Jun Song, PhD, MA
Professor
Epidemiology & Biostatistics
School of Medicine

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.

Grants and Projects

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• Bridge to the Doctorate at University of Illinois at Urbana-Champaign, NIH, 2021-2026
• Development of Technologies for Efficient In Vivo Prime Editing, NIH, 2021-2025
• Center for Research, Innovation and Training in Reproduction and Infertility, NIH, 2007-2023
• Predicting Transcriptional and Epigenetic Networks in Cancer from Sequencing Data, NIH, 2011-2022
• Integrative Genomics, Epigenomics and Bioinformatics Analyses of Human Uterine Fibroids, NIH, 2016-2021
• KnowEng, a Scalable Knowledge Engine for Large-Scale Genomic Data-OVERALL, NIH, 2014-2021
• Origins and Biological Consequences of Human Infertility, NIH, 2007-2017

Publications (58)

Top publication keywords:
Chromosomes, FungalRectumSequence Analysis, DNAChromatin ImmunoprecipitationPromoter Regions, GeneticGA-Binding Protein Transcription FactorGenome, HumanTranscription, GeneticEpigenomicsNucleic Acid ProbesOligonucleotide Array Sequence AnalysisNucleosomesMicrophthalmia-Associated Transcription FactorMonte Carlo MethodRadiotherapy Planning, Computer-Assisted

• Novel SOX10 indel mutations drive schwannomas through impaired transactivation of myelination gene programs.
  Neuro-oncology 2023 Williams EA, Ravindranathan A, Gupta R, Stevers NO, Suwala AK, Hong C, Kim S, Yuan JB, Wu J, Barreto J, Lucas CG, Chan E, Pekmezci M, LeBoit PE, Mully T, Perry A, Bollen A, Van Ziffle J, Devine WP, …
• Chd1 protects genome integrity at promoters to sustain hypertranscription in embryonic stem cells.
  Nature communications 2021 Bulut-Karslioglu A, Jin H, Kim YK, Cho B, Guzman-Ayala M, Williamson AJK, Hejna M, Stötzel M, Whetton AD, Song JS, Ramalho-Santos M
• Single-Cell Profiling Reveals Divergent, Globally Patterned Immune Responses in Murine Skin Inflammation.
  iScience 2020 Liu Y, Cook C, Sedgewick AJ, Zhang S, Fassett MS, Ricardo-Gonzalez RR, Harirchian P, Kashem SW, Hanakawa S, Leistico JR, North JP, Taylor MA, Zhang W, Man MQ, Charruyer A, Beliakova-Bethell N, Benz SC…
• Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution.
  Cell reports 2018 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 …
• Disruption of the β1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner.
  Cancer cell 2018 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…

