Alexander J. Hartemink | Scholars@Duke

Alexander J. Hartemink
Professor in the Department of Computer Science

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

Current Appointments & Affiliations

Professor in the Department of Computer Science, Computer Science, Trinity College of Arts & Sciences 2013
Bass Fellow, Computer Science, Trinity College of Arts & Sciences 2014

Contact Information

308 Research Drive, LSRC D239, Durham, NC 27708-0129
amink@cs.duke.edu (919) 660-6514
http://www.cs.duke.edu/~amink/

Background
Education, Training, & Certifications
- Ph.D., Massachusetts Institute of Technology 2001
- M.Phil., University of Oxford (UK) 1996
- B.S., Duke University 1994
Duke Appointment History
- Professor in the Department of Biology, Biology, Trinity College of Arts & Sciences 2013 - 2016
- Professor in the Department of Statistical Science, Statistical Science, Trinity College of Arts & Sciences 2013 - 2016
- Director of the Computational Biology and Bioinformatics Program, Institutes and Centers, School of Medicine 2012 - 2015
- Investigator in the Institute for Genome Sciences & Policy, University Institutes and Centers, Institutes and Provost's Academic Units 2008 - 2014
- Associate Professor of Computer Science, Computer Science, Trinity College of Arts & Sciences 2008 - 2013
- Associate Professor in the Department of Statistical Science, Statistical Science, Trinity College of Arts & Sciences 2010 - 2013
- Associate Professor of Biology, Biology, Trinity College of Arts & Sciences 2012 - 2013
- Assistant Professor of Computer Science, Computer Science, Trinity College of Arts & Sciences 2001 - 2008
Recognition
In the News
- FEB 22, 2016
  
