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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;
The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Tett, Adrian; Huang, Kun D; Asnicar, Francesco; Fehlner-Peach, Hannah; Pasolli, Edoardo; Karcher, Nicolai; Armanini, Federica; Manghi, Paolo; Bonham, Kevin; Zolfo, Moreno; De Filippis, Francesca; Magnabosco, Cara; Bonneau, Richard; Lusingu, John; Amuasi, John; Reinhard, Karl; Rattei, Thomas; Boulund, Fredrik; Engstrand, Lars; Zink, Albert; Collado, Maria Carmen; Littman, Dan R; Eibach, Daniel; Ercolini, Danilo; Rota-Stabelli, Omar; Huttenhower, Curtis; Maixner, Frank; Segata, Nicola Cell host & microbe. 31607556 2019 11 13;
Nonoptimal Vaginal Microbiota After Azithromycin Treatment for Chlamydia trachomatis Infection. Tamarelle, Jeanne; Ma, Bing; Gajer, Pawel; Humphrys, Mike S; Terplan, Mishka; Mark, Katrina S; Thiébaut, Anne C M; Forney, Larry J; Brotman, Rebecca M; Delarocque-Astagneau, Elisabeth; Bavoil, Patrik M; Ravel, Jacques The Journal of infectious diseases. 31573603 2020 02 03;
Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly. Ivey, Kerry L; Chan, Andrew T; Izard, Jacques; Cassidy, Aedin; Rogers, Geraint B; Rimm, Eric B mBio. 31551328 2019 Sep 24;
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HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences. Danaher, Robert J; Fouts, Derrick E; Chan, Agnes P; Choi, Yongwook; DePew, Jessica; McCorrison, Jamison M; Nelson, Karen E; Wang, Chunmei; Miller, Craig S Journal of neurovirology. 27739035 2017 Apr;
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A New Catalog of Microbiological Tools for Women's Infectious Disease Research. Lewis, Amanda L; Lewis, Warren G Genome announcements. 27688331 2016 Sep 29;
Genome Sequences of Nine Gram-Negative Vaginal Bacterial Isolates. Deitzler, Grace E; Ruiz, Maria J; Lu, Wendy; Weimer, Cory; Park, SoEun; Robinson, Lloyd S; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G; Lewis, Amanda L Genome announcements. 27688330 2016 Sep 29;
Genome Sequences of 14 Firmicutes Strains Isolated from the Human Vagina. Deitzler, Grace E; Ruiz, Maria J; Weimer, Cory; Park, SoEun; Robinson, Lloyd; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Amanda L; Lewis, Warren G Genome announcements. 27688329 2016 Sep 29;
Genome Sequences of 11 Human Vaginal Actinobacteria Strains. Lewis, Amanda L; Deitzler, Grace E; Ruiz, Maria J; Weimer, Cory; Park, SoEun; Robinson, Lloyd S; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G Genome announcements. 27688328 2016 Sep 29;
Genome Sequences of 12 Bacterial Isolates Obtained from the Urine of Pregnant Women. Weimer, Cory M; Deitzler, Grace E; Robinson, Lloyd S; Park, SoEun; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G; Lewis, Amanda L Genome announcements. 27688327 2016 Sep 29;
Genome Sequences of 15 Gardnerella vaginalis Strains Isolated from the Vaginas of Women with and without Bacterial Vaginosis. Robinson, Lloyd S; Perry, Justin; Lek, Sai; Wollam, Aye; Sodergren, Erica; Weinstock, George; Lewis, Warren G; Lewis, Amanda L Genome announcements. 27688326 2016 Sep 29;
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Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung. Segal, Leopoldo N; Clemente, Jose C; Wu, Benjamin G; Wikoff, William R; Gao, Zhan; Li, Yonghua; Ko, Jane P; Rom, William N; Blaser, Martin J; Weiden, Michael D Thorax. 27486204 2017 Jan;
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Global prevalence and distribution of genes and microorganisms involved in mercury methylation. Podar, Mircea; Gilmour, Cynthia C; Brandt, Craig C; Soren, Allyson; Brown, Steven D; Crable, Bryan R; Palumbo, Anthony V; Somenahally, Anil C; Elias, Dwayne A Science advances 26601305 2015 Oct
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The influence of non-steroidal anti-inflammatory drugs on the gut microbiome. Rogers, M A M; Aronoff, D M Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. 26482265 2016 Feb;
Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease. Lewis, James D; Chen, Eric Z; Baldassano, Robert N; Otley, Anthony R; Griffiths, Anne M; Lee, Dale; Bittinger, Kyle; Bailey, Aubrey; Friedman, Elliot S; Hoffmann, Christian; Albenberg, Lindsey; Sinha, Rohini; Compher, Charlene; Gilroy, Erin; Nessel, Lisa; Grant, Amy; Chehoud, Christel; Li, Hongzhe; Wu, Gary D; Bushman, Frederic D Cell host & microbe. 26468751 2015 Oct 14;
