Modeling protein families using probabilistic suffix trees. - Gill Bejerano; Golan Yona (RECOMB, 1999)

Optimal Amnesic Probabilistic Automata or How to Learn and Classify Proteins in Linear Time and Space. - Alberto Apostolico; Gill Bejerano (J. Comput. Biol., 2000)

Automatic Modeling of Musical Style. - Olivier Lartillot; Shlomo Dubnov; Gérard Assayag; Gill Bejerano (ICMC, 2001)

Unsupervised Sequence Segmentation by a Mixture of Switching Variable Memory Markov Sources. - Yevgeny Seldin; Gill Bejerano; Naftali Tishby (ICML, 2001)

A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites. - Yoseph Barash; Gill Bejerano; Nir Friedman (WABI, 2001)

Markovian domain fingerprinting: statistical segmentation of protein sequences. - Gill Bejerano; Yevgeny Seldin; Hanah Margalit; Naftali Tishby (Bioinform., 2001)

Variations on probabilistic suffix trees: statistical modeling and prediction of protein families. - Gill Bejerano; Golan Yona (Bioinform., 2001)

PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. - Ruti Hershberg; Gill Bejerano; Alberto Santos-Zavaleta; Hanah Margalit (Nucleic Acids Res., 2001)

Efficient exact value computation and applications to biosequence analysis. - Gill Bejerano (RECOMB, 2003)

Using Machine-Learning Methods for Musical Style Modeling. - Shlomo Dubnov; Gérard Assayag; Olivier Lartillot; Gill Bejerano (Computer, 2003)

Discriminative Feature Selection via Multiclass Variable Memory Markov Model. - Noam Slonim; Gill Bejerano; Shai Fine; Naftali Tishby (EURASIP J. Adv. Signal Process., 2003)

Automata learning and stocahstic modeling for biosequence analysis (למידת אוטומטים ומידול סטוכסטי לצרכי ניתוח רצפי מולקולות ביולוגיות.). - Gill Bejerano (2003)

Into the heart of darkness: large-scale clustering of human non-coding DNA. - Gill Bejerano; David Haussler; Mathieu Blanchette (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Algorithms for variable length Markov chain modeling. - Gill Bejerano (Bioinform., 2004)

Efficient Exact p-Value Computation for Small Sample, Sparse, and Surprising Categorical Data. - Gill Bejerano; Nir Friedman; Naftali Tishby (J. Comput. Biol., 2004)

Branch and bound computation of exact p-values. - Gill Bejerano (Bioinform., 2006)

The UCSC Genome Browser Database: update 2006. - Angela S. Hinrichs; Donna Karolchik; Robert Baertsch; Galt P. Barber; Gill Bejerano; Hiram Clawson; Mark Diekhans; Terrence S. Furey; Rachel A. Harte; Fan Hsu; Jennifer Hillman-Jackson; Robert M. Kuhn; et al. (Nucleic Acids Res., 2006)

Identification and Classification of Conserved RNA Secondary Structures in the Human Genome. - Jakob Skou Pedersen; Gill Bejerano; Adam C. Siepel; Kate R. Rosenbloom; Kerstin Lindblad-Toh; Eric S. Lander; Jim Kent; Webb Miller; David Haussler (PLoS Comput. Biol., 2006)

The UCSC genome browser database: update 2007. - Robert M. Kuhn; Donna Karolchik; Ann S. Zweig; Heather Trumbower; Daryl J. Thomas; Archana Thakkapallayil; Charles W. Sugnet; Mario Stanke; Kayla E. Smith; Adam C. Siepel; Kate R. Rosenbloom; Brooke L. Rhead; et al. (Nucleic Acids Res., 2007)

Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data. - Geetu Tuteja; Karen Betancourt Moreira; Tisha Chung; Jenny Chen; Aaron M. Wenger; Gill Bejerano (PLoS Comput. Biol., 2014)

Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories. - Harendra Guturu; Sandeep Chinchali; Shoa L. Clarke; Gill Bejerano (PLoS Comput. Biol., 2016)

Darwin: A Genomics Co-processor Provides up to 15, 000X Acceleration on Long Read Assembly. - Yatish Turakhia; Gill Bejerano; William J. Dally (ASPLOS, 2018)

Darwin-WGA: A Co-processor Provides Increased Sensitivity in Whole Genome Alignments with High Speedup. - Yatish Turakhia; Sneha D. Goenka; Gill Bejerano; William J. Dally (HPCA, 2019)

Darwin: A Genomics Coprocessor. - Yatish Turakhia; Gill Bejerano; William J. Dally (IEEE Micro, 2019)

Avoiding genetic racial profiling in criminal DNA profile databases. - Jacob A. Blindenbach; Karthik Anand Jagadeesh; Gill Bejerano; David J. Wu 001 (Nat. Comput. Sci., 2021)

WhichTF is functionally important in your open chromatin data? - Yosuke Tanigawa; Ethan Dyer; Gill Bejerano (PLoS Comput. Biol., 2022)

Enriched phenotypes in rare variant carriers suggest pathogenic mechanisms in rare disease patients. - Lane Fitzsimmons; Maria T. Acosta; David R. Adams; Ben Afzali; Ali Al-Beshri; Eric Allenspach; Aimee Allworth; Raquel L. Alvarez; Justin Alvey; Ashley Andrews; Euan A. Ashley; Carlos A. Bacino; et al. (BioData Min., 2025)