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Biodata Mining and Discovery Section
The overall mission of the Biodata Mining and Discovery Section is to assist and to participate in biomedical research with computational and bioinformatics approaches in support of the ultimate research goals of the NIAMS IRP. We are currently providing NGS (next generation sequencing) data analysis related bioinformatics support, focusing mainly on ChIP-Seq and RNA-Seq based research projects. We implement established data analysis approaches and apply them to a wide range of biological and biomedical studies. We also develop new data analysis algorithms and strategies, and conduct research to evaluate emerging methods and techniques in the rapidly evolving field of applied bioinformatics and computational biology.
Callen E, Faryabi RB, Luckey M, Hao B, Daniel JA, Yang W, Sun HW, Dressler G, Peng W, Chi H, Ge K, Krangel MS, Park JH, Nussenzweig A. The DNA Damage- and Transcription-Associated Protein Paxip1 Controls Thymocyte Development and Emigration. Immunity. 2012 Nov 13. pii: S1074-7613(12)00456-6. doi: 10.1016/j.immuni.2012.10.007.
Vahedi G, Takahashi H, Nakayamada S, Sun HW, Sartorelli V, Kanno Y, O'Shea JJ. STATs Shape the Active Enhancer Landscape of T Cell Populations. Cell. 2012 Nov 21;151(5):981-93. doi: 10.1016/j.cell.2012.09.044.
Okano J, Levy C, Lichti U, Sun HW, Yuspa SH, Sakai Y, Morasso MI. Cutaneous retinoic Acid levels determine hair follicle development and downgrowth. J Biol Chem. 2012 Nov 16;287(47):39304-15. doi: 10.1074/jbc.M112.397273. Epub 2012 Sep 24.
Hirahara K, Ghoreschi K, Yang XP, Takahashi H, Laurence A, Vahedi G, Sciumè G, Hall AO, Dupont CD, Francisco LM, Chen Q, Tanaka M, Kanno Y, Sun HW, Sharpe AH, Hunter CA, O'Shea JJ. Interleukin-27 Priming of T Cells Controls IL-17 Production In trans via Induction of the Ligand PD-L1. Immunity. 2012 Jun 21. [Epub ahead of print]
Nakayamada S, Kanno Y, Takahashi H, Jankovic D, Lu KT, Johnson TA, Sun HW, Vahedi G, Hakim O, Handon R, Schwartzberg PL, Hager GL, O'Shea JJ. Early Th1 Cell Differentiation Is Marked by a Tfh Cell-like Transition. Immunity. 2011 Dec 23;35(6):919-31.
Lu KT, Kanno Y, Cannons JL, Handon R, Bible P, Elkahloun AG, Anderson SM, Wei L, Sun H, O'Shea JJ, Schwartzberg PL. Functional and Epigenetic Studies Reveal Multistep Differentiation and Plasticity of In Vitro-Generated and In Vivo-Derived Follicular T Helper Cells.Immunity. 2011 Oct 19.
Yang XP, Ghoreschi K, Steward-Tharp SM, Rodriguez-Canales J, Zhu J, Grainger JR, Hirahara K, Sun HW, Wei L, Vahedi G, Kanno Y, O'Shea JJ, Laurence A. Opposing regulation of the locus encoding IL-17 through direct, reciprocal actions of STAT3 and STAT5. Nature Immunology. 2011 Mar;12(3):247-54.
Yamane A, Resch W, Kuo N, Kuchen S, Li Z, Sun HW, Robbiani DF, McBride K, Nussenzweig MC, Casellas R. Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes. Nature Immunology 2011 Jan;12(1):62-9.
Ghoreschi K, Laurence A, Yang XP, Tato CM, McGeachy MJ, Konkel JE, Ramos HL, Wei L, Davidson TS, Bouladoux N, Grainger JR, Chen Q, Kanno Y, Watford WT, Sun HW, Eberl G, Shevach EM, Belkaid Y, Cua DJ, Chen W, O'Shea JJ. Generation of pathogenic T(H)17 cells in the absence of TGF-β signalling. Nature. 2010 Oct 21;467(7318):967-71.
Daniel JA, Santos MA, Wang Z, Zang C, Schwab KR, Jankovic M, Filsuf D, Chen HT, Gazumyan A, Yaname A, Cho YW, Sun HW, Ge K, Peng W, Nussenzweig MC, Casellas R, Dressler GR, Zhao K, Nussenzweig A. PTIP promotes chromatin changes critical for immunoglobulin class switch recombination. Science 2010 Aug 20;329(5994):917-23.See extended list of publications
Reviewed December 14, 2012