Alexander J. Hartemink

Professor of Biology

308 Research Drive, LSRC D239, Durham, NC 27708-0129
Campus Box: 
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


  • Ph.D., Massachusetts Institute of Technology 2001

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

  • B.S., Duke University 1994

Welch, JD, Hartemink, A, and Prins, JF. E pluribus unum: United states of single cells(Accepted)..

McDowell, IC, Barrera, A, D'Ippolito, AM, Vockley, CM, Hong, LK, Leichter, SM, Bartelt, LC, Majoros, WH, Song, L, Safi, A, Koçak, DD, Gersbach, CA, Hartemink, AJ, Crawford, GE, Engelhardt, BE, and Reddy, TE. "Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding." Genome Res 28, no. 9 (September 2018): 1272-1284. Full Text

Welch, JD, Hartemink, AJ, and Prins, JF. "MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics." Genome Biology 18, no. 1 (July 24, 2017): 138-null. Full Text

Mayhew, MB, Iversen, ES, and Hartemink, AJ. "Characterization of dependencies between growth and division in budding yeast." Journal of the Royal Society, Interface 14, no. 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, no. 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, no. 1 (May 23, 2016): 106-null. 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, no. 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, no. 2 (January 2015): 212-224. Full Text

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, no. 6215 (December 2014): 1256780-null. Full Text Open Access Copy

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, no. 6215 (December 2014): 1256846-null. Full Text Open Access Copy


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. "Epigenomics." January 1, 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.

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

Bulyk, ML, Hartemink, AJ, Fraenkel, E, and Stormo, G. "DNA-protein interactions: Integrating structure, sequence, and function." December 1, 2007.

Bulyk, ML, Hartemink, AJ, Fraenkel, E, and Stormo, GD. "Session Introduction." World Scientific, 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, A, Carin, L, and Figueiredo, MAT. "On semi-supervised classification." January 1, 2005.


Selected Grants

Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health (Mentor). 2005 to 2021

Exploring the Role of Dynamic Chromatin Occupancy in Transcriptional Regulation - Non-competing renewal III 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 2018

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