• 8573 Citations
  • 27 h-Index
19962018

Research output per year

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Research Output

  • 8573 Citations
  • 27 h-Index
  • 36 Article
  • 1 Chapter
  • 1 Short survey
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Article
2018

PASNet: Pathway-associated sparse deep neural network for prognosis prediction from high-throughput data

Hao, J., Kim, Y., Kim, T. & Kang, M., Dec 17 2018, In : BMC Bioinformatics. 19, 1, 510.

Research output: Contribution to journalArticle

3 Scopus citations
2017

An Intrinsic Transcriptional Program Underlying Synaptic Scaling during Activity Suppression

Schaukowitch, K., Reese, A. L., Kim, S. K., Kilaru, G., Joo, J. Y., Kavalali, E. T. & Kim, T. K., Feb 7 2017, In : Cell Reports. 18, 6, p. 1512-1526 15 p.

Research output: Contribution to journalArticle

10 Scopus citations

Emerging themes in neuronal activity-dependent gene expression

Madabhushi, R. & Kim, T. K., Jan 1 2017, (Accepted/In press) In : Molecular and Cellular Neuroscience.

Research output: Contribution to journalArticle

11 Scopus citations

HDAC5 and Its Target Gene, Npas4, Function in the Nucleus Accumbens to Regulate Cocaine-Conditioned Behaviors

Taniguchi, M., Carreira, M. B., Cooper, Y. A., Bobadilla, A. C., Heinsbroek, J. A., Koike, N., Larson, E. B., Balmuth, E. A., Hughes, B. W., Penrod, R. D., Kumar, J., Smith, L. N., Guzman, D., Takahashi, J. S., Kim, T. K., Kalivas, P. W., Self, D. W., Lin, Y. & Cowan, C. W., Sep 27 2017, In : Neuron. 96, 1, p. 130-144 15 p.

Research output: Contribution to journalArticle

28 Scopus citations
2016

Diverse regulatory interactions of long noncoding RNAs

Kim, T. K. & Shiekhattar, R., Feb 1 2016, In : Current Opinion in Genetics and Development. 36, p. 73-82 10 p.

Research output: Contribution to journalArticle

10 Scopus citations

Erratum: Stimulus-specific combinatorial functionality of neuronal c-fos enhancers (Nature Neuroscience (2016) 19 (75-83))

Joo, J. Y., Schaukowitch, K., Farbiak, L., Kilaru, G. & Kim, T. K., Mar 29 2016, In : Nature Neuroscience. 19, 4, p. 642 1 p.

Research output: Contribution to journalArticle

1 Scopus citations
2015

Architectural and Functional Commonalities between Enhancers and Promoters

Kim, T. K. & Shiekhattar, R., Aug 27 2015, In : Cell. 162, 5, p. 948-959 12 p.

Research output: Contribution to journalArticle

133 Scopus citations

Enhancer RNAs: A class of long noncoding RNAs synthesized at enhancers

Kim, T. K., Hemberg, M. & Gray, J. M., Jan 1 2015, In : Cold Spring Harbor perspectives in biology. 7, 1, a018622.

Research output: Contribution to journalArticle

49 Scopus citations

Genomic views of transcriptional enhancers: Essential determinants of cellular identity and activity-dependent responses in the CNS

Gray, J. M., Kim, T. K., West, A. E., Nord, A. S., Markenscoff-Papadimitriou, E. & Lomvardas, S., Oct 14 2015, In : Journal of Neuroscience. 35, 41, p. 13819-13826 8 p.

Research output: Contribution to journalArticle

17 Scopus citations

Stimulus-specific combinatorial functionality of neuronal c-fos enhancers

Joo, J. Y., Schaukowitch, K., Farbiak, L., Kilaru, G. & Kim, T. K., Dec 29 2015, In : Nature Neuroscience. 19, 1, p. 75-83 9 p.

Research output: Contribution to journalArticle

67 Scopus citations
2014

ChIP-seq and RNA-seq Methods to Study Circadian Control of Transcription in Mammals

Takahashi, J. S., Kumar, V., Nakashe, P., Koike, N., Huang, H. C., Green, C. B. & Kim, T. K., 2014, (Accepted/In press) In : Methods in Enzymology.

Research output: Contribution to journalArticle

10 Scopus citations

Emerging epigenetic mechanisms of long non-coding RNAs

Schaukowitch, K. & Kim, T. K., Apr 4 2014, In : Neuroscience. 264, p. 25-38 14 p.

Research output: Contribution to journalArticle

58 Scopus citations

Enhancer RNA facilitates NELF release from immediate early genes

Schaukowitch, K., Joo, J. Y., Liu, X., Watts, J. K., Martinez, C. & Kim, T. K., 2014, In : Molecular Cell. 56, 1, p. 29-42 14 p.

Research output: Contribution to journalArticle

157 Scopus citations

SET7/9 methylation of the pluripotency factor LIN28A is a nucleolar localization mechanism that blocks let-7 biogenesis in human ESCs

Kim, S. K., Lee, H., Han, K., Kim, S. C., Choi, Y., Park, S. W., Bak, G., Lee, Y., Choi, J. K., Kim, T. K., Han, Y. M. & Lee, D., Dec 4 2014, In : Cell Stem Cell. 15, 6, p. 735-749 15 p.

