Alexander J. Hartemink | Scholars@Duke

Alexander J. Hartemink
Professor in the Department of Computer Science

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

Current Appointments & Affiliations

Professor in the Department of Computer Science, Computer Science, Trinity College of Arts & Sciences 2013
Professor of Biology, Biology, 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
Box 90129, Durham, NC 27708-0129
amink@cs.duke.edu (919) 660-6514
ORC ID
http://www.cs.duke.edu/~amink/

Background
Education, Training, & Certifications
- Ph.D., Massachusetts Institute of Technology 2001
- M.Phil., University of Oxford (United Kingdom) 1996
- B.S., Duke University 1994
Previous Appointments & Affiliations
- 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
- Alexander F. Hehmeyer Professor of Computer Science, Computer Science, Trinity College of Arts & Sciences 2013 - 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
- JAN 10, 2022
  
  Babs Wise: Paving the Road to a Rhodes
- 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
- Faculty Early Career Development (CAREER) Program. National Science Foundation. 2004
Expertise
Subject Headings
Global Scholarship
- Expertise
  - United Kingdom (Country)
- Teaching
  - Kenya (Country)
Research
Selected Grants
- Methods to Elucidate the Dynamic Interplay of Transcriptional Regulation and Chromatin Occupancy awarded by National Institutes of Health 2021 - 2026
- Elucidating the Molecular Basis of Cellular Metal Stress by using Mass Spectrometry-Based Proteomic Methods awarded by National Institutes of Health 2022 - 2026
- IRES Track 1 IRTG Engaged in Dissecting and Reengineering the Regulatory Genome awarded by National Science Foundation 2019 - 2023
- 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 III awarded by National Institutes of Health 2016 - 2021
- 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
- missing activity
External Relationships
- Apostle, Inc.
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Luo, Kaixuan, Jianling Zhong, Alexias Safi, Linda K. Hong, Alok K. Tewari, Lingyun Song, Timothy E. Reddy, Li Ma, Gregory E. Crawford, and Alexander J. Hartemink. “Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data.” Genome Res 32, no. 6 (June 2022): 1183–98. https://doi.org/10.1101/gr.272203.120.
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  - Li, Yulong, Alexander J. Hartemink, and David M. MacAlpine. “Cell-Cycle-Dependent Chromatin Dynamics at Replication Origins.” Genes (Basel) 12, no. 12 (December 16, 2021). https://doi.org/10.3390/genes12121998.
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  - Li, Yulong, Alexander J. Hartemink, and David M. MacAlpine. “Cell cycle-dependent chromatin dynamics at replication origins,” November 18, 2021. https://doi.org/10.1101/2021.11.15.468728.
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  - Mitra, Sneha, Jianling Zhong, Trung Q. Tran, David M. MacAlpine, and Alexander J. Hartemink. “RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data.” Nucleic Acids Res 49, no. 14 (August 20, 2021): 7925–38. https://doi.org/10.1093/nar/gkab553.
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  - Tran, Trung Q., Heather K. MacAlpine, Vinay Tripuraneni, Sneha Mitra, David M. MacAlpine, and Alexander J. Hartemink. “Linking the dynamics of chromatin occupancy and transcription with predictive models.” Genome Res 31, no. 6 (June 2021): 1035–46. https://doi.org/10.1101/gr.267237.120.
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  - Tripuraneni, Vinay, Gonen Memisoglu, Heather K. MacAlpine, Trung Q. Tran, Wei Zhu, Alexander J. Hartemink, James E. Haber, and David M. MacAlpine. “Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication.” Genome Research 31, no. 5 (May 2021): 775–88. https://doi.org/10.1101/gr.271155.120.
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  - Luo, Kaixuan, Jianling Zhong, Alexias Safi, Linda K. Hong, Alok K. Tewari, Lingyun Song, Timothy E. Reddy, Li Ma, Gregory E. Crawford, and Alexander J. Hartemink. “Quantitative occupancy of myriad transcription factors from one DNase experiment enables efficient comparisons across conditions,” June 29, 2020. https://doi.org/10.1101/2020.06.28.171587.
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  - Tran, Trung Q., Heather K. MacAlpine, Vinay Tripuraneni, Sneha Mitra, David M. MacAlpine, and Alexander J. Hartemink. “Linking the dynamics of chromatin occupancy and transcription with predictive models,” June 29, 2020. https://doi.org/10.1101/2020.06.28.176545.
