Program Publications
Program Publications
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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Authors | Journal | PubMedID | Publication Date |
|---|---|---|---|---|
| Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit. | Schwartz, Drew J; Shalon, Nitan; Wardenburg, Kate; DeVeaux, Anna; Wallace, Meghan A; Hall-Moore, Carla; Ndao, I Malick; Sullivan, Janice E; Radmacher, Paula; Escobedo, Marilyn; Burnham, Carey-Ann D; Warner, Barbara B; Tarr, Phillip I; Dantas, Gautam | Science translational medicine | 37134153 | 2023 May 03 |
| The Microbiome and Big Data. | Navas-Molina, Jose A; Hyde, Embriette R; Sanders, Jon; Knight, Rob | Current opinion in systems biology | 36937228 | 2017 Aug |
| History of childhood physical abuse is associated with gut microbiota diversity among adult psychiatric inpatients. | Rohr, Jessica C; Bourassa, Katelynn A; Thompson, Dominique S; Fowler, J Christopher; Frueh, B Christopher; Weinstein, Benjamin L; Petrosino, Joseph; Madan, Alok | Journal of affective disorders | 36933668 | 2023 Jun 15 |
| Does the Vaginal Microbiome Operate Differently by Race to Influence Risk of Precervical Cancer? | Tossas, Katherine Y; Zhu, Bin; Perera, Robert A; Serrano, Myrna G; Sullivan, Stephanie; Sayeed, Sadia; Strauss 3rd, Jerome F; Winn, Robert A; Buck, Gregory A; Seewaldt, Victoria L | Journal of women's health (2002) | 36897755 | 2023 May |
| Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth. | Liao, Jingqiu; Shenhav, Liat; Urban, Julia A; Serrano, Myrna; Zhu, Bin; Buck, Gregory A; Korem, Tal | bioRxiv : the preprint server for biology | 36711990 | 2023 Jun 17 |
| Persistence and In Vivo Evolution of Vaginal Bacterial Strains over a Multiyear Time Period. | France, Michael; Ma, Bing; Ravel, Jacques | mSystems | 36413016 | 2022 Dec 20 |
| Roles of the Microbiota of the Female Reproductive Tract in Gynecological and Reproductive Health. | Zhu, Bin; Tao, Zhi; Edupuganti, Laahirie; Serrano, Myrna G; Buck, Gregory A | Microbiology and molecular biology reviews : MMBR | 36222685 | 2022 Dec 21 |
| Differential co-expression networks of the gut microbiota are associated with depression and anxiety treatment resistance among psychiatric inpatients. | Thompson, Dominique S; Fu, Chenlian; Gandhi, Tanmay; Fowler, J Christopher; Frueh, B Christopher; Weinstein, Benjamin L; Petrosino, Joseph; Hadden, Julia K; Carlson, Marianne; Coarfa, Cristian; Madan, Alok | Progress in neuro-psychopharmacology & biological psychiatry | 36122838 | 2023 Jan 10 |
| "What is the FDA Going to Think?": Negotiating Values through Reflective and Strategic Category Work in Microbiome Science. | Darling, Katherine W; Boyce, Angie M; Cho, Mildred K; Sankar, Pamela L | Science, technology & human values | 36119463 | 2015 Jan |
| Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression. | Delgado-Diaz, David Jose; Jesaveluk, Brianna; Hayward, Joshua A; Tyssen, David; Alisoltani, Arghavan; Potgieter, Matthys; Bell, Liam; Ross, Elizabeth; Iranzadeh, Arash; Allali, Imane; Dabee, Smritee; Barnabas, Shaun; Gamieldien, Hoyam; Blackburn, Jonathan M; Mulder, Nicola; Smith, Steven B; Edwards, Vonetta L; Burgener, Adam D; Bekker, Linda-Gail; Ravel, Jacques; Passmore, Jo-Ann S; Masson, Lindi; Hearps, Anna C; Tachedjian, Gilda | Microbiome | 36045402 | 2022 08 31 |
| A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria. | Yao, Lina; D'Agostino, Gabriel D; Park, Jinseok; Hang, Saiyu; Adhikari, Arijit A; Zhang, Yancong; Li, Wei; Avila-Pacheco, Julian; Bae, Sena; Clish, Clary B; Franzosa, Eric A; Huttenhower, Curtis; Huh, Jun R; Devlin, A Sloan | Nature microbiology | 35982310 | 2022 09 |
| Factors Associated With Incidence and Spontaneous Clearance of Molecular-Bacterial Vaginosis: Results From a Longitudinal Frequent-Sampling Observational Study. | Tamarelle, Jeanne; Shardell, Michelle D; Ravel, Jacques; Brotman, Rebecca M | Sexually transmitted diseases | 35969846 | 2022 Sep 01 |
| Complete Genome Sequences of Ezakiella coagulans C0061C1 and Fenollaria massiliensis C0061C2. | France, Michael T; Clifford, Jack; Narina, Shilpa; Rutt, Lindsay; Ravel, Jacques | Microbiology resource announcements | 35861554 | 2022 Jul 21 |
| High-sensitivity pattern discovery in large, paired multiomic datasets. | Ghazi, Andrew R; Sucipto, Kathleen; Rahnavard, Ali; Franzosa, Eric A; McIver, Lauren J; Lloyd-Price, Jason; Schwager, Emma; Weingart, George; Moon, Yo Sup; Morgan, Xochitl C; Waldron, Levi; Huttenhower, Curtis | Bioinformatics (Oxford, England) | 35758795 | 2022 06 24 |
| Progressive dysbiosis of human orodigestive microbiota along the sequence of gastroesophageal reflux, Barrett's esophagus and esophageal adenocarcinoma. | Hao, Yuhan; Karaoz, Ulas; Yang, Liying; Yachimski, Patrick S; Tseng, Wenzhi; Nossa, Carlos W; Ye, Weimin; Tseng, Mengkao; Poles, Michael; Francois, Fritz; Traube, Morris; Brown, Stuart M; Chen, Yu; Torralba, Manolito; Peek, Richard M; Brodie, Eoin L; Pei, Zhiheng | International journal of cancer | 35751398 | 2022 Jun 24 |
| Douching cessation and molecular bacterial vaginosis: a reanalysis of archived specimens. | Brown, Sarah Elizabeth; He, Xin; Shardell, Michelle D; Ravel, Jacques; Ghanem, Khalil G; Zenilman, Jonathan M; Brotman, Rebecca M | Sexually transmitted infections | 35636931 | 2022 May 30 |
| Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants. | Kaelin, Emily A; Rodriguez, Cynthia; Hall-Moore, Carla; Hoffmann, Julie A; Linneman, Laura A; Ndao, I Malick; Warner, Barbara B; Tarr, Phillip I; Holtz, Lori R; Lim, Efrem S | Nature microbiology | 35449461 | 2022 May |
| Dietary lignans, plasma enterolactone levels, and metabolic risk in men: exploring the role of the gut microbiome. | Li, Yanping; Wang, Fenglei; Li, Jun; Ivey, Kerry L; Wilkinson, Jeremy E; Wang, Dong D; Li, Ruifeng; Liu, Gang; Eliassen, Heather A; Chan, Andrew T; Clish, Clary B; Huttenhower, Curtis; Hu, Frank B; Sun, Qi; Rimm, Eric B | BMC microbiology | 35350985 | 2022 03 29 |
| Associations Between Vaginal Bacteria and Bacterial Vaginosis Signs and Symptoms: A Comparative Study of Kenyan and American Women. | Carter, Kayla A; Balkus, Jennifer E; Anzala, Omu; Kimani, Joshua; Hoffman, Noah G; Fiedler, Tina L; Mochache, Vernon; Fredricks, David N; McClelland, Raymond Scott; Srinivasan, Sujatha | Frontiers in cellular and infection microbiology | 35310847 | 2022 |
| Exerkines in health, resilience and disease. | Chow, Lisa S; Gerszten, Robert E; Taylor, Joan M; Pedersen, Bente K; van Praag, Henriette; Trappe, Scott; Febbraio, Mark A; Galis, Zorina S; Gao, Yunling; Haus, Jacob M; Lanza, Ian R; Lavie, Carl J; Lee, Chih-Hao; Lucia, Alejandro; Moro, Cedric; Pandey, Ambarish; Robbins, Jeremy M; Stanford, Kristin I; Thackray, Alice E; Villeda, Saul; Watt, Matthew J; Xia, Ashley; Zierath, Juleen R; Goodpaster, Bret H; Snyder, Michael P | Nature reviews. Endocrinology | 35304603 | 2022 05 |
