Alexander J. Hartemink


Professor in the Department of Computer Science

Computational biology, machine learning, Bayesian statistics, transcriptional regulation, genomics and epigenomics, graphical models, Bayesian networks, hidden Markov models, systems biology, computational neurobiology, classification, feature selection

Appointments and Affiliations

  • Professor in the Department of Computer Science
  • Professor of Biology
  • Bass Fellow

Contact Information


  • Ph.D. Massachusetts Institute of Technology, 2001
  • M.Phil. University of Oxford (United Kingdom), 1996
  • B.S. Duke University, 1994

Awards, Honors, and Distinctions

  • Sloan Research Fellowship-Molecular Biology. Alfred P. Sloan Foundation. 2005
  • Faculty Early Career Development (CAREER) Program. National Science Foundation. 2004

Courses Taught

  • COMPSCI 260: Introduction to Computational Genomics
  • COMPSCI 391: Independent Study
  • COMPSCI 393: Research Independent Study
  • COMPSCI 394: Research Independent Study
  • ETHICS 89S: Special Topic: First-Year Seminar in Ethics
  • ETHICS 291: Independent Study

In the News

Representative Publications

  • Luo, K; Zhong, J; Safi, A; Hong, LK; Tewari, AK; Song, L; Reddy, TE; Ma, L; Crawford, GE; Hartemink, AJ, Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data., Genome Res, vol 32 no. 6 (2022), pp. 1183-1198 [10.1101/gr.272203.120] [abs].
  • Li, Y; Hartemink, AJ; MacAlpine, DM, Cell-Cycle-Dependent Chromatin Dynamics at Replication Origins., Genes, vol 12 no. 12 (2021) [10.3390/genes12121998] [abs].
  • Li, Y; Hartemink, AJ; MacAlpine, DM, Cell cycle-dependent chromatin dynamics at replication origins (2021) [10.1101/2021.11.15.468728] [abs].
  • Mitra, S; Zhong, J; Tran, TQ; MacAlpine, DM; Hartemink, AJ, RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data., Nucleic Acids Res, vol 49 no. 14 (2021), pp. 7925-7938 [10.1093/nar/gkab553] [abs].
  • Tran, TQ; MacAlpine, HK; Tripuraneni, V; Mitra, S; MacAlpine, DM; Hartemink, AJ, Linking the dynamics of chromatin occupancy and transcription with predictive models., Genome Res, vol 31 no. 6 (2021), pp. 1035-1046 [10.1101/gr.267237.120] [abs].