Now showing items 1-20 of 54

    • Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome 

      Hartmann, Erica M.; Hickey, Roxana; Hsu, Tiffany; Betancourt Román, Clarisse M.; Chen, Jing; Schwager, Randall; Kline, Jeff; Brown, G. Z.; Halden, Rolf U.; Huttenhower, Curtis; Green, Jessica L. (American Chemical Society, 2016)
      Antibiotic resistance is increasingly widespread, largely due to human influence. Here, we explore the relationship between antibiotic resistance genes and the antimicrobial chemicals triclosan, triclocarban, and methyl-, ...
    • Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease 

      Morgan, Xochitl C; Kabakchiev, Boyko; Waldron, Levi; Tyler, Andrea D; Tickle, Timothy L; Milgrom, Raquel; Stempak, Joanne M; Gevers, Dirk; Xavier, Ramnik J; Silverberg, Mark S; Huttenhower, Curtis (BioMed Central, 2015)
      Background: Pouchitis is common after ileal pouch-anal anastomosis (IPAA) surgery for ulcerative colitis (UC). Similar to inflammatory bowel disease (IBD), both host genetics and the microbiota are implicated in its ...
    • Bioinformatics for the Human Microbiome Project 

      Gevers, Dirk; Pop, Mihai; Schloss, Patrick D.; Huttenhower, Curtis (Public Library of Science, 2012)
    • A Case Study for Large-Scale Human Microbiome Analysis Using JCVI’s Metagenomics Reports (METAREP) 

      Goll, Johannes; Thiagarajan, Mathangi; Abubucker, Sahar; Huttenhower, Curtis; Yooseph, Shibu; Methé, Barbara A. (Public Library of Science, 2012)
      As metagenomic studies continue to increase in their number, sequence volume and complexity, the scalability of biological analysis frameworks has become a rate-limiting factor to meaningful data interpretation. To address ...
    • CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types 

      Nelms, Bradlee D.; Waldron, Levi; Barrera, Luis A.; Weflen, Andrew W.; Goettel, Jeremy A.; Guo, Guoji; Montgomery, Robert K.; Neutra, Marian R.; Breault, David T.; Snapper, Scott B.; Orkin, Stuart H.; Bulyk, Martha L.; Huttenhower, Curtis; Lencer, Wayne I. (BioMed Central, 2016)
      We present a sensitive approach to predict genes expressed selectively in specific cell types, by searching publicly available expression data for genes with a similar expression profile to known cell-specific markers. Our ...
    • Chapter 12: Human Microbiome Analysis 

      Morgan, Xochitl C.; Huttenhower, Curtis (Public Library of Science, 2012)
      Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, archaeal, fungal, and viral. ...
    • The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone 

      Lee, Kevin C.; Stott, Matthew B.; Dunfield, Peter F.; Huttenhower, Curtis; McDonald, Ian R.; Morgan, Xochitl C. (American Society for Microbiology, 2016)
      ABSTRACT Chthonomonas calidirosea T49T is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that the C. calidirosea genome would be highly ...
    • Compact graphical representation of phylogenetic data and metadata with GraPhlAn 

      Asnicar, Francesco; Weingart, George; Tickle, Timothy L.; Huttenhower, Curtis; Segata, Nicola (PeerJ Inc., 2015)
      The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We ...
    • Composition of the Adult Digestive Tract Bacterial Microbiome Based on Seven Mouth Surfaces, Tonsils, Throat and Stool Samples 

      Segata, Nicholas; Haake, Susan Kinder; Mannon, Peter; Lemon, Katherine Paige; Waldron, Levi D.; Gevers, Dirk; Huttenhower, Curtis; Izard, Jacques Georges (BioMed Central, 2012)
      Background: To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human ...
    • Computational biology: plus c'est la même chose, plus ça change 

      Huttenhower, Curtis (BioMed Central, 2011)
      A report on the joint 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)/10th Annual European Conference on Computational Biology (ECCB) meetings and the 7th International Society for ...
    • Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer 

