Found: 13

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  • Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.

    Published in:
    Genome Biology, 2012, v. 13, n. 9, p. r79, doi. 10.1186/gb-2012-13-9-r79
    By:
    • Morgan, Xochitl C.;
    • Tickle, Timothy L.;
    • Sokol, Harry;
    • Gevers, Dirk;
    • Devaney, Kathryn L.;
    • Ward, Doyle V.;
    • Reyes, Joshua A.;
    • Shah, Samir A.;
    • LeLeiko, Neal;
    • Snapper, Scott B.;
    • Bousvaros, Athos;
    • Korzenik, Joshua;
    • Sands, Bruce E.;
    • Xavier, Ramnik J.;
    • Huttenhower, Curtis
    Publication type:
    Article

  • Computational Tools and Resources for Analysis and Exploration of Single-Cell Rnaseq Data in Agriculture.

    Published in:
    Journal of Animal Science, 2023, v. 101, p. 267, doi. 10.1093/jas/skad341.303
    By:
    • Kapoor, Muskan;
    • Tuggle, Christopher K.;
    • Burdett, Tony;
    • Tickle, Timothy;
    • Harrison, Peter;
    • Elsik, Christine;
    • Provart, Nicholas;
    • Libault, Marc;
    • Warren, Wes;
    • Koltes, James E.;
    • Sokolov, Alexey;
    • Ventura, Enrique Sapena;
    • Yordanova, Galabina;
    • Papatheodorou, Irene;
    • George, Nancy;
    • Ware, Doreen;
    • Kumari, Sunita;
    • Daharsh, Lance;
    • Cole, Benjamin
    Publication type:
    Article

  • Multivariable association discovery in population-scale meta-omics studies.

    Published in:
    PLoS Computational Biology, 2021, v. 17, n. 11, p. 1, doi. 10.1371/journal.pcbi.1009442
    By:
    • 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
    Publication type:
    Article

  • A statistical model for describing and simulating microbial community profiles.

    Published in:
    PLoS Computational Biology, 2021, v. 17, n. 9, p. 1, doi. 10.1371/journal.pcbi.1008913
    By:
    • Ma, Siyuan;
    • Ren, Boyu;
    • Mallick, Himel;
    • Moon, Yo Sup;
    • Schwager, Emma;
    • Maharjan, Sagun;
    • Tickle, Timothy L.;
    • Lu, Yiren;
    • Carmody, Rachel N.;
    • Franzosa, Eric A.;
    • Janson, Lucas;
    • Huttenhower, Curtis
    Publication type:
    Article

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

    Published in:
    ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2014, v. 8, n. 7, p. 1403, doi. 10.1038/ismej.2014.3
    By:
    • 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 A;
    • Morgan, Xochitl C;
    • Glickman, Jonathan N;
    • Gevers, Dirk;
    • Huttenhower, Curtis;
    • Garrett, Wendy S
    Publication type:
    Article

  • Two-stage microbial community experimental design.

    Published in:
    ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2013, v. 7, n. 12, p. 2330, doi. 10.1038/ismej.2013.139
    By:
    • Tickle, Timothy L;
    • Segata, Nicola;
    • Waldron, Levi;
    • Weingart, Uri;
    • Huttenhower, Curtis
    Publication type:
    Article

  • MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data.

    Published in:
    Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03349-w
    By:
    • Sarfraz, Irzam;
    • Wang, Yichen;
    • Shastry, Amulya;
    • Teh, Wei Kheng;
    • Sokolov, Artem;
    • Herb, Brian R.;
    • Creasy, Heather H.;
    • Virshup, Isaac;
    • Dries, Ruben;
    • Degatano, Kylee;
    • Mahurkar, Anup;
    • Schnell, Daniel J.;
    • Madrigal, Pedro;
    • Hilton, Jason;
    • Gehlenborg, Nils;
    • Tickle, Timothy;
    • Campbell, Joshua D.
    Publication type:
    Article

  • MetaPhlAn2 for enhanced metagenomic taxonomic profiling.

    Published in:
    Nature Methods, 2015, v. 12, n. 10, p. 902, doi. 10.1038/nmeth.3589
    By:
    • Truong, Duy Tin;
    • Franzosa, Eric A;
    • Tickle, Timothy L;
    • Scholz, Matthias;
    • Weingart, George;
    • Pasolli, Edoardo;
    • Tett, Adrian;
    • Huttenhower, Curtis;
    • Segata, Nicola
    Publication type:
    Article

  • Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.

    Published in:
    Journal of Clinical Investigation, 2014, v. 124, n. 8, p. 3617, doi. 10.1172/JCI75436
    By:
    • Haberman, Yael;
    • Tickle, Timothy L.;
    • Dexheimer, Phillip J.;
    • Mi-Ok Kim;
    • 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.
    Publication type:
    Article

  • Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.

    Published in:
    Genome Medicine, 2016, v. 8, p. 1, doi. 10.1186/s13073-016-0271-6
    By:
    • Yassour, Moran;
    • Mi Young Lim;
    • Hyun Sun Yun;
    • Tickle, Timothy L.;
    • Joohon Sung;
    • Yun-Mi Song;
    • Kayoung Lee;
    • Franzosa, Eric A.;
    • Morgan, Xochitl C.;
    • Gevers, Dirk;
    • Lander, Eric S.;
    • Xavier, Ramnik J.;
    • Birren., Bruce W.;
    • GwangPyo Ko;
    • Huttenhower, Curtis
    Publication type:
    Article

  • Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.

    Published in:
    Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0637-x
    By:
    • 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
    Publication type:
    Article

  • Toward a data infrastructure for the Plant Cell Atlas.

    Published in:
    Plant Physiology, 2023, v. 191, n. 1, p. 35, doi. 10.1093/plphys/kiac468
    By:
    • Fahlgren, Noah;
    • Kapoor, Muskan;
    • Yordanova, Galabina;
    • Papatheodorou, Irene;
    • Waese, Jamie;
    • Cole, Benjamin;
    • Harrison, Peter;
    • Ware, Doreen;
    • Tickle, Timothy;
    • Paten, Benedict;
    • Burdett, Tony;
    • Elsik, Christine G.;
    • Tuggle, Christopher K.;
    • Provart, Nicholas J.
    Publication type:
    Article

  • Computational meta’omics for microbial community studies.

    Published in:
    Molecular Systems Biology, 2013, v. 9, n. 1, p. 1, doi. 10.1038/msb.2013.22
    By:
    • Segata, Nicola;
    • Boernigen, Daniela;
    • Tickle, Timothy L;
    • Morgan, Xochitl C;
    • Garrett, Wendy S;
    • Huttenhower, Curtis
    Publication type:
    Article