| Human gut bacteria produce ΤΗ17-modulating bile acid metabolites. | Paik, Donggi; Yao, Lina; Zhang, Yancong; Bae, Sena; D'Agostino, Gabriel D; Zhang, Minghao; Kim, Eunha; Franzosa, Eric A; Avila-Pacheco, Julian; Bisanz, Jordan E; Rakowski, Christopher K; Vlamakis, Hera; Xavier, Ramnik J; Turnbaugh, Peter J; Longman, Randy S; Krout, Michael R; Clish, Clary B; Rastinejad, Fraydoon; Huttenhower, Curtis; Huh, Jun R; Devlin, A Sloan | Nature | 35296854 | 2022 03 |
| Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data. | France, Michael T; Fu, Li; Rutt, Lindsay; Yang, Hongqiu; Humphrys, Michael S; Narina, Shilpa; Gajer, Pawel M; Ma, Bing; Forney, Larry J; Ravel, Jacques | Genome biology | 35232471 | 2022 Mar 01 |
| Corrigendum to: Spec-seq: determining protein-DNA-binding specificity by sequencing. | Zuo, Zheng; Chang, Yiming Kenny; Stormo, Gary D | Briefings in functional genomics | 34923581 | 2022 Apr 11 |
| Unique roles of vaginal Megasphaera phylotypes in reproductive health. | Glascock, Abigail L; Jimenez, Nicole R; Boundy, Sam; Koparde, Vishal N; Brooks, J Paul; Edwards, David J; Strauss Iii, Jerome F; Jefferson, Kimberly K; Serrano, Myrna G; Buck, Gregory A; Fettweis, Jennifer M | Microbial genomics | 34898422 | 2021 12 |
| The vaginal microbiome in women of reproductive age with healthy weight versus overweight/obesity. | Allen, Natalie G; Edupuganti, Laahirie; Edwards, David J; Jimenez, Nicole R; Buck, Gregory A; Jefferson, Kimberly K; Strauss 3rd, Jerome F; Vaginal Microbiome Consortium; Wickham 3rd, Edmond P; Fettweis, Jennifer M | Obesity (Silver Spring, Md.) | 34806323 | 2022 01 |
| Multivariable association discovery in population-scale meta-omics studies. | Mallick, Himel; Rahnavard, Ali; McIver, Lauren J; Ma, Siyuan; Zhang, Yancong; Nguyen, Long H; Tickle, Timothy L; Weingart, George; Ren, Boyu; Schwager, Emma H; Chatterjee, Suvo; Thompson, Kelsey N; Wilkinson, Jeremy E; Subramanian, Ayshwarya; Lu, Yiren; Waldron, Levi; Paulson, Joseph N; Franzosa, Eric A; Bravo, Hector Corrada; Huttenhower, Curtis | PLoS computational biology | 34784344 | 2021 11 |
| Metagenomic profiling of placental tissue suggests DNA virus infection of the placenta is rare. | Witney, Adam A; Aller, Sean; Strang, Blair L | The Journal of general virology | 34723784 | 2021 11 |
| Complex species and strain ecology of the vaginal microbiome from pregnancy to postpartum and association with preterm birth. | Pace, Ryan M; Chu, Derrick M; Prince, Amanda L; Ma, Jun; Seferovic, Maxim D; Aagaard, Kjersti M | Med (New York, N.Y.) | 34617072 | 2021 Sep 10 |
| Vaginal microbiome Lactobacillus crispatus is heritable among European American women. | Wright, Michelle L; Fettweis, Jennifer M; Eaves, Lindon J; Silberg, Judy L; Neale, Michael C; Serrano, Myrna G; Jimenez, Nicole R; Prom-Wormley, Elizabeth; Girerd, Philippe H; Borzelleca Jr, Joseph F; Jefferson, Kimberly K; Strauss 3rd, Jerome F; York, Timothy P; Buck, Gregory A | Communications biology | 34354222 | 2021 08 05 |
| The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men. | Sikavi, Daniel R; Nguyen, Long H; Haruki, Koichiro; Ugai, Tomotaka; Ma, Wenjie; Wang, Dong D; Thompson, Kelsey N; Yan, Yan; Branck, Tobyn; Wilkinson, Jeremy E; Akimoto, Naohiko; Zhong, Rong; Lau, Mai Chan; Mima, Kosuke; Kosumi, Keisuke; Morikawa, Teppei; Rimm, Eric B; Garrett, Wendy S; Izard, Jacques; Cao, Yin; Song, Mingyang; Huttenhower, Curtis; Ogino, Shuji; Chan, Andrew T | Clinical and translational gastroenterology | 34333506 | 2021 08 01 |
| Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment. | Roodgar, Morteza; Good, Benjamin H; Garud, Nandita R; Martis, Stephen; Avula, Mohan; Zhou, Wenyu; Lancaster, Samuel M; Lee, Hayan; Babveyh, Afshin; Nesamoney, Sophia; Pollard, Katherine S; Snyder, Michael P | Genome research | 34301627 | 2021 08 |
| Assessing the Concordance Between Urogenital and Vaginal Microbiota: Can Urine Specimens Be Used as a Proxy for Vaginal Samples? | Brown, Sarah E; Robinson, Courtney K; Shardell, Michelle D; Holm, Johanna B; Ravel, Jacques; Ghanem, Khalil G; Brotman, Rebecca M | Frontiers in cellular and infection microbiology | 34268137 | 2021 |
| Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. | Thänert, Robert; Thänert, Anna; Ou, Jocelyn; Bajinting, Adam; Burnham, Carey-Ann D; Engelstad, Holly J; Tecos, Maria E; Ndao, I Malick; Hall-Moore, Carla; Rouggly-Nickless, Colleen; Carl, Mike A; Rubin, Deborah C; Davidson, Nicholas O; Tarr, Phillip I; Warner, Barbara B; Dantas, Gautam; Warner, Brad W | Gut microbes | 34264786 | 2021 Jan-Dec |
| Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men. | Ma, Wenjie; Nguyen, Long H; Song, Mingyang; Wang, Dong D; Franzosa, Eric A; Cao, Yin; Joshi, Amit; Drew, David A; Mehta, Raaj; Ivey, Kerry L; Strate, Lisa L; Giovannucci, Edward L; Izard, Jacques; Garrett, Wendy; Rimm, Eric B; Huttenhower, Curtis; Chan, Andrew T | Genome medicine | 34140026 | 2021 06 17 |
| Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome. | Li, Yanping; Wang, Dong D; Satija, Ambika; Ivey, Kerry L; Li, Jun; Wilkinson, Jeremy E; Li, Ruifeng; Baden, Megu; Chan, Andrew T; Huttenhower, Curtis; Rimm, Eric B; Hu, Frank B; Sun, Qi | The Journal of nutrition | 34114015 | 2021 Jun 10 |
| Wearable sensors enable personalized predictions of clinical laboratory measurements. | Dunn, Jessilyn; Kidzinski, Lukasz; Runge, Ryan; Witt, Daniel; Hicks, Jennifer L; Schüssler-Fiorenza Rose, Sophia Miryam; Li, Xiao; Bahmani, Amir; Delp, Scott L; Hastie, Trevor; Snyder, Michael P | Nature medicine | 34031607 | 2021 Jun |
| Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. | Beghini, Francesco; McIver, Lauren J; Blanco-Míguez, Aitor; Dubois, Leonard; Asnicar, Francesco; Maharjan, Sagun; Mailyan, Ana; Manghi, Paolo; Scholz, Matthias; Thomas, Andrew Maltez; Valles-Colomer, Mireia; Weingart, George; Zhang, Yancong; Zolfo, Moreno; Huttenhower, Curtis; Franzosa, Eric A; Segata, Nicola | eLife | 33944776 | 2021 May 04 |
| Biogenic Amines Increase the Odds of Bacterial Vaginosis and Affect the Growth of and Lactic Acid Production by Vaginal Lactobacillus spp. | Borgogna, Joanna-Lynn C; Shardell, Michelle D; Grace, Savannah G; Santori, Elisa K; Americus, Benjamin; Li, Zhong; Ulanov, Alexander; Forney, Larry; Nelson, Tiffanie M; Brotman, Rebecca M; Ravel, Jacques; Yeoman, Carl J | Applied and environmental microbiology | 33674429 | 2021 04 27 |
| Megasphaera lornae sp. nov., Megasphaera hutchinsoni sp. nov., and Megasphaera vaginalis sp. nov.: novel bacteria isolated from the female genital tract. | Srinivasan, Sujatha; Beamer, May A; Fiedler, Tina L; Austin, Michele N; Sizova, Maria V; Strenk, Susan M; Agnew, Kathy J; Gowda, G A Nagana; Raftery, Daniel; Epstein, Slava S; Fredricks, David N; Hillier, Sharon L | International journal of systematic and evolutionary microbiology | 33616513 | 2019 Jun |
| Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease. | Somineni, Hari K; Nagpal, Sini; Venkateswaran, Suresh; Cutler, David J; Okou, David T; Haritunians, Talin; Simpson, Claire L; Begum, Ferdouse; Datta, Lisa W; Quiros, Antonio J; Seminerio, Jenifer; Mengesha, Emebet; Alexander, Jonathan S; Baldassano, Robert N; Dudley-Brown, Sharon; Cross, Raymond K; Dassopoulos, Themistocles; Denson, Lee A; Dhere, Tanvi A; Iskandar, Heba; Dryden, Gerald W; Hou, Jason K; Hussain, Sunny Z; Hyams, Jeffrey S; Isaacs, Kim L; Kader, Howard; Kappelman, Michael D; Katz, Jeffry; Kellermayer, Richard; Kuemmerle, John F; Lazarev, Mark; Li, Ellen; Mannon, Peter; Moulton, Dedrick E; Newberry, Rodney D; Patel, Ashish S; Pekow, Joel; Saeed, Shehzad A; Valentine, John F; Wang, Ming-Hsi; McCauley, Jacob L; Abreu, Maria T; Jester, Traci; Molle-Rios, Zarela; Palle, Sirish; Scherl, Ellen J; Kwon, John; Rioux, John D; Duerr, Richard H; Silverberg, Mark S; Zwick, Michael E; Stevens, Christine; Daly, Mark J; Cho, Judy H; Gibson, Greg; McGovern, Dermot P B; Brant, Steven R; Kugathasan, Subra | American journal of human genetics | 33600772 | 2021 03 04 |
| The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. | Wang, Dong D; Nguyen, Long H; Li, Yanping; Yan, Yan; Ma, Wenjie; Rinott, Ehud; Ivey, Kerry L; Shai, Iris; Willett, Walter C; Hu, Frank B; Rimm, Eric B; Stampfer, Meir J; Chan, Andrew T; Huttenhower, Curtis | Nature medicine | 33574608 | 2021 02 |
| Sequence Comparison of Vaginolysin from Different Gardnerella Species. | Garcia, Erin M; Serrano, Myrna G; Edupuganti, Laahirie; Edwards, David J; Buck, Gregory A; Jefferson, Kimberly K | Pathogens (Basel, Switzerland) | 33498226 | 2021 Jan 20 |
| Fructan-sensitive children with irritable bowel syndrome have distinct gut microbiome signatures. | Chumpitazi, Bruno P; Hoffman, Kristi L; Smith, Daniel P; McMeans, Ann R; Musaad, Salma; Versalovic, James; Petrosino, Joseph F; Shulman, Robert J | Alimentary pharmacology & therapeutics. | 33314183 | 2020 Dec 13; |
| HMPDACC: a Human Microbiome Project Multi-omic data resource. | Creasy, Heather Huot; Felix, Victor; Aluvathingal, Jain; Crabtree, Jonathan; Ifeonu, Olukemi; Matsumura, James; McCracken, Carrie; Nickel, Lance; Orvis, Joshua; Schor, Mike; Giglio, Michelle; Mahurkar, Anup; White, Owen | Nucleic acids research | 33305317 | 2021 01 08 |
| VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition. | France, Michael T; Ma, Bing; Gajer, Pawel; Brown, Sarah; Humphrys, Michael S; Holm, Johanna B; Waetjen, L Elaine; Brotman, Rebecca M; Ravel, Jacques | Microbiome. | 33228810 | 2020 11 23; |
| Identification of Natural CRISPR Systems and Targets in the Human Microbiome. | Münch, Philipp C; Franzosa, Eric A; Stecher, Bärbel; McHardy, Alice C; Huttenhower, Curtis | Cell host & microbe. | 33217332 | 2020 Nov 16; |
| Genetic Variation in Toll-Like Receptor 5 and Colonization with Flagellated Bacterial Vaginosis-Associated Bacteria. | Dela Cruz, Erin J; Fiedler, Tina L; Liu, Congzhou; Munch, Matthew M; Kohler, Christina M; Oot, Antoinette R; Wallis, Jacqueline M; Wang, Junhui; Frishman, Anna; Garcia, Kristina; Wiser, Andrew; Balkus, Jennifer E; Srinivasan, Sujatha; Golob, Jonathan L; Sycuro, Laura K; Marrazzo, Jeanne M; Hawn, Thomas R; Fredricks, David N | Infection and immunity | 33199356 | 2021 Feb 16 |
| Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut. | Nishiyama, Hiroki; Endo, Hisashi; Blanc-Mathieu, Romain; Ogata, Hiroyuki | Microorganisms. | 33121006 | 2020 Oct 27; |
| Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial 'dark matter'. | Tan, James Y; Wang, Sida; Dick, Gregory J; Young, Vincent B; Sherman, David H; Burns, Mark A; Lin, Xiaoxia N | Integrative biology : quantitative biosciences from nano to macro. | 33089329 | 2020 11 18; |
| Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California. | Sailani, M Reza; Metwally, Ahmed A; Zhou, Wenyu; Rose, Sophia Miryam Schüssler-Fiorenza; Ahadi, Sara; Contrepois, Kevin; Mishra, Tejaswini; Zhang, Martin Jinye; Kidzi?ski, ?ukasz; Chu, Theodore J; Snyder, Michael P | Nature communications. | 33004787 | 2020 10 01; |
| Association of diet with circulating trimethylamine-N-oxide concentration. | Hamaya, Rikuta; Ivey, Kerry L; Lee, Dong H; Wang, Molin; Li, Jun; Franke, Adrian; Sun, Qi; Rimm, Eric B | The American journal of clinical nutrition. | 32936862 | 2020 12 10; |
| Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz. | Wagner, Justin; Kancherla, Jayaram; Braccia, Domenick; Matsumara, James; Felix, Victor; Crabtree, Jonathan; Mahurkar, Anup; Corrada Bravo, Héctor | F1000Research | 32742640 | 2020 |
| Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. | Karcher, Nicolai; Pasolli, Edoardo; Asnicar, Francesco; Huang, Kun D; Tett, Adrian; Manara, Serena; Armanini, Federica; Bain, Debbie; Duncan, Sylvia H; Louis, Petra; Zolfo, Moreno; Manghi, Paolo; Valles-Colomer, Mireia; Raffaetà, Roberta; Rota-Stabelli, Omar; Collado, Maria Carmen; Zeller, Georg; Falush, Daniel; Maixner, Frank; Walker, Alan W; Huttenhower, Curtis; Segata, Nicola | Genome biology. | 32513234 | 2020 06 08; |
| PICRUSt2 for prediction of metagenome functions. | Douglas, Gavin M; Maffei, Vincent J; Zaneveld, Jesse R; Yurgel, Svetlana N; Brown, James R; Taylor, Christopher M; Huttenhower, Curtis; Langille, Morgan G I | Nature biotechnology. | 32483366 | 2020 Jun; |
| Molecular Choreography of Acute Exercise. | Contrepois, Kévin; Wu, Si; Moneghetti, Kegan J; Hornburg, Daniel; Ahadi, Sara; Tsai, Ming-Shian; Metwally, Ahmed A; Wei, Eric; Lee-McMullen, Brittany; Quijada, Jeniffer V; Chen, Songjie; Christle, Jeffrey W; Ellenberger, Mathew; Balliu, Brunilda; Taylor, Shalina; Durrant, Matthew G; Knowles, David A; Choudhry, Hani; Ashland, Melanie; Bahmani, Amir; Enslen, Brooke; Amsallem, Myriam; Kobayashi, Yukari; Avina, Monika; Perelman, Dalia; Schüssler-Fiorenza Rose, Sophia Miryam; Zhou, Wenyu; Ashley, Euan A; Montgomery, Stephen B; Chaib, Hassan; Haddad, Francois; Snyder, Michael P | Cell. | 32470399 | 2020 May 28; |
| Complete Genome Sequences of Six Lactobacillus iners Strains Isolated from the Human Vagina. | France, Michael T; Rutt, Lindsay; Narina, Shilpa; Arbaugh, Sarah; McComb, Elias; Humphrys, Mike S; Ma, Bing; Hayward, Matthew R; Costello, Elizabeth K; Relman, David A; Kwon, Douglas S; Ravel, Jacques | Microbiology resource announcements. | 32409537 | 2020 May 14; |
| MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data. | Bangayan, Nathanael J; Shi, Baochen; Trinh, Jerry; Barnard, Emma; Kasimatis, Gabriela; Curd, Emily; Li, Huiying | Microorganisms. | 32397065 | 2020 May 08; |
| Asymptomatic Bacterial Vaginosis Is Associated With Depletion of Mature Superficial Cells Shed From the Vaginal Epithelium. | O'Hanlon, D Elizabeth; Gajer, Pawel; Brotman, Rebecca M; Ravel, Jacques | Frontiers in cellular and infection microbiology. | 32211347 | 2020; |
| Associations of Sleep Characteristics With Cognitive Function and Decline Among Older Adults. | McSorley, V Eloesa; Bin, Yu Sun; Lauderdale, Diane S | American journal of epidemiology. | 32181824 | 2019 06 01; |
| Maternal activation of the EGFR prevents translocation of gut-residing pathogenic Escherichia coli in a model of late-onset neonatal sepsis. | Knoop, Kathryn A; Coughlin, Paige E; Floyd, Alexandria N; Ndao, I Malick; Hall-Moore, Carla; Shaikh, Nurmohammad; Gasparrini, Andrew J; Rusconi, Brigida; Escobedo, Marilyn; Good, Misty; Warner, Barbara B; Tarr, Phillip I; Newberry, Rodney D | Proceedings of the National Academy of Sciences of the United States of America. | 32179676 | 2020 04 07; |
