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Research Output

  • 81 Article
  • 4 Review article
  • 1 Chapter
  • 1 Conference contribution
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Article
2020

Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform

Blatti, C., Emad, A., Berry, M. J., Gatzke, L., Epstein, M., Lanier, D., Rizal, P., Ge, J., Liao, X., Sobh, O., Lambert, M., Post, C. S., Xiao, J., Groves, P., Epstein, A. T., Chen, X., Srinivasan, S., Lehnert, E., Kalari, K. R., Wang, L. & 8 others, Weinshilboum, R. M., Song, J. S., Jongeneel, C. V., Han, J., Ravaioli, U., Sobh, N., Bushell, C. B. & Sinha, S., Jan 1 2020, In : PLoS biology. 18, 1, e3000583.

Research output: Contribution to journalArticle

Open Access
2019

Local genomic features predict the distinct and overlapping binding patterns of the bHLH-Zip family oncoproteins MITF and MYC-MAX

Hejna, M., Moon, W. M., Cheng, J., Kawakami, A., Fisher, D. E. & Song, J. S., Jul 2019, In : Pigment Cell and Melanoma Research. 32, 4, p. 500-509 10 p.

Research output: Contribution to journalArticle

Sequenceng: An interactive knowledge base of sequencing techniques

Zhang, Y., Manjunath, M., Kim, Y., Heintz, J. & Song, J. S., Jan 1 2019, In : Bioinformatics. 35, 8, p. 1438-1440 3 p.

Research output: Contribution to journalArticle

Single-cell transcriptomics reveals spatial and temporal turnover of keratinocyte differentiation regulators

Finnegan, A., Cho, R. J., Luu, A., Harirchian, P., Lee, J., Cheng, J. B. & Song, J. S., Jan 1 2019, In : Frontiers in Genetics. 10, JUL, 775.

Research output: Contribution to journalArticle

Open Access

Targeted exon skipping with AAV-mediated split adenine base editors

Winter, J., Luu, A., Gapinske, M., Manandhar, S., Shirguppe, S., Woods, W. S., Song, J. S. & Perez-Pinera, P., Dec 1 2019, In : Cell Discovery. 5, 1, 41.

Research output: Contribution to journalArticle

Open Access

The cancer-associated genetic variant rs3903072 modulates immune cells in the tumor microenvironment

Zhang, Y., Manjunath, M., Yan, J., Baur, B. A., Zhang, S., Roy, S. & Song, J. S., Jan 1 2019, In : Frontiers in Genetics. 10, JUL, 754.

Research output: Contribution to journalArticle

Open Access
2018

A unified computational framework for modeling genome-wide nucleosome landscape

Jin, H., Finnegan, A. I. & Song, J. S., Sep 12 2018, In : Physical Biology. 15, 6, 066011.

Research output: Contribution to journalArticle

ClusterEnG: An interactive educational web resource for clustering and visualizing high-dimensional data

Manjunath, M., Zhang, Y., Kim, Y., Yeo, S. H., Sobh, O., Russell, N., Followell, C., Bushell, C., Ravaioli, U. & Song, J. S., Jan 1 2018, In : PeerJ Computer Science. 2018, 5, e155.

Research output: Contribution to journalArticle

Open Access

CRISPR-SKIP: Programmable gene splicing with single base editors

Gapinske, M., Luu, A., Winter, J., Woods, W. S., Kostan, K. A., Shiva, N., Song, J. S. & Perez-Pinera, P., Aug 15 2018, In : Genome biology. 19, 1, 107.

