Affiliated Research Centers

Knoweldge Engine for Genomics (KnowEnG)

NIH Center of Excellence in Big Data Computing (Co-PI)

Center for the Physics of Living Cells (CPLC)

NSF Physics Frontiers Center (Co-Investigator)

Research Interests

Understanding gene regulation in eukaryotes presents exciting challenges in biology today. Eukaryotic DNA is not naked but wraps around millions of histone proteins, forming a very complicated three-dimensional structure called chromatin. Chromatin structure and other epigenetic factors play crucial roles in gene regulation, selectively enhancing or silencing transcriptional activities specific to various cell types. My main research interest focuses on using integrative genomics to study the interplay among transcription factors, chromatin structure, non-coding RNAs, and gene regulation in development and diseases.

Publication in Genomics

C. Zhao and J.S. Song. Quantum transport senses community structure in networks. arXiv:1711.04979 [quant-ph], (2017)

H. Jin, A.I. Finnegan, J.S. Song. A unified computational framework for modeling genome-wide nucleosome landscape, BIORXIV/2017/202580, (2017).

C. Zhao and J.S. Song. Exact heat kernel on a hypersphere and its applications in kernel SVM. Front. Appl. Math. Stat, (2018). arXiv:1702.01373 [stat.ML]

J. Ye*, H. Jin*, A. Pankov, J.S. Song, R. Blelloch. (*co-first authors, co-corresponding authors). NF45 and NF90/NF110 coordinately regulate ESC pluripotency and differentiation, RNA 23, 1270-1284, (2017)

N. Salma, J.S. Song, A. Kawakami, S.P. Devi, M. Khaled, J.M. Cacicedo, and D.E. Fisher. Tfe3 and Tfeb transcriptionally regulate Pparg2 expression in adipocytes and mediate adiponectin and glucose levels in mice. Mol. Cell Biol. 37(15), e00608-16, (2017).

M. Hejna*, A. Jorapur*, J.S. Song, R.L. Judson. (*co-first authors, co-corresponding authors). High accuracy label-free classification of single-cell kinetic states from holographic cytometry of human melanoma cells. Scientific Reports, 7, 11943, (2017). BIORXIV/2017/127449

M. Manjunath, Y. Zhang, S.H. Yeo, O. Sobh, N. Russell, C. Followell, C. Bushell, U. Ravaioli and J.S. Song. ClusterEnG: An interactive educational web resource for clustering big data. BIORXIV/2017/120915, (2017).

M. Kim, Y. Kim, L. Qian, J.S. Song. TeachEnG: a Teaching Engine for Genomics. Bioinformatics, 33(20), 3296-3298, (2017). BIORXIV/2017/111054

A.I. Finnegan and J.S. Song. Maximum Entropy Methods for Extracting the Learned Features of Deep Neural Networks, PLoS Computational Biology, 13(10): e1005836, (2017). BIORXIV/2017/105957

C. Zhao and J.S. Song. Emergent community agglomeration from data set geometry, Physical Review E, 95, 042307, (2017). BIORXIV/2017/109587

A. Bulut-Karslioglu, S. Biechele, H. Jin, T.A. Macrae, M. Hejna, M. Gertsenstein, J.S. Song and M. Ramalho-Santos. Inhibition of mTOR induces a paused pluripotent state, Nature, 540, 119-123, (2016).

M. Kim*, A. Kreig*, C.-Y. Lee, H.T. Rube, J. Calvert, J.S. Song and Sua Myong (*co-first authors, co-corresponding authors). Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA, Nucleic Acids Research, 44(10), 4807-17, (2016).

T. Mazor*, A. Pankov*, J.S. Song, J.F. Costello (*co-first authors). Intratumoral Heterogeneity of the Epigenome. Cancer Cell, 29, 440-451, (2016).

H.T. Rube*, W. Lee*, M. Hejna, H. Chen, D.H. Yasui, J.F. Hess, J.M. LaSalle, J.S. Song†,# Q. Gong†,#. (*co-first authors, co-senior authors, #co-corresponding authors). Sequence features accurately predict genome-wide MeCP2 binding in vivo. Nature Communications, 7, 11025, (2016).

