Now showing items 1-10 of 10

    • A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development 

      Hill, Jennifer Hampton; Franzosa, Eric A; Huttenhower, Curtis; Guillemin, Karen (eLife Sciences Publications, Ltd, 2016)
      Resident microbes play important roles in the development of the gastrointestinal tract, but their influence on other digestive organs is less well explored. Using the gnotobiotic zebrafish, we discovered that the normal ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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, ...
    • Multi-Omics of the Gut Microbial Ecosystem in Inflammatory Bowel Diseases 

      Lloyd-Price, Jason; Arze, Cesar; Schirmer, Melanie; Andrews, Elizabeth; Ajami, Nadim J.; Brislawn, Colin J.; Courtney, Holly; Gonzalez, Antonio; Graeber, Thomas G.; Hall, A. Brantley; Mallick, Himel; Rahnavard, Gholamali; Sauk, Jenny; Shungin, Dmitry; Vázquez-Baeza, Yoshiki; White, Richard A.; Braun, Jonathan; Denson, Lee A.; Jansson, Janet K.; Knight, Robert; Kugathasan, Subra; McGovern, Dermot P. B.; Stappenbeck, Thaddeus S.; Vlamakis, Hera; Huttenhower, Curtis; Ananthakrishnan, Ashwin; Avila-Pacheco, Julian; Poon, Tiffany; Bonham, Kevin; Casero, David; Casero, David; Lake, Kathleen; Landers, Carol; Plichta, Damian; Prasad, Mahadev; Winter, Harland; Clish, Clary; Franzosa, Eric; Xavier, Ramnik; Petrosino, Joseph (Springer Science and Business Media LLC, 2019-05)
      Inflammatory bowel diseases (IBD), which include Crohn’s disease (CD) and ulcerative colitis (UC), affect several million individuals worldwide. CD and UC are complex diseases and heterogeneous at the clinical, immunological, ...
    • A reproducible approach to high-throughput biological data acquisition and integration 

      Börnigen, Daniela; Moon, Yo Sup; Rahnavard, Gholamali; Waldron, Levi; McIver, Lauren; Shafquat, Afrah; Franzosa, Eric A.; Miropolsky, Larissa; Sweeney, Christopher; Morgan, Xochitl C.; Garrett, Wendy S.; Huttenhower, Curtis (PeerJ Inc., 2015)
      Modern biological research requires rapid, complex, and reproducible integration of multiple experimental results generated both internally and externally (e.g., from public repositories). Although large systematic ...
    • Signatures of Pleiotropy, Economy and Convergent Evolution in a Domain-Resolved Map of Human–Virus Protein–Protein Interaction Networks 

      Garamszegi, Sara; Franzosa, Eric A.; Xia, Yu (Public Library of Science, 2013)
      A central challenge in host-pathogen systems biology is the elucidation of general, systems-level principles that distinguish host-pathogen interactions from within-host interactions. Current analyses of host-pathogen and ...
    • Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes 

      Yassour, Moran; Lim, Mi Young; Yun, Hyun Sun; Tickle, Timothy L.; Sung, Joohon; Song, Yun-Mi; Lee, Kayoung; Franzosa, Eric A.; Morgan, Xochitl C.; Gevers, Dirk; Lander, Eric S.; Xavier, Ramnik J.; Birren, Bruce W.; Ko, GwangPyo; Huttenhower, Curtis (BioMed Central, 2016)
      Background: Obesity and type 2 diabetes (T2D) are linked both with host genetics and with environmental factors, including dysbioses of the gut microbiota. However, it is unclear whether these microbial changes precede ...