Research output: Contribution to journalArticle

Disruption of the β1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner

Mancini, A., Xavier-Magalhães, A., Woods, W. S., Nguyen, K. T., Amen, A. M., Hayes, J. L., Fellmann, C., Gapinske, M., McKinney, A. M., Hong, C., Jones, L. E., Walsh, K. M., Bell, R. J. A., Doudna, J. A., Costa, B. M., Song, J. S., Perez-Pinera, P. & Costello, J. F., Sep 10 2018, In : Cancer Cell. 34, 3, p. 513-528.e8

Research output: Contribution to journalArticle

Integrative genomic analysis predicts causative cis-regulatory mechanisms of the breast cancer–associated genetic variant rs4415084

Zhang, Y., Manjunath, M., Zhang, S., Chasman, D., Roy, S. & Song, J. S., Apr 1 2018, In : Cancer Research. 78, 7, p. 1579-1591 13 p.

Research output: Contribution to journalArticle

Quantum transport senses community structure in networks

Zhao, C. & Song, J. S., Aug 3 2018, In : Physical Review E. 98, 2, 022301.

Research output: Contribution to journalArticle

Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution

Cheng, J. B., Sedgewick, A. J., Finnegan, A. I., Harirchian, P., Lee, J., Kwon, S., Fassett, M. S., Golovato, J., Gray, M., Ghadially, R., Liao, W., Perez White, B. E., Mauro, T. M., Mully, T., Kim, E. A., Sbitany, H., Neuhaus, I. M., Grekin, R. C., Yu, S. S., Gray, J. W. & 6 others, Purdom, E., Paus, R., Vaske, C. J., Benz, S. C., Song, J. S. & Cho, R. J., Oct 23 2018, In : Cell Reports. 25, 4, p. 871-883 13 p.

Research output: Contribution to journalArticle

2017

Emergent community agglomeration from data set geometry

Zhao, C. & Song, J. S., Apr 13 2017, In : Physical Review E. 95, 4, 042307.

Research output: Contribution to journalArticle

High accuracy label-free classification of single-cell kinetic states from holographic cytometry of human melanoma cells

Hejna, M., Jorapur, A., Song, J. S. & Judson, R. L., Dec 1 2017, In : Scientific reports. 7, 1, 11943.

Research output: Contribution to journalArticle

Maximum entropy methods for extracting the learned features of deep neural networks

Finnegan, A. & Song, J. S., Oct 2017, In : PLoS computational biology. 13, 10, e1005836.

Research output: Contribution to journalArticle

Nanomagnetic System for Rapid Diagnosis of Acute Infection

Park, K. S., Kim, H., Kim, S., Lee, K., Park, S., Song, J., Min, C., Khanam, F., Rashu, R., Bhuiyan, T. R., Ryan, E. T., Qadri, F., Weissleder, R., Cheon, J., Charles, R. C. & Lee, H., Nov 28 2017, In : ACS Nano. 11, 11, p. 11425-11432 8 p.

Research output: Contribution to journalArticle

NF45 and NF90/NF110 coordinately regulate ESC pluripotency and differentiation

Ye, J., Jin, H., Pankov, A., Song, J. S. & Blelloch, R., Aug 2017, In : RNA. 23, 8, p. 1270-1284 15 p.

Research output: Contribution to journalArticle

TeachEnG: A Teach ing en gine for G enomics

Kim, M., Kim, Y., Qian, L. & Song, J. S., Oct 15 2017, In : Bioinformatics. 33, 20, p. 3296-3298 3 p.

Research output: Contribution to journalArticle

Tfe3 and Tfeb transcriptionally regulate peroxisome proliferator-activated receptor γ2 expression in adipocytes and mediate adiponectin and glucose levels in mice

Salma, N., Song, J. S., Kawakami, A., Devi, S. P., Khaled, M., Cacicedo, J. M. & Fisher, D. E., Aug 1 2017, In : Molecular and cellular biology. 37, 15, e00608-16.

Research output: Contribution to journalArticle

2016

Categorical spectral analysis of periodicity in nucleosomal DNA

Jin, H., Rube, H. T. & Song, J. S., Feb 17 2016, In : Nucleic acids research. 44, 5, p. 2047-2057 11 p.

