Alexander J. Hartemink

According to our database, Alexander J. Hartemink authored at least 48 papers between 1997 and 2020.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2020

RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy.

Sneha Mitra, Jianling Zhong, David M. MacAlpine, Alexander J. Hartemink

Proceedings of the Research in Computational Molecular Biology, 2020

2017

E Pluribus Unum: United States of Single Cells.

Joshua D. Welch, Alexander J. Hartemink, Jan F. Prins

Proceedings of the Research in Computational Molecular Biology, 2017

2016

SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data.

Joshua D. Welch, Ziqing Liu, Li Wang, Junjie Lu, Paul Lerou, Jeremy E. Purvis, Li Qian, Alexander J. Hartemink, Jan F. Prins

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

Learning a Hybrid Architecture for Sequence Regression and Annotation.

Yizhe Zhang, Ricardo Henao, Lawrence Carin, Jianling Zhong, Alexander J. Hartemink

Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence, 2016

2014

Learning protein-DNA interaction landscapes by integrating experimental data through computational models.

Jianling Zhong, Todd Wasson, Alexander J. Hartemink

Bioinform., 2014

2013

Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program.

Xin Guo, Allister Bernard, David A. Orlando, Steven B. Haase, Alexander J. Hartemink

Proc. Natl. Acad. Sci. USA, 2013

Stability selection for regression-based models of transcription factor-DNA binding specificity.

Fantine Mordelet, John Horton, Alexander J. Hartemink, Barbara E. Engelhardt, Raluca Gordân

Bioinform., 2013

Using DNase Digestion Data to Accurately Identify Transcription Factor Binding Sites.

Kaixuan Luo, Alexander J. Hartemink

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Session Introduction.

Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Cell-cycle phenotyping with conditional random fields: A case study in Saccharomyces cerevisiae.

Michael B. Mayhew, Alexander J. Hartemink

Proceedings of the 10th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2013

2012

Close Encounters of the Collaborative Kind.

Michael B. Mayhew, Xin Guo, Steven B. Haase, Alexander J. Hartemink

Computer, 2012

Intrinsic Disorder Within and Flanking the DNA-Binding Domains of Human Transcription Factors.

Xin Guo, Martha L. Bulyk, Alexander J. Hartemink

Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

2011

A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments.

Michael B. Mayhew, Joshua W. Robinson, Boyoun Jung, Steven B. Haase, Alexander J. Hartemink

Bioinform., 2011

2010

Learning Non-Stationary Dynamic Bayesian Networks.

Joshua W. Robinson, Alexander J. Hartemink

J. Mach. Learn. Res., 2010

Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions.

Raluca Gordân, Alexander J. Hartemink, Martha L. Bulyk

Proceedings of the Research in Computational Molecular Biology, 2010

2009

Domain-oriented edge-based alignment of protein interaction networks.

Xin Guo, Alexander J. Hartemink

Bioinform., 2009

2008

A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery.

Raluca Gordân, Leelavati Narlikar, Alexander J. Hartemink

Proceedings of the Research in Computational Molecular Biology, 2008

Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery.

Raluca Gordân, Alexander J. Hartemink

Proceedings of the Biocomputing 2008, 2008

Session Introduction.

Martha L. Bulyk, Ernest Fraenkel, Alexander J. Hartemink, Yael Mandel-Gutfreund

Proceedings of the Biocomputing 2008, 2008

Non-stationary dynamic Bayesian networks.

Joshua W. Robinson, Alexander J. Hartemink

Proceedings of the Advances in Neural Information Processing Systems 21, 2008

2007

A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast.

Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink

PLoS Comput. Biol., 2007

Nucleosome Occupancy Information Improves <i>de novo</i> Motif Discovery.

Leelavati Narlikar, Raluca Gordân, Alexander J. Hartemink

Proceedings of the Research in Computational Molecular Biology, 2007

Reconstructing the Topology of Protein Complexes.

Allister Bernard, David S. Vaughn, Alexander J. Hartemink

Proceedings of the Research in Computational Molecular Biology, 2007

Session Introduction.

