Browsing by Author "Huttenhower, Curtis"

Now showing items 21-40 of 62

    • Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis 

      Scher, Jose U; Sczesnak, Andrew; Longman, Randy S; Segata, Nicola; Ubeda, Carles; Bielski, Craig; Rostron, Tim; Cerundolo, Vincenzo; Pamer, Eric G; Abramson, Steven B; Huttenhower, Curtis; Littman, Dan R (eLife Sciences Publications, Ltd, 2013)
      Rheumatoid arthritis (RA) is a prevalent systemic autoimmune disease, caused by a combination of genetic and environmental factors. Animal models suggest a role for intestinal bacteria in supporting the systemic immune ...

    • A Framework for Human Microbiome Research 

      Methé, Barbara A.; Nelson, Karen E.; Pop, Mihai; Creasy, Heather H.; Giglio, Michelle G.; Gevers, Dirk; Petrosino, Joseph F.; Abubucker, Sahar; Badger, Jonathan H.; Chinwalla, Asif T.; Earl, Ashlee M.; Fulton, Robert S.; Hallsworth-Pepin, Kymberlie; Lobos, Elizabeth A.; Madupu, Ramana; Magrini, Vincent; Mitreva, Makedonka; Muzny, Donna M.; Sodergren, Erica J.; Versalovic, James; Wollam, Aye M.; Worley, Kim C.; Wortman, Jennifer R.; Zeng, Qiandong; Aagaard, Kjersti M.; Abolude, Olukemi O.; Allen-Vercoe, Emma; Alm, Eric J.; Alvarado, Lucia; Andersen, Gary L.; Appelbaum, Elizabeth; Arachchi, Harindra M.; Armitage, Gary; Arze, Cesar A.; Ayvaz, Tulin; Baker, Carl C.; Begg, Lisa; Belachew, Tsegahiwot; Bhonagiri, Veena; Bihan, Monika; Blaser, Martin J.; Bloom, Toby; Vivien Bonazzi, J.; Brooks, Paul; Buck, Gregory A.; Buhay, Christian J.; Busam, Dana A.; Campbell, Joseph L.; Canon, Shane R.; Cantarel, Brandi L.; Chain, Patrick S.; Chen, I-Min A.; Chen, Lei; Chhibba, Shaila; Ciulla, Dawn M.; Clemente, Jose C.; Clifton, Sandra W.; Conlan, Sean; Crabtree, Jonathan; Cutting, Mary A.; Davidovics, Noam J.; Davis, Catherine C.; DeSantis, Todd Z.; Deal, Carolyn; Delehaunty, Kimberley D.; Deych, Elena; Dooling, David J.; Dugan, Shannon P.; Farmer, Candace N.; Faust, Karoline; Feldgarden, Michael; Felix, Victor M.; Fisher, Sheila; Fodor, Anthony A.; Forney, Larry; Foster, Leslie; Di Francesco, Valentina; Friedman, Jonathan; Friedrich, Dennis C.; Fronick, Catrina C.; Fulton, Lucinda L.; Gao, Hongyu; Garcia, Nathalia; Giannoukos, Georgia; Giblin, Christina; Giovanni, Maria Y.; Goll, Johannes; Gonzalez, Antonio; Griggs, Allison; Gujja, Sharvari; Haas, Brian J.; Hamilton, Holli A.; Hepburn, Theresa A.; Herter, Brandi; Hoffmann, Diane E.; Holder, Michael E.; Howarth, Clinton; Huse, Susan M.; Jansson, Janet K.; Jiang, Huaiyang; Jordan, Catherine; Joshi, Vandita; Katancik, James A.; Keitel, Wendy A.; Kelley, Scott T.; Kells, Cristyn; Kinder-Haake, Susan; King, Nicholas B.; Knight, Rob; Kong, Heidi H.; Koren, Omry; Koren, Sergey; Kota, Karthik