      Börnigen, Daniela; Tyekucheva, Svitlana; Wang, Xiaodong; Rider, Jennifer R.; Lee, Gwo-Shu; Mucci, Lorelei A.; Sweeney, Christopher; Huttenhower, Curtis (Public Library of Science, 2016)
      Molecular research in cancer is one of the largest areas of bioinformatic investigation, but it remains a challenge to understand biomolecular mechanisms in cancer-related pathways from high-throughput genomic data. This ...
    • Concordance of gene expression in human protein complexes reveals tissue specificity and pathology 

      Börnigen, Daniela; Pers, Tune H.; Thorrez, Lieven; Huttenhower, Curtis; Moreau, Yves; Brunak, Søren (Oxford University Press, 2013)
      Disease-causing variants in human genes usually lead to phenotypes specific to only a few tissues. Here, we present a method for predicting tissue specificity based on quantitative deregulation of protein complexes. The ...
    • Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast 

      Brauer, M. J.; Huttenhower, Curtis; Airoldi, Edoardo Maria; Rosenstein, R.; Matese, J. C.; Gresham, D.; Boer, V. M.; Troyanskaya, O. G.; Botstein, D. (American Society for Cell Biology (ASCB), 2008)
      We studied the relationship between growth rate and genome-wide gene expression, cell cycle progression, and glucose metabolism in 36 steady-state continuous cultures limited by one of six different nutrients (glucose, ...
    • Cross-biome comparison of microbial association networks 

      Faust, Karoline; Lima-Mendez, Gipsi; Lerat, Jean-Sébastien; Sathirapongsasuti, Jarupon F.; Knight, Rob; Huttenhower, Curtis; Lenaerts, Tom; Raes, Jeroen (Frontiers Media S.A., 2015)
      Clinical and environmental meta-omics studies are accumulating an ever-growing amount of microbial abundance data over a wide range of ecosystems. With a sufficiently large sample number, these microbial communities can ...
    • curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome 

      Ganzfried, Benjamin Frederick; Riester, Markus; Haibe-Kains, Benjamin; Risch, Thomas; Tyekucheva, Svitlana; Jazic, Ina; Wang, Xin Victoria; Ahmadifar, Mahnaz; Birrer, Michael James; Parmigiani, Giovanni; Huttenhower, Curtis; Waldron, Levi D. (Oxford University Press, 2013)
      This article introduces a manually curated data collection for gene expression meta-analysis of patients with ovarian cancer and software for reproducible preparation of similar databases. This resource provides uniformly ...
    • Dysfunction of the Intestinal Microbiome in Inflammatory Bowel Disease and Treatment 

      Morgan, Xochitl C; Sokol, Harry; Gevers, Dirk; Ward, Doyle V; LeLeiko, Neal; Sands, Bruce E; Tickle, Timothy L.; Devaney, Kathryn L; Reyes, Joshua Anthony; Shah, Samir A; Snapper, Scott Brian; Bousvaros, Athos; Korzenik, Joshua; Xavier, Ramnik; Huttenhower, Curtis (BioMed Central, 2012)
      Background: The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis result from alterations in intestinal microbes and the immune system. However, the precise dysfunctions of microbial metabolism in ...
    • Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants 

      Morrow, Ardythe L; Lagomarcino, Anne J; Schibler, Kurt R; Taft, Diana H; Yu, Zhuoteng; Wang, Bo; Altaye, Mekibib; Wagner, Michael; Gevers, Dirk; Ward, Doyle V; Kennedy, Michael A; Huttenhower, Curtis; Newburg, David S (BioMed Central, 2013)
      Background: Necrotizing enterocolitis (NEC) is a devastating intestinal disease that afflicts 10% of extremely preterm infants. The contribution of early intestinal colonization to NEC onset is not understood, and predictive ...
    • Epigenomic Diversity of Colorectal Cancer Indicated by LINE-1 Methylation in a Database of 869 Tumors 

      Baba, Yoshifumi; Huttenhower, Curtis; Nosho, Katsuhiko; Tanaka, Noriko; Shima, Kaori; Hazra, Aditi; Schernhammer, Eva S; Hunter, David J.; Giovannucci, Edward L.; Fuchs, Charles Stewart; Ogino, Shuji (BioMed Central, 2010)
      Background: Genome-wide DNA hypomethylation plays a role in genomic instability and carcinogenesis. LINE-1 (L1 retrotransposon) constitutes a substantial portion of the human genome, and LINE-1 methylation correlates with ...
    • 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 ...