H. Jin, H.T. Rube, J.S. Song. Categorical spectral analysis of periodicity in nucleosomal DNA. Categorical spectral analysis of periodicity in nucleosomal DNA. Nucleic Acids Research, 44(5), 2047-2057, (2016).

H. Qin, M. Hejna, Y. Liu, M. Percharde, M. Wossidlo, L. Blouin, J. Durruthy-Durruthy, P. Wong, Z. Qi, J. Yu, L.S. Qi, V. Sebastiano, J.S. Song, M. Ramalho-Santos. YAP Induces Human Naive Pluripotency. Cell Reports, 14(10), 2301-2312, (2016).

R.J.A. Bell, H.T. Rube, A. Xavier-Magalhaes, B.M. Costa, A. Mancini, J.S. Song, J.F. Costello. Understanding TERT Promoter Mutations: a Common Path to Immortality. Molecular Cancer Research, 14(4), 315-23, (2016).

T. Mazor1, A. Pankov1, B.E. Johnson, C. Hong, E.G. Hamilton, R.J.A. Bell, I.V. Smirnov, G.F. Reis, J.J. Phillips, M.J. Barnes, A. Idbaih, A. Alentorn, J.J. Kloezeman, M.L.M. Lamfers, A.W. Bollen, B.S. Taylor, A.M. Molinaro, A.B. Olshen, S.M. Chang, J.S. Song,2,* and J.F. Costello2,*. (1co-first authors, 2co-senior authors, *co-corresponding authors). DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors, Cancer Cell, 28(3), 307-317, (2015)

S. Sinha, J.S. Song, R. Weinshilboum, V. Jongeneel, J. Han. KnowEnG: A knowledge engine for genomics. J Am Med Inform Assoc, (2015).

R.J.A. Bell, H.T. Rube, A. Kreig, A. Mancini, S.D. Fouse, R.P. Nagarajan, S. Choi, C. Hong, D. He, M. Pekmezci, J.K. Wiencke, M.R. Wrensch, S.M. Chang, K.M. Walsh, S. Myong, J.S. Song*,# and J.F. Costello*,#. (*co-corresponding authors, #equal contribution). The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer, Science, 348, 1036-1039, (2015). Abstract, PDF

H.A. Wong, R.E. Fatimy, C. Onodera, Z. Wei, M. Yi, A. Mohan, S. Gowrisankaran, P. Karmali, E. Marcusson, H. Wakimoto, R. Stephens, E.J. Uhlmann, J.S. Song, B. Tannous and A.M. Krichevsky. TCGA analysis predicts microRNA for targeting cancer growth and vascularization in glioblastoma, Molecular Therapy, 23(7), 1234-47, (2015).

N. Salma, J.S. Song, Z. Arany, D.E. Fisher. Transcription factor Tfe3 directly regulates Pgc-1alpha in muscle, J. Cell. Physiology, 230(10), 2330-6, (2015).

Chen J, Hackett CS, Zhang S, Song YK, Bell RJA, 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(4), 380-95, (2015).

A. Diaz1, H. Qin1, M. Ramalho-Santos*, J.S. Song* (1co-first authors, *co-corresponding authors). HiTSelect: A Comprehensive Tool for High-Complexity Pooled Screen Analysis, Nucleic Acids Research, 43(3):e16, (2015).

M. Guzman-Ayala, M. Sachs, F.M. Koh, C. Onodera, A. Bulut-Karslioglu, C.J. Lin, P. Wong, R. Nitta, J.S. Song, and M. Ramalho-Santos. Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast, Development, 142(1), 118-27, (2015).

H. Qin1, A. Diaz1, L. Blouin, R.J. Lebbink, W. Patena, P. Tanbun, E.M. LeProust, M.T. McManus2, J.S. Song2,*, M. Ramalho-Santos2,* (1co-first authors, 2co-senior authors, *co-corresponding authors). Systematic Identification of Barriers to Human iPSC Generation, Cell, 158(2), 449-461, (2014).