| Global chemical effects of the microbiome include new bile-acid conjugations. | Quinn, Robert A; Melnik, Alexey V; Vrbanac, Alison; Fu, Ting; Patras, Kathryn A; Christy, Mitchell P; Bodai, Zsolt; Belda-Ferre, Pedro; Tripathi, Anupriya; Chung, Lawton K; Downes, Michael; Welch, Ryan D; Quinn, Melissa; Humphrey, Greg; Panitchpakdi, Morgan; Weldon, Kelly C; Aksenov, Alexander; da Silva, Ricardo; Avila-Pacheco, Julian; Clish, Clary; Bae, Sena; Mallick, Himel; Franzosa, Eric A; Lloyd-Price, Jason; Bussell, Robert; Thron, Taren; Nelson, Andrew T; Wang, Mingxun; Leszczynski, Eric; Vargas, Fernando; Gauglitz, Julia M; Meehan, Michael J; Gentry, Emily; Arthur, Timothy D; Komor, Alexis C; Poulsen, Orit; Boland, Brigid S; Chang, John T; Sandborn, William J; Lim, Meerana; Garg, Neha; Lumeng, Julie C; Xavier, Ramnik J; Kazmierczak, Barbara I; Jain, Ruchi; Egan, Marie; Rhee, Kyung E; Ferguson, David; Raffatellu, Manuela; Vlamakis, Hera; Haddad, Gabriel G; Siegel, Dionicio; Huttenhower, Curtis; Mazmanian, Sarkis K; Evans, Ronald M; Nizet, Victor; Knight, Rob; Dorrestein, Pieter C | Nature. | 32103176 | 2020 03; |
| Single-Cell Genomics and the Oral Microbiome. | Balachandran, M; Cross, K L; Podar, M | Journal of dental research | 32091935 | 2020 06 |
| Association Between Sulfur-Metabolizing Bacterial Communities in Stool and Risk of Distal Colorectal Cancer in Men. | Nguyen, Long H; Ma, Wenjie; Wang, Dong D; Cao, Yin; Mallick, Himel; Gerbaba, Teklu K; Lloyd-Price, Jason; Abu-Ali, Galeb; Hall, A Brantley; Sikavi, Daniel; Drew, David A; Mehta, Raaj S; Arze, Cesar; Joshi, Amit D; Yan, Yan; Branck, Tobyn; DuLong, Casey; Ivey, Kerry L; Ogino, Shuji; Rimm, Eric B; Song, Mingyang; Garrett, Wendy S; Izard, Jacques; Huttenhower, Curtis; Chan, Andrew T | Gastroenterology. | 31972239 | 2020 04; |
| Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. | Fornelos, Nadine; Franzosa, Eric A; Bishai, Jason; Annand, John W; Oka, Akihiko; Lloyd-Price, Jason; Arthur, Timothy D; Garner, Ashley; Avila-Pacheco, Julian; Haiser, Henry J; Tolonen, Andrew C; Porter, Jeffrey A; Clish, Clary B; Sartor, R Balfour; Huttenhower, Curtis; Vlamakis, Hera; Xavier, Ramnik J | Nature microbiology. | 31959971 | 2020 03; |
| Personal aging markers and ageotypes revealed by deep longitudinal profiling. | Ahadi, Sara; Zhou, Wenyu; Schüssler-Fiorenza Rose, Sophia Miryam; Sailani, M Reza; Contrepois, Kévin; Avina, Monika; Ashland, Melanie; Brunet, Anne; Snyder, Michael | Nature medicine. | 31932806 | 2020 01; |
| Windows Into Human Health Through Wearables Data Analytics. | Witt, Daniel; Kellogg, Ryan; Snyder, Michael; Dunn, Jessilyn | Current opinion in biomedical engineering. | 31832566 | 2019 Mar; |
| Discordant transmission of bacteria and viruses from mothers to babies at birth. | Maqsood, Rabia; Rodgers, Rachel; Rodriguez, Cynthia; Handley, Scott A; Ndao, I Malick; Tarr, Phillip I; Warner, Barbara B; Lim, Efrem S; Holtz, Lori R | Microbiome | 31823811 | 2019 12 10 |
| Comparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains. | Kirmiz, Nina; Galindo, Kadir; Cross, Karissa L; Luna, Estefani; Rhoades, Nicholas; Podar, Mircea; Flores, Gilberto E | Applied and environmental microbiology. | 31757822 | 2020 Jan 21; |
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| Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. | Kuleshov, Volodymyr; Jiang, Chao; Zhou, Wenyu; Jahanbani, Fereshteh; Batzoglou, Serafim; Snyder, Michael | Nature biotechnology. | 26655498 | 2016 Jan; |
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| Oral microbiota and host innate immune response in bisphosphonate-related osteonecrosis of the jaw. | Pushalkar, Smruti; Li, Xin; Kurago, Zoya; Ramanathapuram, Lalitha V; Matsumura, Satoko; Fleisher, Kenneth E; Glickman, Robert; Yan, Wenbo; Li, Yihong; Saxena, Deepak | International journal of oral science. | 25105817 | 2014 Dec; |
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| Phase variation of poly-N-acetylglucosamine expression in Staphylococcus aureus. | Brooks, Jamie L; Jefferson, Kimberly K | PLoS pathogens. | 25077798 | 2014 Jul; |
| Differences in vaginal microbiome in African American women versus women of European ancestry. | Fettweis, Jennifer M; Brooks, J Paul; Serrano, Myrna G; Sheth, Nihar U; Girerd, Philippe H; Edwards, David J; Strauss, Jerome F; Reimers, Mark A; Rivera, Maria C; Puma, Federico A; Huang, Bernice; Shyu, Conrad; Koparde, Vishal N; Lee, Vladimir; Jefferson, | Microbiology (Reading, England) | 25073854 | 2014 Jul 29 |
| The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention. | Hampton, Thomas H; Green, Deanna M; Cutting, Garry R; Morrison, Hilary G; Sogin, Mitchell L; Gifford, Alex H; Stanton, Bruce A; O'Toole, George A | Microbiome | 25071935 | 2014 |
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| Conducting a microbiome study. | Goodrich, Julia K; Di Rienzi, Sara C; Poole, Angela C; Koren, Omry; Walters, William A; Caporaso, J Gregory; Knight, Rob; Ley, Ruth E | Cell. | 25036628 | 2014 Jul 17; |
| Serum profiling using protein microarrays to identify disease related antigens. | Sharon, Donald; Snyder, Michael | Methods in molecular biology (Clifton, N.J.). | 25030927 | 2014; |
| Microfluidic molecular assay platform for the detection of miRNAs, mRNAs, proteins, and posttranslational modifications at single-cell resolution. | Wu, Meiye; Singh, Anup K | Journal of laboratory automation. | 25027027 | 2014 Dec; |
| Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays. | VanDussen, Kelli L; Marinshaw, Jeffrey M; Shaikh, Nurmohammad; Miyoshi, Hiroyuki; Moon, Clara; Tarr, Phillip I; Ciorba, Matthew A; Stappenbeck, Thaddeus S | Gut. | 25007816 | 2015 Jun; |
| Analysis of a food-borne fungal pathogen outbreak: virulence and genome of a Mucor circinelloides isolate from yogurt. | Lee, Soo Chan; Billmyre, R Blake; Li, Alicia; Carson, Sandra; Sykes, Sean M; Huh, Eun Young; Mieczkowski, Piotr; Ko, Dennis C; Cuomo, Christina A; Heitman, Joseph | mBio | 25006230 | 2014 |
| Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. | Haberman, Yael; Tickle, Timothy L; Dexheimer, Phillip J; Kim, Mi-Ok; Tang, Dora; Karns, Rebekah; Baldassano, Robert N; Noe, Joshua D; Rosh, Joel; Markowitz, James; Heyman, Melvin B; Griffiths, Anne M; Crandall, Wallace V; Mack, David R; Baker, Susan S; Huttenhower, Curtis; Keljo, David J; Hyams, Jeffrey S; Kugathasan, Subra; Walters, Thomas D; Aronow, Bruce; Xavier, Ramnik J; Gevers, Dirk; Denson, Lee A | The Journal of clinical investigation. | 25003194 | 2014 Aug; |
| Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. | Pop, Mihai; Walker, Alan W; Paulson, Joseph; Lindsay, Brianna; Antonio, Martin; Hossain, M Anowar; Oundo, Joseph; Tamboura, Boubou; Mai, Volker; Astrovskaya, Irina; Corrada Bravo, Hector; Rance, Richard; Stares, Mark; Levine, Myron M; Panchalingam, Sandra | Genome biology | 24995464 | 2014 |
| Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. | Parfrey, Laura Wegener; Walters, William A; Lauber, Christian L; Clemente, Jose C; Berg-Lyons, Donna; Teiling, Clotilde; Kodira, Chinnappa; Mohiuddin, Mohammed; Brunelle, Julie; Driscoll, Mark; Fierer, Noah; Gilbert, Jack A; Knight, Rob | Frontiers in microbiology. | 24995004 | 2014; |
| Lactobacillus rhamnosus L34 and Lactobacillus casei L39 suppress Clostridium difficile-induced IL-8 production by colonic epithelial cells. | Boonma, Prapaporn; Spinler, Jennifer K; Venable, Susan F; Versalovic, James; Tumwasorn, Somying | BMC microbiology | 24989059 | 2014 |
| Gene-targeted microfluidic cultivation validated by isolation of a gut bacterium listed in Human Microbiome Project's Most Wanted taxa. | Ma, Liang; Kim, Jungwoo; Hatzenpichler, Roland; Karymov, Mikhail A; Hubert, Nathaniel; Hanan, Ira M; Chang, Eugene B; Ismagilov, Rustem F | Proceedings of the National Academy of Sciences of the United States of America | 24965364 | 2014 Jul 8 |
| Oligotyping analysis of the human oral microbiome. | Eren, A Murat; Borisy, Gary G; Huse, Susan M; Mark Welch, Jessica L | Proceedings of the National Academy of Sciences of the United States of America | 24965363 | 2014 Jul 15 |
| Defining a personal, allele-specific, and single-molecule long-read transcriptome. | Tilgner, Hagen; Grubert, Fabian; Sharon, Donald; Snyder, Michael P | Proceedings of the National Academy of Sciences of the United States of America. | 24961374 | 2014 Jul 8; |
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| From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions. | Spinler, Jennifer K; Sontakke, Amrita; Hollister, Emily B; Venable, Susan F; Oh, Phaik Lyn; Balderas, Miriam A; Saulnier, Delphine M A; Mistretta, Toni-Ann; Devaraj, Sridevi; Walter, Jens; Versalovic, James; Highlander, Sarah K | Genome biology and evolution | 24951561 | 2014 Jul |
| Inflammatory bowel disease as a model for translating the microbiome. | Huttenhower, Curtis; Kostic, Aleksandar D; Xavier, Ramnik J | Immunity | 24950204 | 2014 Jun 19 |
| Finding the missing links among metabolites, microbes, and the host. | Dorrestein, Pieter C; Mazmanian, Sarkis K; Knight, Rob | Immunity. | 24950202 | 2014 Jun 19; |
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| Evidence of extensive DNA transfer between bacteroidales species within the human gut. | Coyne, Michael J; Zitomersky, Naamah Levy; McGuire, Abigail Manson; Earl, Ashlee M; Comstock, Laurie E | mBio | 24939888 | 2014 |
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| Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251). | Cuomo, Christina A; Rodriguez-Del Valle, Nuri; Perez-Sanchez, Lizaida; Abouelleil, Amr; Goldberg, Jonathan; Young, Sarah; Zeng, Qiandong; Birren, Bruce W | Genome announcements. | 24855299 | 2014; |
| Microbiome in reflux disorders and esophageal adenocarcinoma. | Yang, Liying; Chaudhary, Noami; Baghdadi, Jonathan; Pei, Zhiheng | Cancer journal (Sudbury, Mass.) | 24855009 | 2014 May-Jun |
| The placenta harbors a unique microbiome. | Aagaard, Kjersti; Ma, Jun; Antony, Kathleen M; Ganu, Radhika; Petrosino, Joseph; Versalovic, James | Science translational medicine | 24848255 | 2014 May 21 |
| Relating the metatranscriptome and metagenome of the human gut. | Franzosa, Eric A; Morgan, Xochitl C; Segata, Nicola; Waldron, Levi; Reyes, Joshua; Earl, Ashlee M; Giannoukos, Georgia; Boylan, Matthew R; Ciulla, Dawn; Gevers, Dirk; Izard, Jacques; Garrett, Wendy S; Chan, Andrew T; Huttenhower, Curtis | Proceedings of the National Academy of Sciences of the United States of America | 24843156 | 2014 Jun 3 |
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| Oribacterium parvum sp. nov. and Oribacterium asaccharolyticum sp. nov., obligately anaerobic bacteria from the human oral cavity, and emended description of the genus Oribacterium. | Sizova, Maria V; Muller, Paul A; Stancyk, David; Panikov, Nicolai S; Mandalakis, Manolis; Hazen, Amanda; Hohmann, Tine; Doerfert, Sebastian N; Fowle, William; Earl, Ashlee M; Nelson, Karen E; Epstein, Slava S | International journal of systematic and evolutionary microbiology. | 24824639 | 2014 Aug; |
| Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. | Schubert, Alyxandria M; Rogers, Mary A M; Ring, Cathrin; Mogle, Jill; Petrosino, Joseph P; Young, Vincent B; Aronoff, David M; Schloss, Patrick D | mBio | 24803517 | 2014 |
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| Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. | Vital, Marius; Howe, Adina Chuang; Tiedje, James M | mBio | 24757212 | 2014 |
| Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. | Swan, Brandon K; Chaffin, Mark D; Martinez-Garcia, Manuel; Morrison, Hilary G; Field, Erin K; Poulton, Nicole J; Masland, E Dashiell P; Harris, Christopher C; Sczyrba, Alexander; Chain, Patrick S G; Koren, Sergey; Woyke, Tanja; Stepanauskas, Ramunas | PloS one | 24743558 | 2014 |
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| Transferable vancomycin resistance in a community-associated MRSA lineage. | Rossi, Flavia; Diaz, Lorena; Wollam, Aye; Panesso, Diana; Zhou, Yanjiao; Rincon, Sandra; Narechania, Apurva; Xing, Galen; Di Gioia, Thais S R; Doi, Andre; Tran, Truc T; Reyes, Jinnethe; Munita, Jose M; Carvajal, Lina P; Hernandez-Roldan, Alejandra; Branda | The New England journal of medicine | 24738669 | 2014 Apr 17 |
| Diversity and genomic insights into the uncultured Chloroflexi from the human microbiota. | Campbell, Alisha G; Schwientek, Patrick; Vishnivetskaya, Tatiana; Woyke, Tanja; Levy, Shawn; Beall, Clifford J; Griffen, Ann; Leys, Eugene; Podar, Mircea | Environmental microbiology | 24738594 | 2014 Apr 17 |
| Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis. | Hyde, Embriette R; Andrade, Fernando; Vaksman, Zalman; Parthasarathy, Kavitha; Jiang, Hong; Parthasarathy, Deepa K; Torregrossa, Ashley C; Tribble, Gena; Kaplan, Heidi B; Petrosino, Joseph F; Bryan, Nathan S | PloS one | 24670812 | 2014 |
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| Gut microbiota influences low fermentable substrate diet efficacy in children with irritable bowel syndrome. | Chumpitazi, Bruno P; Hollister, Emily B; Oezguen, Numan; Tsai, Cynthia M; McMeans, Ann R; Luna, Ruth A; Savidge, Tor C; Versalovic, James; Shulman, Robert J | Gut microbes | 24637601 | 2014 Mar-Apr |
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| Functional and phylogenetic assembly of microbial communities in the human microbiome. | Shafquat, Afrah; Joice, Regina; Simmons, Sheri L; Huttenhower, Curtis | Trends in microbiology | 24618403 | 2014 Mar 4 |
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| History and impact of RDP: a legacy from Carl Woese to microbiology. | Cole, James R; Tiedje, James M | RNA biology | 24607969 | 2014 Mar |
