Alexander J. Hartemink

Professor of Biology

Office: 
308 Research Drive, LSRC D239, Durham, NC 27708-0129
Campus Box: 
Box 90129, Durham, NC 27708-0129
Phone: 
(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

  • Ph.D., Massachusetts Institute of Technology 2001

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

  • B.S., Duke University 1994

Welch, J. D., A. Hartemink, and J. F. Prins. E pluribus unum: United states of single cells. Vol. 10229 LNCS, 2017.

McDowell, Ian C., Alejandro Barrera, Anthony M. D’Ippolito, Christopher M. Vockley, Linda K. Hong, Sarah M. Leichter, Luke C. Bartelt, et al. “Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.Genome Res 28, no. 9 (September 2018): 1272–84. https://doi.org/10.1101/gr.233346.117. Full Text

Welch, Joshua D., Alexander J. Hartemink, and Jan F. Prins. “MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics.Genome Biology 18, no. 1 (July 24, 2017): 138. https://doi.org/10.1186/s13059-017-1269-0. Full Text

Mayhew, Michael B., Edwin S. Iversen, and Alexander J. Hartemink. “Characterization of dependencies between growth and division in budding yeast.Journal of the Royal Society, Interface 14, no. 127 (February 2017). https://doi.org/10.1098/rsif.2016.0993. Full Text

Sparks, Erin E., Colleen Drapek, Allison Gaudinier, Song Li, Mitra Ansariola, Ning Shen, Jessica H. Hennacy, et al. “Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.Dev Cell 39, no. 5 (December 5, 2016): 585–96. https://doi.org/10.1016/j.devcel.2016.09.031. Full Text

Welch, Joshua D., Alexander J. Hartemink, and Jan F. Prins. “SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data.Genome Biology 17, no. 1 (May 23, 2016): 106. https://doi.org/10.1186/s13059-016-0975-3. Full Text Open Access Copy

Zhong, Jianling, Kaixuan Luo, Peter S. Winter, Gregory E. Crawford, Edwin S. Iversen, and Alexander J. Hartemink. “Mapping nucleosome positions using DNase-seq.Genome Res 26, no. 3 (March 2016): 351–64. https://doi.org/10.1101/gr.195602.115. Full Text

Zhang, Y., R. Henao, L. Carin, J. Zhong, and A. J. Hartemink. “Learning a hybrid architecture for sequence regression and annotation.” 30th Aaai Conference on Artificial Intelligence, Aaai 2016, January 1, 2016, 1415–21. Open Access Copy

Belsky, Jason A., Heather K. MacAlpine, Yoav Lubelsky, Alexander J. Hartemink, and David M. MacAlpine. “Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly.Genes Dev 29, no. 2 (January 15, 2015): 212–24. https://doi.org/10.1101/gad.247924.114. Full Text

Pfenning, Andreas R., Erina Hara, Osceola Whitney, Miriam V. Rivas, Rui Wang, Petra L. Roulhac, Jason T. Howard, et al. “Convergent transcriptional specializations in the brains of humans and song-learning birds.Science 346, no. 6215 (December 12, 2014): 1256846. https://doi.org/10.1126/science.1256846. Full Text Open Access Copy

Whitney, Osceola, Andreas R. Pfenning, Jason T. Howard, Charles A. Blatti, Fang Liu, James M. Ward, Rui Wang, et al. “Core and region-enriched networks of behaviorally regulated genes and the singing genome.Science 346, no. 6215 (December 12, 2014): 1256780. https://doi.org/10.1126/science.1256780. Full Text Open Access Copy

Pages

Zhong, J., T. Wasson, and A. J. Hartemink. “Learning protein-DNA interaction landscapes by integrating experimental data through computational models.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 8394 LNBI:433–47, 2014. https://doi.org/10.1007/978-3-319-05269-4_34. Full Text

Perez-Pinera, Pablo, David G. Ousterout, Jonathan M. Brunger, Alicia M. Farin, Katherine A. Glass, Farshid Guilak, Gregory E. Crawford, Alexander J. Hartemink, and Charles A. Gersbach. “Synergistic and Tunable Gene Activation by Combinations of Synthetic Transcription Factors.” In Molecular Therapy, 21:S93–S93. NATURE PUBLISHING GROUP, 2013.

Hartemink, A. J., M. Kellis, W. S. Noble, and Z. Weng. “Epigenomics.” In Pacific Symposium on Biocomputing, 2013.

Hartemink, Alexander J., Manolis Kellis, William Stafford Noble, and Zhiping Weng. “Session Introduction.” In Pacific Symposium on Biocomputing, edited by Russ B. Altman, A Keith Dunker, Lawrence Hunter, Tiffany Murray, and Teri E. Klein, 65–68. World Scientific Publishing, 2013.

Gordân, Raluca, Alexander J. Hartemink, and Martha L. Bulyk. “Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions.” In Recomb, edited by Bonnie Berger, 6044:574–574. Springer, 2010.

Bulyk, Martha L., Ernest Fraenkel, Alexander J. Hartemink, and Yael Mandel-Gutfreund. “Session Introduction.” In Pacific Symposium on Biocomputing, edited by Russ B. Altman, A Keith Dunker, Lawrence Hunter, Tiffany Murray, and Teri E. Klein, 438–40. World Scientific, 2008.

Bulyk, M. L., A. J. Hartemink, E. Fraenkel, and G. Stormo. “DNA-protein interactions: Integrating structure, sequence, and function.” In Pacific Symposium on Biocomputing 2007, Psb 2007, 470–71, 2007.

Bulyk, Martha L., Alexander J. Hartemink, Ernest Fraenkel, and Gary D. Stormo. “Session Introduction.” In Pacific Symposium on Biocomputing, edited by Russ B. Altman, A Keith Dunker, Lawrence Hunter, Tiffany Murray, and Teri E. Klein, 470–71. World Scientific, 2007.

Krishnapuram, B., D. Williams, Y. Xue, A. Hartemink, L. Carin, and M. A. T. Figueiredo. “On semi-supervised classification.” In Advances in Neural Information Processing Systems, 2005.

Hartemink, Alexander J., and Eran Segal. “Session Introduction: Joint Learning from Multiple Types of Genomic Data.” In Pacific Symposium on Biocomputing, edited by Russ B. Altman, Tiffany A. Jung, Teri E. Klein, A Keith Dunker, and Lawrence Hunter. World Scientific, 2005.

Pages

Selected Grants

IRES Track 1 IRTG Engaged in Dissecting and Reengineering the Regulatory Genome awarded by National Science Foundation (Mentor). 2019 to 2022

Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health (Mentor). 2005 to 2020

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