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Jun S. Song - Publications

Affiliations: 
Institute for Genomic Biology University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 
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42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Manjunath M, Zhang Y, Zhang S, Roy S, Perez-Pinera P, Song JS. ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants. Frontiers in Genetics. 11: 730. PMID 32765587 DOI: 10.3389/Fgene.2020.00730  0.329
2020 Finnegan AI, Kim S, Jin H, Gapinske M, Woods WS, Perez-Pinera P, Song JS. Epigenetic engineering of yeast reveals dynamic molecular adaptation to methylation stress and genetic modulators of specific DNMT3 family members. Nucleic Acids Research. PMID 32187373 DOI: 10.1093/Nar/Gkaa161  0.309
2019 Winter J, Luu A, Gapinske M, Manandhar S, Shirguppe S, Woods WS, Song JS, Perez-Pinera P. Targeted exon skipping with AAV-mediated split adenine base editors. Cell Discovery. 5: 41. PMID 31636954 DOI: 10.1038/S41421-019-0109-7  0.318
2019 Finnegan A, Cho RJ, Luu A, Harirchian P, Lee J, Cheng JB, Song JS. Single-Cell Transcriptomics Reveals Spatial and Temporal Turnover of Keratinocyte Differentiation Regulators. Frontiers in Genetics. 10: 775. PMID 31552090 DOI: 10.3389/Fgene.2019.00775  0.34
2019 Zhang Y, Manjunath M, Yan J, Baur BA, Zhang S, Roy S, Song JS. The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment. Frontiers in Genetics. 10: 754. PMID 31507631 DOI: 10.3389/Fgene.2019.00754  0.311
2018 Hejna M, Moon WM, Cheng J, Kawakami A, Fisher DE, Song JS. Local Genomic Features Predict the Distinct and Overlapping Binding Patterns of the bHLH-Zip Family Oncoproteins MITF and MYC-MAX. Pigment Cell & Melanoma Research. PMID 30548162 DOI: 10.1111/Pcmr.12762  0.319
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, et al. Disruption of the β1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner. Cancer Cell. 34: 513-528.e8. PMID 30205050 DOI: 10.1016/J.Ccell.2018.08.003  0.305
2018 Jin H, Finnegan AI, Song J. A unified computational framework for modeling genome-wide nucleosome landscape. Physical Biology. PMID 30113318 DOI: 10.1088/1478-3975/Aadad2  0.344
2018 Gapinske M, Luu A, Winter J, Woods WS, Kostan KA, Shiva N, Song JS, Perez-Pinera P. CRISPR-SKIP: programmable gene splicing with single base editors. Genome Biology. 19: 107. PMID 30107853 DOI: 10.1186/S13059-018-1482-5  0.304
2018 Zhang Y, Manjunath M, Zhang S, Chasman D, Roy S, Song JS. Integrative genomic analysis predicts causative cis-regulatory mechanisms of the breast cancer-associated genetic variant rs4415084. Cancer Research. PMID 29351903 DOI: 10.1158/0008-5472.Can-17-3486  0.31
2018 Zhang Y, Manjunath M, Zhang S, Chasman D, Roy S, Song JS. Abstract 1220: Integrative genomic analysis discovers the causative regulatory mechanisms of a breast cancer-associated genetic variant Epidemiology. 78: 1220-1220. DOI: 10.1158/1538-7445.Am2018-1220  0.316
2017 Salma N, Song JS, Kawakami A, Devi SP, Khaled M, Cacicedo JM, Fisher DE. Tfe3 and Tfeb transcriptionally regulate Pparγ2 expression in adipocytes and mediate adiponectin and glucose levels in mice. Molecular and Cellular Biology. PMID 28483914 DOI: 10.1128/Mcb.00608-16  0.306
2016 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. PMID 27880763 DOI: 10.1038/Nature20578  0.304
2016 Kim M, Kreig A, Lee CY, Rube HT, Calvert J, Song JS, Myong S. Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA. Nucleic Acids Research. PMID 27095201 DOI: 10.1093/Nar/Gkw272  0.305
2016 Rube HT, Lee W, Hejna M, Chen H, Yasui DH, Hess JF, LaSalle JM, Song JS, Gong Q. Sequence features accurately predict genome-wide MeCP2 binding in vivo. Nature Communications. 7: 11025. PMID 27008915 DOI: 10.1038/Ncomms11025  0.321
2016 Bell RJ, Rube HT, Xavier-Magalhães A, Costa BM, Mancini A, Song JS, Costello JF. Understanding TERT Promoter Mutations: a Common Path to Immortality. Molecular Cancer Research : McR. PMID 26941407 DOI: 10.1158/1541-7786.Mcr-16-0003  0.315
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, et al. Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer. Science (New York, N.Y.). 348: 1036-9. PMID 25977370 DOI: 10.1126/Science.Aab0015  0.32
2015 Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp PA. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell. 160: 1246-60. PMID 25748654 DOI: 10.1016/J.Cell.2015.02.038  0.302
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. The genetics of splicing in neuroblastoma. Cancer Discovery. 5: 380-95. PMID 25637275 DOI: 10.1158/2159-8290.Cd-14-0892  0.362
