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Jun Song, PhD, MA

Title(s)Professor, Epidemiology & Biostatistics
SchoolSchool of Medicine
Address550 16th. Street
San Francisco CA 94158
Phone415-476-6933
ORCID ORCID Icon0000-0002-0422-2175 Additional info
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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 - Sep 29, 2011
    Role: Co-Investigator
    Center for Research, Innovation and Training in Reproduction and Infertility
    NIH/NICHD P50HD055764Apr 1, 2007 - Mar 31, 2023
    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution. Cell Rep. 2018 10 23; 25(4):871-883. 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. PMID: 30355494.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    2. Disruption of the ß1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner. Cancer Cell. 2018 09 10; 34(3):513-528.e8. 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. PMID: 30205050.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    3. NF45 and NF90/NF110 coordinately regulate ESC pluripotency and differentiation. RNA. 2017 08; 23(8):1270-1284. Ye J, Jin H, Pankov A, Song JS, Blelloch R. PMID: 28487382.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    4. Inhibition of mTOR induces a paused pluripotent state. Nature. 2016 12 01; 540(7631):119-123. Bulut-Karslioglu A, Biechele S, Jin H, Macrae TA, Hejna M, Gertsenstein M, Song JS, Ramalho-Santos M. PMID: 27880763.
      View in: PubMed   Mentions: 21     Fields:    Translation:AnimalsCells
    5. Intratumoral Heterogeneity of the Epigenome. Cancer Cell. 2016 Apr 11; 29(4):440-451. Mazor T, Pankov A, Song JS, Costello JF. PMID: 27070699.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    6. YAP Induces Human Naive Pluripotency. Cell Rep. 2016 Mar 15; 14(10):2301-12. 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. PMID: 26947063.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    7. Understanding TERT Promoter Mutations: A Common Path to Immortality. Mol Cancer Res. 2016 Apr; 14(4):315-23. Bell RJ, Rube HT, Xavier-Magalhães A, Costa BM, Mancini A, Song JS, Costello JF. PMID: 26941407.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    8. 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. 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. PMID: 26373278.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    9. Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer. Science. 2015 May 29; 348(6238):1036-9. 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. PMID: 25977370.
      View in: PubMed   Mentions: 118     Fields:    Translation:HumansCells
    10. The genetics of splicing in neuroblastoma. Cancer Discov. 2015 Apr; 5(4):380-95. 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. PMID: 25637275.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    11. Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast. Development. 2015 Jan 01; 142(1):118-27. Guzman-Ayala M, Sachs M, Koh FM, Onodera C, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song JS, Ramalho-Santos M. PMID: 25480920.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    12. HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis. Nucleic Acids Res. 2015 Feb 18; 43(3):e16. Diaz AA, Qin H, Ramalho-Santos M, Song JS. PMID: 25428347.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    13. Systematic identification of barriers to human iPSC generation. Cell. 2014 Jul 17; 158(2):449-461. Qin H, Diaz A, Blouin L, Lebbink RJ, Patena W, Tanbun P, LeProust EM, McManus MT, Song JS, Ramalho-Santos M. PMID: 25036638.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    14. Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma. Science. 2014 Jan 10; 343(6167):189-193. 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. PMID: 24336570.
      View in: PubMed   Mentions: 340     Fields:    Translation:Humans
    15. Quantifying the role of steric constraints in nucleosome positioning. Nucleic Acids Res. 2014 Feb; 42(4):2147-58. Rube HT, Song JS. PMID: 24288372.
      View in: PubMed   Mentions: 7     Fields:    Translation:AnimalsCells
    16. Somatic cells regulate maternal mRNA translation and developmental competence of mouse oocytes. Nat Cell Biol. 2013 Dec; 15(12):1415-23. 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. PMID: 24270888.
      View in: PubMed   Mentions: 33     Fields:    Translation:AnimalsCells
    17. Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo. Cell Rep. 2013 Jun 27; 3(6):1777-84. Sachs M, Onodera C, Blaschke K, Ebata KT, Song JS, Ramalho-Santos M. PMID: 23727241.
      View in: PubMed   Mentions: 50     Fields:    Translation:AnimalsCells
    18. 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. Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA. PMID: 23583100.