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  - Mitra, Sneha, Jianling Zhong, David M. MacAlpine, and Alexander J. Hartemink. “RoboCOP: Jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data,” June 4, 2020. https://doi.org/10.1101/2020.06.03.132001.
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  - Tripuraneni, Vinay, Gonen Memisoglu, Wei Zhu, Trung Tran, Alexander J. Hartemink, James E. Haber, and David M. MacAlpine. “Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication,” December 6, 2019. https://doi.org/10.1101/866673.
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  - 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.
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  - Welch, Joshua D., Alexander J. Hartemink, and Jan F. Prins. “MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics.” Genome Biol 18, no. 1 (July 24, 2017): 138. https://doi.org/10.1186/s13059-017-1269-0.
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  - Welch, Joshua D., Alexander J. Hartemink, and Jan F. Prins. “Manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics,” April 24, 2017. https://doi.org/10.1101/130336.
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  - Mayhew, Michael B., Edwin S. Iversen, and Alexander J. Hartemink. “Characterization of dependencies between growth and division in budding yeast.” J R Soc Interface 14, no. 127 (February 2017). https://doi.org/10.1098/rsif.2016.0993.
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  - 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.
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  - Welch, Joshua D., Alexander J. Hartemink, and Jan F. Prins. “SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data.” Genome Biol 17, no. 1 (May 23, 2016): 106. https://doi.org/10.1186/s13059-016-0975-3.
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  - 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.
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  - 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.
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  - 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.
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  - 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.
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  - Zhong, Jianling, Todd Wasson, and Alexander J. Hartemink. “Learning protein-DNA interaction landscapes by integrating experimental data through computational models.” Bioinformatics 30, no. 20 (October 15, 2014): 2868–74. https://doi.org/10.1093/bioinformatics/btu408.
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  - Meyer, Pablo, Geoffrey Siwo, Danny Zeevi, Eilon Sharon, Raquel Norel, Raquel DREAM6 Promoter Prediction Consortium, Eran Segal, and Gustavo Stolovitzky. “Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach.” Genome Res 23, no. 11 (November 2013): 1928–37. https://doi.org/10.1101/gr.157420.113.
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  - Mordelet, Fantine, John Horton, Alexander J. Hartemink, Barbara E. Engelhardt, and Raluca Gordân. “Stability selection for regression-based models of transcription factor-DNA binding specificity.” Bioinformatics 29, no. 13 (July 1, 2013): i117–25. https://doi.org/10.1093/bioinformatics/btt221.
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  - Guo, Xin, Allister Bernard, David A. Orlando, Steven B. Haase, and Alexander J. Hartemink. “Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program.” Proceedings of the National Academy of Sciences of the United States of America 110, no. 10 (March 2013): E968–77. https://doi.org/10.1073/pnas.1120991110.
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  - 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 human gene activation by combinations of synthetic transcription factors.” Nat Methods 10, no. 3 (March 2013): 239–42. https://doi.org/10.1038/nmeth.2361.
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  - Luo, Kaixuan, and Alexander J. Hartemink. “Using DNase digestion data to accurately identify transcription factor binding sites.” Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, January 2013, 80–91.
  - Landt, Stephen G., Georgi K. Marinov, Anshul Kundaje, Pouya Kheradpour, Florencia Pauli, Serafim Batzoglou, Bradley E. Bernstein, et al. “ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.” Genome Res 22, no. 9 (September 2012): 1813–31. https://doi.org/10.1101/gr.136184.111.
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  - Mayhew, Michael B., Xin Guo, Steven B. Haase, and Alexander J. Hartemink. “Close Encounters of the Collaborative Kind.” Computer 45, no. 3 (March 2012): 24–30. https://doi.org/10.1109/mc.2012.85.
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  - Guo, Xin, Martha L. Bulyk, and Alexander J. Hartemink. “Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors.” Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, January 2012, 104–15.
  - Meyer, Pablo, Leonidas G. Alexopoulos, Thomas Bonk, Andrea Califano, Carolyn R. Cho, Alberto de la Fuente, David de Graaf, et al. “Verification of systems biology research in the age of collaborative competition.” Nature Biotechnology 29, no. 9 (September 2011): 811–15. https://doi.org/10.1038/nbt.1968.
