Publications
- Mitra, S., Malik, R., Wong, W., Rahman, A., Hartemink, A., Pritykin, Y., Dey, K., & Leslie, C. (2023)
“Single-cell multiome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis.”
Nature Genetics, 56, April 2024.
pp. 627–636.
Online Access.
- Chen, B., MacAlpine, H., Hartemink, A., & MacAlpine, D. (2023)
“Spatiotemporal kinetics of CAF-1–dependent chromatin maturation ensures transcription fidelity during S-phase.”
Genome Research, 33, December 2023.
pp. 2108–2118.
[Supp. Info.]
- Luo, K., Zhong, J., Safi, A., Hong, L., Tewari, A., Song, L., Reddy, T., Ma, L., Crawford, G., & Hartemink, A. (2022)
“Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data.”
Genome Research, 32, June 2022.
pp. 1183–1198.
[Supp. Info.]
- Li, Y., Hartemink, A., & MacAlpine, D. (2021)
“Cell-cycle–dependent chromatin dynamics at replication origins.”
Genes, 12, December 2021.
pp. 1998:1–13.
- Mitra, S., Zhong, J., Tran, T., MacAlpine, D., & Hartemink, A. (2021)
“RoboCOP: Jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data.”
Nucleic Acids Research, 49, August 2021.
pp. 7925–7938.
[Supp. Info.]
- Tran, T., MacAlpine, H., Tripuraneni, V., Mitra, S., MacAlpine, D., & Hartemink, A. (2021)
“Linking the dynamics of chromatin occupancy and transcription with predictive models.”
Genome Research, 31, June 2021.
pp. 1035–1046.
[Supp. Info.]
- Tripuraneni, V., Memisoglu, G., MacAlpine, H., Tran, T., Zhu, W., Hartemink, A., Haber, J., & MacAlpine, D. (2021)
“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, May 2021.
pp. 775–788.
[Supp. Info.]
- Mitra, S., Zhong, J., MacAlpine, D. & Hartemink, A. (2020)
“RoboCOP: Multivariate state space model integrating epigenomic accessibility data to elucidate genome-wide chromatin occupancy.”
Research in Computational Molecular Biology 2020 (RECOMB20), Lecture Notes in Bioinformatics, Schwartz, R., ed. 12074, May 2020.
pp. 136–151.
[Supp. Info.]
- McDowell, I., Barrera, A., D'Ippolito, A., Vockley, C., Hong, L., Leichter, S., Bartelt, L., Majoros, W., Song, L., Safi, A., Koçak, D., Gersbach, C., Hartemink, A., Crawford, G., Engelhardt, B., & Reddy, T. (2018)
“Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.”
Genome Research, 28, September 2018.
pp. 1272–1284.
- Welch, J., Hartemink, A., & Prins, J. (2017)
“MATCHER: Manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics.”
Genome Biology, 18, 24 July 2017.
138 (pp. 1–19).
[Supp. Info.]
- Welch, J., Hartemink, A., & Prins, J. (2017)
“E pluribus unum: United states of single cells.”
Research in Computational Molecular Biology 2017 (RECOMB17), Lecture Notes in Bioinformatics, Sahinalp, S.C., ed. 10229, May 2017.
pp. 400–401.
- Mayhew, M., Iversen, E., & Hartemink, A. (2017)
“Characterization of dependencies between growth and division in budding yeast.”
Journal of the Royal Society Interface, 14, February 2017.
20160993 (pp. 1–12).
- Sparks, E., Drapek, C., Gaudinier, A., Li, S., Ansariola, M., Shen, N., Hennacy, J., Zhang, J., Turco, G., Petricka, J., Foret, J., Hartemink, A., Gordân, R., Megraw, M., Brady, S., & Benfey, P. (2016)
“Establishment of expression in the SHORTROOT-SCARECROW transcriptional cascade through opposing activities of both activators and repressors.”
Developmental Cell, 39, 5 December 2016.
pp. 585–596.
- Welch, J., Hartemink, A., & Prins, J. (2016)
“SLICER: Inferring branched, nonlinear cellular trajectories from single cell RNA-seq data.”
Genome Biology, 17, 23 May 2016.
106 (pp. 1–15).