      View in: PubMed   Mentions: 90     Fields:    Translation:HumansAnimalsCells
    19. Oncogenic BRAF regulates oxidative metabolism via PGC1a and MITF. Cancer Cell. 2013 Mar 18; 23(3):302-15. 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. PMID: 23477830.
      View in: PubMed   Mentions: 203     Fields:    Translation:HumansCells
    20. 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. 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. PMID: 23447565.
      View in: PubMed   Mentions: 69     Fields:    Translation:HumansCells
    21. NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data. Front Genet. 2012; 3:320. Nellore A, Bobkov K, Howe E, Pankov A, Diaz A, Song JS. PMID: 23335939.
      View in: PubMed   Mentions:
    22. Categorical spectral analysis of periodicity in human and viral genomes. Nucleic Acids Res. 2013 Feb 01; 41(3):1395-405. Howe ED, Song JS. PMID: 23241388.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    23. CHANCE: comprehensive software for quality control and validation of ChIP-seq data. Genome Biol. 2012 Oct 15; 13(10):R98. Diaz A, Nellore A, Song JS. PMID: 23068444.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansAnimals
    24. Sox1 marks an activated neural stem/progenitor cell in the hippocampus. Development. 2012 Nov; 139(21):3938-49. Venere M, Han YG, Bell R, Song JS, Alvarez-Buylla A, Blelloch R. PMID: 22992951.
      View in: PubMed   Mentions: 23     Fields:    Translation:AnimalsCells
    25. YY1 regulates melanocyte development and function by cooperating with MITF. PLoS Genet. 2012; 8(5):e1002688. Li J, Song JS, Bell RJ, Tran TN, Haq R, Liu H, Love KT, Langer R, Anderson DG, Larue L, Fisher DE. PMID: 22570637.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    26. Normalization, bias correction, and peak calling for ChIP-seq. Stat Appl Genet Mol Biol. 2012 Mar 31; 11(3):Article 9. Diaz A, Park K, Lim DA, Song JS. PMID: 22499706.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    27. Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal. PLoS Genet. 2012; 8(3):e1002576. Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF. PMID: 22438827.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
    28. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol. 2011 May; 13(5):541-9. 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. PMID: 21499256.
      View in: PubMed   Mentions: 240     Fields:    Translation:HumansCells
    29. Epigenomics: From Chromatin Biology to Therapeutics. Nucleosome positioning in promoters: significance and open questions. 2011. J.S. Song and D.E. Fisher..
    30. Intronic miR-211 assumes the tumor suppressive function of its host gene in melanoma. Mol Cell. 2010 Dec 10; 40(5):841-9. 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. PMID: 21109473.
      View in: PubMed   Mentions: 89     Fields:    Translation:HumansCells
    31. Negative regulation of tumor suppressor p53 by microRNA miR-504. Mol Cell. 2010 Jun 11; 38(5):689-99. Hu W, Chan CS, Wu R, Zhang C, Sun Y, Song JS, Tang LH, Levine AJ, Feng Z. PMID: 20542001.
      View in: PubMed   Mentions: 113     Fields:    Translation:HumansAnimalsCells
    32. Lineage-specific transcriptional regulation of DICER by MITF in melanocytes. Cell. 2010 Jun 11; 141(6):994-1005. 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. PMID: 20550935.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansAnimalsCells
    33. Chromatin structure analyses identify miRNA promoters. Genes Dev. 2008 Nov 15; 22(22):3172-83. Ozsolak F, Poling LL, Wang Z, Liu H, Liu XS, Roeder RG, Zhang X, Song JS, Fisher DE. PMID: 19056895.
      View in: PubMed   Mentions: 267     Fields:    Translation:HumansCells
    34. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics. 2008 Nov 13; 9:537. Zhang Y, Shin H, Song JS, Lei Y, Liu XS. PMID: 19014516.