Research output: Contribution to journalArticle

Inhibition of mTOR induces a paused pluripotent state

Bulut-Karslioglu, A., Biechele, S., Jin, H., MacRae, T. A., Hejna, M., Gertsenstein, M., Song, J. S. & Ramalho-Santos, M., Dec 1 2016, In : Nature. 540, 7631, p. 119-123 5 p.

Research output: Contribution to journalArticle

Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA

Kim, M., Kreig, A., Lee, C. Y., Rube, H. T., Calvert, J., Song, J. S. & Myong, S., Jun 2 2016, In : Nucleic acids research. 44, 10, p. 4807-4817 11 p.

Research output: Contribution to journalArticle

Sequence features accurately predict genome-wide MeCP2 binding in vivo

Rube, H. T., Lee, W., Hejna, M., Chen, H., Yasui, D. H., Hess, J. F., Lasalle, J. M., Song, J. S. & Gong, Q., Mar 24 2016, In : Nature communications. 7, 11025.

Research output: Contribution to journalArticle

Sparsity-based pixel super resolution for lens-free digital in-line holography

Song, J., Leon Swisher, C., Im, H., Jeong, S., Pathania, D., Iwamoto, Y., Pivovarov, M., Weissleder, R. & Lee, H., Apr 21 2016, In : Scientific reports. 6, 24681.

Research output: Contribution to journalArticle

YAP Induces Human Naive Pluripotency

Qin, H., Hejna, M., Liu, Y., Percharde, M., Wossidlo, M., Blouin, L., Durruthy-Durruthy, J., Wong, P., Qi, Z., Yu, J., Qi, L. S., Sebastiano, V., Song, J. S. & Ramalho-Santos, M., Mar 15 2016, In : Cell Reports. 14, 10, p. 2301-2312 12 p.

Research output: Contribution to journalArticle

2015

Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast

Guzman-Ayala, M., Sachs, M., Koh, F. M., Onodera, C., Bulut-Karslioglu, A., Lin, C. J., Wong, P., Nitta, R., Song, J. S. & Ramalho-Santos, M., Jan 1 2015, In : Development (Cambridge). 142, 1, p. 118-127 10 p.

Research output: Contribution to journalArticle

Digital diffraction analysis enables low-cost molecular diagnostics on a smartphone

Im, H., Castro, C. M., Shao, H., Liong, M., Song, J., Pathania, D., Fexon, L., Min, C., Avila-Wallace, M., Zurkiya, O., Rho, J., Magaoay, B., Tambouret, R. H., Pivovarov, M., Weissleder, R. & Lee, H., May 5 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 18, p. 5613-5618 6 p.

Research output: Contribution to journalArticle

DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors

Mazor, T., Pankov, A., Johnson, B. E., Hong, C., Hamilton, E. G., Bell, R. J. A., Smirnov, I. V., Reis, G. F., Phillips, J. J., Barnes, M. J., Idbaih, A., Alentorn, A., Kloezeman, J. J., Lamfers, M. L. M., Bollen, A. W., Taylor, B. S., Molinaro, A. M., Olshen, A. B., Chang, S. M., Song, J. S. & 1 others, Costello, J. F., Sep 14 2015, In : Cancer Cell. 28, 3, p. 307-317 11 p.

Research output: Contribution to journalArticle

Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis

Chen, S., Sanjana, N. E., Zheng, K., Shalem, O., Lee, K., Shi, X., Scott, D. A., Song, J., Pan, J. Q., Weissleder, R., Lee, H., Zhang, F. & Sharp, P. A., Mar 15 2015, In : Cell. 160, 6, p. 1246-1260 15 p.

Research output: Contribution to journalArticle

HiTSelect: A comprehensive tool for high-complexity-pooled screen analysis

Diaz, A. A., Qin, H., Ramalho-Santos, M. & Song, J. S., Jan 1 2015, In : Nucleic acids research. 43, 3, p. e16

Research output: Contribution to journalArticle

KnowEnG: A knowledge engine for genomics

Sinha, S., Song, J., Weinshilboum, R., Jongeneel, V. & Han, J., Jan 1 2015, In : Journal of the American Medical Informatics Association. 22, 6, p. 1115-1119 5 p.