- Welch, J., Liu, Z., Wang, L., Lu, J., Lerou, P., Purvis, J., Qian, L., Hartemink, A., & Prins, J. (2016)
“SLICER: Inferring branched, nonlinear cellular trajectories from single cell RNA-seq data.”
Research in Computational Molecular Biology 2016 (RECOMB16), Lecture Notes in Bioinformatics, Singh, M., ed. 9649, April 2016.
pp. 239–240.
- Zhong, J., Luo, K., Winter, P., Crawford, G., Iversen, E., & Hartemink, A. (2016)
“Mapping nucleosome positions using DNase-seq.”
Genome Research, 26, March 2016.
pp. 351–364.
- Zhang, Y., Henao, R., Carin, L., Zhong, J., & Hartemink, A. (2016)
“Learning a hybrid architecture for sequence regression and annotation.”
AAAI Conference on Artificial Intelligence 2016 (AAAI16), February 2016.
pp. 1415–1421.
Also available at arXiv, arXiv:1512.05219.
- Scholl, Z., Zhong, J., & Hartemink, A. (2015)
“Chromatin interactions correlate with local transcriptional activity in Saccharomyces cerevisiae.”
bioRxiv, bioRxiv:021725.
- Belsky, J., MacAlpine, H., Lubelsky, Y., Hartemink, A., & MacAlpine, D. (2015)
“Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly.”
Genes and Development, 29, 15 January 2015.
pp. 212–224.
- Pfenning, A., Hara, E., Whitney, O., Rivas, M., Wang, R., Roulhac, P., Howard, J., Wirthlin, M., Lovell, P., Ganapathy, G., Mouncastle, J., Moseley, M., Thompson, J., Soderblom, E., Iriki, A., Kato, M., Gilbert, M., Zhang, G., Bakken, T., Bongaarts, A., Bernard, A., Lein, E., Mello, C., Hartemink, A., & Jarvis, E. (2014)
“Convergent transcriptional specializations in the brains of humans and song-learning birds.”
Science, 346, 12 December 2014.
pp. 1256846-1–13.
[Author Summary]
[Kavli Biggest Science Stories 2014]
[Nature]
[Science]
[New Scientist]
[Washington Post]
[MIT News]
- Whitney, O., Pfenning, A., Howard, J., Blatti, C., Liu, F., Ward, J., Wang, R., Audet, J.-N., Kellis, M., Mukherjee, S., Sinha, S., Hartemink, A., West, A., & Jarvis, E. (2014)
“Core and region-enriched networks of behaviorally regulated genes and the singing genome.”
Science, 346, 12 December 2014.
pp. 1256780-1–11.
[Author Summary]
- Zhong, J., Wasson, T., & Hartemink, A. (2014)
“Learning protein-DNA interaction landscapes by integrating experimental data through computational models.”
Bioinformatics, 30, 15 October 2014.
pp. 2868–2874.
- Zhong, J., Wasson, T., & Hartemink, A. (2014)
“Learning protein-DNA interaction landscapes by integrating experimental data through computational models.”
Research in Computational Molecular Biology 2014 (RECOMB14), Lecture Notes in Bioinformatics, Sharan, R., ed. 8394, April 2014.
pp. 433–447.
- Meyer, P., Siwo, G., Zeevi, D., Sharon, E., Norel, R., DREAM6 Promoter Prediction Consortium, Segal, E., & Stolovitsky, G. (2013)
“Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach.”
Genome Research, 23, November 2013.
pp. 1928–1937.
- Mordelet, F., Horton, J., Hartemink, A., Engelhardt, B., & Gordân, R. (2013)
“Stability selection for regression-based models of transcription factor-DNA binding specificity.”
Intelligent Systems in Molecular Biology 2013 (ISMB13), Bioinformatics, 29, July 2013.
pp. i117–i125.
- Mayhew, M. & Hartemink, A. (2013)
“Cell-cycle phenotyping with conditional random fields: A case study in Saccharomyces cerevisiae.”
IEEE International Symposium on Biomedical Imaging 2013: From Nano to Macro (ISBI 2013), April 2013.
pp. 1062–1065.
- Guo, X., Bernard, A., Orlando, D., Haase, S., & Hartemink, A. (2013)
“Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program.”
PNAS, 110, 5 March 2013.
pp. E968–E977.
[Deconvolution Website]
[Author Summary]
[Supp. Info.]