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| Single cell genomics of uncultured, health-associated Tannerella BU063 (Oral Taxon 286) and comparison to the closely related pathogen Tannerella forsythia. | Beall, Clifford J; Campbell, Alisha G; Dayeh, Daniel M; Griffen, Ann L; Podar, Mircea; Leys, Eugene J | PloS one | 24551246 | 2014 |
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| Experiences of patients with chronic gastrointestinal conditions: in their own words. | McCormick, Jennifer B; Hammer, Rachel R; Farrell, Ruth M; Geller, Gail; James, Katherine M; Loftus Jr, Edward V; Mercer, Mary Beth; Tilburt, Jon C; Sharp, Richard R | Health and quality of life outcomes | 22401607 | 2012 |
| Standard colonic lavage alters the natural state of mucosal-associated microbiota in the human colon. | Harrell, Laura; Wang, Yunwei; Antonopoulos, Dionysios; Young, Vincent; Lichtenstein, Lev; Huang, Yong; Hanauer, Stephen; Chang, Eugene | PloS one | 22389708 | 2012 |
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| Molecular pathways: pathogenesis and clinical implications of microbiome alteration in esophagitis and Barrett esophagus. | Yang, Liying; Francois, Fritz; Pei, Zhiheng | Clinical cancer research : an official journal of the American Association for Cancer Research | 22344232 | 2012 Apr 15 |
| Host response to probiotics determined by nutritional status of rotavirus-infected neonatal mice. | Preidis, Geoffrey A; Saulnier, Delphine M; Blutt, Sarah E; Mistretta, Toni-Ann; Riehle, Kevin P; Major, Angela M; Venable, Susan F; Barrish, James P; Finegold, Milton J; Petrosino, Joseph F; Guerrant, Richard L; Conner, Margaret E; Versalovic, James | Journal of pediatric gastroenterology and nutrition | 22343914 | 2012 Sep |
| Altered vaginal microbiota are associated with perinatal mother-to-child transmission of HIV in African women from Burkina Faso. | Frank, Daniel N; Manigart, Olivier; Leroy, Valeriane; Meda, Nicolas; Valea, Diane; Zhang, Weiming; Dabis, Francois; Pace, Norman R; Van de Perre, Philippe; Janoff, Edward N | Journal of acquired immune deficiency syndromes (1999) | 22343176 | 2012 Jul 1 |
| Cxcr2 and Cxcl5 regulate the IL-17/G-CSF axis and neutrophil homeostasis in mice. | Mei, Junjie; Liu, Yuhong; Dai, Ning; Hoffmann, Christian; Hudock, Kristin M; Zhang, Peggy; Guttentag, Susan H; Kolls, Jay K; Oliver, Paula M; Bushman, Frederic D; Worthen, G Scott | The Journal of clinical investigation | 22326959 | 2012 Mar 1 |
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| The under-recognized dominance of Verrucomicrobia in soil bacterial communities. | Bergmann, Gaddy T; Bates, Scott T; Eilers, Kathryn G; Lauber, Christian L; Caporaso, J Gregory; Walters, William A; Knight, Rob; Fierer, Noah | Soil biology & biochemistry | 22267877 | 2011 Jul |
| Probiotics stimulate enterocyte migration and microbial diversity in the neonatal mouse intestine. | Preidis, Geoffrey A; Saulnier, Delphine M; Blutt, Sarah E; Mistretta, Toni-Ann; Riehle, Kevin P; Major, Angela M; Venable, Susan F; Finegold, Milton J; Petrosino, Joseph F; Conner, Margaret E; Versalovic, James | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 22267340 | 2012 May |
| Perturbation dynamics of the rumen microbiota in response to exogenous butyrate. | Li, Robert W; Wu, Sitao; Baldwin 6th, Ransom L; Li, Weizhong; Li, Congjun | PloS one | 22253719 | 2012 |
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| Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments. | Ozok, A R; Persoon, I F; Huse, S M; Keijser, B J F; Wesselink, P R; Crielaard, W; Zaura, E | International endodontic journal | 22251411 | 2012 Jun |
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| Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. | Schatz, Michael C; Phillippy, Adam M; Sommer, Daniel D; Delcher, Arthur L; Puiu, Daniela; Narzisi, Giuseppe; Salzberg, Steven L; Pop, Mihai | Briefings in bioinformatics | 22199379 | 2013 Mar |
| Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws. | Smajs, David; Norris, Steven J; Weinstock, George M | Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases | 22198325 | 2012 Mar |
| GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease. | Haft, Daniel H; Varghese, Neha | PloS one | 22194940 | 2011 |
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| IMG: the Integrated Microbial Genomes database and comparative analysis system. | Markowitz, Victor M; Chen, I-Min A; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos | Nucleic acids research | 22194640 | 2012 Jan |
| Human microbiome and HIV/AIDS. | Saxena, Deepak; Li, Yihong; Yang, Liying; Pei, Zhiheng; Poles, Michael; Abrams, William R; Malamud, Daniel | Current HIV/AIDS reports | 22193889 | 2012 Mar |
| Single-cell protein analysis. | Wu, Meiye; Singh, Anup K | Current opinion in biotechnology | 22189001 | 2012 Feb |
| Experimental and analytical tools for studying the human microbiome. | Kuczynski, Justin; Lauber, Christian L; Walters, William A; Parfrey, Laura Wegener; Clemente, Jose C; Gevers, Dirk; Knight, Rob | Nature reviews. Genetics | 22179717 | 2012 Jan |
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| Advancing analytical algorithms and pipelines for billions of microbial sequences. | Gonzalez, Antonio; Knight, Rob | Current opinion in biotechnology | 22172529 | 2012 Feb |
| SitePainter: a tool for exploring biogeographical patterns. | Gonzalez, Antonio; Stombaugh, Jesse; Lauber, Christian L; Fierer, Noah; Knight, Rob | Bioinformatics (Oxford, England) | 22171330 | 2012 Feb 1 |
| Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences. | Wang, Xiaoyu; Cai, Yunpeng; Sun, Yijun; Knight, Rob; Mai, Volker | The ISME journal | 22170430 | 2012 Jul |
| Using QIIME to analyze 16S rRNA gene sequences from microbial communities. | Kuczynski, Justin; Stombaugh, Jesse; Walters, William Anton; Gonzalez, Antonio; Caporaso, J Gregory; Knight, Rob | Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] | 22161565 | 2011 Dec |
| Single cell genome sequencing. | Yilmaz, Suzan; Singh, Anup K | Current opinion in biotechnology | 22154471 | 2012 Jun |
| Characterizing microbial communities through space and time. | Gonzalez, Antonio; King, Andrew; Robeson 2nd, Michael S; Song, Sejin; Shade, Ashley; Metcalf, Jessica L; Knight, Rob | Current opinion in biotechnology | 22154467 | 2012 Jun |
| GAGE: A critical evaluation of genome assemblies and assembly algorithms. | Salzberg, Steven L; Phillippy, Adam M; Zimin, Aleksey; Puiu, Daniela; Magoc, Tanja; Koren, Sergey; Treangen, Todd J; Schatz, Michael C; Delcher, Arthur L; Roberts, Michael; Marcais, Guillaume; Pop, Mihai; Yorke, James A | Genome research | 22147368 | 2012 Mar |
| CharProtDB: a database of experimentally characterized protein annotations. | Madupu, Ramana; Richter, Alexander; Dodson, Robert J; Brinkac, Lauren; Harkins, Derek; Durkin, Scott; Shrivastava, Susmita; Sutton, Granger; Haft, Daniel | Nucleic acids research | 22140108 | 2012 Jan |
| The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. | Pagani, Ioanna; Liolios, Konstantinos; Jansson, Jakob; Chen, I-Min A; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor M; Kyrpides, Nikos C | Nucleic acids research | 22135293 | 2012 Jan |
