Jun Song, PhD, MA
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Title(s) | Professor, Epidemiology & Biostatistics |
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School | School of Medicine |
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Address | 550 16th. Street San Francisco CA 94158
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Phone | 415-476-6933 |
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ORCID
.gif) | 0000-0002-0422-2175  |
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vCard | Download vCard |
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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.
Research Bibliographic
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.
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Single-Cell Profiling Reveals Divergent, Globally Patterned Immune Responses in Murine Skin Inflammation. iScience. 2020 Oct 23; 23(10):101582.
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, Ghadially R, Mauro TM, Kaplan DH, Kabashima K, Choi J, Song JS, Cho RJ, Cheng JB. PMID: 33205009.
View in: PubMed Mentions:
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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: 19 Fields: Translation: HumansCells
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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: 13 Fields: Translation: HumansAnimalsCells
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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
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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: 27 Fields: Translation: AnimalsCells
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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: 50 Fields: Translation: HumansCells
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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: 42 Fields: Translation: HumansCells
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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: 36 Fields: Translation: HumansCells
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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: 60 Fields: Translation: HumansCells
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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: 141 Fields: Translation: HumansCells
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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: 7 Fields: Translation: AnimalsCells
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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: 26 Fields: Translation: AnimalsCells
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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: 15 Fields: Translation: Cells
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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: 37 Fields: Translation: HumansCells
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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: 413 Fields: Translation: Humans
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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
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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: 39 Fields: Translation: AnimalsCells
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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: 52 Fields: Translation: AnimalsCells
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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: 104 Fields: Translation: HumansAnimalsCells
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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: 252 Fields: Translation: HumansCells
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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: 77 Fields: Translation: HumansCells
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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:
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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: 3 Fields: Translation: HumansCells
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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: 31 Fields: Translation: HumansAnimals
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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: 26 Fields: Translation: AnimalsCells
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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: 20 Fields: Translation: HumansAnimalsCells
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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: 27 Fields: Translation: Cells
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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: 36 Fields: Translation: AnimalsCells
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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: 259 Fields: Translation: HumansCells
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Epigenomics: From Chromatin Biology to Therapeutics. Nucleosome positioning in promoters: significance and open questions. 2011.
J.S. Song and D.E. Fisher. .
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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: 102 Fields: Translation: HumansCells
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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: 125 Fields: Translation: HumansAnimalsCells
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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: 44 Fields: Translation: HumansAnimalsCells
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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: 277 Fields: Translation: HumansCells
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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: 73 Fields: Translation: HumansCells
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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: 19 Fields: Translation: HumansCells
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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
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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
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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: 76 Fields: Translation: HumansCells
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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
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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: 10 Fields: Translation: Humans
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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:
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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: 29 Fields: Translation: Humans
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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: 158 Fields: Translation: HumansCells
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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: 74 Fields: Translation: AnimalsCells
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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
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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: 3 Fields: Translation: Humans
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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: 659 Fields: Translation: HumansCells
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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: 18 Fields:
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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: 111 Fields: Translation: HumansCells
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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.
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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.
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On a Conjecture of Givental. J Math Phys. 2004; 45:4539-4550.
Song JS, Song YS.
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Of McKay Correspondence, Non-linear Sigma-model and Conformed Field Theory. Adv Theo Math Phys. 2000; 4:747-790.
He YH, Song JS. .
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Three-Dimensional Gorenstein Singularities and SU(3) Modular Invariants. Adv Theo Math Phys. 2000; 4:791-822.
Song JS. .
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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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Year | Publications |
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1999 | 1 | 2000 | 2 | 2004 | 2 | 2005 | 1 | 2006 | 4 | 2007 | 7 | 2008 | 6 | 2010 | 3 | 2011 | 2 | 2012 | 6 | 2013 | 8 | 2014 | 3 | 2015 | 3 | 2016 | 4 | 2017 | 1 | 2018 | 2 | 2020 | 1 |
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This graph shows the number and percent of publications by field.
Fields are based on how the National Library of Medicine (NLM) classifies the publications' journals and might not represent the specific topics of the publications.
Note that an individual publication can be assigned to more than one field. As a result, the publication counts in this graph might add up to more than the number of publications the person has written.
To see the data as text, click here.
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