Alexander J. Hartemink

Publication Activity (10 Years)

Years Active: 1997-2020
Publications (10 Years): 4

Top Venues

RECOMB

Pacific Symposium on Biocomputing

Bioinform.

ISBI

Massachusetts Institute of Technology, Cambridge, MA, USA (PHD)

Education History

Massachusetts Institute of Technology, Cambridge, MA, USA

PHD

Publications

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)
Joshua D. Welch, Alexander J. Hartemink, Jan F. Prins
E Pluribus Unum: United States of Single Cells. RECOMB (2017)
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)
Yizhe Zhang, Ricardo Henao, Lawrence Carin, Jianling Zhong, Alexander J. Hartemink
Learning a Hybrid Architecture for Sequence Regression and Annotation. AAAI (2016)
Jianling Zhong, Todd Wasson, Alexander J. Hartemink
Learning Protein-DNA Interaction Landscapes by Integrating Experimental Data through Computational Models. RECOMB (2014)
Jianling Zhong, Todd Wasson, Alexander J. Hartemink
Learning protein-DNA interaction landscapes by integrating experimental data through computational models. Bioinform. 30 (20) (2014)
Kaixuan Luo, Alexander J. Hartemink
Using DNase Digestion Data to Accurately Identify Transcription Factor Binding Sites. Pacific Symposium on Biocomputing (2013)
Michael B. Mayhew, Alexander J. Hartemink
Cell-cycle phenotyping with conditional random fields: A case study in Saccharomyces cerevisiae. ISBI (2013)
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) (2013)
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) (2013)
Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng
Session Introduction. Pacific Symposium on Biocomputing (2013)
Michael B. Mayhew, Xin Guo, Steven B. Haase, Alexander J. Hartemink
Close Encounters of the Collaborative Kind. Computer 45 (3) (2012)
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)
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) (2011)
Joshua W. Robinson, Alexander J. Hartemink
Learning Non-Stationary Dynamic Bayesian Networks. J. Mach. Learn. Res. 11 (2010)
Raluca Gordân, Alexander J. Hartemink, Martha L. Bulyk
Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions. RECOMB (2010)
Xin Guo, Alexander J. Hartemink
Domain-oriented edge-based alignment of protein interaction networks. Bioinform. 25 (12) (2009)
Raluca Gordân, Leelavati Narlikar, Alexander J. Hartemink
A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery. RECOMB (2008)
Joshua W. Robinson, Alexander J. Hartemink
Non-stationary dynamic Bayesian networks. NIPS (2008)
Martha L. Bulyk, Ernest Fraenkel, Alexander J. Hartemink, Yael Mandel-Gutfreund
Session Introduction. Pacific Symposium on Biocomputing (2008)
Raluca Gordân, Alexander J. Hartemink
Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery. Pacific Symposium on Biocomputing (2008)
Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink
A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast. PLoS Comput. Biol. 3 (11) (2007)
Allister Bernard, David S. Vaughn, Alexander J. Hartemink
Reconstructing the Topology of Protein Complexes. RECOMB (2007)
Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink
Motif Discovery. RECOMB (2007)
Martha L. Bulyk, Alexander J. Hartemink, Ernest Fraenkel, Gary D. Stormo
Session Introduction. Pacific Symposium on Biocomputing (2007)
Leelavati Narlikar, Raluca Gordân, Uwe Ohler, Alexander J. Hartemink
motif discovery. ISMB (Supplement of Bioinformatics) (2006)
Leelavati Narlikar, Alexander J. Hartemink
Sequence features of DNA binding sites reveal structural class of associated transcription factor. Bioinform. 22 (2) (2006)
Pallavi N. Pratapa, Edward F. Patz Jr., Alexander J. Hartemink
Finding Diagnostic Biomarkers in Proteomic Spectra. Pacific Symposium on Biocomputing (2006)
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)
Peng Yin, Alexander J. Hartemink
Theoretical and practical advances in genome halving. Bioinform. 21 (7) (2005)
Alexander J. Hartemink, Eran Segal
Session Introduction: Joint Learning from Multiple Types of Genomic Data. Pacific Symposium on Biocomputing (2005)
Allister Bernard, Alexander J. Hartemink
Informative Structure Priors: Joint Learning of Dynamic Regulatory Networks from Multiple Types of Data. Pacific Symposium on Biocomputing (2005)
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) (2005)
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) (2004)
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) (2004)
Balaji Krishnapuram, David Williams, Ya Xue, Alexander J. Hartemink, Lawrence Carin, Mário A. T. Figueiredo
On Semi-Supervised Classification. NIPS (2004)
Alexander J. Hartemink, Eran Segal
Session Introduction. Pacific Symposium on Biocomputing (2004)
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) (2004)
Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink
Joint classifier and feature optimization for cancer diagnosis using gene expression data. RECOMB (2003)
Peter D. Karp, Eric P. Neumann, Alexander J. Hartemink, Pedro Romero
Genome, Pathway, and Interaction Bioinformatics - Session Introduction. Pacific Symposium on Biocomputing (2003)
V. Anne Smith, Erich D. Jarvis, Alexander J. Hartemink
Influence of Network Topology and Data Collection on Network Inference. Pacific Symposium on Biocomputing (2003)
Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young
Bayesian Methods for Elucidating Genetic Regulatory Networks. IEEE Intell. Syst. 17 (2) (2002)
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)
V. Anne Smith, Erich D. Jarvis, Alexander J. Hartemink
Evaluating functional network inference using simulations of complex biological systems. ISMB (2002)
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)
Stuart E. Schechter, Todd Parnell, Alexander J. Hartemink
Anonymous Authentication of Membership in Dynamic Groups. Financial Cryptography (1999)
Alexander J. Hartemink, Tarjei S. Mikkelsen, David K. Gifford
Simulating biological reactions: A modular approach. DNA Based Computers (1999)
Alexander J. Hartemink, David K. Gifford
Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation. DNA Based Computers (1997)

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Publication Activity (10 Years)

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Alexander J. Hartemink