C.; Kovar, Christie L.; Kyrpides, Nikos C.; La Rosa, Patricio S.; Lewis, Cecil M.; Lewis, Lora; Ley, Ruth E.; Li, Kelvin; Liolios, Konstantinos; Lo, Chien-Chi; Lozupone, Catherine A.; Lunsford, R. Dwayne; Madden, Tessa; Mahurkar, Anup A.; Mannon, Peter J.; Mardis, Elaine R.; Markowitz, Victor M.; Mavrommatis, Konstantinos; McCorrison, Jamison M.; McEwen, Jean; McGuire, Amy L.; McInnes, Pamela; Mehta, Teena; Mihindukulasuriya, Kathie A.; Minx, Patrick J.; Newsham, Irene; Nusbaum, Chad; O’Laughlin, Michelle; Orvis, Joshua; Pagani, Ioanna; Palaniappan, Krishna; Patel, Shital M.; Peterson, Jane; Podar, Mircea; Pohl, Craig; Pollard, Katherine S.; Priest, Margaret E.; Proctor, Lita M.; Qin, Xiang; Raes, Jeroen; Ravel, Jacques; Reid, Jeffrey G.; Rho, Mina; Rhodes, Rosamond; Riehle, Kevin P.; Rivera, Maria C.; Rodriguez-Mueller, Beltran; Rogers, Yu-Hui; Ross, Matthew C.; Russ, Carsten; Sanka, Ravi K.; Pamela Sankar, J.; Sathirapongsasuti, Fah; Schloss, Jeffery A.; Schloss, Patrick D.; Scholz, Matthew; Schriml, Lynn; Schubert, Alyxandria M.; Segata, Nicola; Segre, Julia A.; Shannon, William D.; Sharp, Richard R.; Sharpton, Thomas J.; Shenoy, Narmada; Sheth, Nihar U.; Simone, Gina A.; Singh, Indresh; Sobel, Jack D.; Sommer, Daniel D.; Spicer, Paul; Sutton, Granger G.; Tabbaa, Diana G.; Thiagarajan, Mathangi; Tomlinson, Chad M.; Torralba, Manolito; Treangen, Todd J.; Truty, Rebecca M.; Vishnivetskaya, Tatiana A.; Walker, Jason; Wang, Zhengyuan; Ward, Doyle V.; Warren, Wesley; Watson, Mark A.; Wellington, Christopher; Wetterstrand, Kris A.; Wilczek-Boney, Katarzyna; Wu, Yuan Qing; Wylie, Kristine M.; Wylie, Todd; Yandava, Chandri; Ye, Yuzhen; Yooseph, Shibu; Youmans, Bonnie P.; Zhou, Yanjiao; Zhu, Yiming; Zoloth, Laurie; Birren, Bruce W.; Gibbs, Richard A.; Highlander, Sarah K.; Weinstock, George M.; White, Owen; Huttenhower, Curtis; FitzGerald, Michael G.; Martin, John C.; Young, Sarah K.; Anderson, Scott; Chu, Ken; Dewhirst, Floyd Everett; Ding, Yan; Dunne, Wm. Michael; Durkin, A. Scott; Edgar, Robert C.; Erlich, Rachel L.; Farrell, Ruth M.; Goldberg, Jonathan M.; Harris, Emily L.; Huang, Katherine H.; Izard, Jacques Georges; Knights, Dan; Lee, Sandra L.; Lemon, Katherine Paige; Lennon, Niall; Liu, Bo; Liu, Yue; McDonald, Daniel; Miller, Jason R.; Pearson, Matthew; Schmidt, Thomas M.; Smillie, Chris Scott; Sykes, Sean M.; Wang, Lu; White, James R.; Ye, Liang; Zhang, Lan; Zucker, Jeremy Daniel Hofeld; Wilson, Richard K. (Nature Publishing Group, 2012)
      A variety of microbial communities and their genes (microbiome) exist throughout the human body, playing fundamental roles in human health and disease. The NIH funded Human Microbiome Project (HMP) Consortium has established ...