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  - Mayhew, Michael B., Joshua W. Robinson, Boyoun Jung, Steven B. Haase, and Alexander J. Hartemink. “A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments.” Bioinformatics (Oxford, England) 27, no. 13 (July 2011): i295–303. https://doi.org/10.1093/bioinformatics/btr244.
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  - Miller, Heather B., Timothy J. Robinson, Raluca Gordân, Alexander J. Hartemink, and Mariano A. Garcia-Blanco. “Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing.” Rna 17, no. 4 (April 2011): 665–74. https://doi.org/10.1261/rna.2462011.
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  - Robinson, J. W., and A. J. Hartemink. “Learning non-stationary dynamic bayesian networks.” Journal of Machine Learning Research 11 (December 1, 2010): 3647–80.
  - Gordân, Raluca, Leelavati Narlikar, and Alexander J. Hartemink. “Finding regulatory DNA motifs using alignment-free evolutionary conservation information.” Nucleic Acids Res 38, no. 6 (April 2010): e90. https://doi.org/10.1093/nar/gkp1166.
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  - MacAlpine, Heather K., Raluca Gordân, Sara K. Powell, Alexander J. Hartemink, and David M. MacAlpine. “Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading.” Genome Res 20, no. 2 (February 2010): 201–11. https://doi.org/10.1101/gr.097873.109.
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  - Gordân, R., L. Narlikar, and A. J. Hartemink. “Finding regulatory DNA motifs using alignment-free evolutionary conservation information.” Nucleic Acids Research 38, no. 6 (January 4, 2010). https://doi.org/10.1093/nar/gkp1166.
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  - Robinson, J. W., and A. J. Hartemink. “Non-stationary dynamic Bayesian networks.” Advances in Neural Information Processing Systems 21 Proceedings of the 2008 Conference, December 1, 2009, 1369–76.
  - Wasson, Todd, and Alexander J. Hartemink. “An ensemble model of competitive multi-factor binding of the genome.” Genome Research 19, no. 11 (November 2009): 2101–12. https://doi.org/10.1101/gr.093450.109.
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  - Gordân, Raluca, Alexander J. Hartemink, and Martha L. Bulyk. “Distinguishing direct versus indirect transcription factor-DNA interactions.” Genome Res 19, no. 11 (November 2009): 2090–2100. https://doi.org/10.1101/gr.094144.109.
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  - Guo, Xin, and Alexander J. Hartemink. “Domain-oriented edge-based alignment of protein interaction networks.” Bioinformatics (Oxford, England) 25, no. 12 (June 2009): i240–46. https://doi.org/10.1093/bioinformatics/btp202.
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  - Orlando, David A., Edwin S. Iversen, Alexander J. Hartemink, and Steven B. Haase. “A branching process model for flow cytometry and budding index measurements in cell synchrony experiments.” The Annals of Applied Statistics 3, no. 4 (January 2009): 1521–41. https://doi.org/10.1214/09-aoas264.
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  - Orlando, David A., Charles Y. Lin, Allister Bernard, Jean Y. Wang, Joshua E. S. Socolar, Edwin S. Iversen, Alexander J. Hartemink, and Steven B. Haase. “Global control of cell-cycle transcription by coupled CDK and network oscillators.” Nature 453, no. 7197 (June 2008): 944–47. https://doi.org/10.1038/nature06955.
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  - Luedi, Philippe P., Fred S. Dietrich, Jennifer R. Weidman, Jason M. Bosko, Randy L. Jirtle, and Alexander J. Hartemink. “Computational and experimental identification of novel human imprinted genes.” Genome Res 17, no. 12 (December 2007): 1723–30. https://doi.org/10.1101/gr.6584707.
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  - Narlikar, Leelavati, Raluca Gordân, and Alexander J. Hartemink. “A nucleosome-guided map of transcription factor binding sites in yeast.” Plos Comput Biol 3, no. 11 (November 2007): e215. https://doi.org/10.1371/journal.pcbi.0030215.
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  - Orlando, David A., Charles Y. Lin, Allister Bernard, Edwin S. Iversen, Alexander J. Hartemink, and Steven B. Haase. “A probabilistic model for cell cycle distributions in synchrony experiments.” Cell Cycle (Georgetown, Tex.) 6, no. 4 (February 2007): 478–88. https://doi.org/10.4161/cc.6.4.3859.