- Perez-Pinera, P., Ousterout, D., Brunger, J., Farin, A., Glass, K., Guilak, F., Crawford, G., Hartemink, A., & Gersbach, C. (2013)
“Synergistic and tunable gene activation in human cells by combinations of synthetic transcription factors.”
Nature Methods, 10, 3 February 2013.
pp. 239–242.
[Supp. Info.]
- Luo, K. & Hartemink, A. (2013)
“Using DNase digestion data to accurately identify transcription factor binding sites.”
In Pacific Symposium on Biocomputing 2013 (PSB13), Altman, R., Dunker, A.K., Hunter, L., Murray, T., & Klein, T., eds. World Scientific: New Jersey.
pp. 80–91.
[Supp. Info.]
[Code]
- Landt, S., Marinov, G., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B., Bickel, P., Brown, B., Cayting, P., Chen, Y., DeSalvo, G., Epstein, C., Euskirchen, G., Fisher-Aylor, K., Gerstein, M., Gertz, J., Hartemink, A., Hoffman, M., Iyer, V., Jung, Y., Karmakar, S., Kellis, M., Kharchenko, P., Li, Q., Liu, T., Liu, X., Ma, L., Milosavljevic, A., Myers, R., Park, P., Pazin, M., Perry, M., Raha, D., Reddy, T., Rozowsky, J., Shoresh, N., Sidow, A., Slattery, M., Stammatoyonnopoulous, J., Tolstorukov, M., White, K., Xi, S., Farnham, P., Lieb, J., Wold, B., & Snyder, M. (2012)
“ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.”
Genome Research, 22, September 2012.
pp. 1813–1831.
- Mayhew, M., Guo, X., Haase, S., & Hartemink, A. (2012)
“Close encounters of the collaborative kind.”
IEEE Computer, Special Issue on Computationally Driven Experimental Biology, 45, March 2012.
pp. 24–30.
[Cover Feature]
- Guo, X., Bulyk, M., & Hartemink, A. (2012)
“Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors.”
In Pacific Symposium on Biocomputing 2012 (PSB12), Altman, R., Dunker, A.K., Hunter, L., Murray, T., & Klein, T., eds. World Scientific: New Jersey.
pp. 104–115.
- Meyer, P., Alexopoulos, L., Bonk, T., Califano, A., Cho, C., de la Fuente, A., de Graaf, D., Hartemink, A., Hoeng, J., Ivanov, N., Koeppl, H., Linding, R., Marbach, D., Norel, R., Peitsch, M., Rice, J., Royyuru, A., Schacherer, F., Sprengel, J., Stolle, K., Vitkup, D., & Stolovitzky, G. (2011)
“Verification of systems biology research in the age of collaborative competition.”
Nature Biotechnology, 29, September 2011.
pp. 811–815.
- Mayhew, M., Robinson, J., Jung, B., Haase, S., & Hartemink, A. (2011)
“A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments.”
Intelligent Systems in Molecular Biology 2011 (ISMB11), Bioinformatics, 27, July 2011.
pp. i295–i303.
- Miller, H., Robinson, T., Gordân, R., Hartemink, A., & Garcia-Blanco, M. (2011)
“Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing.”
RNA, 17, April 2011.
pp. 665–674.
- Robinson, J. & Hartemink, A. (2010)
“Learning non-stationary dynamic Bayesian networks.”
Journal of Machine Learning Research, 11, December 2010.
pp. 3647–3680.
- Gordân, R., Narlikar, L., & Hartemink, A. (2010)
“Finding regulatory DNA motifs using alignment-free evolutionary conservation information.”
Nucleic Acids Research, 38, April 2010.
p. e90.
[Supp. Info.]
- MacAlpine, H., Gordân, R., Powell, S., Hartemink, A., & MacAlpine, D. (2010)
“Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading.”
Genome Research, 20, February 2010.
pp. 201–211.
- Orlando, D., Iversen, E., Hartemink, A., & Haase, S. (2009)
“A branching process model for flow cytometry and budding index measurements in cell synchrony experiments.”
Annals of Applied Statistics, 3, December 2009.
pp. 1521–1541.
- Wasson, T. & Hartemink, A. (2009)
“An ensemble model of competitive multi-factor binding of the genome.”
Genome Research, 19, November 2009.
pp. 2101–2112.