    • A Framework for Microbiome Science in Public Health 

      Wilkinson, Jeremy E.; Franzosa, Eric; Everett, Christine; Li, Chengchen; Hu, Frank; Wirth, Dyann; Song, Mingyang; Chan, Andrew; Rimm, Eric; Garrett, Wendy; Huttenhower, Curtis (Nature / Springer, 2021-04-05)
      Human microbiome science has advanced rapidly and reached a scale at which basic biology, clinical translation, and population health are increasingly integrated. It is thus now possible for public health researchers, ...

    • Functional profiling of the gut microbiome in disease-associated inflammation 

      Börnigen, Daniela; Morgan, Xochitl C; Franzosa, Eric A; Ren, Boyu; Xavier, Ramnik J; Garrett, Wendy S; Huttenhower, Curtis (BioMed Central, 2013)
      The microbial residents of the human gut are a major factor in the development and lifelong maintenance of health. The gut microbiota differs to a large degree from person to person and has an important influence on health ...

    • Genomic analysis identifies association of Fusobacterium with colorectal carcinoma 

      Kostic, Aleksandar David; Gevers, D.; Pedamallu, Chandra Sekhar; Michaud, Monia; Duke, F.; Earl, A. M.; Ojesina, Akinyemi Ifedapo; Jung, J.; Bass, Adam Joel; Tabernero, J.; Baselga, J.; Liu, C.; Shivdasani, Ramesh Arjun; Ogino, Shuji; Birren, B. W.; Huttenhower, Curtis; Garrett, Wendy S.; Meyerson, Matthew Langer (Cold Spring Harbor Laboratory Press, 2011)
      The tumor microenvironment of colorectal carcinoma is a complex community of genomically altered cancer cells, nonneoplastic cells, and a diverse collection of microorganisms. Each of these components may contribute to ...

    • Global Assessment of Genomic Regions Required for Growth in Mycobacterium tuberculosis 

      Zhang, Yanjia Jason; Ioerger, Thomas R.; Huttenhower, Curtis; Long, Jarukit E.; Sassetti, Christopher M.; Sacchettini, James C.; Rubin, Eric Joseph (Public Library of Science, 2012)
      Identifying genomic elements required for viability is central to our understanding of the basic physiology of bacterial pathogens. Recently, the combination of high-density mutagenesis and deep sequencing has allowed for ...

    • Global Chemical Impact of the Microbiome Includes Novel Bile Acid Conjugations 

      Quinn, Robert; Melnik, Alexey; Vrbanac, Alison; Patras, Kathryn; Christy, Mitchell; Zsolt, Bodai; Belda-Ferre, Pedro; Tripathi, Anupriya; Chung, Lawton; Quinn, Melissa; Humphrey, Greg; Panitchpakdi, Morgan; Weldon, Kelly; Aksenov, Alexander; da Silva, Ricardo; Avila-Pacheco, Julian; Clish, Clary; Bae, Sena; Mallick, Himel; Franzosa, Eric; Lloyd-Price, Jason; Bussell, Robert; Thron, Taren; Nelson, Andrew; Wang, Mingxun; Leszczynski, Eric; Vargas, Fernando; Gauglitz, Julia; Meehan, Michael; Gentry, Emily; Arthur, Timothy; Downes, Michael; Fu, Ting; Welch, Ryan; Komor, Alexis; Poulsen, Orit; Boland, Brigid; Chang, John; Sandborn, William; Lim, Meerana; Garg, Neha; Lumeng, Julie; Xavier, Ramnik; Kazmierczak, Barbara; Jain, Ruchi; Egan, Marie; Rhee, Kyung; Ferguson, David; Evans, Ronald; Raffatellu, Manuela; Vlamakis, Hera; Haddad, Gabriel; Siegel, Dionicio; Huttenhower, Curtis; Mazmanian, Sarkis; Nizet, Victor; Knight, Rob; Dorrestein, Pieter (Springer Nature, 2020-02-26)
      A mosaic of cross-phyla chemical interactions occurs between all metazoans and their microbiomes. In humans, the gut harbors the heaviest microbial load, but many organs, particularly those with a mucosal surface, associate ...