      View in: PubMed   Mentions: 71     Fields:    Translation:HumansCells
    35. CCCTC-binding factor confines the distal action of estrogen receptor. Cancer Res. 2008 Nov 01; 68(21):9041-9. Chan CS, Song JS. PMID: 18974150.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    36. Nkx3-1 and LEF-1 function as transcriptional inhibitors of estrogen receptor activity. Cancer Res. 2008 Sep 15; 68(18):7380-5. Holmes KA, Song JS, Liu XS, Brown M, Carroll JS. PMID: 18794125.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    37. A high-resolution map of nucleosome positioning on a fission yeast centromere. Genome Res. 2008 Jul; 18(7):1064-72. Song JS, Liu X, Liu XS, He X. PMID: 18411404.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    38. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 2008 Mar; 18(3):393-403. 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. PMID: 18258921.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansCells
    39. Defining the rectal dose constraint for permanent radioactive seed implantation of the prostate. Urol Oncol. 2008 Mar-Apr; 26(2):147-52. 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. PMID: 18312933.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    40. 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. Xiang HF, Song JS, Chin DW, Cormack RA, Tishler RB, Makrigiorgos GM, Court LE, Chin LM. PMID: 17500458.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    41. Microarray blob-defect removal improves array analysis. Bioinformatics. 2007 Apr 15; 23(8):966-71. Song JS, Maghsoudi K, Li W, Fox E, Quackenbush J, Shirley Liu X. PMID: 17332024.
      View in: PubMed   Mentions: 9     Fields:    
    42. 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. Landis DM, Luo W, Song J, Bellon JR, Punglia RS, Wong JS, Killoran JH, Gelman R, Harris JR. PMID: 17275202.
      View in: PubMed   Mentions: 24     Fields:    Translation:Humans
    43. High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol. 2007 Feb; 25(2):244-8. Ozsolak F, Song JS, Liu XS, Fisher DE. PMID: 17220878.
      View in: PubMed   Mentions: 157     Fields:    Translation:HumansCells
    44. Model-based analysis of two-color arrays (MA2C). Genome Biol. 2007; 8(8):R178. Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS. PMID: 17727723.
      View in: PubMed   Mentions: 73     Fields:    Translation:AnimalsCells
    45. Monte Carlo calculation of rectal dose when using an intrarectal balloon during prostate radiation therapy. Med Dosim. 2007; 32(3):151-6. Song JS, Court LE, Cormack RA. PMID: 17707193.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    46. 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. Court LE, Jahnke L, Chin D, Song J, Cormack R, Zygmanski P, Tishler RB, Chin L. PMID: 16981791.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    47. Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 2006 Nov; 38(11):1289-97. 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. PMID: 17013392.
      View in: PubMed   Mentions: 646     Fields:    Translation:HumansCells
    48. Analytic computation of the expectation of the linkage disequilibrium coefficient r2. Theor Popul Biol. 2007 Feb; 71(1):49-60. Song YS, Song JS. PMID: 17069867.
      View in: PubMed   Mentions: 17     Fields:    
    49. CEAS: cis-regulatory element annotation system. Nucleic Acids Res. 2006 Jul 01; 34(Web Server issue):W551-4. Ji X, Li W, Song J, Wei L, Liu XS. PMID: 16845068.
      View in: PubMed   Mentions: 108     Fields:    Translation:HumansCells
    50. A comparative study of rectal dose histograms in prostate brachytherapy: some analytic and numerical results. Med Phys. 2005 Feb; 32(2):437-47. Song JS, Albert M, D'Amico AV, Cormack RA. PMID: 15789590.
      View in: PubMed   Mentions:    Fields:    Translation:HumansPHPublic HealthCTClinical Trials
    51. The Hurwitz Enumeration Problem of Branched Covers and Hodge Integrals. Journal of Geometry and Physics. 2004; 50:223-256. Monni S, Song JS, Song YS.
    52. On a Conjecture of Givental. J Math Phys. 2004; 45:4539-4550. Song JS, Song YS.
    53. Of McKay Correspondence, Non-linear Sigma-model and Conformed Field Theory. Adv Theo Math Phys. 2000; 4:747-790. He YH, Song JS..
    54. Three-Dimensional Gorenstein Singularities and SU(3) Modular Invariants. Adv Theo Math Phys. 2000; 4:791-822. Song JS..
    55. Descendant Gromov-Witten Invariants, Simple Hurwitz Numbers, and the Virasoro Conjecture for P^1. Adv Theo Math Phys. 1999; 3:1721-1768. Song JS..
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