  12 Duke Graduates Named Fulbright Scholars
- JAN 6, 2015
  
  Genomics Team Wins $5.9 Million Grant
- DEC 10, 2014
  
  Genes Tell Story of Birdsong and Human Speech
- MAR 24, 2014
  
  Duke Announces Reorganization of Genome Sciences
Awards & Honors
- Sloan Research Fellowship-Molecular Biology. Alfred P. Sloan Foundation. 2005
Expertise
Subject Headings
Global Scholarship
- Expertise
  - United Kingdom (Country)
- Teaching
  - Kenya (Country)
Research
Selected Grants
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- Exploring the Role of Dynamic Chromatin Occupancy in Transcriptional Regulation - Non-competing renewal I awarded by National Institutes of Health 2016 - 2020
- Decoding and Reprogramming the Corticosteroid Transcriptional Regulatory Network awarded by National Institutes of Health 2015 - 2018
- CRCNS: Neural Flow Networks in Songbirds awarded by National Institutes of Health 2005 - 2012
- Identification and Characterization of Epigenetically Labile Genes awarded by National Institutes of Health 2006 - 2010
- High-performance Computing System for Bioinformatics awarded by National Institutes of Health 2009 - 2010
- CAREER: Computational Methods for Learning Dynamic Networks of Regulation and Control awarded by National Science Foundation 2004 - 2009
Publications & Artistic Works
Selected Publications
- Books
  - Welch, JD, Hartemink, A, and Prins, JF. E pluribus unum: United states of single cells. January 1, 2017.
- Conference Papers
  - Zhong, J, Wasson, T, and Hartemink, AJ. "Learning protein-DNA interaction landscapes by integrating experimental data through computational models." January 1, 2014. 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. Link to Item
  - 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, G. "DNA-protein interactions: Integrating structure, sequence, and function." 2007. Link to Item
  - 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.
  - Hartemink, AJ, and Segal, E. "Session Introduction." World Scientific, 2004.
  - Krishnapuram, B, Williams, D, Xue, Y, Hartemink, AJ, Carin, L, and Figueiredo, MAT. "On Semi-Supervised Classification." 2004.
  - Karp, PD, Neumann, EP, Hartemink, AJ, and Romero, P. "Genome, Pathway, and Interaction Bioinformatics - Session Introduction." 2003.
  - Hartemink, AJ, Mikkelsen, TS, and Gifford, DK. "Simulating biological reactions: A modular approach." DIMACS/AMS, 1999.
  - Schechter, SE, Parnell, T, and Hartemink, AJ. "Anonymous Authentication of Membership in Dynamic Groups." Springer, 1999. Full Text
  - Hartemink, AJ, and Gifford, DK. "Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation." DIMACS/AMS, 1997.
- Journal Articles
  - 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-. 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-. 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
  - 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-. 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, no. 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, no. 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, no. 13 (July 1, 2013): i117-i125. Full Text Open Access Copy Link to Item
  - Guo, X, Bernard, A, Orlando, DA, Haase, SB, and Hartemink, AJ. "Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program." Proc Natl Acad Sci U S A 110, no. 10 (March 5, 2013): E968-E977. Full Text Link to Item
  - Perez-Pinera, P, Ousterout, DG, Brunger, JM, Farin, AM, Glass, KA, Guilak, F, Crawford, GE, Hartemink, AJ, and Gersbach, CA. "Synergistic and tunable human gene activation by combinations of synthetic transcription factors." Nat Methods 10, no. 3 (March 2013): 239-242. Full Text Link to Item
  - Hartemink, AJ, Kellis, M, Noble, WS, and Weng, Z. "Epigenomics." Pac Symp Biocomput (2013): 65-68. Link to Item
  - Luo, K, and Hartemink, AJ. "Using DNase digestion data to accurately identify transcription factor binding sites." Pac Symp Biocomput (2013): 80-91. Link to Item
  - Mayhew, MB, and Hartemink, AJ. "Cell-cycle phenotyping with conditional random fields: A case study in Saccharomyces cerevisiae." Proceedings - International Symposium on Biomedical Imaging (2013): 1062-1065. Full Text
  - Landt, SG, Marinov, GK, Kundaje, A, Kheradpour, P, Pauli, F, Batzoglou, S, Bernstein, BE, Bickel, P, Brown, JB, Cayting, P, Chen, Y, DeSalvo, G, Epstein, C, Fisher-Aylor, KI, Euskirchen, G, Gerstein, M, Gertz, J, Hartemink, AJ, Hoffman, MM, Iyer, VR, Jung, YL, Karmakar, S, Kellis, M, Kharchenko, PV, Li, Q, Liu, T, Liu, XS, Ma, L, Milosavljevic, A, Myers, RM, Park, PJ, Pazin, MJ, Perry, MD, Raha, D, Reddy, TE, Rozowsky, J, Shoresh, N, Sidow, A, Slattery, M, and Stamatoyannopoulos, JA et al. "ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia." Genome Res 22, no. 9 (September 2012): 1813-1831. Full Text Link to Item
  - Guo, X, Bulyk, ML, and Hartemink, AJ. "Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors." Pac Symp Biocomput (2012): 104-115. Link to Item
