada | The American journal of bioethics : AJOB | 2011 Nov | 44-5 | 22047127 |
| De minimis risk: a proposal for a new category of research risk. | Rhodes, Rosamond; Azzouni, Jody; Baumrin, Stefan Bernard; Benkov, Keith; Blaser, Martin J; Brenner, Barbara; Dauben, Joseph W; Earle, William J; Frank, Lily; Gligorov, Nada; Goldfarb, Joseph; Hirschhorn, Kurt; Hirschhorn, Rochelle; Holzman, Ian; Indyk, De | The American journal of bioethics : AJOB | 2011 Nov | 1-7 | 22047112 |
| RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. | Zhao, Yongan; Tang, Haixu; Ye, Yuzhen | Bioinformatics (Oxford, England) | 2012 Jan 1 | 125-6 | 22039206 |
| Graph accordance of next-generation sequence assemblies. | Yao, Guohui; Ye, Liang; Gao, Hongyu; Minx, Patrick; Warren, Wesley C; Weinstock, George M | Bioinformatics (Oxford, England) | 2012 Jan 1 | 13-6 | 22025481 |
| Microbiome and malignancy. | Plottel, Claudia S; Blaser, Martin J | Cell host & microbe | 2011 Oct 20 | 324-35 | 22018233 |
| Human-associated microbial signatures: examining their predictive value. | Knights, Dan; Parfrey, Laura Wegener; Zaneveld, Jesse; Lozupone, Catherine; Knight, Rob | Cell host & microbe. | 2011 Oct 20; | 22018228 | |
| Fluorescent labeling of antibody fragments using split GFP. | Ferrara, Fortunato; Listwan, Pawel; Waldo, Geoffrey S; Bradbury, Andrew R M | PloS one | 2011 | e25727 | 21998685 |
| Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. | Liu, Bo; Gibbons, Theodore; Ghodsi, Mohammad; Treangen, Todd; Pop, Mihai | BMC genomics | 2011 | S4 | 21989143 |
| Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data. | Liu, Zhenqiu; Hsiao, William; Cantarel, Brandi L; Drabek, Elliott Franco; Fraser-Liggett, Claire | Bioinformatics (Oxford, England) | 2011 Dec 1 | 3242-9 | 21984758 |
| Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. | Segata, Nicola; Huttenhower, Curtis | PloS one | 2011 | e24704 | 21931822 |
| Bambus 2: scaffolding metagenomes. | Koren, Sergey; Treangen, Todd J; Pop, Mihai | Bioinformatics (Oxford, England) | 2011 Nov 1 | 2964-71 | 21926123 |
| The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. | Sczesnak, Andrew; Segata, Nicola; Qin, Xiang; Gevers, Dirk; Petrosino, Joseph F; Huttenhower, Curtis; Littman, Dan R; Ivanov, Ivaylo I | Cell host & microbe | 2011 Sep 15 | 260-72 | 21925113 |
| Applying an optical space-time coding method to enhance light scattering signals in microfluidic devices. | Mei, Zhe; Wu, Tsung-Feng; Pion-Tonachini, Luca; Qiao, Wen; Zhao, Chao; Liu, Zhiwen; Lo, Yu-Hwa | Biomicrofluidics. | 2011 Sep; | 21915241 | |
| Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). | Youssef, Noha H; Blainey, Paul C; Quake, Stephen R; Elshahed, Mostafa S | Applied and environmental microbiology | 2011 Nov | 7804-14 | 21908640 |
| TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. | Pirrung, Meg; Kennedy, Ryan; Caporaso, J Gregory; Stombaugh, Jesse; Wendel, Doug; Knight, Rob | Bioinformatics (Oxford, England) | 2011 Nov 1 | 3067-9 | 21903626 |
| WebMGA: a customizable web server for fast metagenomic sequence analysis. | Wu, Sitao; Zhu, Zhengwei; Fu, Liming; Niu, Beifang; Li, Weizhong | BMC genomics | 2011 | 444 | 21899761 |
| Genetic basis for in vivo daptomycin resistance in enterococci. | Arias, Cesar A; Panesso, Diana; McGrath, Danielle M; Qin, Xiang; Mojica, Maria F; Miller, Corwin; Diaz, Lorena; Tran, Truc T; Rincon, Sandra; Barbu, E Magda; Reyes, Jinnethe; Roh, Jung H; Lobos, Elizabeth; Sodergren, Erica; Pasqualini, Renata; Arap, Wadih | The New England journal of medicine | 2011 Sep 8 | 892-900 | 21899450 |
| Linking long-term dietary patterns with gut microbial enterotypes. | Wu, Gary D; Chen, Jun; Hoffmann, Christian; Bittinger, Kyle; Chen, Ying-Yu; Keilbaugh, Sue A; Bewtra, Meenakshi; Knights, Dan; Walters, William A; Knight, Rob; Sinha, Rohini; Gilroy, Erin; Gupta, Kernika; Baldassano, Robert; Nessel, Lisa; Li, Hongzhe; Bus | Science (New York, N.Y.) | 2011 Oct 7 | 105-8 | 21885731 |
| Antibiotic effects on bacterial profile in osteonecrosis of the jaw. | Ji, X; Pushalkar, S; Li, Y; Glickman, R; Fleisher, K; Saxena, D | Oral diseases | 2012 Jan | 85-95 | 21883710 |
| Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. | Zaneveld, Jesse R R; Parfrey, Laura Wegener; Van Treuren, Will; Lozupone, Catherine; Clemente, Jose C; Knights, Dan; Stombaugh, Jesse; Kuczynski, Justin; Knight, Rob | Trends in microbiology | 2011 Oct | 472-82 | 21872475 |
| Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison. | Ahn, Jiyoung; Yang, Liying; Paster, Bruce J; Ganly, Ian; Morris, Luc; Pei, Zhiheng; Hayes, Richard B | PloS one | 2011 | e22788 | 21829515 |
| Specific sorting of single bacterial cells with microfabricated fluorescence-activated cell sorting and tyramide signal amplification fluorescence in situ hybridization. | Chen, Chun H; Cho, Sung H; Chiang, Hsin-I; Tsai, Frank; Zhang, Kun; Lo, Yu-Hwa | Analytical chemistry | 2011 Oct 1 | 7269-75 | 21809842 |
| The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection. | Reeves, Angela E; Theriot, Casey M; Bergin, Ingrid L; Huffnagle, Gary B; Schloss, Patrick D; Young, Vincent B | Gut microbes | 2011 May-Jun | 145-58 | 21804357 |
| The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. | He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong | The ISME journal | 2012 Feb | 259-72 | 21796217 |
| Investigating the biological and clinical significance of human dysbioses. | Frank, Daniel N; Zhu, Wei; Sartor, R Balfour; Li, Ellen | Trends in microbiology | 2011 Sep | 427-34 | 21775143 |
| Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting through the Growing Pains and Moving Forward. | Young, Vincent B; Kahn, Stacy A; Schmidt, Thomas M; Chang, Eugene B | Frontiers in microbiology | 2011 | 144 | 21772835 |
| Bayesian community-wide culture-independent microbial source tracking. | Knights, Dan; Kuczynski, Justin; Charlson, Emily S; Zaneveld, Jesse; Mozer, Michael C; Collman, Ronald G; Bushman, Frederic D; Knight, Rob; Kelley, Scott T | Nature methods | 2011 Sep | 761-3 | 21765408 |
| Microfluidic fluorescence in situ hybridization and flow cytometry (ýýFlowFISH). | Liu, Peng; Meagher, Robert J; Light, Yooli K; Yilmaz, Suzan; Chakraborty, Romy; Arkin, Adam P; Hazen, Terry C; Singh, Anup K | Lab on a chip | 2011 Aug 21 | 2673-9 | 21755095 |
| Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. | Saulnier, Delphine M; Riehle, Kevin; Mistretta, Toni-Ann; Diaz, Maria-Alejandra; Mandal, Debasmita; Raza, Sabeen; Weidler, Erica M; Qin, Xiang; Coarfa, Cristian; Milosavljevic, Aleksandar; Petrosino, Joseph F; Highlander, Sarah; Gibbs, Richard; Lynch, Sus | Gastroenterology | 2011 Nov | 1782-91 | 21741921 |
| Extrapolation of urn models via poissonization: accurate measurements of the microbial unknown. | Lladser, Manuel E; Gouet, Raul; Reeder, Jens | PloS one | 2011 | e21105 | 21738613 |
| DNACLUST: accurate and efficient clustering of phylogenetic marker genes. | Ghodsi, Mohammadreza; Liu, Bo; Pop, Mihai | BMC bioinformatics | 2011 | 271 | 21718538 |
| Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. | Werner, Jeffrey J; Koren, Omry; Hugenholtz, Philip; DeSantis, Todd Z; Walters, William A; Caporaso, J Gregory; Angenent, Largus T; Knight, Rob; Ley, Ruth E | The ISME journal | 2012 Jan | 94-103 | 21716311 |
| How patients view probiotics: findings from a multicenter study of patients with inflammatory bowel disease and irritable bowel syndrome. | Mercer, MaryBeth; Brinich, Margaret A; Geller, Gail; Harrison, Krista; Highland, Janelle; James, Katherine; Marshall, Patricia; McCormick, Jennifer B; Tilburt, Jon; Achkar, Jean-Paul; Farrell, Ruth M; Sharp, Richard R | Journal of clinical gastroenterology | 2012 Feb | 138-44 | 21716123 |
| Metagenomic biomarker discovery and explanation. | Segata, Nicola; Izard, Jacques; Waldron, Levi; Gevers, Dirk; Miropolsky, Larisa; Garrett, Wendy S; Huttenhower, Curtis | Genome biology | 2011 | R60 | 21702898 |
| UCHIME improves sensitivity and speed of chimera detection. | Edgar, Robert C; Haas, Brian J; Clemente, Jose C; Quince, Christopher; Knight, Rob | Bioinformatics (Oxford, England) | 2011 Aug 15 | 2194-200 | 21700674 |
| Bacterial DNA content in the intestinal wall from infants with necrotizing enterocolitis. | Bucher, Brian T; McDuffie, Lucas A; Shaikh, Nurmohammad; Tarr, Phillip I; Warner, Barbara B; Hamvas, Aaron; White, Frances V; Erwin, Christopher R; Warner, Brad W | Journal of pediatric surgery | 2011 Jun | 1029-33 | 21683193 |
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| Boulder ALignment Editor (ALE): a web-based RNA alignment tool. | Stombaugh, Jesse; Widmann, Jeremy; McDonald, Daniel; Knight, Rob | Bioinformatics (Oxford, England) | 2011 Jun 15 | 1706-7 | 21546392 |
