Jun S. Song - Publications

Affiliations: 
Institute for Genomic Biology University of Illinois, Urbana-Champaign, Urbana-Champaign, IL 

52 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
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  0.4
2018 Manjunath M, Zhang Y, Yeo SH, Sobh O, Russell N, Followell C, Bushell C, Ravaioli U, Song JS. ClusterEnG: an interactive educational web resource for clustering and visualizing high-dimensional data. Peerj. Computer Science. 4. PMID 30906871 DOI: 10.7717/peerj-cs.155  0.4
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  0.48
2018 Zhao C, Song JS. Quantum transport senses community structure in networks. Physical Review. E. 98: 022301. PMID 30253552 DOI: 10.1103/PhysRevE.98.022301  0.44
2018 Zhang Y, Manjunath M, Kim Y, Heintz J, Song JS. SequencEnG: an Interactive Knowledge Base of Sequencing Techniques. Bioinformatics (Oxford, England). PMID 30202870 DOI: 10.1093/bioinformatics/bty794  0.4
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  0.32
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  0.4
2017 Salma N, Song JS, Kawakami A, Devi SP, Khaled M, Cacicedo JM, Fisher DE. Erratum for Salma et al., "Tfe3 and Tfeb Transcriptionally Regulate Peroxisome Proliferator-Activated Receptor γ2 Expression in Adipocytes and Mediate Adiponectin and Glucose Levels in Mice". Molecular and Cellular Biology. 37. PMID 29030472 DOI: 10.1128/MCB.00466-17  0.48
2017 Hejna M, Jorapur A, Song JS, Judson RL. High accuracy label-free classification of single-cell kinetic states from holographic cytometry of human melanoma cells. Scientific Reports. 7: 11943. PMID 28931937 DOI: 10.1038/s41598-017-12165-1  0.44
2017 Zhao C, Song JS. Emergent community agglomeration from data set geometry. Physical Review. E. 95: 042307. PMID 28505848 DOI: 10.1103/PhysRevE.95.042307  0.44
2017 Ye J, Jin H, Pankov A, Song J, Blelloch R. NF45 and NF90/NF110 coordinately regulate ESC pluripotency and differentiation. Rna (New York, N.Y.). PMID 28487382 DOI: 10.1261/rna.061499.117  0.32
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  0.48
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  0.44
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  0.72
2016 Mazor T, Pankov A, Song JS, Costello JF. Intratumoral Heterogeneity of the Epigenome. Cancer Cell. 29: 440-51. PMID 27070699 DOI: 10.1016/j.ccell.2016.03.009  0.72
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  0.72
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. YAP Induces Human Naive Pluripotency. Cell Reports. PMID 26947063 DOI: 10.1016/j.celrep.2016.02.036  0.4
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  0.72
2016 Jin H, Rube HT, Song JS. Categorical spectral analysis of periodicity in nucleosomal DNA. Nucleic Acids Research. PMID 26893354 DOI: 10.1093/nar/gkw101  0.44
2015 Mazor T, Pankov A, Johnson BE, Hong C, Hamilton EG, Bell RJ, Smirnov IV, Reis GF, Phillips JJ, Barnes MJ, Idbaih A, Alentorn A, Kloezeman JJ, Lamfers ML, Bollen AW, ... ... Song JS, et al. DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors. Cancer Cell. 28: 307-17. PMID 26373278 DOI: 10.1016/j.ccell.2015.07.012  0.72
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  0.72
2015 Wong HK, Fatimy RE, Onodera C, Wei Z, Yi M, Mohan A, Gowrisankaran S, Karmali P, Marcusson E, Wakimoto H, Stephens R, Uhlmann EJ, Song JS, Tannous B, Krichevsky AM. The Cancer Genome Atlas Analysis Predicts MicroRNA for Targeting Cancer Growth and Vascularization in Glioblastoma. Molecular Therapy : the Journal of the American Society of Gene Therapy. 23: 1234-47. PMID 25903473 DOI: 10.1038/mt.2015.72  0.72
2015 Salma N, Song JS, Arany Z, Fisher DE. Transcription Factor Tfe3 Directly Regulates Pgc-1alpha in Muscle. Journal of Cellular Physiology. 230: 2330-6. PMID 25736533 DOI: 10.1002/jcp.24978  0.48
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  0.72
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  0.72
2015 Diaz AA, Qin H, Ramalho-Santos M, Song JS. HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis. Nucleic Acids Research. 43: e16. PMID 25428347 DOI: 10.1093/nar/gku1197  0.4
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  0.72
2014 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, ... ... Song JS, et al. Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma. Science (New York, N.Y.). 343: 189-93. PMID 24336570 DOI: 10.1126/science.1239947  0.72
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  0.44
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. Somatic cells regulate maternal mRNA translation and developmental competence of mouse oocytes. Nature Cell Biology. 15: 1415-23. PMID 24270888 DOI: 10.1038/ncb2873  0.72
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  0.72
2013 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. 12: 616-28. PMID 23583100 DOI: 10.1016/j.stem.2013.03.003  0.72
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. Oncogenic BRAF regulates oxidative metabolism via PGC1α and MITF. Cancer Cell. 23: 302-15. PMID 23477830 DOI: 10.1016/j.ccr.2013.02.003  0.72
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, ... ... Song JS, et al. 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. 110: 4321-6. PMID 23447565 DOI: 10.1073/pnas.1205575110  0.72
2013 Howe ED, Song JS. Categorical spectral analysis of periodicity in human and viral genomes Nucleic Acids Research. 41: 1395-1405. PMID 23241388 DOI: 10.1093/nar/gks1261  0.72
2012 Nellore A, Bobkov K, Howe E, Pankov A, Diaz A, Song JS. NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data. Frontiers in Genetics. 3: 320. PMID 23335939 DOI: 10.3389/fgene.2012.00320  0.72
2012 Diaz A, Nellore A, Song JS. CHANCE: comprehensive software for quality control and validation of ChIP-seq data. Genome Biology. 13: R98. PMID 23068444 DOI: 10.1186/gb-2012-13-10-r98  0.72
2012 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 (Cambridge, England). 139: 3938-49. PMID 22992951 DOI: 10.1242/dev.081133  0.72
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  0.72
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  0.72
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  0.72
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, et al. Intronic miR-211 assumes the tumor suppressive function of its host gene in melanoma. Molecular Cell. 40: 841-9. PMID 21109473 DOI: 10.1016/j.molcel.2010.11.020  0.72
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. Lineage-specific transcriptional regulation of DICER by MITF in melanocytes. Cell. 141: 994-1005. PMID 20550935 DOI: 10.1016/j.cell.2010.05.004  0.72
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  0.72
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  0.52
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  0.72
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  0.52
2008 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. Urologic Oncology. 26: 147-52. PMID 18312933 DOI: 10.1016/j.urolonc.2007.03.026  0.72
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  0.72
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  0.72
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  0.72
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  0.52
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