  - Mayhew, MB, Guo, X, Haase, SB, and Hartemink, AJ. "Close encounters of the collaborative kind." Computer 45, no. 3 (2012): 24-30. Full Text
  - Meyer, P, Alexopoulos, LG, Bonk, T, Califano, A, Cho, CR, de la Fuente, A, de Graaf, D, Hartemink, AJ, Hoeng, J, Ivanov, NV, Koeppl, H, Linding, R, Marbach, D, Norel, R, Peitsch, MC, Rice, JJ, Royyuru, A, Schacherer, F, Sprengel, J, Stolle, K, Vitkup, D, and Stolovitzky, G. "Verification of systems biology research in the age of collaborative competition. (Published online)" Nat Biotechnol 29, no. 9 (September 8, 2011): 811-815. Full Text Link to Item
  - Mayhew, MB, Robinson, JW, Jung, B, Haase, SB, and Hartemink, AJ. "A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments." Bioinformatics 27, no. 13 (July 1, 2011): i295-i303. Full Text Link to Item
  - Miller, HB, Robinson, TJ, Gordân, R, Hartemink, AJ, and Garcia-Blanco, MA. "Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing." RNA 17, no. 4 (April 2011): 665-674. Full Text Link to Item
  - Gordân, R, Narlikar, L, and Hartemink, AJ. "Finding regulatory DNA motifs using alignment-free evolutionary conservation information." Nucleic Acids Res 38, no. 6 (April 2010): e90-. Full Text Open Access Copy Link to Item
  - MacAlpine, HK, Gordân, R, Powell, SK, Hartemink, AJ, and MacAlpine, DM. "Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading." Genome Res 20, no. 2 (February 2010): 201-211. Full Text Link to Item
  - Gordân, R, Narlikar, L, and Hartemink, AJ. "Finding regulatory DNA motifs using alignment-free evolutionary conservation information." Nucleic Acids Research 38, no. 6 (2010): e90.1-e90.12. Full Text
  - Robinson, JW, and Hartemink, AJ. "Learning non-stationary dynamic bayesian networks." Journal of Machine Learning Research 11 (2010): 3647-3680.
  - Gordân, R, Hartemink, AJ, and Bulyk, ML. "Distinguishing direct versus indirect transcription factor-DNA interactions." Genome Res 19, no. 11 (November 2009): 2090-2100. Full Text Link to Item
  - Wasson, T, and Hartemink, AJ. "An ensemble model of competitive multi-factor binding of the genome." Genome Res 19, no. 11 (November 2009): 2101-2112. Full Text Link to Item
  - Guo, X, and Hartemink, AJ. "Domain-oriented edge-based alignment of protein interaction networks." Bioinformatics 25, no. 12 (June 15, 2009): i240-i246. Full Text Open Access Copy Link to Item
  - Orlando, DA, Iversen, ES, Hartemink, AJ, and Haase, SB. "A branching process model for flow cytometry and budding index measurements in cell synchrony experiments." Ann Appl Stat 3, no. 4 (2009): 1521-1541. Full Text Open Access Copy Link to Item
  - Robinson, JW, and Hartemink, AJ. "Non-stationary dynamic Bayesian networks." Advances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference (2009): 1369-1376.
  - Orlando, DA, Lin, CY, Bernard, A, Wang, JY, Socolar, JES, Iversen, ES, Hartemink, AJ, and Haase, SB. "Global control of cell-cycle transcription by coupled CDK and network oscillators." Nature 453, no. 7197 (June 12, 2008): 944-947. Full Text Link to Item
  - Bulyk, ML, Hartemink, AJ, Fraenkel, E, and Mandel-Gutfreund, Y. "Protein-nucleic acid interactions: Integrating structure, sequence, and function." Pacific Symposium on Biocomputing 2008, PSB 2008 (2008): 438-440.
  - Gordân, R, Narlikar, L, and Hartemink, AJ. "A fast, alignment-free, conservation-based method for transcription factor binding site discovery." Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4955 LNBI (2008): 98-111. Full Text
  - Gordân, R, and Hartemink, AJ. "Using DNA duplex stability information for transcription factor binding site discovery." Pac Symp Biocomput (2008): 453-464. Link to Item
  - Luedi, PP, Dietrich, FS, Weidman, JR, Bosko, JM, Jirtle, RL, and Hartemink, AJ. "Computational and experimental identification of novel human imprinted genes." Genome Res 17, no. 12 (December 2007): 1723-1730. Full Text Link to Item
  - Narlikar, L, Gordân, R, and Hartemink, AJ. "A nucleosome-guided map of transcription factor binding sites in yeast." PLoS Comput Biol 3, no. 11 (November 2007): e215-. Full Text Open Access Copy Link to Item
  - Orlando, DA, Lin, CY, Bernard, A, Iversen, ES, Hartemink, AJ, and Haase, SB. "A probabilistic model for cell cycle distributions in synchrony experiments." Cell Cycle 6, no. 4 (February 15, 2007): 478-488. Full Text Link to Item
  - Bernard, A, Vaughn, DS, and Hartemink, AJ. "Reconstructing the topology of protein complexes." Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4453 LNBI (2007): 32-46.
  - Narlikar, L, Gordân, R, and Hartemink, AJ. "Nucleosome occupancy information improves de novo motif discovery." Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4453 LNBI (2007): 107-121.
  - Smith, VA, Yu, J, Smulders, TV, Hartemink, AJ, and Jarvis, ED. "Computational inference of neural information flow networks." PLoS Comput Biol 2, no. 11 (November 24, 2006): e161-. Full Text Open Access Copy Link to Item