Research output: Contribution to journalArticle

32 Scopus citations
2013

Usf1, a suppressor of the circadian Clock mutant, reveals the nature of the DNA-binding of the CLOCK: BMAL1 complex in mice

Shimomura, K., Kumar, V., Koike, N., Kim, T. K., Chong, J., Buhr, E. D., Whiteley, A. R., Low, S. S., Omura, C., Fenner, D., Owens, J. R., Richards, M., Yoo, S. H., Hong, H. K., Vitaterna, M. H., Bass, J., Pletcher, M. T., Wiltshire, T., Hogenesch, J., Lowrey, P. L. & 1 others, Takahashi, J. S., Apr 9 2013, In : eLife. 2013, 2, e00426.

Research output: Contribution to journalArticle

37 Scopus citations
2012

Bhlhb5 and Prdm8 Form a Repressor Complex Involved in Neuronal Circuit Assembly

Ross, S., McCord, A., Jung, C., Atan, D., Mok, S., Hemberg, M., Kim, T. K., Salogiannis, J., Hu, L., Cohen, S., Lin, Y., Harrar, D., McInnes, R. & Greenberg, M., Jan 26 2012, In : Neuron. 73, 2, p. 292-303 12 p.

Research output: Contribution to journalArticle

61 Scopus citations

Systematic evaluation of factors influencing ChIP-seq fidelity

Chen, Y., Negre, N., Li, Q., Mieczkowska, J. O., Slattery, M., Liu, T., Zhang, Y., Kim, T. K., He, H. H., Zieba, J., Ruan, Y., Bickel, P. J., Myers, R. M., Wold, B. J., White, K. P., Lieb, J. D. & Liu, X. S., Jun 2012, In : Nature Methods. 9, 6, p. 609-614 6 p.

Research output: Contribution to journalArticle

89 Scopus citations

Transcriptional architecture and chromatin landscape of the core circadian clock in mammals

Koike, N., Yoo, S. H., Huang, H. C., Kumar, V., Lee, C., Kim, T. K. & Takahashi, J. S., Oct 19 2012, In : Science. 338, 6105, p. 349-354 6 p.

Research output: Contribution to journalArticle

634 Scopus citations
2010

Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways

Pfenning, A. R., Kim, T. K., Spotts, J. M., Hemberg, M., Su, D. & West, A. E., 2010, In : PLoS One. 5, 5, e10870.

Research output: Contribution to journalArticle

18 Scopus citations

The Angelman Syndrome Protein Ube3A Regulates Synapse Development by Ubiquitinating Arc

Greer, P. L., Hanayama, R., Bloodgood, B. L., Mardinly, A. R., Lipton, D. M., Flavell, S. W., Kim, T. K., Griffith, E. C., Waldon, Z., Maehr, R., Ploegh, H. L., Chowdhury, S., Worley, P. F., Steen, J. & Greenberg, M. E., Mar 5 2010, In : Cell. 140, 5, p. 704-716 13 p.

Research output: Contribution to journalArticle

385 Scopus citations

Widespread transcription at neuronal activity-regulated enhancers

Kim, T. K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., Markenscoff-Papadimitriou, E., Kuhl, D., Bito, H., Worley, P. F., Kreiman, G. & Greenberg, M. E., May 13 2010, In : Nature. 465, 7295, p. 182-187 6 p.

Research output: Contribution to journalArticle

1296 Scopus citations
2009

A retrograde neuronal survival response: Target-derived neurotrophins regulate MEF2D and bcl-w

Pazyra-Murphy, M. F., Hans, A., Courchesne, S. L., Karch, C., Cosker, K. E., Heerssen, H. M., Watson, F. L., Kim, T., Greenberg, M. E. & Segal, R. A., May 20 2009, In : Journal of Neuroscience. 29, 20, p. 6700-6709 10 p.

Research output: Contribution to journalArticle

55 Scopus citations

Mef2-mediated transcription of the miR379-410 cluster regulates activity-dependent dendritogenesis by fine-tuning Pumilio2 protein levels

Fiore, R., Khudayberdiev, S., Christensen, M., Siegel, G., Flavell, S. W., Kim, T. K., Greenberg, M. E. & Schratt, G., Mar 18 2009, In : EMBO Journal. 28, 6, p. 697-710 14 p.

Research output: Contribution to journalArticle

278 Scopus citations
2008

Activity-dependent regulation of inhibitory synapse development by Npas4

Lin, Y., Bloodgood, B. L., Hauser, J. L., Lapan, A. D., Koon, A. C., Kim, T. K., Hu, L. S., Malik, A. N. & Greenberg, M. E., Oct 30 2008, In : Nature. 455, 7217, p. 1198-1204 7 p.