- Gordân, R., Hartemink, A., & Bulyk, M. (2009)
“Distinguishing direct versus indirect transcription factor-DNA interactions.”
Genome Research, 19, November 2009.
pp. 2090–2100.
[Supp. Info.]
- Guo, X. & Hartemink, A. (2009)
“Domain-oriented edge-based alignment of protein interaction networks.”
Intelligent Systems in Molecular Biology 2009 (ISMB09), Bioinformatics, 25, 15 June 2009.
pp. i240–i246.
- Robinson, J. & Hartemink, A. (2009)
“Non-stationary dynamic Bayesian networks.”
In Advances in Neural Information Processing Systems 21 (NIPS08), Koller, D., Schuurmans, D., Bengio, Y., & Bottou, L., eds. MIT Press: Cambridge, MA.
pp. 1369–1376.
[Appendix]
- Orlando, D., Lin, C., Bernard, A., Wang, J., Socolar, J., Iversen, E., Hartemink, A., & Haase, S. (2008)
“Global control of cell-cycle transcription by coupled CDK and network oscillators.”
Nature, 453, 12 June 2008.
pp. 944–947.
[Supp. Info.]
- Gordân, R., Narlikar, L., & Hartemink, A. (2008)
“A fast, alignment-free, conservation-based method for transcription factor binding site discovery.”
Research in Computational Molecular Biology 2008 (RECOMB08), Lecture Notes in Bioinformatics, Vingron, M. & Wong, L., eds. 4955, April 2008.
pp. 98–111.
[Supp. Info.]
- Gordân, R. & Hartemink, A. (2008)
“Using DNA duplex stability information for transcription factor binding site discovery.”
In Pacific Symposium on Biocomputing 2008 (PSB08), Altman, R., Dunker, A.K., Hunter, L., Murray, T., & Klein, T., eds. World Scientific: New Jersey.
pp. 453–464.
[Supp. Info.]
- Lüdi, P., Dietrich, F., Weidman, J., Bosko, J., Jirtle, R., & Hartemink, A. (2007)
“Computational and experimental identification of novel human imprinted genes.”
Genome Research, 17, December 2007.
pp. 1723–1730.
[Supp. Info.]
[Cover]
[Nature Reviews Genetics]
[Science]
[AP]
[Wired]
- Narlikar, L., Gordân, R., & Hartemink, A. (2007)
“A nucleosome-guided map of transcription factor binding sites in yeast.”
PLoS Computational Biology, 3, November 2007.
pp. 2199–2208.
- Bernard, A., Vaughn, D., & Hartemink, A. (2007)
“Reconstructing the topology of protein complexes.”
Research in Computational Molecular Biology 2007 (RECOMB07), Lecture Notes in Bioinformatics, Speed, T. & Huang, H., eds. 4453, April 2007.
pp. 32–46.
- Narlikar, L., Gordân, R., & Hartemink, A. (2007)
“Nucleosome occupancy information improves de novo motif discovery.”
Research in Computational Molecular Biology 2007 (RECOMB07), Lecture Notes in Bioinformatics, Speed, T. & Huang, H., eds. 4453, April 2007.
pp. 107–121.
[Supp. Info.]
- Orlando, D., Lin, C., Bernard, A., Iversen, E., Hartemink, A., & Haase, S. (2007)
“A probabilistic model for cell cycle distributions in synchrony experiments.”
RECOMB Satellite Conference on Systems Biology 2006, Cell Cycle, 6, February 2007.
pp. 478–488.
- Smith, V., Yu, J., Smulders, T., Hartemink, A., & Jarvis, E. (2006)
“Computational inference of neural information flow networks.”
PLoS Computational Biology, 2, November 2006.
pp. 1436–1449.
[Supp. Info.]
[Code]
[Most Viewed Research Article at PLoS Computational Biology]
- Bernard, A. & Hartemink, A. (2006)
“Evaluating algorithms for learning biological networks.”
DREAM Workshop, September 2006.
- Narlikar, L., Gordân, R., Ohler, U., & Hartemink, A. (2006)
“Informative priors based on transcription factor structural class improve de novo motif discovery.”
Intelligent Systems in Molecular Biology 2006 (ISMB06), Bioinformatics, 22, July 2006.
pp. e384–e392.
[Supp. Info.]
