Charles Danko
Assistant Professor
Charles Danko




Department of Biomedical Sciences
Baker Institute for Animal Health
Cornell University
235 Hungerford Hill Road
Ithaca, NY  14853


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Charles Danko received a B.S. degree in Engineering from Johns Hopkins University in 2003 and a Ph.D. degree from the Department of Pharmacology, SUNY Upstate Medical University in 2009.  From 2009-2014, he was a Postdoctoral Fellow in the Department of Biological Statistics and Computation Biology at Cornell University, jointly supervised by Dr. Adam Siepel and Dr. W. Lee Kraus.  In July 2014, he was appointed as an Assistant Professor in the Department of Biomedical Sciences, Baker Institute for Animal Science at Cornell University.

Research Description

We study how patterns of gene expression are encoded in mammalian DNA sequences, and how these ‘regulatory codes’ contribute to evolution, development, and disease. Our specialty is developing statistics and machine-learning approaches to analyze ‘functional genomic’ sequencing data, prepared using DNase-I-seq, PRO-seq, RNA-seq, and related assays. Our tools borrow a wide variety of ideas from the fields of statistics and machine-learning, including recent uses of hidden Markov models, support vector machines, and artificial neural networks.


Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, and Siepel A. (2014) Accurate identification of active transcriptional regulatory elements from global run-on and sequencing data. Submitted. Preprint: bioRxiv.

Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT. (2014) Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nature Genetics 46, 1311-1320.

Luo X, Chae M, Krishnakumar R, Danko CG, Kraus WL. (2014) Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFalpha signaling revealed by integrated genomic analyses. BMC Genomics 15, 155.

Oxford EM, Danko CG, Fox PR, Kornreich BG, Moïse NS. (2014) Change in ß-catenin localization suggests involvement of the canonical Wnt pathway in boxer dogs with arrhythmogenic right ventricular cardiomyopathy.  J. Vet. Internal Med. 28, 92-101.

Hah N, Murakami S, Nagari A, Danko CG, Kraus WL. (2013) Enhancer transcripts mark active estrogen receptor binding sites.  Genome Research 23, 1210-1223.

Zeng L, Sang Chul C, Danko CG, Siepel A, Stanhope MJ, Burne RA. (2013) Gene regulation by CcpA and catabolite repression explored by RNA-seq in Streptococcus mutans.  PLoS ONE 8(3), e60465. Doi: 10.1371/journal.pone.0060465.

Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL. (2013) Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells.  Molec. Cell 50, 212-222.

Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. (2011) Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43, 1031-1034.

Oxford EM, Danko CG, Kornreich BG, Maass K, Hemsley SA, Raskolnikov D, Fox PR, Delmar M, Moïse NS. (2011) Ultrastructural changes in cardiac myocytes from Boxer dogs with arrhythmogenic right ventricular cardiomyopathy.  J. Vet. Cardiology 13, 101-113.

Hah N*, Danko CG*, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. (2011 )A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 145, 622-634.

Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM. (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature 463, 943-947.

Danko CG, Pertsov AM. (2009) Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease. BMC Medical Genomics 2, 31.

Danko CG, McIlvain VA, Qin M, Knox BE, Pertsov AM. (2007) Bioinformatic identification of novel putative photoreceptor specific cis-elements. BMC Bioinformatics 8, 407.

Jarrar MH, Danko CG, Reddy S, Lee YJ, Bibat G, Kaufmann WE. (2003) MeCP2 expression in human cerebral cortex and lymphoid cells: immunochemical characterization of a novel higher-molecular-weight form. J. Child Neurology 18, 675-682.