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  - Smith, V Anne, Jing Yu, Tom V. Smulders, Alexander J. Hartemink, and Erich D. Jarvis. “Computational inference of neural information flow networks.” Plos Comput Biol 2, no. 11 (November 24, 2006): e161. https://doi.org/10.1371/journal.pcbi.0020161.
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  - Narlikar, Leelavati, Raluca Gordân, Uwe Ohler, and Alexander J. Hartemink. “Informative priors based on transcription factor structural class improve de novo motif discovery.” Bioinformatics 22, no. 14 (July 15, 2006): e384–92. https://doi.org/10.1093/bioinformatics/btl251.
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  - Narlikar, Leelavati, and Alexander J. Hartemink. “Sequence features of DNA binding sites reveal structural class of associated transcription factor.” Bioinformatics (Oxford, England) 22, no. 2 (January 2006): 157–63. https://doi.org/10.1093/bioinformatics/bti731.
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  - Krishnapuram, Balaji, Lawrence Carin, Mário A. T. Figueiredo, and Alexander J. Hartemink. “Sparse multinomial logistic regression: fast algorithms and generalization bounds.” Ieee Transactions on Pattern Analysis and Machine Intelligence 27, no. 6 (June 2005): 957–68. https://doi.org/10.1109/tpami.2005.127.
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  - Luedi, Philippe P., Alexander J. Hartemink, and Randy L. Jirtle. “Genome-wide prediction of imprinted murine genes.” Genome Research 15, no. 6 (June 2005): 875–84. https://doi.org/10.1101/gr.3303505.
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  - Hartemink, Alexander J. “Reverse engineering gene regulatory networks.” Nature Biotechnology 23, no. 5 (May 2005): 554–55. https://doi.org/10.1038/nbt0505-554.
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  - Yin, Peng, and Alexander J. Hartemink. “Theoretical and practical advances in genome halving.” Bioinformatics (Oxford, England) 21, no. 7 (April 2005): 869–79. https://doi.org/10.1093/bioinformatics/bti107.
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  - Yu, Jing, V Anne Smith, Paul P. Wang, Alexander J. Hartemink, and Erich D. Jarvis. “Advances to Bayesian network inference for generating causal networks from observational biological data.” Bioinformatics 20, no. 18 (December 12, 2004): 3594–3603. https://doi.org/10.1093/bioinformatics/bth448.
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  - Krishnapuram, Balaji, Alexander J. Hartemink, Lawrence Carin, and Mário A. T. Figueiredo. “A Bayesian approach to joint feature selection and classifier design.” Ieee Transactions on Pattern Analysis and Machine Intelligence 26, no. 9 (September 2004): 1105–11. https://doi.org/10.1109/tpami.2004.55.
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  - Krishnapuram, Balaji, Lawrence Carin, and Alexander J. Hartemink. “Joint classifier and feature optimization for comprehensive cancer diagnosis using gene expression data.” Journal of Computational Biology : A Journal of Computational Molecular Cell Biology 11, no. 2–3 (January 2004): 227–42. https://doi.org/10.1089/1066527041410463.
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  - Jarvis, E. D., V. A. Smith, K. Wada, M. V. Rivas, M. McElroy, T. V. Smulders, P. Carninci, et al. “A framework for integrating the songbird brain.” J Comp Physiol a Neuroethol Sens Neural Behav Physiol 188, no. 11–12 (December 2002): 961–80. https://doi.org/10.1007/s00359-002-0358-y.
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  - Hartemink, A. J., D. K. Gifford, T. S. Jaakkola, and R. A. Young. “Bayesian methods for elucidating genetic regulatory networks.” Ieee Intelligent Systems and Their Applications 17, no. 2 (March 1, 2002): 37–43. https://doi.org/10.1109/5254.999218.
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  - Hartemink, A. J., D. K. Gifford, T. S. Jaakkola, and R. A. Young. “Bayesian Methods for Elucidating Genetic Regulatory Networks.” Ieee Intelligent Systems 17, no. 2 (January 1, 2002): 37–43. https://doi.org/10.1109/MIS.2002.999218.
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  - Smith, V Anne, Erich D. Jarvis, and Alexander J. Hartemink. “Evaluating functional network inference using simulations of complex biological systems.” Bioinformatics 18 Suppl 1 (2002): S216–24. https://doi.org/10.1093/bioinformatics/18.suppl_1.s216.