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• NF45 and NF90/NF110 coordinately regulate ESC pluripotency and differentiation.
  RNA (New York, N.Y.) 2017 Ye J, Jin H, Pankov A, Song JS, Blelloch R
• Inhibition of mTOR induces a paused pluripotent state.
  Nature 2016 Bulut-Karslioglu A, Biechele S, Jin H, Macrae TA, Hejna M, Gertsenstein M, Song JS, Ramalho-Santos M
• Intratumoral Heterogeneity of the Epigenome.
  Cancer cell 2016 Mazor T, Pankov A, Song JS, Costello JF
• Understanding TERT Promoter Mutations: A Common Path to Immortality.
  Molecular cancer research : MCR 2016 Bell RJ, Rube HT, Xavier-Magalhães A, Costa BM, Mancini A, Song JS, Costello JF
• YAP Induces Human Naive Pluripotency.
  Cell reports 2016 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
• DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors.
  Cancer cell 2015 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…
• Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer.
  Science (New York, N.Y.) 2015 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
• The genetics of splicing in neuroblastoma.
  Cancer discovery 2015 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
• Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast.
  Development (Cambridge, England) 2014 Guzman-Ayala M, Sachs M, Koh FM, Onodera C, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song JS, Ramalho-Santos M
• HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.
  Nucleic acids research 2014 Diaz AA, Qin H, Ramalho-Santos M, Song JS
• Systematic identification of barriers to human iPSC generation.
  Cell 2014 Qin H, Diaz A, Blouin L, Lebbink RJ, Patena W, Tanbun P, LeProust EM, McManus MT, Song JS, Ramalho-Santos M
• Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma.
  Science (New York, N.Y.) 2013 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…
• Quantifying the role of steric constraints in nucleosome positioning.
  Nucleic acids research 2013 Rube HT, Song JS
• Somatic cells regulate maternal mRNA translation and developmental competence of mouse oocytes.
  Nature cell biology 2013 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
• Bivalent chromatin marks developmental regulatory genes in the mouse embryonic germline in vivo.
  Cell reports 2013 Sachs M, Onodera C, Blaschke K, Ebata KT, Song JS, Ramalho-Santos M
• Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo.
  Cell stem cell 2013 Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA
• Oncogenic BRAF regulates oxidative metabolism via PGC1α and MITF.
  Cancer cell 2013 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
• BCL2A1 is a lineage-specific antiapoptotic melanoma oncogene that confers resistance to BRAF inhibition.
  Proceedings of the National Academy of Sciences of the United States of America 2013 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
• NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data.
  Frontiers in genetics 2013 Nellore A, Bobkov K, Howe E, Pankov A, Diaz A, Song JS
• Categorical spectral analysis of periodicity in human and viral genomes.
  Nucleic acids research 2012 Howe ED, Song JS
• CHANCE: comprehensive software for quality control and validation of ChIP-seq data.
  Genome biology 2012 Diaz A, Nellore A, Song JS
• Sox1 marks an activated neural stem/progenitor cell in the hippocampus.
  Development (Cambridge, England) 2012 Venere M, Han YG, Bell R, Song JS, Alvarez-Buylla A, Blelloch R
• YY1 regulates melanocyte development and function by cooperating with MITF.
  PLoS genetics 2012 Li J, Song JS, Bell RJ, Tran TN, Haq R, Liu H, Love KT, Langer R, Anderson DG, Larue L, Fisher DE
• Normalization, bias correction, and peak calling for ChIP-seq.
  Statistical applications in genetics and molecular biology 2012 Diaz A, Park K, Lim DA, Song JS
• Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.
  PLoS genetics 2012 Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF
• Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells.
  Nature cell biology 2011 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
• Epigenomics: From Chromatin Biology to Therapeutics
  Nucleosome positioning in promoters: significance and open questions 2011 J.S. Song and D.E. Fisher
• Intronic miR-211 assumes the tumor suppressive function of its host gene in melanoma.
  Molecular cell 2010 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
• Lineage-specific transcriptional regulation of DICER by MITF in melanocytes.
  Cell 2010 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
• Negative regulation of tumor suppressor p53 by microRNA miR-504.
  Molecular cell 2010 Hu W, Chan CS, Wu R, Zhang C, Sun Y, Song JS, Tang LH, Levine AJ, Feng Z
• Chromatin structure analyses identify miRNA promoters.
  Genes & development 2008 Ozsolak F, Poling LL, Wang Z, Liu H, Liu XS, Roeder RG, Zhang X, Song JS, Fisher DE
• Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq.
  BMC genomics 2008 Zhang Y, Shin H, Song JS, Lei Y, Liu XS
• CCCTC-binding factor confines the distal action of estrogen receptor.
  Cancer research 2008 Chan CS, Song JS
• Nkx3-1 and LEF-1 function as transcriptional inhibitors of estrogen receptor activity.
  Cancer research 2008 Holmes KA, Song JS, Liu XS, Brown M, Carroll JS
• A high-resolution map of nucleosome positioning on a fission yeast centromere.
  Genome research 2008 Song JS, Liu X, Liu XS, He X
• Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
  Genome research 2008 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, …
• Defining the rectal dose constraint for permanent radioactive seed implantation of the prostate.
  Urologic oncology 2007 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
• 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.
  Medical physics 2007 Xiang HF, Song JS, Chin DW, Cormack RA, Tishler RB, Makrigiorgos GM, Court LE, Chin LM
• Microarray blob-defect removal improves array analysis.
  Bioinformatics (Oxford, England) 2007 Song JS, Maghsoudi K, Li W, Fox E, Quackenbush J, Shirley Liu X
• Variability among breast radiation oncologists in delineation of the postsurgical lumpectomy cavity.
  International journal of radiation oncology, biology, physics 2007 Landis DM, Luo W, Song J, Bellon JR, Punglia RS, Wong JS, Killoran JH, Gelman R, Harris JR
• High-throughput mapping of the chromatin structure of human promoters.
  Nature biotechnology 2007 Ozsolak F, Song JS, Liu XS, Fisher DE
• Model-based analysis of two-color arrays (MA2C).
  Genome biology 2007 Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS
• Monte Carlo calculation of rectal dose when using an intrarectal balloon during prostate radiation therapy.
  Medical dosimetry : official journal of the American Association of Medical Dosimetrists 2007 Song JS, Court LE, Cormack RA
• Dynamic IMRT treatments of sinus region tumors: comparison of Monte Carlo calculations with treatment planning system calculations and ion chamber measurements.
  Technology in cancer research & treatment 2006 Court LE, Jahnke L, Chin D, Song J, Cormack R, Zygmanski P, Tishler RB, Chin L
• Genome-wide analysis of estrogen receptor binding sites.
  Nature genetics 2006 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
• Analytic computation of the expectation of the linkage disequilibrium coefficient r2.
  Theoretical population biology 2006 Song YS, Song JS
• CEAS: cis-regulatory element annotation system.
  Nucleic acids research 2006 Ji X, Li W, Song J, Wei L, Liu XS
• A comparative study of rectal dose histograms in prostate brachytherapy: some analytic and numerical results.
  Medical physics 2005 Song JS, Albert M, D'Amico AV, Cormack RA
• On a Conjecture of Givental
  J Math Phys 2004 Song JS, Song YS
• The Hurwitz Enumeration Problem of Branched Covers and Hodge Integrals
  Journal of Geometry and Physics 2004 Monni S, Song JS, Song YS
• Of McKay Correspondence, Non-linear Sigma-model and Conformed Field Theory
  Adv Theo Math Phys 2000 He YH, Song JS
• Three-Dimensional Gorenstein Singularities and SU(3) Modular Invariants
  Adv Theo Math Phys 2000 Song JS
• Descendant Gromov-Witten Invariants, Simple Hurwitz Numbers, and the Virasoro Conjecture for P^1
  Adv Theo Math Phys. 1999 Song JS