2015 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 (Cambridge, England). 142: 118-27. PMID 25480920 DOI: 10.1242/Dev.114843  0.34
2015 Bell RJA, Rube HT, Kreig A, Mancini A, Fouse SF, Nagarajan RP, Choi S, Hong C, He D, Pekmezci M, Wiencke JK, Wrensch MR, Chang SM, Walsh KM, Myong S, ... Song JS, et al. Abstract B12: GABP selectively binds and activates the mutant TERT promoter across multiple cancer types Brain. 75. DOI: 10.1158/1538-7445.Brain15-B12  0.315
2015 Bell R, Rube HT, Kreig A, Mancini A, Fouse S, Nagarajan R, Choi S, Hong C, He D, Pekmezci M, Wiencke J, Wrensch M, Chang S, Walsh K, Myong S, ... Song J, et al. GENO-07A MECHANISM OF MUTANT TERT PROMOTER ACTIVATION SHARED ACROSS CANCER TYPES Neuro-Oncology. 17: v92.3-v92. DOI: 10.1093/Neuonc/Nov215.07  0.336
2014 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. 158: 449-61. PMID 25036638 DOI: 10.1016/J.Cell.2014.05.040  0.339
2014 Nagarajan RP, Zhang B, Bell RJ, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, Smirnov I, Song J, Paris PL, Wang T, Costello JF. Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Research. 24: 761-74. PMID 24709822 DOI: 10.1101/Gr.164707.113  0.346
2014 Rube HT, Song JS. Quantifying the role of steric constraints in nucleosome positioning. Nucleic Acids Research. 42: 2147-58. PMID 24288372 DOI: 10.1093/Nar/Gkt1239  0.319
2014 Costello JF, Mazor T, Pankov A, Johnson BE, Hong C, Bell RJA, Smirnov IV, Reis GF, Phillips JJ, Barnes M, Bollen AW, Taylor BS, Molinaro AM, Olshen AB, Song JS, et al. CLONAL EVOLUTION OF GLIOMAS IS ENCODED IN THE EVOLUTIONARY DYNAMICS OF DNA METHYLATION Neuro-Oncology. 16: iii51-iii52. DOI: 10.1093/Neuonc/Nou209.38  0.308
2013 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 Reports. 3: 1777-84. PMID 23727241 DOI: 10.1016/J.Celrep.2013.04.032  0.338
2012 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 Genetics. 8: e1002688. PMID 22570637 DOI: 10.1371/Journal.Pgen.1002688  0.33
2012 Diaz A, Park K, Lim DA, Song JS. Normalization, bias correction, and peak calling for ChIP-seq. Statistical Applications in Genetics and Molecular Biology. 11: Article 9. PMID 22499706 DOI: 10.1515/1544-6115.1750  0.322
2012 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 Genetics. 8: e1002576. PMID 22438827 DOI: 10.1371/Journal.Pgen.1002576  0.325
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, et al. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nature Cell Biology. 13: 541-9. PMID 21499256 DOI: 10.1038/Ncb2239  0.316
2008 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 & Development. 22: 3172-83. PMID 19056895 DOI: 10.1101/Gad.1706508  0.513
2008 Zhang Y, Shin H, Song JS, Lei Y, Liu XS. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. Bmc Genomics. 9: 537. PMID 19014516 DOI: 10.1186/1471-2164-9-537  0.542
2008 Chan CS, Song JS. CCCTC-binding factor confines the distal action of estrogen receptor. Cancer Research. 68: 9041-9. PMID 18974150 DOI: 10.1158/0008-5472.Can-08-2632  0.346
2008 Holmes KA, Song JS, Liu XS, Brown M, Carroll JS. Nkx3-1 and LEF-1 function as transcriptional inhibitors of estrogen receptor activity. Cancer Research. 68: 7380-5. PMID 18794125 DOI: 10.1158/0008-5472.Can-08-0133  0.557
2008 Song JS, Liu X, Liu XS, He X. A high-resolution map of nucleosome positioning on a fission yeast centromere. Genome Research. 18: 1064-72. PMID 18411404 DOI: 10.1101/Gr.075374.107  0.327
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, ... ... Song JS, et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research. 18: 393-403. PMID 18258921 DOI: 10.1101/Gr.7080508  0.341
2007 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 Biology. 8: R178. PMID 17727723 DOI: 10.1186/Gb-2007-8-8-R178  0.528
2007 Song JS, Maghsoudi K, Li W, Fox E, Quackenbush J, Shirley Liu X. Microarray blob-defect removal improves array analysis. Bioinformatics (Oxford, England). 23: 966-71. PMID 17332024 DOI: 10.1093/Bioinformatics/Btm043  0.301
2007 Ozsolak F, Song JS, Liu XS, Fisher DE. High-throughput mapping of the chromatin structure of human promoters. Nature Biotechnology. 25: 244-8. PMID 17220878 DOI: 10.1038/Nbt1279  0.578
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, et al. Genome-wide analysis of estrogen receptor binding sites. Nature Genetics. 38: 1289-97. PMID 17013392 DOI: 10.1038/Ng1901  0.577
2006 Ji X, Li W, Song J, Wei L, Liu XS. CEAS: cis-regulatory element annotation system. Nucleic Acids Research. 34: W551-4. PMID 16845068 DOI: 10.1093/Nar/Gkl322  0.583
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