R.P. Nagarajan , B. Zhang, R.J. Bell, B.E. Johnson, A.B. Olshen, V. Sundaram, D. Li, A.E. Graham, A. Diaz, S.D Fouse, I. Smirnov, J. Song, P.L. Paris, T. Wang, J.F. Costello, Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Research, 24(5), 761-74, (2014).

B.E. Johnson, T. Mazor, et al. Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma, Science, 343(6167), 189-93, (2014).

T. Rube and J.S. Song, Quantifying the Role of Steric Constraints in Nucleosome Positioning, Nucleic Acids Research, 42(4), 2147-58, (2014).

J. Chen, S. Torcia, F. Xie, C-J Lin, H. Cakmak, F. Franciosi, K. Horner, C. Onodera, J.S. Song, M.I. Cedars, M. Ramalho-Santos, and M. Conti. Somatic cells regulate maternal mRNA translation and development competence of mouse oocytes, Nature Cell Biology, 15(12), 1415-23, (2013).

M. Sachs, C. Onodera, K. Blaschke, K.T. Ebata, J.S. Song, M. Ramalho-Santos. Bivalent Chromatin Marks Developmental Regulatory Genes in the Mouse Embryonic Germline in vivo, Cell Reports, 3(6), 1777-84, (2013).

A.D. Ramos, A. Diaz, A. Nellore, R.N. Delgado, K.-Y. Park, G. Gonzales-Roybal, M.C. Oldham, J.S. Song, D.A. Lim. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell 12, 616-628, (2013).

R. Haq, J. Shoag, P. Andreu-Perez, S. Yokoyama, A. Edelman, A.D. Hunley, A. Nellore, J. Wargo, J.S. Song, D.E. Fisher, Z. Arany, H. Widlund. Oncogenic BRAF regulates oxidative metabolism via PGC1α and MITF. Cancer Cell, 23 (3), 302-315, (2013).

R. Haq, S. Yokoyama, K. McHenry, J. Li, D. Porter, L. Duncan, J.S. Song*, D.E. Fisher* (*co-corresponding authors). BCL2A1 is a lineage-specific anti-apoptotic melanoma oncogene that confers resistance to BRAF inhibition, PNAS, 110(11), 4321-4326, (2013).

A. Nellore, K. Bobkov, E. Howe, A. Pankov, A. Diaz, J.S. Song. NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data, Frontiers in Genetics, 3:320 (2013).

E. Howe and J.S. Song. Categorical spectral analysis of periodicity in human and viral genomes, Nucleic Acids Research, 41(3), 1395-1405, (2013).

A. Diaz, A. Nellore, J.S. Song. CHANCE - CHip-seq ANalytics and Confidence Estimation: comprehensive software for quality control and validation of ChIP-seq data, Genome Biology 13:R98, (2012).

M. Venere, Y.-G. Han, R. Bell, J.S. Song, A. Alvarez-Buylla, R. Blelloch, Sox1 marks an activated neural stem/progenitor cell in the hippocampus, Development 139, 3938-3949 (2012).

J. Li#, J.S. Song#,*, R.J.A. Bell, T-N T. Tran, R. Haq, H. Liu, K.T. Love, R. Langer, D.G. Anderson, L. Larue, D.E. Fisher* (#co-first authors, *co-corresponding authors). YY1 regulates melanocyte development and function by co-operating with MITF, PLoS Genetics 8(5): e1002688, (2012).

J. Hunkapiller, Y. Shen, A. Diaz, G. Cagney, D. McCleary, M. Ramalho-Santos, N. Krogan, B. Ren, J.S. Song*, and J.F. Reiter* (*co-corresponding authors). Polycomb-like 3 promotes Polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal, PLoS Genetics 8(3): e1002576, (2012).

