CS Faculty Photo

Professor of Computer Science, Professor of Biology, Bass Fellow, Faculty Director of the Duke University Office of Undergraduate Scholars and Fellows

Faculty Area:
Artificial Intelligence
amink at cs.duke.edu
(919) 660-6514
Web page:

Ph.D., Electrical Engineering and Computer Science, MIT, 2001
S.M., Electrical Engineering and Computer Science, MIT, 1997
M.Phil., Economics, Oxford University, 1996
B.S., Mathematics, Duke University, 1994
B.S., Physics, Duke University, 1994
A.B., Economics, Duke University, 1994

Honors & Awards

DARPA Computer Science Study Panel, 2008; David and Janet Vaughn Brooks Distinguished Teaching Award, 2007;Alfred P. Sloan Fellowship, 2004; NSF Faculty Early Career Development Award (CAREER), 2004; ORAU Ralph E. Powe Junior Faculty Award, 2002; Merck/MIT Graduate Fellowship in Informatics, 2000; Rhodes Scholarship, 1994; NSF Graduate Research Fellowship, 1994; Julia Dale Prize for Mathematics, 1994; Karl Menger Award for Mathematics, 1993; Barry M. Goldwater Memorial Scholarship, 1992; Presidential Scholarship (White House Commission), 1990; Angier B. Duke Scholarship, 1990; Kalin Award for Mathematics, 1990.


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

Selected Publications
  • J Zhong, K Luo, P Winter, G Crawford, E Iversen, & A Hartemink (2016) “Mapping nucleosome positions using DNase-seq.” Genome Research, 26, March 2016, pp. 351–364.
  • J Belsky, H MacAlpine, Y Lubelsky, A Hartemink, & D MacAlpine (2015) “Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly.” Genes and Development, 29, 15 January 2015. pp. 212–224.
  • J Zhong, T Wasson, & A Hartemink (2014) “Learning protein–DNA interaction landscapes by integrating experimental data through computational models.” Research in Computational Molecular Biology 2014 (RECOMB14). Bioinformatics, 30, 15 October 2014. pp. 2868–2874.
  • A Pfenning, E Hara, …, A Hartemink, & E Jarvis (2014) “Convergent transcriptional specializations in the brains of humans and song-learning birds.” Science, 346, 12 December 2014. pp. 1256846-1–13.
  • X Guo, A Bernard, D Orlando, S Haase, & A Hartemink (2013) “Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program.” PNAS, 110, Mar 2013. E968–E977.
  • T Wasson & A Hartemink (2009) “An ensemble model of competitive multi-factor binding of the genome.” Genome Research, 19, November 2009. pp. 2101–2112.
  • D Orlando, C Lin, A Bernard, J Wang, J Socolar, E Iversen, A Hartemink, & S Haase (2008) “Global control of cell-cycle transcription by coupled CDK and network oscillators.” Nature, 453, 12 Jun 2008. 944–947.
Extended List of Publications

Publications by Alexander J. Hartemink