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  - Hartemink, A. J., D. K. Gifford, and J. Khodor. “Automated constraint-based nucleotide sequence selection for DNA computation.” Bio Systems 52, no. 1–3 (October 1999): 227–35. https://doi.org/10.1016/s0303-2647(99)00050-7.
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- Book Sections
  - Hartemink, Alexander J., Manolis Kellis, William Stafford Noble, and Zhiping Weng. “(Session Introduction) Epigenomics.” In Proceedings of the Pacific Symposium on Biocomputing, PSB 2013, Kohala Coast, Hawaii, USA, January 3-7, 2013, edited by Russ B. Altman, A Keith Dunker, Lawrence Hunter, Tiffany Murray, and Teri E. Klein, 65–68. World Scientific Publishing, 2013.
  - Bulyk, Martha L., Ernest Fraenkel, Alexander J. Hartemink, and Yael Mandel-Gutfreund. “(Session Introduction) Protein-nucleic acid interactions: Integrating structure, sequence, and function.” In Proceedings of the Pacific Symposium on Biocomputing, PSB 2008, Kohala Coast, Hawaii, USA, 4-8 January 2008, edited by Russ B. Altman, A Keith Dunker, Lawrence Hunter, Tiffany Murray, and Teri E. Klein, 438–40. World Scientific, 2008.
  - Bulyk, Martha L., Alexander J. Hartemink, Ernest Fraenkel, and Gary D. Stormo. “(Session Introduction) DNA-protein interactions: Integrating structure, sequence, and function.” In Proceedings of the Pacific Symposium on Biocomputing, PSB 2007, Maui, Hawaii, USA, 3-7 January 2007, edited by Russ B. Altman, A Keith Dunker, Lawrence Hunter, Tiffany Murray, and Teri E. Klein, 470–71. World Scientific, 2007.
  - Hartemink, Alexander J. “Bayesian Networks and Informative Priors: Transcriptional Regulatory Network Models.” In BAYESIAN INFERENCE FOR GENE EXPRESSION AND PROTEOMICS, 401–24, 2006.
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  - Hartemink, Alexander J., and Eran Segal. “(Session Introduction) Joint Learning from Multiple Types of Genomic Data.” In Proceedings of the 10th Pacific Symposium on Biocomputing, PSB 2005, Hawaii, USA, 4-8 January 2005, edited by Russ B. Altman, Tiffany A. Jung, Teri E. Klein, A Keith Dunker, and Lawrence Hunter. World Scientific, 2005.
  - Hartemink, Alexander J., and Eran Segal. “(Session Introduction) Joint Learning from Multiple Types of Genomic Data.” In Proceedings of the 9th Pacific Symposium on Biocomputing, PSB 2004, Hawaii, USA, 6-10 January 2004, edited by Russ B. Altman, A Keith Dunker, Lawrence Hunter, Tiffany A. Jung, and Teri E. Klein, 262–63. World Scientific, 2004.
  - Karp, Peter D., Eric P. Neumann, Alexander J. Hartemink, and Pedro Romero. “(Session Introduction) Genome, Pathway, and Interaction Bioinformatics.” In Proceedings of the 8th Pacific Symposium on Biocomputing, PSB 2003, Lihue, Hawaii, USA, January 3-7, 2003, edited by Russ B. Altman, A Keith Dunker, Lawrence Hunter, and Teri E. Klein, 101–3, 2003.
- Conference Papers
  - Mitra, Sneha, Jianling Zhong, David M. MacAlpine, and Alexander J. Hartemink. “RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy.” In Res Comput Mol Biol, 12074:136–51, 2020. https://doi.org/10.1007/978-3-030-45257-5_9.
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  - Welch, J. D., A. Hartemink, and J. F. Prins. “E pluribus unum: United states of single cells.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 10229 LNCS:400–401, 2017.
  - Zhang, Yizhe, Ricardo Henao, Lawrence Carin, Jianling Zhong, and Alexander J. Hartemink. “Learning a Hybrid Architecture for Sequence Regression and Annotation.” In Aaai, edited by Dale Schuurmans and Michael P. Wellman, 1415–21. AAAI Press, 2016.
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  - Zhong, Jianling, Todd Wasson, and Alexander J. Hartemink. “Learning Protein-DNA Interaction Landscapes by Integrating Experimental Data through Computational Models.” In Recomb, edited by Roded Sharan, 8394:433–47. Springer, 2014.
  - 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.
