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ORCIDAlexander J. Hartemink
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2020 – today
- 2020
[c32]Sneha Mitra, Jianling Zhong, David M. MacAlpine, Alexander J. Hartemink:
RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy. RECOMB 2020: 136-151
2010 – 2019
- 2017
- [c31]Joshua D. Welch, Alexander J. Hartemink, Jan F. Prins:
E Pluribus Unum: United States of Single Cells. RECOMB 2017: 400-401 - 2016
- [c30]Yizhe Zhang, Ricardo Henao, Lawrence Carin, Jianling Zhong, Alexander J. Hartemink:
Learning a Hybrid Architecture for Sequence Regression and Annotation. AAAI 2016: 1415-1421 - [c29]Joshua D. Welch, Ziqing Liu, Li Wang, Junjie Lu, Paul Lerou, Jeremy E. Purvis, Li Qian, Alexander J. Hartemink, Jan F. Prins:
SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data. RECOMB 2016: 239-240 - 2014
- [j16]Jianling Zhong, Todd Wasson, Alexander J. Hartemink:
Learning protein-DNA interaction landscapes by integrating experimental data through computational models. Bioinform. 30(20): 2868-2874 (2014) - [c28]Jianling Zhong, Todd Wasson, Alexander J. Hartemink:
Learning Protein-DNA Interaction Landscapes by Integrating Experimental Data through Computational Models. RECOMB 2014: 433-447 - 2013
- [j15]Fantine Mordelet, John Horton, Alexander J. Hartemink, Barbara E. Engelhardt
, Raluca Gordân:
Stability selection for regression-based models of transcription factor-DNA binding specificity. Bioinform. 29(13): 117-125 (2013) - [j14]Xin Guo, Allister Bernard, David A. Orlando, Steven B. Haase, Alexander J. Hartemink:
Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program. Proc. Natl. Acad. Sci. USA 110(10): E968-E977 (2013) - [c27]Michael B. Mayhew, Alexander J. Hartemink:
Cell-cycle phenotyping with conditional random fields: A case study in Saccharomyces cerevisiae. ISBI 2013: 1062-1065 - [c26]Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng:
Session Introduction. Pacific Symposium on Biocomputing 2013: 65-68 - [c25]Kaixuan Luo, Alexander J. Hartemink:
Using DNase Digestion Data to Accurately Identify Transcription Factor Binding Sites. Pacific Symposium on Biocomputing 2013: 80-91 - 2012
- [j13]Michael B. Mayhew, Xin Guo, Steven B. Haase, Alexander J. Hartemink:
Close Encounters of the Collaborative Kind. Computer 45(3): 24-30 (2012) - [c24]Xin Guo, Martha L. Bulyk, Alexander J. Hartemink:
Intrinsic Disorder Within and Flanking the DNA-Binding Domains of Human Transcription Factors. Pacific Symposium on Biocomputing 2012: 104-115 - 2011
- [j12]Michael B. Mayhew, Joshua W. Robinson, Boyoun Jung, Steven B. Haase, Alexander J. Hartemink:
A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments. Bioinform. 27(13): 295-303 (2011) - 2010
- [j11]Joshua W. Robinson, Alexander J. Hartemink:
Learning Non-Stationary Dynamic Bayesian Networks. J. Mach. Learn. Res. 11: 3647-3680 (2010) - [c23]Raluca Gordân, Alexander J. Hartemink, Martha L. Bulyk:
Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions. RECOMB 2010: 574
2000 – 2009
- 2009
- [j10]Xin Guo, Alexander J. Hartemink:
Domain-oriented edge-based alignment of protein interaction networks. Bioinform. 25(12) (2009) - 2008
- [c22]Joshua W. Robinson, Alexander J. Hartemink:
Non-stationary dynamic Bayesian networks. NIPS 2008: 1369-1376 - [c21]Martha L. Bulyk, Ernest Fraenkel, Alexander J. Hartemink, Yael Mandel-Gutfreund:
Session Introduction. Pacific Symposium on Biocomputing 2008: 438-440 - [c20]Raluca Gordân, Alexander J. Hartemink:
Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery. Pacific Symposium on Biocomputing 2008: 453-464 - [c19]Raluca Gordân, Leelavati Narlikar, Alexander J. Hartemink:
A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery. RECOMB 2008: 98-111 - 2007
- [j9]Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink:
A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast. PLoS Comput. Biol. 3(11) (2007) - [c18]Martha L. Bulyk, Alexander J. Hartemink, Ernest Fraenkel, Gary D. Stormo:
Session Introduction. Pacific Symposium on Biocomputing 2007: 470-471 - [c17]Allister Bernard, David S. Vaughn, Alexander J. Hartemink:
Reconstructing the Topology of Protein Complexes. RECOMB 2007: 32-46 - [c16]Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink:
Nucleosome Occupancy Information Improves de novo Motif Discovery. RECOMB 2007: 107-121 - 2006