  - Narlikar, L, Gordân, R, Ohler, U, and Hartemink, AJ. "Informative priors based on transcription factor structural class improve de novo motif discovery." Bioinformatics 22, no. 14 (July 15, 2006): e384-e392. Full Text Link to Item
  - Narlikar, L, and Hartemink, AJ. "Sequence features of DNA binding sites reveal structural class of associated transcription factor." Bioinformatics 22, no. 2 (January 15, 2006): 157-163. Full Text Link to Item
  - Pratapa, PN, Patz, EF, and Hartemink, AJ. "Finding diagnostic biomarkers in proteomic spectra." Pac Symp Biocomput (2006): 279-290. Link to Item
  - Krishnapuram, B, Carin, L, Figueiredo, MAT, and Hartemink, AJ. "Sparse multinomial logistic regression: fast algorithms and generalization bounds." IEEE Trans Pattern Anal Mach Intell 27, no. 6 (June 2005): 957-968. Full Text Link to Item
  - Luedi, PP, Hartemink, AJ, and Jirtle, RL. "Genome-wide prediction of imprinted murine genes." Genome Res 15, no. 6 (June 2005): 875-884. Full Text Link to Item
  - Hartemink, AJ. "Reverse engineering gene regulatory networks." Nat Biotechnol 23, no. 5 (May 2005): 554-555. Full Text Link to Item
  - Yin, P, and Hartemink, AJ. "Theoretical and practical advances in genome halving." Bioinformatics 21, no. 7 (April 1, 2005): 869-879. Full Text Link to Item
  - Bernard, A, and Hartemink, AJ. "Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data." Pac Symp Biocomput (2005): 459-470. Link to Item
  - Hartemink, AJ, and Segal, E. "Joint learning from multiple types of genomic data." Pac Symp Biocomput (2005): 445-446. Link to Item
  - Yu, J, Smith, VA, Wang, PP, Hartemink, AJ, and Jarvis, ED. "Advances to Bayesian network inference for generating causal networks from observational biological data." Bioinformatics 20, no. 18 (December 12, 2004): 3594-3603. Full Text Open Access Copy Link to Item
  - Krishnapuram, B, Hartemink, AJ, Carin, L, and Figueiredo, MAT. "A Bayesian approach to joint feature selection and classifier design." IEEE Trans Pattern Anal Mach Intell 26, no. 9 (September 2004): 1105-1111. Full Text Link to Item
  - Krishnapuram, B, Carin, L, and Hartemink, AJ. "Joint classifier and feature optimization for comprehensive cancer diagnosis using gene expression data." J Comput Biol 11, no. 2-3 (2004): 227-242. Full Text Link to Item
  - Krishnapuram, B, Carin, L, and Hartemink, AJ. "Joint classifier and feature optimization for cancer diagnosis using gene expression data." Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB (2003): 167-175.
  - Liu, Q, Krishnapuram, B, Pratapa, P, Liao, X, Hartemink, A, and Carin, L. "Identification of differentially expressed proteins using MALDI-TOF mass spectra." Conference Record of the Asilomar Conference on Signals, Systems and Computers 2 (2003): 1323-1327.
  - Smith, VA, Jarvis, ED, and Hartemink, AJ. "Influence of network topology and data collection on network inference." Pac Symp Biocomput (2003): 164-175. Open Access Copy Link to Item
  - Jarvis, ED, Smith, VA, Wada, K, Rivas, MV, McElroy, M, Smulders, TV, Carninci, P, Hayashizaki, Y, Dietrich, F, Wu, X, McConnell, P, Yu, J, Wang, PP, Hartemink, AJ, and Lin, S. "A framework for integrating the songbird brain." J Comp Physiol A Neuroethol Sens Neural Behav Physiol 188, no. 11-12 (December 2002): 961-980. (Review) Full Text Open Access Copy Link to Item
  - Hartemink, AJ, Gifford, DK, Jaakkola, TS, and Young, RA. "Bayesian methods for elucidating genetic regulatory networks." IEEE Intelligent Systems and Their Applications 17, no. 2 (2002): 37-43. Full Text
  - Hartemink, AJ, Gifford, DK, Jaakkola, TS, and Young, RA. "Combining location and expression data for principled discovery of genetic regulatory network models." Pac Symp Biocomput (2002): 437-449. Link to Item
  - Hartemink, AJ, Gifford, DK, Jaakkola, TS, and Young, RA. "Bayesian Methods for Elucidating Genetic Regulatory Networks." IEEE Intelligent Systems 17 (2002): 37-43. Full Text
  - Smith, VA, Jarvis, ED, and Hartemink, AJ. "Evaluating functional network inference using simulations of complex biological systems." Bioinformatics 18 Suppl 1 (2002): S216-S224. Open Access Copy Link to Item
  - Hartemink, AJ, Gifford, DK, Jaakkola, TS, and Young, RA. "Maximum likelihood estimation of optimal scaling factors for expression array normalization." Proceedings of SPIE - The International Society for Optical Engineering 4266 (2001): 132-140. Full Text
  - Hartemink, AJ, Gifford, DK, Jaakkola, TS, and Young, RA. "Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks." Pac Symp Biocomput (2001): 422-433. Link to Item
  - Hartemink, AJ, Gifford, DK, and Khodor, J. "Automated constraint-based nucleotide sequence selection for DNA computation." Biosystems 52, no. 1-3 (October 1999): 227-235. Link to Item
Teaching & Mentoring
Recent Courses

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Education, Training, & Certifications

Duke Appointment History

In the News

Awards & Honors

Subject Headings

Global Scholarship

Expertise

Teaching

Selected Grants

Selected Publications

Books

Conference Papers

Journal Articles

Recent Courses