CS Faculty Photo

Professor of Computer Science, Professor of Biology, Bass Fellow, Faculty Director of the Office of University Scholars and Fellows, Center for Genomic and Computational Biology, Center for Applied Genomic Technologies

Faculty Area:
Computational biology, machine learning, and artificial intelligence
Email:
amink at cs.duke.edu
Office:
D239 LSRC
Phone:
(919) 660-6514
Web page:
http://www.cs.duke.edu/~amink
Education

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

Research

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

Selected Publications
  • McDowell, I., Barrera, A., ..., Hartemink, A., Crawford, G., Engelhardt, B., & Reddy, T. (2018) “Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.” Genome Research, 28, September 2018. pp. 1272–1284.
  • Welch, J., Hartemink, A., & Prins, J. (2017) “MATCHER: Manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics.” Genome Biology, 18, 24 July 2017. 138 (pp. 1–19).
  • Mayhew, M., Iversen, E., & Hartemink, A. (2017) “Characterization of dependencies between growth and division in budding yeast.” Journal of the Royal Society Interface, 14, February 2017. 20160993 (pp. 1–12).
  • Welch, J., Hartemink, A., & Prins, J. (2016) “SLICER: Inferring branched, nonlinear cellular trajectories from single cell RNA-seq data.” Genome Biology, 17, 23 May 2016. 106 (pp. 1–15).
  • Zhong, J., Luo, K., Winter, P., Crawford, G., Iversen, E., & Hartemink, A. (2016) “Mapping nucleosome positions using DNase-seq.” Genome Research, 26, March 2016. pp. 351–364.
  • Belsky, J., MacAlpine, H., Lubelsky, Y., Hartemink, A., & MacAlpine, D. (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.
  • Pfenning, A., Hara, E., ..., Hartemink, A., & Jarvis, E. (2014) “Convergent transcriptional specializations in the brains of humans and song-learning birds.” Science, 346, 12 December 2014. pp. 1256846-1–13.
  • Guo, X., Bernard, A., Orlando, D., Haase, S., & Hartemink, A. (2013) “Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program.” PNAS, 110, 5 March 2013. pp. E968–E977.
  • Wasson, T. & Hartemink, A. (2009) “An ensemble model of competitive multi-factor binding of the genome.”Genome Research, 19, November 2009. pp. 2101–2112.
  • Orlando, D., Lin, C., Bernard, A., Wang, J., Socolar, J., Iversen, E., Hartemink, A., & Haase, S. (2008) “Global control of cell-cycle transcription by coupled CDK and network oscillators.” Nature, 453, 12 June 2008. pp. 944–947.
Extended List of Publications

Publications by Alexander Hartemink