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| A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. | Sun, Yijun; Cai, Yunpeng; Huse, Susan M; Knight, Rob; Farmerie, William G; Wang, Xiaoyu; Mai, Volker | Briefings in bioinformatics | 2012 Jan | 107-21 | 21525143 |
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| Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. | Blainey, Paul C; Mosier, Annika C; Potanina, Anastasia; Francis, Christopher A; Quake, Stephen R | PloS one | 2011 | e16626 | 21364937 |
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| The microbe-derived short chain fatty acid butyrate targets miRNA-dependent p21 gene expression in human colon cancer. | Hu, Shien; Dong, Tien Sy; Dalal, Sushila R; Wu, Feng; Bissonnette, Marc; Kwon, John H; Chang, Eugene B | PloS one | 2011 | e16221 | 21283757 |
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| Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth. | Zhou, Xia; Brotman, Rebecca M; Gajer, Pawel; Abdo, Zaid; Schuette, Ursel; Ma, Sam; Ravel, Jacques; Forney, Larry J | Infectious diseases in obstetrics and gynecology | 2010 | 737425 | 21197076 |
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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 B | PloS one | 2010 | e13607 | 21042588 |
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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 H | Biochemistry | 2010 Nov 30 | 10117-30 | 20961038 |
| Human oral, gut, and plaque microbiota in patients with atherosclerosis. | Koren, Omry; Spor, Ayme; Felin, Jenny; Fak, Frida; Stombaugh, Jesse; Tremaroli, Valentina; Behre, Carl Johan; Knight, Rob; Fagerberg, Bjorn; Ley, Ruth E; Backhed, Fredrik | Proceedings of the National Academy of Sciences of the United States of America | 2011 Mar 15 | 4592-8 | 20937873 |
| Growth and Development Symposium: promoting healthier humans through healthier livestock: animal agriculture enters the metagenomics era. | Frank, D N | Journal of animal science | 2011 Mar | 835-44 | 20935136 |
| Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. | Wang, Yunwei; Antonopoulos, Dionysios A; Zhu, Xiaorong; Harrell, Laura; Hanan, Ira; Alverdy, John C; Meyer, Folker; Musch, Mark W; Young, Vincent B; Chang, Eugene B | Applied microbiology and biotechnology | 2010 Dec | 1333-42 | 20931185 |
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| Regional differences in colonic mucosa-associated microbiota determine the physiological expression of host heat shock proteins. | Hu, Shien; Wang, Yunwei; Lichtenstein, Lev; Tao, Yun; Musch, Mark W; Jabri, Bana; Antonopoulos, Dionysios; Claud, Erika C; Chang, Eugene B | American journal of physiology. Gastrointestinal and liver physiology | 2010 Dec | G1266-75 | 20864653 |
| Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. | Frank, Daniel N; Robertson, Charles E; Hamm, Christina M; Kpadeh, Zegbeh; Zhang, Tianyi; Chen, Hongyan; Zhu, Wei; Sartor, R Balfour; Boedeker, Edgar C; Harpaz, Noam; Pace, Norman R; Li, Ellen | Inflammatory bowel diseases | 2011 Jan | 179-84 | 20839241 |
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| Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. | Nossa, Carlos W; Oberdorf, William E; Yang, Liying; Aas, Jorn A; Paster, Bruce J; Desantis, Todd Z; Brodie, Eoin L; Malamud, Daniel; Poles, Michael A; Pei, Zhiheng | World journal of gastroenterology : WJG | 2010 Sep 7 | 4135-44 | 20806429 |
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| Genome sequencing reveals widespread virulence gene exchange among human Neisseria species. | Marri, Pradeep Reddy; Paniscus, Mary; Weyand, Nathan J; Rendon, Maria A; Calton, Christine M; Hernandez, Diana R; Higashi, Dustin L; Sodergren, Erica; Weinstock, George M; Rounsley, Steven D; So, Magdalene | PloS one | 2010 | e11835 | 20676376 |
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| The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. | Redford, Amanda J; Bowers, Robert M; Knight, Rob; Linhart, Yan; Fierer, Noah | Environmental microbiology | 2010 Nov | 2885-93 | 20545741 |
| Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies. | Harwich Jr, Michael D; Alves, Joao M; Buck, Gregory A; Strauss 3rd, Jerome F; Patterson, Jennifer L; Oki, Aminat T; Girerd, Philippe H; Jefferson, Kimberly K | BMC genomics | 2010 | 375 | 20540756 |
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