Alexander J. Hartemink

Professor in the Department of Computer Science

External address: 
308 Research Drive, LSRC D239, Durham, NC 27708-0129
Internal office address: 
Box 90129, Durham, NC 27708-0129
(919) 660-6514


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

Education & Training

  • Ph.D., Massachusetts Institute of Technology 2001

  • M.Phil., University of Oxford (UK) 1996

  • B.S., Duke University 1994

Exploring the Role of Dynamic Chromatin Occupancy in Transcriptional Regulation - Non-competing renewal I awarded by National Institutes of Health (Principal Investigator). 2016 to 2020

Decoding and Reprogramming the Corticosteroid Transcriptional Regulatory Network awarded by National Institutes of Health (Investigator). 2015 to 2017

Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health (Principal Investigator). 2005 to 2016

CRCNS: Neural Flow Networks in Songbirds awarded by National Institutes of Health (Principal Investigator). 2005 to 2012

Identification and Characterization of Epigenetically Labile Genes awarded by National Institutes of Health (Co Investigator). 2006 to 2010

High-performance Computing System for Bioinformatics awarded by National Institutes of Health (Major User). 2009 to 2010

CAREER: Computational Methods for Learning Dynamic Networks of Regulation and Control awarded by National Science Foundation (Principal Investigator). 2004 to 2009

Mayhew, MB, Iversen, ES, and Hartemink, AJ. "Characterization of dependencies between growth and division in budding yeast." Journal of the Royal Society, Interface 14.127 (February 2017). Full Text

Sparks, EE, Drapek, C, Gaudinier, A, Li, S, Ansariola, M, Shen, N, Hennacy, JH, Zhang, J, Turco, G, Petricka, JJ, Foret, J, Hartemink, AJ, Gordân, R, Megraw, M, Brady, SM, and Benfey, PN. "Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors." Developmental cell 39.5 (December 2016): 585-596. Full Text

Welch, JD, Hartemink, AJ, and Prins, JF. "SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data." Genome biology 17.1 (May 23, 2016): 106-. Full Text Open Access Copy

Zhong, J, Luo, K, Winter, PS, Crawford, GE, Iversen, ES, and Hartemink, AJ. "Mapping nucleosome positions using DNase-seq." Genome research 26.3 (March 2016): 351-364. Full Text

Zhang, Y, Henao, R, Carin, L, Zhong, J, and Hartemink, AJ. "Learning a hybrid architecture for sequence regression and annotation." 30th AAAI Conference on Artificial Intelligence, AAAI 2016 (January 1, 2016): 1415-1421. Open Access Copy

Belsky, JA, MacAlpine, HK, Lubelsky, Y, Hartemink, AJ, and MacAlpine, DM. "Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly." Genes & development 29.2 (January 2015): 212-224. Full Text

Pfenning, AR, Hara, E, Whitney, O, Rivas, MV, Wang, R, Roulhac, PL, Howard, JT, Wirthlin, M, Lovell, PV, Ganapathy, G, Mouncastle, J, Moseley, MA, Thompson, JW, Soderblom, EJ, Iriki, A, Kato, M, Gilbert, MTP, Zhang, G, Bakken, T, Bongaarts, A, Bernard, A, Lein, E, Mello, CV, Hartemink, AJ, and Jarvis, ED. "Convergent transcriptional specializations in the brains of humans and song-learning birds." Science (New York, N.Y.) 346.6215 (December 2014): 1256846-. Full Text Open Access Copy

Whitney, O, Pfenning, AR, Howard, JT, Blatti, CA, Liu, F, Ward, JM, Wang, R, Audet, J-N, Kellis, M, Mukherjee, S, Sinha, S, Hartemink, AJ, West, AE, and Jarvis, ED. "Core and region-enriched networks of behaviorally regulated genes and the singing genome." Science (New York, N.Y.) 346.6215 (December 2014): 1256780-. Full Text Open Access Copy

Zhong, J, Wasson, T, and Hartemink, AJ. "Learning protein-DNA interaction landscapes by integrating experimental data through computational models." Bioinformatics (Oxford, England) 30.20 (October 2014): 2868-2874. Full Text

Mordelet, F, Horton, J, Hartemink, AJ, Engelhardt, BE, and Gordân, R. "Stability selection for regression-based models of transcription factor-DNA binding specificity." Bioinformatics 29.13 (July 1, 2013): i117-i125. Full Text


Perez-Pinera, P, Ousterout, DG, Brunger, JM, Farin, AM, Glass, KA, Guilak, F, Crawford, GE, Hartemink, AJ, and Gersbach, CA. "Synergistic and Tunable Gene Activation by Combinations of Synthetic Transcription Factors." June 2013.

Hartemink, AJ, Kellis, M, Noble, WS, and Weng, Z. "Session Introduction." World Scientific Publishing, 2013.

Gordân, R, Hartemink, AJ, and Bulyk, ML. "Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions." Springer, 2010. Full Text

Bulyk, ML, Fraenkel, E, Hartemink, AJ, and Mandel-Gutfreund, Y. "Session Introduction." World Scientific, 2008.

Bulyk, ML, Hartemink, AJ, Fraenkel, E, and Stormo, GD. "Session Introduction." World Scientific, 2007.

Bulyk, ML, Hartemink, AJ, Fraenkel, E, and Stormo, G. "DNA-protein interactions: Integrating structure, sequence, and function." 2007.

Hartemink, AJ, and Segal, E. "Session Introduction: Joint Learning from Multiple Types of Genomic Data." World Scientific, 2005.

Krishnapuram, B, Williams, D, Xue, Y, Hartemink, AJ, Carin, L, and Figueiredo, MAT. "On Semi-Supervised Classification." 2004.

Hartemink, AJ, and Segal, E. "Session Introduction." World Scientific, 2004.