- [j8]Leelavati Narlikar, Alexander J. Hartemink:
Sequence features of DNA binding sites reveal structural class of associated transcription factor. Bioinform. 22(2): 157-163 (2006) - [j7]V. Anne Smith, Jing Yu, Tom V. Smulders, Alexander J. Hartemink, Erich D. Jarvis:
Computational Inference of Neural Information Flow Networks. PLoS Comput. Biol. 2(11) (2006) - [c15]Leelavati Narlikar, Raluca Gordân, Uwe Ohler, Alexander J. Hartemink:
Informative priors based on transcription factor structural class improve de novo motif discovery. ISMB (Supplement of Bioinformatics) 2006: 384-392 - [c14]Pallavi N. Pratapa, Edward F. Patz Jr., Alexander J. Hartemink:
Finding Diagnostic Biomarkers in Proteomic Spectra. Pacific Symposium on Biocomputing 2006: 279-290 - 2005
- [j6]Peng Yin, Alexander J. Hartemink:
Theoretical and practical advances in genome halving. Bioinform. 21(7): 869-879 (2005) - [j5]Balaji Krishnapuram, Lawrence Carin, Mário A. T. Figueiredo, Alexander J. Hartemink:
Sparse Multinomial Logistic Regression: Fast Algorithms and Generalization Bounds. IEEE Trans. Pattern Anal. Mach. Intell. 27(6): 957-968 (2005) - [c13]Allister Bernard, Alexander J. Hartemink:
Informative Structure Priors: Joint Learning of Dynamic Regulatory Networks from Multiple Types of Data. Pacific Symposium on Biocomputing 2005 - [c12]Alexander J. Hartemink, Eran Segal:
Session Introduction: Joint Learning from Multiple Types of Genomic Data. Pacific Symposium on Biocomputing 2005 - 2004
- [j4]Jing Yu, V. Anne Smith, Paul P. Wang, Alexander J. Hartemink, Erich D. Jarvis:
Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinform. 20(18): 3594-3603 (2004) - [j3]Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink:
Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data. J. Comput. Biol. 11(2/3): 227-242 (2004) - [j2]Balaji Krishnapuram, Alexander J. Hartemink, Lawrence Carin, Mário A. T. Figueiredo:
A Bayesian Approach to Joint Feature Selection and Classifier Design. IEEE Trans. Pattern Anal. Mach. Intell. 26(9): 1105-1111 (2004) - [c11]Balaji Krishnapuram, David Williams, Ya Xue, Alexander J. Hartemink, Lawrence Carin, Mário A. T. Figueiredo:
On Semi-Supervised Classification. NIPS 2004: 721-728 - [c10]Alexander J. Hartemink, Eran Segal:
Session Introduction. Pacific Symposium on Biocomputing 2004: 262-263 - 2003
- [c9]Peter D. Karp, Eric P. Neumann, Alexander J. Hartemink, Pedro Romero:
Genome, Pathway, and Interaction Bioinformatics - Session Introduction. Pacific Symposium on Biocomputing 2003: 101-103 - [c8]V. Anne Smith, Erich D. Jarvis, Alexander J. Hartemink:
Influence of Network Topology and Data Collection on Network Inference. Pacific Symposium on Biocomputing 2003: 164-175 - [c7]Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink:
Joint classifier and feature optimization for cancer diagnosis using gene expression data. RECOMB 2003: 167-175 - 2002
- [j1]Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young:
Bayesian Methods for Elucidating Genetic Regulatory Networks. IEEE Intell. Syst. 17(2): 37-43 (2002) - [c6]V. Anne Smith, Erich D. Jarvis, Alexander J. Hartemink:
Evaluating functional network inference using simulations of complex biological systems. ISMB 2002: 216-224 - [c5]Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young:
Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models. Pacific Symposium on Biocomputing 2002: 437-449 - 2001
- [b1]Alexander J. Hartemink:
Principled computational methods for the validation discovery of genetic regulatory networks. Massachusetts Institute of Technology, Cambridge, MA, USA, 2001 - [c4]Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young:
Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks. Pacific Symposium on Biocomputing 2001: 422-433
1990 – 1999
- 1999
- [c3]Alexander J. Hartemink, Tarjei S. Mikkelsen, David K. Gifford:
Simulating biological reactions: A modular approach. DNA Based Computers 1999: 111-121 - [c2]Stuart E. Schechter, Todd Parnell, Alexander J. Hartemink:
Anonymous Authentication of Membership in Dynamic Groups. Financial Cryptography 1999: 184-195 - 1997
- [c1]Alexander J. Hartemink, David K. Gifford:
Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation. DNA Based Computers 1997: 25-37
Coauthor Index
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