    • Graphle: Interactive Exploration of Large, Dense Graphs 

      Huttenhower, Curtis; Mehmood, Sajid O; Troyanskaya, Olga G (BioMed Central, 2009)
      Background: A wide variety of biological data can be modeled as network structures, including experimental results (e.g. protein-protein interactions), computational predictions (e.g. functional interaction networks), or ...

    • Growth Effects of N-Acylethanolamines on Gut Bacteria Reflect Altered Bacterial Abundances in Inflammatory Bowel Disease 

      Fornelos, Nadine; Franzosa, Eric; 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.; Xavier (Springer Science and Business Media LLC, 2020-01-20)
      Inflammatory bowel diseases (IBD) are associated with alterations in gut microbial abundances and lumenal metabolite concentrations, but the effects of specific metabolites on the gut microbiota in health and disease remain ...

    • A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets 

      Koren, Omry; Knights, Daniel; Gonzalez, Antonio; Waldron, Levi D.; Segata, Nicola; Knight, Rob; Huttenhower, Curtis; Ley, Ruth E. (Public Library of Science, 2013)
      Recent analyses of human-associated bacterial diversity have categorized individuals into ‘enterotypes’ or clusters based on the abundances of key bacterial genera in the gut microbiota. There is a lack of consensus, ...

    • Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission 

      Rooks, Michelle G; Veiga, Patrick; Wardwell-Scott, Leslie H; Tickle, Timothy; Segata, Nicola; Michaud, Monia; Gallini, Carey Ann; Beal, Chloé; van Hylckama-Vlieg, Johan ET; Ballal, Sonia Arora; Morgan, Xochitl C; Glickman, Jonathan Neil; Gevers, Dirk; Huttenhower, Curtis; Garrett, Wendy S. (Springer Nature, 2014)
      Dysregulated immune responses to gut microbes are central to inflammatory bowel disease (IBD), and gut microbial activity can fuel chronic inflammation. Examining how IBD-directed therapies influence gut microbiomes may ...

    • The healthy human microbiome 

      Lloyd-Price, Jason; Abu-Ali, Galeb; Huttenhower, Curtis (BioMed Central, 2016)
      Humans are virtually identical in their genetic makeup, yet the small differences in our DNA give rise to tremendous phenotypic diversity across the human population. By contrast, the metagenome of the human microbiome—the ...

    • High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED 

      Kaminski, James; Gibson, Molly K.; Franzosa, Eric A.; Segata, Nicola; Dantas, Gautam; Huttenhower, Curtis (Public Library of Science, 2015)
      Profiling microbial community function from metagenomic sequencing data remains a computationally challenging problem. Mapping millions of DNA reads from such samples to reference protein databases requires long run-times, ...

    • The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome 

      Gevers, Dirk; Knight, Rob; Petrosino, Joseph F.; Huang, Katherine; McGuire, Amy L.; Birren, Bruce W.; Nelson, Karen E.; White, Owen; Methé, Barbara A.; Huttenhower, Curtis (Public Library of Science, 2012)
      This manuscript describes the NIH Human Microbiome Project, including a brief review of human microbiome research, a history of the project, and a comprehensive overview of the consortium's recent collection of publications ...

    • Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013 

      Ravel, Jacques; Blaser, Martin J; Braun, Jonathan; Brown, Eric; Bushman, Frederic D; Chang, Eugene B; Davies, Julian; Dewey, Kathryn G; Dinan, Timothy; Dominguez-Bello, Maria; Erdman, Susan E; Finlay, B Brett; Garrett, Wendy S; Huffnagle, Gary B; Huttenhower, Curtis; Jansson, Janet; Jeffery, Ian B; Jobin, Christian; Khoruts, Alexander; Kong, Heidi H; Lampe, Johanna W; Ley, Ruth E; Littman, Dan R; Mazmanian, Sarkis K; Mills, David A; Neish, Andrew S; Petrof, Elaine; Relman, David A; Rhodes, Rosamond; Turnbaugh, Peter J; Young, Vincent B; Knight, Rob; White, Owen (BioMed Central, 2014)
      A conference entitled ‘Human microbiome science: Vision for the future’ was organized in Bethesda, MD from July 24 to 26, 2013. The event brought together experts in the field of human microbiome research and aimed at ...