Aaron Diaz, Kiyoub Park, Daniel A. Lim, and Jun S. Song. Normalization, bias correction, and peak calling for ChIP-seq, Statistical Applications in Genetics and Molecular Biology, Vol 11: Iss. 3, Article 9, (2012).

Yuki Ohi#, Han Qin, Chibo Hong, Laure Blouin, Jose M. Polo, Tingxia Guo, Zhongxia Qi, Sara L. Downey, Philip D. Manos, Derrick J. Rossi, Jingwei Yu, Matthias Hebrok, Konrad Hochedlinger, Joseph F. Costello, Jun S. Song#,* & Miguel Ramalho-Santos* (#co-first authors, *co-corresponding authors), Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells, Nature Cell Biology 13 (5), 541-549, (2011).

J.S. Song and D.E. Fisher. Nucleosome positioning in promoters: significance and open questions, in Epigenomics: From Chromatin Biology to Therapeutics. ed. K. Appasani, Cambridge University Press (2010).

C. Levy, M. Khaled, D. Iliopoulos, M.M. Janas, S. Schubert, S. Pinner, P.H. Chen, S. Li, A.L. Fletcher, S. Yokoyama, K.L. Scott, L.A. Garraway, J.S. Song, S.R. Granter, S.J. Turley, D.E. Fisher, C.D. Novina. Intronic miR-211 Assumes the Tumor Suppressive Function of Its Host Gene in Melanoma, Molecular Cell 40(5) 841-849, (2010).

C. Levy, M. Khaled, K.C. Robinson, S. Yokoyama, P.H. Chen, R.A. Veguilla, E. Makino, J. Lu, F. Beermann, L. Chin, M. Bosenberg, J.S. Song, and D.E. Fisher. Lineage-specific transcriptional regulation of DICER by MITF in melanocytes, Cell 141(6) 994-1005, (2010).

W. Hu, C.S. Chan, C. Zhang, Y, Sun, J.S. Song, L. Tang, A.J. Levine, Z. Feng. Negative Regulation of the Tumor Suppressor p53 by the microRNA miR-504, Molecular Cell 38(5) 689-99, (2010).

F. Ozsolak, L.L. Poling, Z. Wang, H. Liu, X.S. Liu, R.G. Roeder, X. Zhang, J.S. Song* and D.E. Fisher* (*co-corresponding authors). Chromatin Structure Analyses Identify miRNA Promoters. Genes & Development 22, 3172–3183, (2008).

Y. Zhang, H. Shin, J.S. Song, Y. Lei, and X.S. Liu. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics 9, 537, (2008).

C.S. Chan and J.S. Song. CTCF Confines the Distal Action of Estrogen Receptor. Cancer Research 68, 9041–9, (2008)

K.A. Holmes, J.S. Song, X.S. Liu, M. Brown, and J.S. Carroll. NKX3-1 and LEF-1 function as transcriptional inhibitors of Estrogen Receptor activity. Cancer Research 68, 7380–7385, (2008).

J.S. Song*, X. Liu*, X.S. Liu, and X. He (*co-first authors). A high-resolution map of nucleosome positioning on a fission yeast centromere. Genome Research 18, 1064–1072, (2008).

D.S. Johnson, W. Li, D.B. Gordon, A. Bhattacharjee, B. Curry, J. Ghosh, L. Brizuela, J.S. Carroll, M. Brown, P. Flicek, C.M. Koch, I. Dunham, M. Bieda, X. Xu, P.J. Farnham, P. Kapranov, D.A. Nix, T.R. Gingeras, X. Zhang, H. Holster, N. Jiang, R.D. Green, J.S. Song, S.A. McCuine, E. Anton, L. Nguyen, N.D. Trinklein, Z. Ye, K. Ching, D. Hawkins, B. Ren, P.C. Scacheri, J. Rozowsky, A. Karpikov, G. Euskirchen, S. Weissman, M. Gerstein, M. Snyder, A. Yang, Z. Moqtaderi, H. Hirsch, H.P. Shulha, Y. Fu, Z. Weng, K. Struhl, R.M. Myers, J.D. Lieb, and X.S. Liu, Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research 18(3), 393-403, (2008).