Research output: Contribution to journalArticle

On chip analysis of CNS lymphoma in cerebrospinal fluid

Turetsky, A., Lee, K., Song, J., Giedt, R. J., Kim, E., Kovach, A. E., Hochberg, E. P., Castro, C. M., Lee, H. & Weissleder, R., Jan 1 2015, In : Theranostics. 5, 8, p. 796-804 9 p.

Research output: Contribution to journalArticle

The cancer genome atlas analysis predicts MicroRNA for targeting cancer growth and vascularization in glioblastoma

Wong, H. K. A., Fatimy, R. E., Onodera, C., Wei, Z., Yi, M., Mohan, A., Gowrisankaran, S., Karmali, P., Marcusson, E., Wakimoto, H., Stephens, R., Uhlmann, E. J., Song, J. S., Tannous, B. & Krichevsky, A. M., Jul 1 2015, In : Molecular Therapy. 23, 7, p. 1234-1247 14 p.

Research output: Contribution to journalArticle

The genetics of splicing in neuroblastoma

Chen, J., Hackett, C. S., Zhang, S., Song, Y. K., Bell, R. J. A., Molinaro, A. M., Quigley, D. A., Balmain, A., Song, J. S., Costello, J. F., Gustafson, W. C., Van Dyke, T., Kwok, P. Y., Khan, J. & Weiss, W. A., Apr 1 2015, In : Cancer Discovery. 5, 4, p. 380-395 16 p.

Research output: Contribution to journalArticle

The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer

Bell, R. J. A., Rube, H. T., Kreig, A., Mancini, A., Fouse, S. D., Nagarajan, R. P., Choi, S., Hong, C., He, D., Pekmezci, M., Wiencke, J. K., Wrensch, M. R., Chang, S. M., Walsh, K. M., Myong, S., Song, J. S. & Costello, J. F., May 29 2015, In : Science. 348, 6238, p. 1036-1039 4 p.

Research output: Contribution to journalArticle

Transcription Factor Tfe3 Directly Regulates Pgc-1alpha in Muscle

Salma, N., Song, J. S., Arany, Z. & Fisher, D. E., Oct 1 2015, In : Journal of Cellular Physiology. 230, 10, p. 2330-2336 7 p.

Research output: Contribution to journalArticle

2014

Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma

Johnson, B. E., Mazor, T., Hong, C., Barnes, M., Aihara, K., McLean, C. Y., Fouse, S. D., Yamamoto, S., Ueda, H., Tatsuno, K., Asthana, S., Jalbert, L. E., Nelson, S. J., Bollen, A. W., Gustafson, W. C., Charron, E., Weiss, W. A., Smirnov, I. V., Song, J. S., Olshen, A. B. & 14 others, Cha, S., Zhao, Y., Moore, R. A., Mungall, A. J., Jones, S. J. M., Hirst, M., Marra, M. A., Saito, N., Aburatani, H., Mukasa, A., Berger, M. S., Chang, S. M., Taylor, B. S. & Costello, J. F., Jan 1 2014, In : Science. 343, 6167, p. 189-193 5 p.

Research output: Contribution to journalArticle

Quantifying the role of steric constraints in nucleosome positioning

Rube, H. T. & Song, J. S., Feb 1 2014, In : Nucleic acids research. 42, 4, p. 2147-2158 12 p.

Research output: Contribution to journalArticle

Recurrent epimutations activate gene body promoters in primary glioblastoma

Nagarajan, R. P., Zhang, B., Bell, R. J. A., Johnson, B. E., Olshen, A. B., Sundaram, V., Li, D., Graham, A. E., Diaz, A., Fouse, S. D., Smirnov, I., Song, J., Paris, P. L., Wang, T. & Costello, J. F., May 2014, In : Genome Research. 24, 5, p. 761-774 14 p.