| An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. | McDonald, Daniel; Price, Morgan N; Goodrich, Julia; Nawrocki, Eric P; DeSantis, Todd Z; Probst, Alexander; Andersen, Gary L; Knight, Rob; Hugenholtz, Philip | The ISME journal | 22134646 | 2012 Mar |
| Strategies for metagenomic-guided whole-community proteomics of complex microbial environments. | Cantarel, Brandi L; Erickson, Alison R; VerBerkmoes, Nathan C; Erickson, Brian K; Carey, Patricia A; Pan, Chongle; Shah, Manesh; Mongodin, Emmanuel F; Jansson, Janet K; Fraser-Liggett, Claire M; Hettich, Robert L | PloS one | 22132090 | 2011 |
| An optical-coding method to measure particle distribution in microfluidic devices. | Wu, Tsung-Feng; Mei, Zhe; Pion-Tonachini, Luca; Zhao, Chao; Qiao, Wen; Arianpour, Ashkan; Lo, Yu-Hwa | AIP advances. | 22125760 | 2011 Jun; |
| The Human Microbiome Project: lessons from human genomics. | Lewis Jr, Cecil M; Obregon-Tito, Alexandra; Tito, Raul Y; Foster, Morris W; Spicer, Paul G | Trends in microbiology | 22112388 | 2012 Jan |
| Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus Alignment. | Ye, Yuzhen | Proceedings. IEEE International Conference on Bioinformatics and Biomedicine | 22102981 | 2011 Feb 4 |
| Astrovirus MLB2 viremia in febrile child. | Holtz, Lori R; Wylie, Kristine M; Sodergren, Erica; Jiang, Yanfang; Franz, Carl J; Weinstock, George M; Storch, Gregory A; Wang, David | Emerging infectious diseases | 22099095 | 2011 Nov |
| IMG/M: the integrated metagenome data management and comparative analysis system. | Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Szeto, Ernest; Palaniappan, Krishna; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Pati, Amrita; Huntemann, Marcel; Liolios, Konstantinos; Pagani, Ioanna; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natali | Nucleic acids research | 22086953 | 2012 Jan |
| The intestinal microbiota in health and disease. | Young, Vincent B | Current opinion in gastroenterology | 22080827 | 2012 Jan |
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| ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. | Basu, Malay K; Selengut, Jeremy D; Haft, Daniel H | BMC bioinformatics | 22070167 | 2011 |
| Tetra-?-acetato-?O:O'-bis-[(3,5-di-methyl-1H-pyrazole-?N)-copper(II)]. | van Wyk, Juanita; Omondi, Bernard; Darkwa, James | Acta crystallographica. Section E, Structure reports online. | 22065823 | 2011 Sep 01; |
| 2,2'-Bis(meth-oxy-meth-oxy)-3-methyl-1,1'-binaphth-yl. | Carrilho, Rui M B; Abreu, Artur R; Pereira, Mariette M; Rodrigues, V H | Acta crystallographica. Section E, Structure reports online. | 22058976 | 2011 Sep 01; |
| Saying privacy, meaning confidentiality. | Schwab, Abraham P; Frank, Lily; Gligorov, Nada | The American journal of bioethics : AJOB | 22047127 | 2011 Nov |
| De minimis risk: a proposal for a new category of research risk. | Rhodes, Rosamond; Azzouni, Jody; Baumrin, Stefan Bernard; Benkov, Keith; Blaser, Martin J; Brenner, Barbara; Dauben, Joseph W; Earle, William J; Frank, Lily; Gligorov, Nada; Goldfarb, Joseph; Hirschhorn, Kurt; Hirschhorn, Rochelle; Holzman, Ian; Indyk, De | The American journal of bioethics : AJOB | 22047112 | 2011 Nov |
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| Microbiome and malignancy. | Plottel, Claudia S; Blaser, Martin J | Cell host & microbe | 22018233 | 2011 Oct 20 |
| Human-associated microbial signatures: examining their predictive value. | Knights, Dan; Parfrey, Laura Wegener; Zaneveld, Jesse; Lozupone, Catherine; Knight, Rob | Cell host & microbe. | 22018228 | 2011 Oct 20; |
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| The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. | Sczesnak, Andrew; Segata, Nicola; Qin, Xiang; Gevers, Dirk; Petrosino, Joseph F; Huttenhower, Curtis; Littman, Dan R; Ivanov, Ivaylo I | Cell host & microbe | 21925113 | 2011 Sep 15 |
| Applying an optical space-time coding method to enhance light scattering signals in microfluidic devices. | Mei, Zhe; Wu, Tsung-Feng; Pion-Tonachini, Luca; Qiao, Wen; Zhao, Chao; Liu, Zhiwen; Lo, Yu-Hwa | Biomicrofluidics. | 21915241 | 2011 Sep; |
| Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). | Youssef, Noha H; Blainey, Paul C; Quake, Stephen R; Elshahed, Mostafa S | Applied and environmental microbiology | 21908640 | 2011 Nov |
| TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. | Pirrung, Meg; Kennedy, Ryan; Caporaso, J Gregory; Stombaugh, Jesse; Wendel, Doug; Knight, Rob | Bioinformatics (Oxford, England) | 21903626 | 2011 Nov 1 |
| WebMGA: a customizable web server for fast metagenomic sequence analysis. | Wu, Sitao; Zhu, Zhengwei; Fu, Liming; Niu, Beifang; Li, Weizhong | BMC genomics | 21899761 | 2011 |
| Genetic basis for in vivo daptomycin resistance in enterococci. | Arias, Cesar A; Panesso, Diana; McGrath, Danielle M; Qin, Xiang; Mojica, Maria F; Miller, Corwin; Diaz, Lorena; Tran, Truc T; Rincon, Sandra; Barbu, E Magda; Reyes, Jinnethe; Roh, Jung H; Lobos, Elizabeth; Sodergren, Erica; Pasqualini, Renata; Arap, Wadih | The New England journal of medicine | 21899450 | 2011 Sep 8 |
| Linking long-term dietary patterns with gut microbial enterotypes. | Wu, Gary D; Chen, Jun; Hoffmann, Christian; Bittinger, Kyle; Chen, Ying-Yu; Keilbaugh, Sue A; Bewtra, Meenakshi; Knights, Dan; Walters, William A; Knight, Rob; Sinha, Rohini; Gilroy, Erin; Gupta, Kernika; Baldassano, Robert; Nessel, Lisa; Li, Hongzhe; Bus | Science (New York, N.Y.) | 21885731 | 2011 Oct 7 |
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| Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. | Zaneveld, Jesse R R; Parfrey, Laura Wegener; Van Treuren, Will; Lozupone, Catherine; Clemente, Jose C; Knights, Dan; Stombaugh, Jesse; Kuczynski, Justin; Knight, Rob | Trends in microbiology | 21872475 | 2011 Oct |
| Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison. | Ahn, Jiyoung; Yang, Liying; Paster, Bruce J; Ganly, Ian; Morris, Luc; Pei, Zhiheng; Hayes, Richard B | PloS one | 21829515 | 2011 |
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| The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection. | Reeves, Angela E; Theriot, Casey M; Bergin, Ingrid L; Huffnagle, Gary B; Schloss, Patrick D; Young, Vincent B | Gut microbes | 21804357 | 2011 May-Jun |
| The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide. | He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong | The ISME journal | 21796217 | 2012 Feb |
| Investigating the biological and clinical significance of human dysbioses. | Frank, Daniel N; Zhu, Wei; Sartor, R Balfour; Li, Ellen | Trends in microbiology | 21775143 | 2011 Sep |
| Studying the Enteric Microbiome in Inflammatory Bowel Diseases: Getting through the Growing Pains and Moving Forward. | Young, Vincent B; Kahn, Stacy A; Schmidt, Thomas M; Chang, Eugene B | Frontiers in microbiology | 21772835 | 2011 |
| Bayesian community-wide culture-independent microbial source tracking. | Knights, Dan; Kuczynski, Justin; Charlson, Emily S; Zaneveld, Jesse; Mozer, Michael C; Collman, Ronald G; Bushman, Frederic D; Knight, Rob; Kelley, Scott T | Nature methods | 21765408 | 2011 Sep |
