Charles Danko, PhD

Charles Danko

Baker Institute for Animal Health

Department of Biomedical Sciences

Associate Professor in Life Science and Technology

Baker Institute for Animal Health

Baker Institute for Animal Health
235 Hungerford Hill Road
Ithaca, NY 14853-6401

Department of Biomedical Sciences
Cornell University College of Veterinary Medicine
Baker, Box 53

Ithaca, NY 14853

Office: 607-256-5620

Research Interest

How do cells read and interpret DNA to regulate life?

Dr. Charles Danko is interested in how DNA, the basic blueprints for all living things, is interpreted by cells to produce living, breathing organisms. He also explores how diseases like cancer change these interpretations and impact health.

  • Understanding how evolution determines human and animal differences. The genes of humans, chimps, rhesus macaques, mice, and rats aren’t all that different, considering how diverse these creatures are. Danko and his collaborators are studying the roles of “gene enhancers” in evolution, small parts of the genome that can ramp-up or -down the number of times a gene is transcribed into RNA and ultimately translated into the proteins that make up the functional differences between the animals.
  • How cancer cells use genes differently. Glioblastoma cancer cells make up many serious brain tumors. To determine how to specifically target those cancers Danko and his team have studied the ways these cells turn their genetic instructions into action, by comparison with normal, healthy cells. They have identified the several proteins called “transcription factors” that drive the out-of-control growth of cancer cells, information that can be used to design cancer therapies specific to each type of cell and its associated cancers.


  • Postdoctoral, Genomics/Bioinformatics , Cornell University, 2009
  • PhD, Bioinformatics, SUNY Upstate Medical University, 2009
  • BS, Biomedical Engineering, Johns Hopkins University, 2003

Biography/Professional Experience

  • 2002–2003: Research Assistant. Kennedy Krieger Institute, Johns Hopkins, Baltimore, MD. Dr. Walter Kaufmann, Advisor
  • 2003–2008: Graduate Student. Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY. Dr. Arkady Pertsov, Advisor
  • 2007–2008: Software Developer. SUNY Microarray Core Facility, Syracuse, NY
  • 2009–2014: Postdoctoral Fellow. Department of Biological Statistics & Computational Biology, Cornell University, Ithaca, NY. Dr. Adam Siepel; Dr. Lee Kraus, Joint Advisors
  • 2014–2021: Assistant Professor. Baker Institute for Animal Health/Department of Biomedical Sciences, Cornell University, Ithaca, NY
  • 2021–Present: Associate Professor. Baker Institute for Animal Health/Department of Biomedical Sciences, Cornell University, Ithaca, NY

Selected Publications

Links and abstracts for all of Dr. Danko's publications can be found at NCBI.

  1. Danko, CG; Wang, Z; Rice, EJ; Chu, T; Martins, AL; Tait Wojno, ED; Lis, JT; Kraus, LW; Siepel, A. (2016). Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells. bioR×iv, doi: 10.1101/083212 
  2. Wang, Z; Martins, AL; Danko, CG. (2016). RTFBSDB: an integrated framework for transcription factor binding site analysisBioinformatics, 32(19), 3024-3026.
  3. Andersson, R; Sandelin, A; Danko, CG. (2015). A unified architecture of transcriptional regulatory elementsCellPress, 31(8), 426-433.
  4. Danko, CG; Hyland, SL; Core, LJ; Martins, AL; Waters, CT; Lee, HW; Cheung, VG; Kraus, WL; Lis, JT; Siepel, A. (2015). Identification of active transcriptional regulatory elements with GRO-seqNature Methods, 12(5), 433-438.
  5. Core, LJ; Martins, AL; Danko, CG; Waters, C; Siepel, A; Lis, JT. (2014). Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancersNature Genetics, 46(12), 1311–1320. 
  6. 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 CellsMolecular Cell, 50(2), 12-222. 
  7. Hah, N; Danko, CG; Core, L; Waterfall, JJ; Siepel, A; Lis, JT; Kraus, L. (2011). A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer CellsCell, 145(4), 622-34.

Awards and Honors

  • 1999 Bausch & Lomb Honorary Science Award. Queen Anne School
  • 2008 Professional and Public Service Award. SUNY Upstate Medical University
  • 2009 Postdoctoral Fellowship. Competitive T32 in Reproductive Genomics
  • 2010 Postdoctoral Fellowship. Biological Informatics, awarded by PhRMA Foundation
  • 2012 Best Poster. Ranked 1 of 30, Reproductive Genomics Retreat Poster Session

Professional/Academic Affiliations

  • 2006–08 Student Representative. Judiciary and Ethical Committee, SUNY Upstate Medical University
  • 2008 Programmer. GCO2PLINK, Converts Affymetrix GCO file into PLINK format
  • 2010 Instructor. Cornell Short Read Sequencing Workshop
  • 2009– Reviewer. For BMC Genomics and PLoS Computational Biology