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Jun Song, PhD

TitleProfessor
SchoolUCSF School of Medicine
DepartmentEpidemiology & Biostatistics
Address550 16th. Street
San Francisco CA 94158
Phone415-476-6933
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    Collapse Overview 
    Collapse 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.


    Collapse Research 
    Collapse Research Activities and Funding
    Integrative Genomics, Epigenomics and Bioinformatics Analyses of Human Uterine Fibroids
    NIH/NICHD R01HD089552Sep 16, 2016 - Jun 30, 2021
    Role: Co-Principal Investigator
    KnowEng, a Scalable Knowledge Engine for Large-Scale Genomic Data-OVERALL
    NIH/NIGMS U54GM114838Sep 29, 2014 - Apr 30, 2018
    Role: Co-Principal Investigator
    Predicting Transcriptional and Epigenetic Networks in Cancer from Sequencing Data
    NIH/NCI R01CA163336Dec 16, 2011 - Nov 30, 2016
    Role: Principal Investigator
    Origins and Biological Consequences of Human Infertility
    NIH/NICHD P50HD055764May 3, 2007 - Mar 31, 2017
    Role: Co-Investigator
    Origins and Biological Consequences of Human Infertility
    NIH/NICHD U54HD055764May 3, 2007 - Mar 31, 2017
    Role: Co-Investigator