| Microfluidic fluorescence in situ hybridization and flow cytometry (ýýFlowFISH). | Liu, Peng; Meagher, Robert J; Light, Yooli K; Yilmaz, Suzan; Chakraborty, Romy; Arkin, Adam P; Hazen, Terry C; Singh, Anup K | Lab on a chip | 21755095 | 2011 Aug 21 |
| Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. | Saulnier, Delphine M; Riehle, Kevin; Mistretta, Toni-Ann; Diaz, Maria-Alejandra; Mandal, Debasmita; Raza, Sabeen; Weidler, Erica M; Qin, Xiang; Coarfa, Cristian; Milosavljevic, Aleksandar; Petrosino, Joseph F; Highlander, Sarah; Gibbs, Richard; Lynch, Sus | Gastroenterology | 21741921 | 2011 Nov |
| Extrapolation of urn models via poissonization: accurate measurements of the microbial unknown. | Lladser, Manuel E; Gouet, Raul; Reeder, Jens | PloS one | 21738613 | 2011 |
| DNACLUST: accurate and efficient clustering of phylogenetic marker genes. | Ghodsi, Mohammadreza; Liu, Bo; Pop, Mihai | BMC bioinformatics | 21718538 | 2011 |
| Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. | Werner, Jeffrey J; Koren, Omry; Hugenholtz, Philip; DeSantis, Todd Z; Walters, William A; Caporaso, J Gregory; Angenent, Largus T; Knight, Rob; Ley, Ruth E | The ISME journal | 21716311 | 2012 Jan |
| How patients view probiotics: findings from a multicenter study of patients with inflammatory bowel disease and irritable bowel syndrome. | Mercer, MaryBeth; Brinich, Margaret A; Geller, Gail; Harrison, Krista; Highland, Janelle; James, Katherine; Marshall, Patricia; McCormick, Jennifer B; Tilburt, Jon; Achkar, Jean-Paul; Farrell, Ruth M; Sharp, Richard R | Journal of clinical gastroenterology | 21716123 | 2012 Feb |
| Metagenomic biomarker discovery and explanation. | Segata, Nicola; Izard, Jacques; Waldron, Levi; Gevers, Dirk; Miropolsky, Larisa; Garrett, Wendy S; Huttenhower, Curtis | Genome biology | 21702898 | 2011 |
| UCHIME improves sensitivity and speed of chimera detection. | Edgar, Robert C; Haas, Brian J; Clemente, Jose C; Quince, Christopher; Knight, Rob | Bioinformatics (Oxford, England) | 21700674 | 2011 Aug 15 |
| Bacterial DNA content in the intestinal wall from infants with necrotizing enterocolitis. | Bucher, Brian T; McDuffie, Lucas A; Shaikh, Nurmohammad; Tarr, Phillip I; Warner, Barbara B; Hamvas, Aaron; White, Frances V; Erwin, Christopher R; Warner, Brad W | Journal of pediatric surgery | 21683193 | 2011 Jun |
| Interleukin-1ýý (IL-1ýý) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis. | Carvalho, Frederic A; Nalbantoglu, Ilke; Ortega-Fernandez, Sophie; Aitken, Jesse D; Su, Yueju; Koren, Omry; Walters, William A; Knight, Rob; Ley, Ruth E; Vijay-Kumar, Matam; Gewirtz, Andrew T | Gut | 21646247 | 2012 Mar |
| Moving pictures of the human microbiome. | Caporaso, J Gregory; Lauber, Christian L; Costello, Elizabeth K; Berg-Lyons, Donna; Gonzalez, Antonio; Stombaugh, Jesse; Knights, Dan; Gajer, Pawel; Ravel, Jacques; Fierer, Noah; Gordon, Jeffrey I; Knight, Rob | Genome biology | 21624126 | 2011 |
| Mammalian Cell Sorting using ýýFACS. | Cho, Sung Hwan; Chen, Chun Hao; Tsai, Frank S; Godin, Jessica; Lo, Yu-Hwa | Conference on Lasers and Electro-optics : (CLEO). Conference on Lasers and Electro-optics | 21614147 | 2010 May 16 |
| The microbial communities in male first catch urine are highly similar to those in paired urethral swab specimens. | Dong, Qunfeng; Nelson, David E; Toh, Evelyn; Diao, Lixia; Gao, Xiang; Fortenberry, J Dennis; Van der Pol, Barbara | PloS one | 21603636 | 2011 |
| Responses of gut microbiota to diet composition and weight loss in lean and obese mice. | Ravussin, Yann; Koren, Omry; Spor, Ayme; LeDuc, Charles; Gutman, Roee; Stombaugh, Jesse; Knight, Rob; Ley, Ruth E; Leibel, Rudolph L | Obesity (Silver Spring, Md.) | 21593810 | 2012 Apr |
| RAPSearch: a fast protein similarity search tool for short reads. | Ye, Yuzhen; Choi, Jeong-Hyeon; Tang, Haixu | BMC bioinformatics | 21575167 | 2011 |
| Evolution and classification of the CRISPR-Cas systems. | Makarova, Kira S; Haft, Daniel H; Barrangou, Rodolphe; Brouns, Stan J J; Charpentier, Emmanuelle; Horvath, Philippe; Moineau, Sylvain; Mojica, Francisco J M; Wolf, Yuri I; Yakunin, Alexander F; van der Oost, John; Koonin, Eugene V | Nature reviews. Microbiology | 21552286 | 2011 Jun |
| Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. | Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn; Knight, Rob; Cole, James R; Amaral-Zettler, Linda; Gilbert, Jack A; Karsch-Mizrachi, Ilene; Johnston, Anjanette; Cochrane, Guy; Vaughan, Robert; Hunter, Christopher; Park, Joonhong; Morrison, Norman; Rocca-Serr | Nature biotechnology | 21552244 | 2011 May |
| Boulder ALignment Editor (ALE): a web-based RNA alignment tool. | Stombaugh, Jesse; Widmann, Jeremy; McDonald, Daniel; Knight, Rob | Bioinformatics (Oxford, England) | 21546392 | 2011 Jun 15 |
| Brief communication: DNA from early Holocene American dog. | Tito, Raul Y; Belknap 3rd, Samuel L; Sobolik, Kristin D; Ingraham, Robert C; Cleeland, Lauren M; Lewis Jr, Cecil M | American journal of physical anthropology | 21541929 | 2011 Aug |
| Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. | Dominguez-Bello, Maria Gloria; Blaser, Martin J; Ley, Ruth E; Knight, Rob | Gastroenterology | 21530737 | 2011 May |
| A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. | Sun, Yijun; Cai, Yunpeng; Huse, Susan M; Knight, Rob; Farmerie, William G; Wang, Xiaoyu; Mai, Volker | Briefings in bioinformatics | 21525143 | 2012 Jan |
| Simrank: Rapid and sensitive general-purpose k-mer search tool. | DeSantis, Todd Z; Keller, Keith; Karaoz, Ulas; Alekseyenko, Alexander V; Singh, Navjeet N S; Brodie, Eoin L; Pei, Zhiheng; Andersen, Gary L; Larsen, Niels | BMC ecology | 21524302 | 2011 |
| FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes. | Niu, Beifang; Zhu, Zhengwei; Fu, Limin; Wu, Sitao; Li, Weizhong | Bioinformatics (Oxford, England) | 21505035 | 2011 Jun 15 |
| Reliability and validity of a modified Bristol Stool Form Scale for children. | Lane, Mariella M; Czyzewski, Danita I; Chumpitazi, Bruno P; Shulman, Robert J | The Journal of pediatrics | 21489557 | 2011 Sep |
| The mind-body-microbial continuum. | Gonzalez, Antonio; Stombaugh, Jesse; Lozupone, Catherine; Turnbaugh, Peter J; Gordon, Jeffrey I; Knight, Rob | Dialogues in clinical neuroscience | 21485746 | 2011 |
| Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. | Haft, Daniel H; Basu, Malay Kumar | Journal of bacteriology | 21478363 | 2011 Jun |
| Overview of the development of personalized genomic medicine and surgery. | Brunicardi, F Charles; Gibbs, Richard A; Wheeler, David A; Nemunaitis, John; Fisher, William; Goss, John; Chen, Changyi | World journal of surgery | 21424870 | 2011 Aug |
| Unravelling the effects of the environment and host genotype on the gut microbiome. | Spor, Ayme; Koren, Omry; Ley, Ruth | Nature reviews. Microbiology | 21407244 | 2011 Apr |
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