[Code]
[Input Data]
- Hartemink, A. (2006)
“Bayesian networks and informative priors: Transcriptional regulatory network models.”
In Bayesian Inference for Gene Expression and Proteomics, Do, K.-A., Müller, P., & Vannucci, M., eds. Cambridge University Press: Cambridge, UK.
pp. 401–424.
- Narlikar, L. & Hartemink, A. (2006)
“Sequence features of DNA binding sites reveal structural class of associated transcription factor.”
Bioinformatics, 22, January 2006.
pp. 157–163.
- Pratapa, P., Patz, E., & Hartemink, A. (2006)
“Finding diagnostic biomarkers in proteomic spectra.”
In Pacific Symposium on Biocomputing 2006 (PSB06), Altman, R., Dunker, A.K., Hunter, L., Murray, T., & Klein, T., eds. World Scientific: New Jersey.
pp. 279–290.
[Larger Figs.]
- Krishnapuram, B., Williams, D., Xue, Y., Carin, L., Figueiredo, M., & Hartemink, A. (2005)
“Active learning of features and labels.”
Learning with Multiple Views Workshop at ICML05, August 2005.
- Lüdi, P., Hartemink, A., & Jirtle, R. (2005)
“Genome-wide prediction of imprinted murine genes.”
Genome Research, 15, June 2005.
pp. 875–884.
- Krishnapuram, B., Figueiredo, M., Carin, L., & Hartemink, A. (2005)
“Sparse multinomial logistic regression: Fast algorithms and generalization bounds.”
IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 27, June 2005.
pp. 957–968.
[Code]
- Hartemink, A. (2005)
“Reverse engineering gene regulatory networks.”
Nature Biotechnology, 23, May 2005.
pp. 554–555.
- Yin, P. & Hartemink, A. (2005)
“Theoretical and practical advances in genome halving.”
Bioinformatics, 21, April 2005.
pp. 869–879.
- Bernard, A. & Hartemink, A. (2005)
“Informative structure priors: Joint learning of dynamic regulatory networks from multiple types of data.”
In Pacific Symposium on Biocomputing 2005 (PSB05), Altman, R., Dunker, A.K., Hunter, L., Jung, T., & Klein, T., eds. World Scientific: New Jersey.
pp. 459–470.
[Supp. Info.]
- Krishnapuram, B., Williams, D., Xue, Y., Hartemink, A., Carin, L., & Figueiredo, M. (2005)
“On semi-supervised classification.”
In Advances in Neural Information Processing Systems 17 (NIPS04), Saul, L., Weiss, Y., & Bottou, L., eds. MIT Press: Cambridge, MA.
pp. 721–728.
- Yu, J., Smith, V., Wang, P., Hartemink, A., & Jarvis, E. (2004)
“Advances to Bayesian network inference for generating causal networks from observational biological data.”
Bioinformatics, 20, December 2004.
pp. 3594–3603.
- Krishnapuram, B., Hartemink, A., Carin, L., & Figueiredo, M. (2004)
“A Bayesian approach to joint feature selection and classifier design.”
IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 26, September 2004.
pp. 1105–1111.
- Krishnapuram, B., Carin, L., & Hartemink, A. (2004)
“Joint classifier and feature optimization for comprehensive cancer diagnosis using gene expression data.”
Journal of Computational Biology, 11, March 2004.
pp. 227–242.
- Krishnapuram, B., Carin, L., & Hartemink, A. (2004)
“Gene expression analysis: Joint feature selection and classifier design.”
In Kernel Methods in Computational Biology, Schölkopf, B., Tsuda, K., & Vert, J.-P., eds. MIT Press: Cambridge, MA.
pp. 299–318.
- Liu, Q., Krishnapuram, B., Pratapa, P., Liao, X., Hartemink, A., & Carin, L. (2003)
“Identification of differentially expressed proteins using MALDI-TOF mass spectra.”
ASILOMAR Conference: Biological Aspects of Signal Processing, November 2003.
- Krishnapuram, B., Carin, L., & Hartemink, A. (2003)
“Joint classifier and kernel design.”
Kernel Methods in Bioinformatics Workshop at RECOMB03, April 2003.
- Krishnapuram, B., Carin, L., & Hartemink, A. (2003)
“Joint classifier and feature optimization for cancer diagnosis using gene expression data.”
