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    Jun Song, PhD, MA

    TitleProfessor
    SchoolUCSF School of Medicine
    DepartmentEpidemiology & Biostatistics
    Address513 Parnassus Ave, Med Sci
    San Francisco CA 94143
    Phone415-476-6933

       Overview 
       Overview
      I am a computational biologist working in epigenetics and transcription networks. I am interested in applying the next generation sequencing technology to study interactions among transcription factors, non-coding RNAs and chromatin structure.


       ORNG Applications 
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       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Qin H, Diaz A, Blouin L, Lebbink RJ, Patena W, Tanbun P, LeProust EM, McManus MT, Song JS, Ramalho-Santos M. Systematic Identification of Barriers to Human iPSC Generation. Cell. 2014 Jul 17; 158(2):449-61.
        View in: PubMed
      2. Johnson BE, Mazor T, Hong C, Barnes M, Aihara K, McLean CY, Fouse SD, Yamamoto S, Ueda H, Tatsuno K, Asthana S, Jalbert LE, Nelson SJ, Bollen AW, Gustafson WC, Charron E, Weiss WA, Smirnov IV, Song JS, Olshen AB, Cha S, Zhao Y, Moore RA, Mungall AJ, Jones SJ, Hirst M, Marra MA, Saito N, Aburatani H, Mukasa A, Berger MS, Chang SM, Taylor BS, Costello JF. Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma. Science. 2014 Jan 10; 343(6167):189-93.
        View in: PubMed
      3. Rube HT, Song JS. Quantifying the role of steric constraints in nucleosome positioning. Nucleic Acids Res. 2014 Feb 1; 42(4):2147-58.
        View in: PubMed
      4. Chen J, Torcia S, Xie F, Lin CJ, Cakmak H, Franciosi F, Horner K, Onodera C, Song JS, Cedars MI, Ramalho-Santos M, Conti M. Somatic cells regulate maternal mRNA translation and developmental competence of mouse oocytes. Nat Cell Biol. 2013 Dec; 15(12):1415-23.
        View in: PubMed
      5. Sachs M, Onodera C, Blaschke K, Ebata KT, Song JS, Ramalho-Santos M. Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo. Cell Rep. 2013 Jun 27; 3(6):1777-84.
        View in: PubMed
      6. Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell. 2013 May 2; 12(5):616-28.
        View in: PubMed
      7. Haq R, Shoag J, Andreu-Perez P, Yokoyama S, Edelman H, Rowe GC, Frederick DT, Hurley AD, Nellore A, Kung AL, Wargo JA, Song JS, Fisher DE, Arany Z, Widlund HR. Oncogenic BRAF regulates oxidative metabolism via PGC1a and MITF. Cancer Cell. 2013 Mar 18; 23(3):302-15.
        View in: PubMed
      8. Haq R, Yokoyama S, Hawryluk EB, Jönsson GB, Frederick DT, McHenry K, Porter D, Tran TN, Love KT, Langer R, Anderson DG, Garraway LA, Duncan LM, Morton DL, Hoon DS, Wargo JA, Song JS, Fisher DE. BCL2A1 is a lineage-specific antiapoptotic melanoma oncogene that confers resistance to BRAF inhibition. Proc Natl Acad Sci U S A. 2013 Mar 12; 110(11):4321-6.
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      9. Nellore A, Bobkov K, Howe E, Pankov A, Diaz A, Song JS. NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data. Front Genet. 2012; 3:320.
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      10. Howe ED, Song JS. Categorical spectral analysis of periodicity in human and viral genomes. Nucleic Acids Res. 2013 Feb 1; 41(3):1395-405.
        View in: PubMed
      11. Diaz A, Nellore A, Song JS. CHANCE: comprehensive software for quality control and validation of ChIP-seq data. Genome Biol. 2012 Oct 15; 13(10):R98.
        View in: PubMed
      12. Venere M, Han YG, Bell R, Song JS, Alvarez-Buylla A, Blelloch R. Sox1 marks an activated neural stem/progenitor cell in the hippocampus. Development. 2012 Nov; 139(21):3938-49.
        View in: PubMed
      13. Li J, Song JS, Bell RJ, Tran TN, Haq R, Liu H, Love KT, Langer R, Anderson DG, Larue L, Fisher DE. YY1 regulates melanocyte development and function by cooperating with MITF. PLoS Genet. 2012; 8(5):e1002688.
        View in: PubMed
      14. Diaz A, Park K, Lim DA, Song JS. Normalization, bias correction, and peak calling for ChIP-seq. Stat Appl Genet Mol Biol. 2012; 11(3):Article 9.
        View in: PubMed
      15. Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF. Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. PLoS Genet. 2012; 8(3):e1002576.
        View in: PubMed
      16. Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, Qi Z, Downey SL, Manos PD, Rossi DJ, Yu J, Hebrok M, Hochedlinger K, Costello JF, Song JS, Ramalho-Santos M. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol. 2011 May; 13(5):541-9.
        View in: PubMed
      17. J.S. Song and D.E. Fisher. Epigenomics: From Chromatin Biology to Therapeutics. Nucleosome positioning in promoters: significance and open questions. 2011.
      18. Levy C, Khaled M, Iliopoulos D, Janas MM, Schubert S, Pinner S, Chen PH, Li S, Fletcher AL, Yokoyama S, Scott KL, Garraway LA, Song JS, Granter SR, Turley SJ, Fisher DE, Novina CD. Intronic miR-211 assumes the tumor suppressive function of its host gene in melanoma. Mol Cell. 2010 Dec 10; 40(5):841-9.
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      19. Hu W, Chan CS, Wu R, Zhang C, Sun Y, Song JS, Tang LH, Levine AJ, Feng Z. Negative regulation of tumor suppressor p53 by microRNA miR-504. Mol Cell. 2010 Jun 11; 38(5):689-99.