F. Ozsolak* , J.S. Song* , X.S. Liu, D.E. Fisher (∗ co-first authors). High-throughput mapping of the chromatin structure of human promoters. Nature Biotech 25, 244–248, (2007).

J.S. Song*, W.E. Johnson*, X. Zhu*, X. Zhang, W. Li, A.K. Manrai, J.S. Liu, R. Chen, and X.S. Liu (*co-first authors). Model-based analysis of two-color arrays (MA2C). Genome Biol 8(8), R178, (2007).

J.S. Song*, K. Maghsoudi*, W. Li, E. Fox, J. Quackenbush, and X. Shirley Liu (*co-first authors). Microarray blob-defect removal improves array analysis. Bioinformatics 23(8), 966-71, (2007).

Y.S. Song and J.S. Song. Analytic Computation of the Expectation of the Linkage Disequilibrium Coefficient r2. Theoretical Population Biology 71, 49-60, (2007).

J. Carroll, C. Meyer, J.S. Song, W. Li, T.R. Geistlinger, J. Eeckhoute, A.S. Brodsky, E.K. Keeton, K.C. Fertuck, G.F. Hall, Q. Wang, S. Bekiranov, V. Sementchenko, E.A. Fox, P.A. Silver, T.R. Gingeras, X.S. Liu, and M. Brown. Genome Wide Analysis of Estrogen Receptor Binding Sites. Nature Genetics 38, 1289–1297, (2006).

X. Ji, W. Li, J. Song, L. Wei, and X.S. Liu. CEAS: cis-regulatory element annotation system. Nucleic Acids Res 34, W551-4, (2006).

Publication in Medical Physics

Song JS., Albert M., D’Amico AV., Cormack RA. A Comparative Study of Rectal Dose Histograms in Prostate Brachytherapy: Some Analytic and Numerical Results. Medical Physics 32: 437-447, (2005).

Court LE., Jahnke L., Chin D., Song JS., Cormack R., Zygmanski P., Tishler RB., Chin L. Dynamic IMRT treatments of sinus region tumors: Comparison of Monte Carlo calculations with treatment planning system calculations and ion chamber measurements. Tech in Cancer Res and Treatment 5, (2006).

Landis DM., Luo W., Song JS., Bellon JR., Punglia RS., Wong JS., Killoran JH., Gelman R., Harris JR. Variability among Breast Radiation Oncologists in Delineation of the Postsurgical Lumpectomy Cavity. Int J Radiation Oncol Biol Phys 67: 1299-1308, (2007).

Song JS., Court LE., Cormack R. Monte Carlo calculation of rectal dose when using an intrarectal balloon during prostate radiation therapy. Medical Dosimetry 32: 151-156, (2007).

Xiang H., Song JS., Chin DW., Cormack RA., Tishler RB., Makrigiorges GM., Court LE., Chin LM. 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 34: 1266-1273, (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. Defining the Rectal Dose Constraint for Permanent Radioactive Seed Implantation of the Prostate. Urol Oncol 26: 147-152, (2008).

Publication in Mathematical Physics

Song JS. Descendant Gromov-Witten Invariants, Simple Hurwitz Numbers, and the Virasoro Conjecture for P1. Adv Theo Math Phys 3: 1721-1768, (1999).

He Y-H., Song JS. Of McKay Correspondence, Non-linear Sigma-model and Conformal Field Theory. Adv Theo Math Phys 4: 747-790, (2000).

Song JS. Three-Dimensional Gorenstein Singularities and SU(3) Modular Invariants. Adv Theo Math Phys 4: 791-822, (2000).

Monni S., Song JS., Song YS. The Hurwitz Enumeration Problem of Branched Covers and Hodge Integrals. Journal of Geometry and Physics 50: 223-256, (2004).

Song JS., Song YS. On a Conjecture of Givental. J Math Phys 45: 4539-4550, (2004).