ModuleFinder: A Tool for Computational Discovery of Cis Regulatory Modules. - Anthony A. Philippakis; Fangxue Sherry He; Martha L. Bulyk (Pacific Symposium on Biocomputing, 2005)

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data. - Bertrand R. Huber; Martha L. Bulyk (BMC Bioinform., 2006)

Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells. - Anthony A. Philippakis; Brian W. Busser; Stephen S. Gisselbrecht; Fangxue Sherry He; Beatriz Estrada; Alan M. Michelson; Martha L. Bulyk (PLoS Comput. Biol., 2006)

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

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

Functional Trends in Structural Classes of the DNA Binding Domains of Regulatory Transcription Factors. - Rachel Patton McCord; Martha L. Bulyk (Pacific Symposium on Biocomputing, 2008)

Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments. - Anthony A. Philippakis; Aaron M. Qureshi; Michael F. Berger; Martha L. Bulyk (J. Comput. Biol., 2008)

Predicting the binding preference of transcription factors to individual DNA k-mers. - Trevis M. Alleyne; Lourdes Peña Castillo; Gwenael Badis; Shaheynoor Talukder; Michael F. Berger; Andrew R. Gehrke; Anthony A. Philippakis; Martha L. Bulyk; Quaid Morris; Timothy R. Hughes (Bioinform., 2009)

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. - Daniel E. Newburger; Martha L. Bulyk (Nucleic Acids Res., 2009)

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

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions. - Kimberly Robasky; Martha L. Bulyk (Nucleic Acids Res., 2011)

Identification of Cell Cycle-Regulated, Putative Hyphal Genes in Candida Albicans. - Raluca Gordân; Saumyadipta Pyne; Martha L. Bulyk (Pacific Symposium on Biocomputing, 2012)

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)

LOESS correction for length variation in gene set-based genomic sequence analysis. - Anton Aboukhalil; Martha L. Bulyk (Bioinform., 2012)

Bayesian hierarchical model of protein-binding microarray k-mer data reduces noise and identifies transcription factor subclasses and preferred k-mers. - Bo Jiang 005; Jun S. Liu; Martha L. Bulyk (Bioinform., 2013)

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions. - Maxwell A. Hume; Luis A. Barrera; Stephen S. Gisselbrecht; Martha L. Bulyk (Nucleic Acids Res., 2015)

Reading between the genes: interpreting non-coding DNA in high-throughput. - Joanne Berghout; Yves A. Lussier; Francesca Vitali; Martha L. Bulyk; Maricel G. Kann; Jason H. Moore (PSB, 2019)

Session introduction. - Steven E. Brenner; Martha L. Bulyk; Dana C. Crawford; Jill P. Mesirov; Alexander A. Morgan; Predrag Radivojac (PSB, 2019)

Session Introduction. - Steven E. Brenner; Martha L. Bulyk; Dana C. Crawford; Alexander A. Morgan; Predrag Radivojac; Nicholas P. Tatonetti (PSB, 2020)

Computational Challenges and Artificial Intelligence in Precision Medicine. - Olga Afanasiev; Joanne Berghout; Steven E. Brenner; Martha L. Bulyk; Dana C. Crawford; Jonathan H. Chen; Roxana Daneshjou; Lukasz Kidzinski (PSB, 2021)