In Research in Computational Molecular Biology 2003 (RECOMB03), Vingron, M., Pevzner, P., Istrail, S. & Waterman, M., eds. ACM: New York.
pp. 167–175.
- Smith, V., Jarvis, E., & Hartemink, A. (2003)
“Influence of network topology and data collection on network inference.”
In Pacific Symposium on Biocomputing 2003 (PSB03), Altman, R., Dunker, A.K., Hunter, L., Jung, T., & Klein, T., eds. World Scientific: New Jersey.
pp. 164–175.
- Yu, J., Smith, V., Wang, P., Hartemink, A., & Jarvis, E. (2002)
“Using Bayesian network inference algorithms to recover molecular genetic regulatory networks.”
International Conference on Systems Biology 2002 (ICSB02), December 2002.
- Jarvis, E., Smith, V., Wada, K., Rivas, M., McElroy, M., Smulders, T., Carninci, P., Hayashisaki, Y., Dietrich, F., Wu, X., McConnell, P., Yu, J., Wang, P., Hartemink, A., & Lin, S. (2002)
“A framework for integrating the songbird brain.”
Journal of Comparative Physiology A, 188, December 2002.
pp. 961–980.
- Krishnapuram, B., Hartemink, A., & Carin, L. (2002)
“Applying logistic regression and RVM to achieve accurate probabilistic cancer diagnosis from gene expression profiles.”
GENSIPS: Workshop on Genomic Signal Processing and Statistics, October 2002.
- Smith, V., Jarvis, E., & Hartemink, A. (2002)
“Evaluating functional network inference using simulations of complex biological systems.”
Intelligent Systems in Molecular Biology 2002 (ISMB02), Bioinformatics, 18:S1.
pp. S216–S224.
- Hartemink, A., Gifford, D., Jaakkola, T., & Young, R. (2002)
“Bayesian methods for elucidating genetic regulatory networks.”
IEEE Intelligent Systems, special issue on Intelligent Systems in Biology, 17, March/April 2002.
pp. 37–43.
- Hartemink, A., Gifford, D., Jaakkola, T., & Young, R. (2002)
“Combining location and expression data for principled discovery of genetic regulatory networks.”
In Pacific Symposium on Biocomputing 2002 (PSB02), Altman, R., Dunker, A.K., Hunter, L., Lauderdale, K., & Klein, T., eds. World Scientific: New Jersey.
pp. 437–449.
- Hartemink, A. (2001)
“Principled Computational Methods for the Validation and Discovery of Genetic Regulatory Networks.”
Massachusetts Institute of Technology, Ph.D. dissertation.
- Hartemink, A., Gifford, D., Jaakkola, T., & Young, R. (2001)
“Maximum likelihood estimation of optimal scaling factors for expression array normalization.”
SPIE International Symposium on Biomedical Optics 2001 (BiOS01). In Microarrays: Optical Technologies and Informatics, Bittner, M., Chen, Y., Dorsel, A., & Dougherty, E., eds. Proceedings of SPIE, 4266.
pp. 132–140.
- Hartemink, A., Gifford, D., Jaakkola, T., & Young, R. (2001)
“Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks.”
In Pacific Symposium on Biocomputing 2001 (PSB01), Altman, R., Dunker, A.K., Hunter, L., Lauderdale, K., & Klein, T., eds. World Scientific: New Jersey.
pp. 422–433.
- Hartemink, A., Mikkelsen, T., & Gifford, D. (2000)
“Simulating biological reactions: A modular approach.”
DNA Based Computers V. Winfree, E. & Gifford, D., eds. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 54, American Mathematical Society.
pp. 111–121.
- Schechter, S., Parnell, T., & Hartemink, A. (1999)
“Anonymous authentication of membership in dynamic groups.”
Financial Cryptography '99. Franklin, M., ed. Lecture Notes in Computer Science, 1648, Springer-Verlag.
pp. 184–195.
- Hartemink, A., Gifford, D., & Khodor, J. (1999)
“Automated constraint-based nucleotide sequence selection for DNA computation.”
Biosystems, 52, October 1999, Elsevier Press.
pp. 227–235.
- Hartemink, A. & Gifford, D. (1999)
“Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation.”
DNA Based Computers III. Rubin, H. & Wood, D., eds. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 48, American Mathematical Society.
pp. 25–38.