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Jun Song, PhD, MA

Title(s)Professor, Epidemiology & Biostatistics
SchoolSchool of Medicine
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, 2022
    Role: Principal Investigator
    Origins and Biological Consequences of Human Infertility
    NIH/NICHD U54HD055764May 3, 2007 - Mar 31, 2017
    Role: Co-Investigator
    Center for Research, Innovation and Training in Reproduction and Infertility
    NIH/NICHD P50HD055764Apr 1, 2007 - Mar 31, 2023
    Role: Co-Investigator

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    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. Cheng JB, Sedgewick AJ, Finnegan AI, Harirchian P, Lee J, Kwon S, Fassett MS, Golovato J, Gray M, Ghadially R, Liao W, Perez White BE, Mauro TM, Mully T, Kim EA, Sbitany H, Neuhaus IM, Grekin RC, Yu SS, Gray JW, Purdom E, Paus R, Vaske CJ, Benz SC, Song JS, Cho RJ. Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution. Cell Rep. 2018 Oct 23; 25(4):871-883. PMID: 30355494.
      View in: PubMed
    2. Mancini A, Xavier-Magalhães A, Woods WS, Nguyen KT, Amen AM, Hayes JL, Fellmann C, Gapinske M, McKinney AM, Hong C, Jones LE, Walsh KM, Bell RJA, Doudna JA, Costa BM, Song JS, Perez-Pinera P, Costello JF. Disruption of the ß1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner. Cancer Cell. 2018 Sep 10; 34(3):513-528.e8. PMID: 30205050.
      View in: PubMed
    3. Ye J, Jin H, Pankov A, Song JS, Blelloch R. NF45 and NF90/NF110 coordinately regulate ESC pluripotency and differentiation. RNA. 2017 08; 23(8):1270-1284. PMID: 28487382.
      View in: PubMed
    4. Bulut-Karslioglu A, Biechele S, Jin H, Macrae TA, Hejna M, Gertsenstein M, Song JS, Ramalho-Santos M. Inhibition of mTOR induces a paused pluripotent state. Nature. 2016 12 01; 540(7631):119-123. PMID: 27880763.
      View in: PubMed
    5. Mazor T, Pankov A, Song JS, Costello JF. Intratumoral Heterogeneity of the Epigenome. Cancer Cell. 2016 Apr 11; 29(4):440-451. PMID: 27070699.
      View in: PubMed
    6. 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 JS, Ramalho-Santos M. YAP Induces Human Naive Pluripotency. Cell Rep. 2016 Mar 15; 14(10):2301-12. PMID: 26947063; PMCID: PMC4807727.
      View in: PubMed, PubMed Central
    7. Bell RJ, Rube HT, Xavier-Magalhães A, Costa BM, Mancini A, Song JS, Costello JF. Understanding TERT Promoter Mutations: A Common Path to Immortality. Mol Cancer Res. 2016 Apr; 14(4):315-23. PMID: 26941407; PMCID: PMC4852159 [Available on 04/01/17].
      View in: PubMed, PubMed Central
    8. Mazor T, Pankov A, Johnson BE, Hong C, Hamilton EG, Bell RJA, Smirnov IV, Reis GF, Phillips JJ, Barnes MJ, Idbaih A, Alentorn A, Kloezeman JJ, Lamfers MLM, Bollen AW, Taylor BS, Molinaro AM, Olshen AB, Chang SM, Song JS, Costello JF. DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors. Cancer Cell. 2015 Sep 14; 28(3):307-317. PMID: 26373278; PMCID: PMC4573399.
      View in: PubMed, PubMed Central
    9. 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 JS, 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
    10. Chen J, Hackett CS, Zhang S, Song YK, Bell RJ, Molinaro AM, Quigley DA, Balmain A, Song JS, 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.
      View in: PubMed
    11. Guzman-Ayala M, Sachs M, Koh FM, Onodera C, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song JS, Ramalho-Santos M. Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast. Development. 2015 Jan 01; 142(1):118-27. PMID: 25480920; PMCID: PMC4299150.
      View in: PubMed, PubMed Central
    12. Diaz AA, Qin H, Ramalho-Santos M, Song JS. 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
    13. 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):449-461. PMID: 25036638; PMCID: PMC4130998.
      View in: PubMed, PubMed Central
    14. 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 SJM, 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):189-193. PMID: 24336570.