    • Infected erythrocyte-derived extracellular vesicles alter vascular function via regulatory Ago2-miRNA complexes in malaria 

      Mantel, Pierre-Yves; Hjelmqvist, Daisy; Walch, Michael; Kharoubi-Hess, Solange; Nilsson, Sandra; Ravel, Deepali; Ribeiro, Marina; Grüring, Christof; Ma, Siyuan; Padmanabhan, Prasad; Trachtenberg, Alexander; Ankarklev, Johan; Brancucci, Nicolas M.; Huttenhower, Curtis; Duraisingh, Manoj T.; Ghiran, Ionita; Kuo, Winston P.; Filgueira, Luis; Martinelli, Roberta; Marti, Matthias (Nature Publishing Group, 2016)
      Malaria remains one of the greatest public health challenges worldwide, particularly in sub-Saharan Africa. The clinical outcome of individuals infected with Plasmodium falciparum parasites depends on many factors including ...

    • Inferring Developmental Stage Composition from Gene Expression in Human Malaria 

      Joice, Regina; Narasimhan, Vagheesh; Montgomery, Jacqui; Sidhu, Amar Bir; Oh, Keunyoung; Meyer, Evan; Pierre-Louis, Willythssa; Seydel, Karl; Milner, Danny; Williamson, Kim; Wiegand, Roger; Ndiaye, Daouda; Daily, Johanna; Wirth, Dyann; Taylor, Terrie; Huttenhower, Curtis; Marti, Matthias (Public Library of Science, 2013)
      In the current era of malaria eradication, reducing transmission is critical. Assessment of transmissibility requires tools that can accurately identify the various developmental stages of the malaria parasite, particularly ...

    • Integrated Functional Networks of Process, Tissue, and Developmental Stage Specific Interactions in Arabidopsis thaliana 

      Pop, Ana; Huttenhower, Curtis; Iyer-Pascuzzi, Anjali; Benfey, Philip N; Troyanskaya, Olga G (BioMed Central, 2010)
      Background: Recent years have seen an explosion in plant genomics, as the difficulties inherent in sequencing and functionally analyzing these biologically and economically significant organisms have been overcome. Arabidopsis ...

    • Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis 

      Dubin, Krista; Callahan, Margaret K.; Ren, Boyu; Khanin, Raya; Viale, Agnes; Ling, Lilan; No, Daniel; Gobourne, Asia; Littmann, Eric; Huttenhower, Curtis; Pamer, Eric G.; Wolchok, Jedd D. (Nature Publishing Group, 2016)
      The composition of the intestinal microbiota influences the development of inflammatory disorders. However, associating inflammatory diseases with specific microbial members of the microbiota is challenging, because ...

    • Meeting report for the 1st skin microbiota workshop, boulder, CO October 15-16 2012 

      Gilbert, Jack A; Ball, Madeleine; Blainey, Paul; Blaser, Martin J; Bohannan, Brendan JM; Bateman, Ashley; Bunge, John; Dominguez-Bello, Maria Gloria; Epstein, Slava; Fierer, Noah; Gevers, Dirk; Grikscheit, Tracy; Hamdan, Leila J; Harvey, James; Huttenhower, Curtis; Kirkup, Benjamin; Kong, Heidi H; Lauber, Christian; Lemon, Katherine P; Lynch, Susan V; Martin, Lance; Mello, Charlene; Palma, Joseph; Parker, Roy; Petrosino, Joseph; Segre, Julia A; Vosshall, Leslie; Yi, Rui; Knight, Rob (BioMed Central, 2014)
      This report details the outcome of the 1st Skin Microbiota Workshop, Boulder, CO, held on October 15th-16th 2012. The workshop was arranged to bring Department of Defense personnel together with experts in microbial ecology, ...