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  - Mayhew, M. B., and A. J. Hartemink. “Cell-cycle phenotyping with conditional random fields: A case study in Saccharomyces cerevisiae.” In Proceedings International Symposium on Biomedical Imaging, 1062–65, 2013. https://doi.org/10.1109/ISBI.2013.6556661.
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  - Gordan, Raluca, Alexander J. Hartemink, and Martha L. Bulyk. “Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions.” In Research in Computational Molecular Biology, Proceedings, edited by B. Berger, 6044:574–574. SPRINGER-VERLAG BERLIN, 2010.
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  - Gordân, Raluca, and Alexander J. Hartemink. “Using DNA duplex stability information for transcription factor binding site discovery.” In Pac Symp Biocomput, 453–64, 2008.
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  - Gordân, Raluca, Leelavati Narlikar, and Alexander J. Hartemink. “A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery.” In Recomb, edited by Martin Vingron and Limsoon Wong, 4955:98–111. Springer, 2008.
  - Bernard, Allister, David S. Vaughn, and Alexander J. Hartemink. “Reconstructing the Topology of Protein Complexes.” In Recomb, edited by Terence P. Speed and Haiyan Huang, 4453:32–46. Springer, 2007.
  - Narlikar, Leelavati, Raluca Gordân, and Alexander J. Hartemink. “Nucleosome Occupancy Information Improves de novo Motif Discovery.” In Recomb, edited by Terence P. Speed and Haiyan Huang, 4453:107–21. Springer, 2007.
  - Pratapa, Pallavi N., Edward F. Patz, and Alexander J. Hartemink. “Finding diagnostic biomarkers in proteomic spectra.” In Pac Symp Biocomput, 279–90, 2006.
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  - Bernard, Allister, and Alexander J. Hartemink. “Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data.” In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 459–70, 2005.
  - 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.
  - Liu, Q., B. Krishnapuram, P. Pratapa, X. Liao, A. Hartemink, and L. Carin. “Identification of differentially expressed proteins using MALDI-TOF mass spectra.” In Conference Record of the Asilomar Conference on Signals, Systems and Computers, 2:1323–27, 2003.
  - Krishnapuram, B., L. Carin, and A. J. Hartemink. “Joint classifier and feature optimization for cancer diagnosis using gene expression data.” In Proceedings of the Annual International Conference on Computational Molecular Biology, Recomb, 167–75, 2003. https://doi.org/10.1145/640075.640097.
    Full Text
  - Smith, V Anne, Erich D. Jarvis, and Alexander J. Hartemink. “Influence of network topology and data collection on network inference.” In Pac Symp Biocomput, 164–75, 2003.
    Open Access Copy Link to Item
  - Hartemink, Alexander J., David K. Gifford, Tommi S. Jaakkola, and Richard A. Young. “Combining location and expression data for principled discovery of genetic regulatory network models.” In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 437–49, 2002.
  - Hartemink, A. J., D. K. Gifford, T. S. Jaakkola, and R. A. Young. “Maximum likelihood estimation of optimal scaling factors for expression array normalization.” In Proceedings of Spie the International Society for Optical Engineering, 4266:132–40, 2001. https://doi.org/10.1117/12.427981.
    Full Text
  - Hartemink, A. J., D. K. Gifford, T. S. Jaakkola, and R. A. Young. “Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks.” In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 422–33, 2001. https://doi.org/10.1142/9789814447362_0042.
    Full Text
  - Hartemink, Alexander J., Tarjei S. Mikkelsen, and David K. Gifford. “Simulating biological reactions: A modular approach.” In Dna Based Computers, edited by Erik Winfree and David K. Gifford, 54:111–22. DIMACS/AMS, 1999.
  - Schechter, S., T. Parnell, and A. Hartemink. “Anonymous authentication of membership in dynamic groups.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 1648:184–95, 1999. https://doi.org/10.1007/3-540-48390-x_14.
    Full Text
  - Hartemink, Alexander J., and David K. Gifford. “Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation.” In Dna Based Computers, edited by Harvey Rubin and David Harlan Wood, 48:25–38. DIMACS/AMS, 1997.
- Datasets
  - Mitra, Sneha, David MacAlpine, Jianling Zhong, and Alexander Hartemink. “Data from: RoboCOP: Multivariate state space model integrating epigenomic accessibility data to elucidate genome-wide chromatin occupancy,” January 24, 2020. https://doi.org/10.7924/r4hx1b43s.
    Data Access
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