Research output: Contribution to journalArticle

304 Scopus citations

Genome-Wide Analysis of MEF2 Transcriptional Program Reveals Synaptic Target Genes and Neuronal Activity-Dependent Polyadenylation Site Selection

Flavell, S. W., Kim, T. K., Gray, J. M., Harmin, D. A., Hemberg, M., Hong, E. J., Markenscoff-Papadimitriou, E., Bear, D. M. & Greenberg, M. E., Dec 26 2008, In : Neuron. 60, 6, p. 1022-1038 17 p.

Research output: Contribution to journalArticle

285 Scopus citations

Identifying autism loci and genes by tracing recent shared ancestry

Morrow, E. M., Yoo, S. Y., Flavell, S. W., Kim, T. K., Lin, Y., Hill, R. S., Mukaddes, N. M., Balkhy, S., Gascon, G., Hashmi, A., Al-Saad, S., Ware, J., Joseph, R. M., Greenblatt, R., Gleason, D., Ertelt, J. A., Apse, K. A., Bodell, A., Partlow, J. N., Barry, B. & 5 others, Yao, H., Markianos, K., Ferland, R. J., Greenberg, M. E. & Walsh, C. A., Jul 11 2008, In : Science. 321, 5886, p. 218-223 6 p.

Research output: Contribution to journalArticle

493 Scopus citations
2007

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T. K., Koche, R. P., Lee, W., Mendenhall, E., O'Donovan, A., Presser, A., Russ, C., Xie, X., Meissner, A., Wernig, M., Jaenisch, R., Nusbaum, C. & 2 others, Lander, E. S. & Bernstein, B. E., Aug 2 2007, In : Nature. 448, 7153, p. 553-560 8 p.

Research output: Contribution to journalArticle

2843 Scopus citations
2006

Activity-dependent regulation of MEF2 transcription factors suppresses excitatory synapse number

Flavell, S. W., Cowan, C. W., Kim, T. K., Greer, P. L., Lin, Y., Paradis, S., Griffith, E. C., Hu, L. S., Chen, C. & Greenberg, M. E., Feb 17 2006, In : Science. 311, 5763, p. 1008-1012 5 p.

Research output: Contribution to journalArticle

380 Scopus citations

START: An automated tool for serial analysis of chromatin occupancy data

Marinescu, V. D., Kohane, I. S., Kim, T. K., Harmin, D. A., Greenberg, M. E. & Riva, A., Apr 2006, In : Bioinformatics. 22, 8, p. 999-1001 3 p.

Research output: Contribution to journalArticle

5 Scopus citations
2005

PARP-1 determines specificity in a retinoid signaling pathway via direct modulation of mediator

Pavri, R., Lewis, B., Kim, T. K., Dilworth, F. J., Erdjument-Bromage, H., Tempst, P., De Murcia, G., Evans, R., Chambon, P. & Reinberg, D., Apr 1 2005, In : Molecular Cell. 18, 1, p. 83-96 14 p.

Research output: Contribution to journalArticle

174 Scopus citations
2000
59 Scopus citations

Mechanism of ATP-dependent promoter melting by transcription factor IIH

Kim, T. K., Ebright, R. H. & Reinberg, D., May 26 2000, In : Science. 288, 5470, p. 1418-1421 4 p.

Research output: Contribution to journalArticle

196 Scopus citations
1999

A protein phosphatase functions to recycle RNA polymerase II

Cho, H., Kim, T. K., Mancebo, H., Lane, W. S., Flores, O. & Reinberg, D., Jun 15 1999, In : Genes and Development. 13, 12, p. 1540-1552 13 p.

Research output: Contribution to journalArticle

161 Scopus citations
1998

The RNA polymerase II general transcription factors: Past, present, and future

Reinberg, D., Orphanides, G., Ebright, R., Akoulitchev, S., Carcamo, J., Cho, H., Cortes, P., Drapkin, R., Flores, O., Ha, I., Inostroza, J. A., Kim, S., Kim, T. K., Kumar, P., Lagrange, T., LeRoy, G., Lu, H., Ma, D. M., Maldonado, E., Merino, A. & 9 others, Mermelstein, F., Olave, I., Sheldon, M., Shiekhattar, R., Stone, N., Sun, X., Weis, L., Yeung, K. & Zawel, L., 1998, In : Cold Spring Harbor Symposia on Quantitative Biology. 63, p. 83-103 21 p.

Research output: Contribution to journalArticle

53 Scopus citations
1997

Trajectory of DNA in the RNA polymerase II transcription preinitiation complex

Kim, T. K., Lagrange, T., Wang, Y. H., Griffith, J. D., Reinberg, D. & Ebright, R. H., Nov 11 1997, In : Proceedings of the National Academy of Sciences of the United States of America. 94, 23, p. 12268-12273 6 p.

Research output: Contribution to journalArticle

88 Scopus citations
1996

High-resolution mapping of nucleoprotein complexes by site-specific protein-DNA photocrosslinking: Organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex

Lagrange, T., Kim, T. K., Orphanides, G., Ebright, Y. W., Ebricht, R. H. & Reinberg, D., Oct 1 1996, In : Proceedings of the National Academy of Sciences of the United States of America. 93, 20, p. 10620-10625 6 p.

Research output: Contribution to journalArticle

90 Scopus citations