    Collapse Bibliographic 
    Collapse 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. Bulut-Karslioglu A, Biechele S, Jin H, Macrae TA, Hejna M, Gertsenstein M, Song J, Ramalho-Santos M. Inhibition of mTOR induces a paused pluripotent state. Nature. 2016 Dec 01; 540(7631):119-123. PMID: 27880763.
      View in: PubMed
    2. Qin H, Hejna M, Liu Y, Percharde M, Wossidlo M, Blouin L, Durruthy-Durruthy J, Wong P, Qi Z, Yu J, Qi LS, Sebastiano V, Song J, Ramalho-Santos M. YAP Induces Human Naive Pluripotency. Cell Rep. 2016 Mar 15; 14(10):2301-12. PMID: 26947063.
      View in: PubMed
    3. Bell RJ, Rube HT, Xavier-Magalhães A, Costa BM, Mancini A, Song J, Costello JF. Understanding TERT Promoter Mutations: A Common Path to Immortality. Mol Cancer Res. 2016 Apr; 14(4):315-23. PMID: 26941407.
      View in: PubMed
    4. Bell RJ, Rube HT, Kreig A, Mancini A, Fouse SD, Nagarajan RP, Choi S, Hong C, He D, Pekmezci M, Wiencke JK, Wrensch MR, Chang SM, Walsh KM, Myong S, Song J, Costello JF. Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer. Science. 2015 May 29; 348(6238):1036-9. PMID: 25977370; PMCID: PMC4456397.
      View in: PubMed, PubMed Central
    5. Chen J, Hackett CS, Zhang S, Song YK, Bell RJ, Molinaro AM, Quigley DA, Balmain A, Song J, Costello JF, Gustafson WC, Van Dyke T, Kwok PY, Khan J, Weiss WA. The genetics of splicing in neuroblastoma. Cancer Discov. 2015 Apr; 5(4):380-95. PMID: 25637275; PMCID: PMC4390477.
      View in: PubMed, PubMed Central
    6. Guzman-Ayala M, Sachs M, Koh FM, Onodera C, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song J, Ramalho-Santos M. Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast. Development. 2015 Jan 1; 142(1):118-27. PMID: 25480920; PMCID: PMC4299150 [Available on 01/01/16].
      View in: PubMed, PubMed Central
    7. Diaz AA, Qin H, Ramalho-Santos M, Song J. HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis. Nucleic Acids Res. 2015 Feb 18; 43(3):e16. PMID: 25428347; PMCID: PMC4330337.
      View in: PubMed, PubMed Central
    8. Rube HT, Song J. Quantifying the role of steric constraints in nucleosome positioning. Nucleic Acids Res. 2014 Feb; 42(4):2147-58. PMID: 24288372; PMCID: PMC3936764.
      View in: PubMed, PubMed Central
    9. Chen J, Torcia S, Xie F, Lin CJ, Cakmak H, Franciosi F, Horner K, Onodera C, Song J, 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. PMID: 24270888; PMCID: PMC4066669.
      View in: PubMed, PubMed Central
    10. Sachs M, Onodera C, Blaschke K, Ebata KT, Song J, 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. PMID: 23727241; PMCID: PMC3700580.
      View in: PubMed, PubMed Central
    11. Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song J, 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. PMID: 23583100; PMCID: PMC3662805.
      View in: PubMed, PubMed Central
    12. Haq R, Shoag J, Andreu-Perez P, Yokoyama S, Edelman H, Rowe GC, Frederick DT, Hurley AD, Nellore A, Kung AL, Wargo JA, Song J, Fisher DE, Arany Z, Widlund HR. Oncogenic BRAF regulates oxidative metabolism via PGC1a and MITF. Cancer Cell. 2013 Mar 18; 23(3):302-15. PMID: 23477830; PMCID: PMC3635826.
      View in: PubMed, PubMed Central
    13. 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 J, 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. PMID: 23447565; PMCID: PMC3600451.
      View in: PubMed, PubMed Central
    14. Nellore A, Bobkov K, Howe E, Pankov A, Diaz A, Song J. NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data. Front Genet. 2012; 3:320. PMID: 23335939; PMCID: PMC3542818.
      View in: PubMed, PubMed Central
    15. Howe ED, Song J. Categorical spectral analysis of periodicity in human and viral genomes. Nucleic Acids Res. 2013 Feb 1; 41(3):1395-405. PMID: 23241388; PMCID: PMC3561982.
      View in: PubMed, PubMed Central
    16. Diaz A, Nellore A, Song J. CHANCE: comprehensive software for quality control and validation of ChIP-seq data. Genome Biol. 2012; 13(10):R98. PMID: 23068444; PMCID: PMC4053734.
      View in: PubMed, PubMed Central
    17. Venere M, Han YG, Bell R, Song J, Alvarez-Buylla A, Blelloch R. Sox1 marks an activated neural stem/progenitor cell in the hippocampus. Development. 2012 Nov; 139(21):3938-49. PMID: 22992951; PMCID: PMC3472585.
      View in: PubMed, PubMed Central
    18. Li J, Song J, 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. PMID: 22570637; PMCID: PMC3342948.
      View in: PubMed, PubMed Central
    19. Diaz A, Park K, Lim DA, Song J. Normalization, bias correction, and peak calling for ChIP-seq. Stat Appl Genet Mol Biol. 2012; 11(3):Article 9. PMID: 22499706; PMCID: PMC3342857.
      View in: PubMed, PubMed Central
    20. Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song J, 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. PMID: 22438827; PMCID: PMC3305387.
      View in: PubMed, PubMed Central
    21. 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 J, 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. PMID: 21499256; PMCID: PMC3987913.
      View in: PubMed, PubMed Central
    22. J.S. Song and D.E. Fisher. Epigenomics: From Chromatin Biology to Therapeutics. Nucleosome positioning in promoters: significance and open questions. 2011.
    23. 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 J, 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. PMID: 21109473; PMCID: PMC3004467.
      View in: PubMed, PubMed Central
    24. Hu W, Chan CS, Wu R, Zhang C, Sun Y, Song J, 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. PMID: 20542001; PMCID: PMC2900922.
      View in: PubMed, PubMed Central
    25. 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 J, Fisher DE. Lineage-specific transcriptional regulation of DICER by MITF in melanocytes. Cell. 2010 Jun 11; 141(6):994-1005. PMID: 20550935; PMCID: PMC2897150.
      View in: PubMed, PubMed Central
    26. Ozsolak F, Poling LL, Wang Z, Liu H, Liu XS, Roeder RG, Zhang X, Song J, Fisher DE. Chromatin structure analyses identify miRNA promoters. Genes Dev. 2008 Nov 15; 22(22):3172-83. PMID: 19056895; PMCID: PMC2593607.
      View in: PubMed, PubMed Central
    27. Zhang Y, Shin H, Song J, Lei Y, Liu XS. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics. 2008; 9:537. PMID: 19014516; PMCID: PMC2596141.
      View in: PubMed, PubMed Central
    28. Chan CS, Song J. CCCTC-binding factor confines the distal action of estrogen receptor. Cancer Res. 2008 Nov 1; 68(21):9041-9. PMID: 18974150.
      View in: PubMed
    29. Holmes KA, Song J, 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. PMID: 18794125.
      View in: PubMed
    30. Song J, 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. PMID: 18411404; PMCID: PMC2493395.
      View in: PubMed, PubMed Central
    31. 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 J, 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. PMID: 18258921; PMCID: PMC2259103.
      View in: PubMed, PubMed Central
    32. Albert M, Song J, 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. PMID: 18312933.
      View in: PubMed
    33. Xiang HF, Song J, 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. PMID: 17500458.
      View in: PubMed
    34. Song J, 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. PMID: 17332024.
      View in: PubMed
    35. 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. PMID: 17275202.
      View in: PubMed
    36. Ozsolak F, Song J, Liu XS, Fisher DE. High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol. 2007 Feb; 25(2):244-8. PMID: 17220878.
      View in: PubMed
    37. Song J, 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. PMID: 17707193.
      View in: PubMed
    38. Song J, 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. PMID: 17727723; PMCID: PMC2375008.
      View in: PubMed, PubMed Central
    39. 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. PMID: 16981791.
      View in: PubMed
    40. 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. PMID: 17013392.
      View in: PubMed
    41. Song YS, Song J. Analytic computation of the expectation of the linkage disequilibrium coefficient r2. Theor Popul Biol. 2007 Feb; 71(1):49-60. PMID: 17069867.
      View in: PubMed
    42. 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. PMID: 16845068; PMCID: PMC1538818.
      View in: PubMed, PubMed Central
    43. Song J, 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. PMID: 15789590.
      View in: PubMed
    44. Song J, Song YS. On a Conjecture of Givental. J Math Phys. 2004; 45:4539-4550.
    45. Monni S, Song J, Song YS. The Hurwitz Enumeration Problem of Branched Covers and Hodge Integrals. Journal of Geometry and Physics. 2004; 50:223-256.
    46. He YH, Song J . Of McKay Correspondence, Non-linear Sigma-model and Conformed Field Theory. Adv Theo Math Phys. 2000; 4:747-790.
    47. Song J . Three-Dimensional Gorenstein Singularities and SU(3) Modular Invariants. Adv Theo Math Phys. 2000; 4:791-822.
    48. Song J . 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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