Martha L. Bulyk, Alexander J. Hartemink, Ernest Fraenkel, Gary D. Stormo

Proceedings of the Biocomputing 2007, 2007

2006

Computational Inference of Neural Information Flow Networks.

V. Anne Smith, Jing Yu, Tom V. Smulders, Alexander J. Hartemink, Erich D. Jarvis

PLoS Comput. Biol., 2006

Sequence features of DNA binding sites reveal structural class of associated transcription factor.

Leelavati Narlikar, Alexander J. Hartemink

Bioinform., 2006

Finding Diagnostic Biomarkers in Proteomic Spectra.

Pallavi N. Pratapa, Edward F. Patz Jr., Alexander J. Hartemink

Proceedings of the Biocomputing 2006, 2006

Informative priors based on transcription factor structural class improve <i>de novo</i> motif discovery.

Leelavati Narlikar, Raluca Gordân, Uwe Ohler, Alexander J. Hartemink

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005

Sparse Multinomial Logistic Regression: Fast Algorithms and Generalization Bounds.

Balaji Krishnapuram, Lawrence Carin, Mário A. T. Figueiredo, Alexander J. Hartemink

IEEE Trans. Pattern Anal. Mach. Intell., 2005

Theoretical and practical advances in genome halving.

Peng Yin, Alexander J. Hartemink

Bioinform., 2005

Session Introduction: Joint Learning from Multiple Types of Genomic Data.

Alexander J. Hartemink, Eran Segal

Proceedings of the Biocomputing 2005, 2005

Informative Structure Priors: Joint Learning of Dynamic Regulatory Networks from Multiple Types of Data.

Allister Bernard, Alexander J. Hartemink

Proceedings of the Biocomputing 2005, 2005

2004

A Bayesian Approach to Joint Feature Selection and Classifier Design.

Balaji Krishnapuram, Alexander J. Hartemink, Lawrence Carin, Mário A. T. Figueiredo

IEEE Trans. Pattern Anal. Mach. Intell., 2004

Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data.

Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink

J. Comput. Biol., 2004

Advances to Bayesian network inference for generating causal networks from observational biological data.

Jing Yu, V. Anne Smith, Paul P. Wang, Alexander J. Hartemink, Erich D. Jarvis

Bioinform., 2004

Session Introduction.

Alexander J. Hartemink, Eran Segal

Proceedings of the Biocomputing 2004, 2004

On Semi-Supervised Classification.

Balaji Krishnapuram, David Williams, Ya Xue, Alexander J. Hartemink, Lawrence Carin, Mário A. T. Figueiredo

Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004

2003

Joint classifier and feature optimization for cancer diagnosis using gene expression data.

Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink

Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

Influence of Network Topology and Data Collection on Network Inference.

V. Anne Smith, Erich D. Jarvis, Alexander J. Hartemink

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Genome, Pathway, and Interaction Bioinformatics - Session Introduction.

Peter D. Karp, Eric P. Neumann, Alexander J. Hartemink, Pedro Romero

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

2002

Bayesian Methods for Elucidating Genetic Regulatory Networks.

Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young

IEEE Intell. Syst., 2002

Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models.

Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young

Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

Evaluating functional network inference using simulations of complex biological systems.

V. Anne Smith, Erich D. Jarvis, Alexander J. Hartemink

Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

2001

Principled computational methods for the validation discovery of genetic regulatory networks.

Alexander J. Hartemink

PhD thesis, 2001

Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks.

Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young

Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

1999

Anonymous Authentication of Membership in Dynamic Groups.

Stuart E. Schechter, Todd Parnell, Alexander J. Hartemink

Proceedings of the Financial Cryptography, 1999

Simulating biological reactions: A modular approach.

Alexander J. Hartemink, Tarjei S. Mikkelsen, David K. Gifford

Proceedings of the DNA Based Computers, 1999

1997

Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation.

Alexander J. Hartemink, David K. Gifford

Proceedings of the DNA Based Computers, 1997