      View in: PubMed
    15. Rube HT, Song JS. Quantifying the role of steric constraints in nucleosome positioning. Nucleic Acids Res. 2014 Feb; 42(4):2147-58. PMID: 24288372.
      View in: PubMed
    16. 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. PMID: 24270888; PMCID: PMC4066669.
      View in: PubMed, PubMed Central
    17. 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. PMID: 23727241.
      View in: PubMed
    18. 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 02; 12(5):616-28. PMID: 23583100; PMCID: PMC3662805.
      View in: PubMed, PubMed Central
    19. 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. PMID: 23477830; PMCID: PMC3635826.
      View in: PubMed, PubMed Central
    20. 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. PMID: 23447565.
      View in: PubMed
    21. 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. PMID: 23335939; PMCID: PMC3542818.
      View in: PubMed, PubMed Central
    22. Howe ED, Song JS. Categorical spectral analysis of periodicity in human and viral genomes. Nucleic Acids Res. 2013 Feb 01; 41(3):1395-405. PMID: 23241388; PMCID: PMC3561982.
      View in: PubMed, PubMed Central
    23. 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. PMID: 23068444; PMCID: PMC4053734.
      View in: PubMed, PubMed Central
    24. 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. PMID: 22992951; PMCID: PMC3472585.
      View in: PubMed, PubMed Central
    25. 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. PMID: 22570637.
      View in: PubMed
    26. Diaz A, Park K, Lim DA, Song JS. Normalization, bias correction, and peak calling for ChIP-seq. Stat Appl Genet Mol Biol. 2012 Mar 31; 11(3):Article 9. PMID: 22499706; PMCID: PMC3342857.
      View in: PubMed, PubMed Central
    27. 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. PMID: 22438827; PMCID: PMC3305387.
      View in: PubMed, PubMed Central
    28. 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. PMID: 21499256; PMCID: PMC3987913.
      View in: PubMed, PubMed Central
    29. J.S. Song and D.E. Fisher.Epigenomics: From Chromatin Biology to Therapeutics. Nucleosome positioning in promoters: significance and open questions. 2011.
    30. 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. PMID: 21109473; PMCID: PMC3004467.
      View in: PubMed, PubMed Central
    31. 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. PMID: 20542001; PMCID: PMC2900922.
      View in: PubMed, PubMed Central
    32. 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. PMID: 20550935; PMCID: PMC2897150.
      View in: PubMed, PubMed Central
    33. 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. PMID: 19056895.
      View in: PubMed
    34. Zhang Y, Shin H, Song JS, Lei Y, Liu XS. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics. 2008 Nov 13; 9:537. PMID: 19014516; PMCID: PMC2596141.
      View in: PubMed, PubMed Central
    35. Chan CS, Song JS. CCCTC-binding factor confines the distal action of estrogen receptor. Cancer Res. 2008 Nov 01; 68(21):9041-9. PMID: 18974150.
      View in: PubMed
    36. 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. PMID: 18794125.
      View in: PubMed
    37. 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. PMID: 18411404; PMCID: PMC2493395.
      View in: PubMed, PubMed Central
    38. 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. PMID: 18258921; PMCID: PMC2259103.
      View in: PubMed, PubMed Central
    39. 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. PMID: 18312933.
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    40. 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. PMID: 17500458.
      View in: PubMed
    41. 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. PMID: 17332024.
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    42. 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 01; 67(5):1299-308. PMID: 17275202.
      View in: PubMed
    43. 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. PMID: 17220878.
      View in: PubMed
    44. 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. PMID: 17707193.
      View in: PubMed
    45. 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. PMID: 17727723.
      View in: PubMed
    46. 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.
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    47. 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
    48. Song YS, Song JS. 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
    49. Ji X, Li W, Song J, Wei L, Liu XS. CEAS: cis-regulatory element annotation system. Nucleic Acids Res. 2006 Jul 01; 34(Web Server issue):W551-4. PMID: 16845068; PMCID: PMC1538818.
      View in: PubMed, PubMed Central
    50. 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. PMID: 15789590.
      View in: PubMed
    51. Song JS, Song YS.On a Conjecture of Givental. J Math Phys. 2004; 45:4539-4550.
    52. 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.
    53. He YH, Song JS.Of McKay Correspondence, Non-linear Sigma-model and Conformed Field Theory. Adv Theo Math Phys. 2000; 4:747-790.
    54. Song JS.Three-Dimensional Gorenstein Singularities and SU(3) Modular Invariants. Adv Theo Math Phys. 2000; 4:791-822.
    55. 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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