Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation. - Alexander J. Hartemink; David K. Gifford (DNA Based Computers, 1997)

Simulating biological reactions: A modular approach. - Alexander J. Hartemink; Tarjei S. Mikkelsen; David K. Gifford (DNA Based Computers, 1999)

Anonymous Authentication of Membership in Dynamic Groups. - Stuart E. Schechter; Todd Parnell; Alexander J. Hartemink (Financial Cryptography, 1999)

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 (Pacific Symposium on Biocomputing, 2001)

Principled computational methods for the validation discovery of genetic regulatory networks. - Alexander J. Hartemink (2001)

Evaluating functional network inference using simulations of complex biological systems. - V. Anne Smith; Erich D. Jarvis; Alexander J. Hartemink (ISMB, 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 (Pacific Symposium on Biocomputing, 2002)

Bayesian Methods for Elucidating Genetic Regulatory Networks. - Alexander J. Hartemink; David K. Gifford; Tommi S. Jaakkola; Richard A. Young (IEEE Intell. Syst., 2002)

Genome, Pathway, and Interaction Bioinformatics - Session Introduction. - Peter D. Karp; Eric P. Neumann; Alexander J. Hartemink; Pedro Romero (Pacific Symposium on Biocomputing, 2003)

Influence of Network Topology and Data Collection on Network Inference. - V. Anne Smith; Erich D. Jarvis; Alexander J. Hartemink (Pacific Symposium on Biocomputing, 2003)

Joint classifier and feature optimization for cancer diagnosis using gene expression data. - Balaji Krishnapuram; Lawrence Carin; Alexander J. Hartemink (RECOMB, 2003)

On Semi-Supervised Classification. - Balaji Krishnapuram; David Williams; Ya Xue; Alexander J. Hartemink; Lawrence Carin; Mário A. T. Figueiredo (NIPS, 2004)

Session Introduction. - Alexander J. Hartemink; Eran Segal (Pacific Symposium on Biocomputing, 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)

Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data. - Balaji Krishnapuram; Lawrence Carin; Alexander J. Hartemink (J. Comput. Biol., 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)

Informative Structure Priors: Joint Learning of Dynamic Regulatory Networks from Multiple Types of Data. - Allister Bernard; Alexander J. Hartemink (Pacific Symposium on Biocomputing, 2005)

Session Introduction: Joint Learning from Multiple Types of Genomic Data. - Alexander J. Hartemink; Eran Segal (Pacific Symposium on Biocomputing, 2005)

Theoretical and practical advances in genome halving. - Peng Yin; Alexander J. Hartemink (Bioinform., 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)

Informative priors based on transcription factor structural class improve de novo motif discovery. - Leelavati Narlikar; Raluca Gordân; Uwe Ohler; Alexander J. Hartemink (ISMB (Supplement of Bioinformatics), 2006)

Finding Diagnostic Biomarkers in Proteomic Spectra. - Pallavi N. Pratapa; Edward F. Patz Jr.; Alexander J. Hartemink (Pacific Symposium on Biocomputing, 2006)

Sequence features of DNA binding sites reveal structural class of associated transcription factor. - Leelavati Narlikar; Alexander J. Hartemink (Bioinform., 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)

Session Introduction. - Martha L. Bulyk; Alexander J. Hartemink; Ernest Fraenkel; Gary D. Stormo (Pacific Symposium on Biocomputing, 2007)

Reconstructing the Topology of Protein Complexes. - Allister Bernard; David S. Vaughn; Alexander J. Hartemink (RECOMB, 2007)

Nucleosome Occupancy Information Improves de novo Motif Discovery. - Leelavati Narlikar; Raluca Gordân; Alexander J. Hartemink (RECOMB, 2007)

A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast. - Leelavati Narlikar; Raluca Gordân; Alexander J. Hartemink (PLoS Comput. Biol., 2007)

Non-stationary dynamic Bayesian networks. - Joshua W. Robinson; Alexander J. Hartemink (NIPS, 2008)

Session Introduction. - Martha L. Bulyk; Ernest Fraenkel; Alexander J. Hartemink; Yael Mandel-Gutfreund (Pacific Symposium on Biocomputing, 2008)

Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery. - Raluca Gordân; Alexander J. Hartemink (Pacific Symposium on Biocomputing, 2008)

A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery. - Raluca Gordân; Leelavati Narlikar; Alexander J. Hartemink (RECOMB, 2008)

Domain-oriented edge-based alignment of protein interaction networks. - Xin Guo; Alexander J. Hartemink (Bioinform., 2009)

Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions. - Raluca Gordân; Alexander J. Hartemink; Martha L. Bulyk (RECOMB, 2010)

Learning Non-Stationary Dynamic Bayesian Networks. - Joshua W. Robinson; Alexander J. Hartemink (J. Mach. Learn. Res., 2010)

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)

Intrinsic Disorder Within and Flanking the DNA-Binding Domains of Human Transcription Factors. - Xin Guo; Martha L. Bulyk; Alexander J. Hartemink (Pacific Symposium on Biocomputing, 2012)

Close Encounters of the Collaborative Kind. - Michael B. Mayhew; Xin Guo; Steven B. Haase; Alexander J. Hartemink (Computer, 2012)

Cell-cycle phenotyping with conditional random fields: A case study in Saccharomyces cerevisiae. - Michael B. Mayhew; Alexander J. Hartemink (ISBI, 2013)

Session Introduction. - Alexander J. Hartemink; Manolis Kellis; William Stafford Noble; Zhiping Weng (Pacific Symposium on Biocomputing, 2013)

Using DNase Digestion Data to Accurately Identify Transcription Factor Binding Sites. - Kaixuan Luo; Alexander J. Hartemink (Pacific Symposium on Biocomputing, 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)

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)

Learning protein-DNA interaction landscapes by integrating experimental data through computational models. - Jianling Zhong; Todd Wasson; Alexander J. Hartemink (Bioinform., 2014)

Learning a Hybrid Architecture for Sequence Regression and Annotation. - Yizhe Zhang 002; Ricardo Henao; Lawrence Carin; Jianling Zhong; Alexander J. Hartemink (AAAI, 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 (RECOMB, 2016)

E Pluribus Unum: United States of Single Cells. - Joshua D. Welch; Alexander J. Hartemink; Jan F. Prins (RECOMB, 2017)

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 (RECOMB, 2020)