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Structure and function of the healthy pre-adolescent pediatric gut microbiome. Hollister, Emily B; Riehle, Kevin; Luna, Ruth Ann; Weidler, Erica M; Rubio-Gonzales, Michelle; Mistretta, Toni-Ann; Raza, Sabeen; Doddapaneni, Harsha V; Metcalf, Ginger A; Muzny, Donna M; Gibbs, Richard A; Petrosino, Joseph F; Shulman, Robert J; Versalovic, James Microbiome. 26306392 2015;
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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. 26247840 2015 Dec 01;
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High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae. Sizova, Maria V; Chilaka, Amanda; Earl, Ashlee M; Doerfert, Sebastian N; Muller, Paul A; Torralba, Manolito; McCorrison, Jamison M; Durkin, A Scott; Nelson, Karen E; Epstein, Slava S Standards in genomic sciences. 26221418 2015;
Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile. Schubert, Alyxandria M; Sinani, Hamide; Schloss, Patrick D mBio. 26173701 2015 Jul 14;
Role of Autophagy in the Maintenance of Intestinal Homeostasis. Baxt, Leigh A; Xavier, Ramnik J Gastroenterology. 26170139 2015 Sep;
Compact graphical representation of phylogenetic data and metadata with GraPhlAn. Asnicar, Francesco; Weingart, George; Tickle, Timothy L; Huttenhower, Curtis; Segata, Nicola PeerJ. 26157614 2015;
Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. Nobel, Yael R; Cox, Laura M; Kirigin, Francis F; Bokulich, Nicholas A; Yamanishi, Shingo; Teitler, Isabel; Chung, Jennifer; Sohn, Jiho; Barber, Cecily M; Goldfarb, David S; Raju, Kartik; Abubucker, Sahar; Zhou, Yanjiao; Ruiz, Victoria E; Li, Huilin; Mitreva, Makedonka; Alekseyenko, Alexander V; Weinstock, George M; Sodergren, Erica; Blaser, Martin J Nature communications. 26123276 2015 Jun 30;
Using an in-vitro biofilm model to assess the virulence potential of bacterial vaginosis or non-bacterial vaginosis Gardnerella vaginalis isolates. Castro, Joana; Alves, Patrícia; Sousa, Cármen; Cereija, Tatiana; França, Ângela; Jefferson, Kimberly K; Cerca, Nuno Scientific reports. 26113465 2015 Jun 26;
Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants. Taft, Diana H; Ambalavanan, Namasivayam; Schibler, Kurt R; Yu, Zhuoteng; Newburg, David S; Deshmukh, Hitesh; Ward, Doyle V; Morrow, Ardythe L PloS one. 26110908 2015 Jun 25;
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Impact of neonatal intensive care bed configuration on rates of late-onset bacterial sepsis and methicillin-resistant Staphylococcus aureus colonization. Julian, Samuel; Burnham, Carey-Ann D; Sellenriek, Patricia; Shannon, William D; Hamvas, Aaron; Tarr, Phillip I; Warner, Barbara B Infection control and hospital epidemiology. 26108888 2015 Oct;
Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome. Chumpitazi, B P; Cope, J L; Hollister, E B; Tsai, C M; McMeans, A R; Luna, R A; Versalovic, J; Shulman, R J Alimentary pharmacology & therapeutics. 26104013 2015 Aug;
Engineering the gut microbiota to treat hyperammonemia. Shen, Ting-Chin David; Albenberg, Lindsey; Bittinger, Kyle; Chehoud, Christel; Chen, Ying-Yu; Judge, Colleen A; Chau, Lillian; Ni, Josephine; Sheng, Michael; Lin, Andrew; Wilkins, Benjamin J; Buza, Elizabeth L; Lewis, James D; Daikhin, Yevgeny; Nissim, Ilana; Yudkoff, Marc; Bushman, Frederic D; Wu, Gary D The Journal of clinical investigation. 26098218 2015 Jul 1;
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Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease. Chehoud, Christel; Albenberg, Lindsey G; Judge, Colleen; Hoffmann, Christian; Grunberg, Stephanie; Bittinger, Kyle; Baldassano, Robert N; Lewis, James D; Bushman, Frederic D; Wu, Gary D Inflammatory bowel diseases. 26083617 2015 Aug;
Effects of Vaccination with 10-Valent Pneumococcal Non-Typeable Haemophilus influenza Protein D Conjugate Vaccine (PHiD-CV) on the Nasopharyngeal Microbiome of Kenyan Toddlers. Feazel, Leah M; Santorico, Stephanie A; Robertson, Charles E; Bashraheil, Mahfudh; Scott, J Anthony G; Frank, Daniel N; Hammitt, Laura L PloS one. 26083474 2015;
Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9. Bryson, Alexandra L; Hwang, Young; Sherrill-Mix, Scott; Wu, Gary D; Lewis, James D; Black, Lindsay; Clark, Tyson A; Bushman, Frederic D mBio. 26081634 2015 June 16;
Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett's Esophagus Cohort. Gall, Alevtina; Fero, Jutta; McCoy, Connor; Claywell, Brian C; Sanchez, Carissa A; Blount, Patricia L; Li, Xiaohong; Vaughan, Thomas L; Matsen, Frederick A; Reid, Brian J; Salama, Nina R PloS one. 26076489 2015 June 15;
Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes. Alkanani, Aimon K; Hara, Naoko; Gottlieb, Peter A; Ir, Diana; Robertson, Charles E; Wagner, Brandie D; Frank, Daniel N; Zipris, Danny Diabetes. 26068542 2015 Oct;
The Fecal Microbiome in Pediatric Patients With Short Bowel Syndrome. Davidovics, Zev H; Carter, Beth A; Luna, Ruth Ann; Hollister, Emily B; Shulman, Robert J; Versalovic, James JPEN. Journal of parenteral and enteral nutrition. 26059898 2016 11;
Lungs, microbes and the developing neonate. Warner, Barbara B; Hamvas, Aaron Neonatology. 26044101 2015 June;
Fast disease progression in simian HIV-infected female macaque is accompanied by a robust local inflammatory innate immune and microbial response. Ren, Wuze; Ma, Yingfei; Yang, Liying; Gettie, Agegnehu; Salas, January; Russell, Kasi; Blanchard, James; Davidow, Amy; Pei, Zhiheng; Chang, Theresa L; Cheng-Mayer, Cecilia AIDS (London, England). 26035329 2015 Jun 19;
Inflammation-associated microbiota in pediatric eosinophilic esophagitis. Benitez, Alain J; Hoffmann, Christian; Muir, Amanda B; Dods, Kara K; Spergel, Jonathan M; Bushman, Frederic D; Wang, Mei-Lun Microbiome 26034601 2015
Carcass mass has little influence on the structure of gravesoil microbial communities. Weiss, Sophie; Carter, David O; Metcalf, Jessica L; Knight, Rob International journal of legal medicine. 26024793 2016 Jan;
Skin-to-Skin Care and the Development of the Preterm Infant Oral Microbiome. Hendricks-Muñoz, Karen D; Xu, Jie; Parikh, Hardik I; Xu, Ping; Fettweis, Jennifer M; Kim, Yang; Louie, Moi; Buck, Gregory A; Thacker, Leroy R; Sheth, Nihar U American journal of perinatology. 26007311 2015 Nov;
High-throughput sequencing technologies. Reuter, Jason A; Spacek, Damek V; Snyder, Michael P Molecular cell. 26000844 2015 May 21;
The Protein Interactome of Mycobacteriophage Giles Predicts Functions for Unknown Proteins. Mehla, Jitender; Dedrick, Rebekah M; Caufield, J Harry; Siefring, Rachel; Mair, Megan; Johnson, Allison; Hatfull, Graham F; Uetz, Peter Journal of bacteriology. 25986902 2015 Aug 1;
An integrative view of microbiome-host interactions in inflammatory bowel diseases. Wlodarska, Marta; Kostic, Aleksandar D; Xavier, Ramnik J Cell host & microbe. 25974300 2015 May 13;
Comparative Effectiveness of Nutritional and Biological Therapy in North American Children with Active Crohn's Disease. Lee, Dale; Baldassano, Robert N; Otley, Anthony R; Albenberg, Lindsey; Griffiths, Anne M; Compher, Charlene; Chen, Eric Z; Li, Hongzhe; Gilroy, Erin; Nessel, Lisa; Grant, Amy; Chehoud, Christel; Bushman, Frederic D; Wu, Gary D; Lewis, James D Inflammatory bowel diseases. 25970545 2015 Aug;
Identifying personal microbiomes using metagenomic codes. Franzosa, Eric A; Huang, Katherine; Meadow, James F; Gevers, Dirk; Lemon, Katherine P; Bohannan, Brendan J M; Huttenhower, Curtis Proceedings of the National Academy of Sciences of the United States of America. 25964341 2015 Jun 2;
Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis. Segal, Leopoldo N; Blaser, Martin J The Journal of pediatrics. 25934071 2015 Jul;
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Franzosa, Eric A; Hsu, Tiffany; Sirota-Madi, Alexandra; Shafquat, Afrah; Abu-Ali, Galeb; Morgan, Xochitl C; Huttenhower, Curtis Nature reviews. Microbiology. 25915636 2015 Jun;
Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Leone, Vanessa; Gibbons, Sean M; Martinez, Kristina; Hutchison, Alan L; Huang, Edmond Y; Cham, Candace M; Pierre, Joseph F; Heneghan, Aaron F; Nadimpalli, Anuradha; Hubert, Nathaniel; Zale, Elizabeth; Wang, Yunwei; Huang, Yong; Theriault, Betty; Dinner, Aaron R; Musch, Mark W; Kudsk, Kenneth A; Prendergast, Brian J; Gilbert, Jack A; Chang, Eugene B Cell host & microbe. 25891358 2015 May 13;
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