Research output: Contribution to journalArticle

Systematic identification of barriers to human Ipsc generation

Qin, H., Diaz, A., Blouin, L., Lebbink, R. J., Patena, W., Tanbun, P., Leproust, E. M., McManus, M. T., Song, J. S. & Ramalho-Santos, M., Jul 17 2014, In : Cell. 158, 2, p. 449-461 13 p.

Research output: Contribution to journalArticle

2013

BCL2A1 is a lineage-specific antiapoptotic melanoma oncogene that confers resistance to BRAF inhibition

Haq, R., Yokoyama, S., Hawryluk, E. B., Jönsson, G. B., Frederick, D. T., McHenry, K., Porter, D., Tran, T. N., Love, K. T., Langer, R., Anderson, D. G., Garraway, L. A., Duncan, L. M. D., Morton, D. L., Hoon, D. S. B., Wargo, J. A., Song, J. S. & Fisher, D. E., Mar 12 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 11, p. 4321-4326 6 p.

Research output: Contribution to journalArticle

Bivalent Chromatin Marks Developmental Regulatory Genes in the Mouse Embryonic Germline InVivo

Sachs, M., Onodera, C., Blaschke, K., Ebata, K. T., Song, J. S. & Ramalho-Santos, M., Mar 27 2013, In : Cell Reports. 3, 6, p. 1777-1784 8 p.

Research output: Contribution to journalArticle

Categorical spectral analysis of periodicity in human and viral genomes

Howe, E. D. & Song, J. S., Feb 1 2013, In : Nucleic acids research. 41, 3, p. 1395-1405 11 p.

Research output: Contribution to journalArticle

Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo

Ramos, A. D., Diaz, A., Nellore, A., Delgado, R. N., Park, K. Y., Gonzales-Roybal, G., Oldham, M. C., Song, J. S. & Lim, D. A., May 2 2013, In : Cell Stem Cell. 12, 5, p. 616-628 13 p.

Research output: Contribution to journalArticle

NSeq: A multithreaded Java application for finding positioned nucleosomes from sequencing data

Nellore, A., Bobkov, K., Howe, E., Pankov, A., Diaz, A. & Song, J. S., Apr 19 2013, In : Frontiers in Genetics. 3, JAN, Article 320.

Research output: Contribution to journalArticle

Oncogenic BRAF regulates oxidative metabolism via PGC1α and MITF

Haq, R., Shoag, J., Andreu-Perez, P., Yokoyama, S., Edelman, H., Rowe, G. C., Frederick, D. T., Hurley, A. D., Nellore, A., Kung, A. L., Wargo, J. A., Song, J. S., Fisher, D. E., Arany, Z. & Widlund, H. R., Mar 18 2013, In : Cancer Cell. 23, 3, p. 302-315 14 p.

Research output: Contribution to journalArticle

Somatic Cells Regulate Maternal mRNA Translation and Developmental Competence of Mouse Oocytes

Chen, J., Torcia, S., Xie, F., Lin, C. J., Cakmak, H., Franciosi, F., Horner, K., Onodera, C., Song, J. S., Cedars, M. I., Ramalho-Santos, M. & Conti, M., Dec 2013, In : Nature Cell Biology. 15, 12, p. 1415-1423 9 p.

Research output: Contribution to journalArticle

2012

CHANCE: comprehensive software for quality control and validation of ChIP-seq data

Diaz, A., Nellore, A. & Song, J. S., Jan 1 2012, In : Genome biology. 13, 10, p. R98

Research output: Contribution to journalArticle

Normalization, bias correction, and peak calling for ChIP-seq.

Diaz, A., Park, K., Lim, D. A. & Song, J. S., 2012, In : Statistical applications in genetics and molecular biology. 11, 3, p. Article 9

Research output: Contribution to journalArticle