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      20. Levy C, Khaled M, Robinson KC, Veguilla RA, Chen PH, Yokoyama S, Makino E, Lu J, Larue L, Beermann F, Chin L, Bosenberg M, Song JS, Fisher DE. Lineage-specific transcriptional regulation of DICER by MITF in melanocytes. Cell. 2010 Jun 11; 141(6):994-1005.
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      21. Ozsolak F, Poling LL, Wang Z, Liu H, Liu XS, Roeder RG, Zhang X, Song JS, Fisher DE. Chromatin structure analyses identify miRNA promoters. Genes Dev. 2008 Nov 15; 22(22):3172-83.
        View in: PubMed
      22. Zhang Y, Shin H, Song JS, Lei Y, Liu XS. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics. 2008; 9:537.
        View in: PubMed
      23. Chan CS, Song JS. CCCTC-binding factor confines the distal action of estrogen receptor. Cancer Res. 2008 Nov 1; 68(21):9041-9.
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      24. Holmes KA, Song JS, Liu XS, Brown M, Carroll JS. Nkx3-1 and LEF-1 function as transcriptional inhibitors of estrogen receptor activity. Cancer Res. 2008 Sep 15; 68(18):7380-5.
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      25. Song JS, Liu X, Liu XS, He X. A high-resolution map of nucleosome positioning on a fission yeast centromere. Genome Res. 2008 Jul; 18(7):1064-72.
        View in: PubMed
      26. Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 2008 Mar; 18(3):393-403.
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      27. Albert M, Song JS, Schultz D, Cormack RA, Tempany CM, Haker S, Devlin PM, Beard C, Hurwitz MD, Suh WW, Jolesz F, D'Amico AV. Defining the rectal dose constraint for permanent radioactive seed implantation of the prostate. Urol Oncol. 2008 Mar-Apr; 26(2):147-52.
        View in: PubMed
      28. Xiang HF, Song JS, Chin DW, Cormack RA, Tishler RB, Makrigiorgos GM, Court LE, Chin LM. Build-up and surface dose measurements on phantoms using micro-MOSFET in 6 and 10 MV x-ray beams and comparisons with Monte Carlo calculations. Med Phys. 2007 Apr; 34(4):1266-73.
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      29. Song JS, Maghsoudi K, Li W, Fox E, Quackenbush J, Shirley Liu X. Microarray blob-defect removal improves array analysis. Bioinformatics. 2007 Apr 15; 23(8):966-71.
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      30. Landis DM, Luo W, Song J, Bellon JR, Punglia RS, Wong JS, Killoran JH, Gelman R, Harris JR. Variability among breast radiation oncologists in delineation of the postsurgical lumpectomy cavity. Int J Radiat Oncol Biol Phys. 2007 Apr 1; 67(5):1299-308.
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      31. Ozsolak F, Song JS, Liu XS, Fisher DE. High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol. 2007 Feb; 25(2):244-8.
        View in: PubMed
      32. Song JS, Court LE, Cormack RA. Monte Carlo calculation of rectal dose when using an intrarectal balloon during prostate radiation therapy. Med Dosim. 2007; 32(3):151-6.
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      33. Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS. Model-based analysis of two-color arrays (MA2C). Genome Biol. 2007; 8(8):R178.
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      34. Court LE, Jahnke L, Chin D, Song J, Cormack R, Zygmanski P, Tishler RB, Chin L. Dynamic IMRT treatments of sinus region tumors: comparison of Monte Carlo calculations with treatment planning system calculations and ion chamber measurements. Technol Cancer Res Treat. 2006 Oct; 5(5):489-95.
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      35. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS, Brown M. Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 2006 Nov; 38(11):1289-97.
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      36. Song YS, Song JS. Analytic computation of the expectation of the linkage disequilibrium coefficient r2. Theor Popul Biol. 2007 Feb; 71(1):49-60.
        View in: PubMed
      37. Ji X, Li W, Song J, Wei L, Liu XS. CEAS: cis-regulatory element annotation system. Nucleic Acids Res. 2006 Jul 1; 34(Web Server issue):W551-4.
        View in: PubMed
      38. Song JS, Albert M, D'Amico AV, Cormack RA. A comparative study of rectal dose histograms in prostate brachytherapy: some analytic and numerical results. Med Phys. 2005 Feb; 32(2):437-47.
        View in: PubMed
      39. Monni S, Song JS, Song YS. The Hurwitz Enumeration Problem of Branched Covers and Hodge Integrals. Journal of Geometry and Physics. 2004; 50:223-256.
      40. Song JS, Song YS. On a Conjecture of Givental. J Math Phys. 2004; 45:4539-4550.
      41. He YH, Song JS. Of McKay Correspondence, Non-linear Sigma-model and Conformed Field Theory. Adv Theo Math Phys. 2000; 4:747-790.
      42. Song JS. Three-Dimensional Gorenstein Singularities and SU(3) Modular Invariants. Adv Theo Math Phys. 2000; 4:791-822.
      43. Song JS. Descendant Gromov-Witten Invariants, Simple Hurwitz Numbers, and the Virasoro Conjecture for P^1. Adv Theo Math Phys. 1999; 3:1721-1768.
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