| 2019 | HPCA | 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 |
| 2019 | USENIX | Darwin: A Genomics Co-processor Provides up to 15, 000X Acceleration on Long Read Assembly. | Yatish Turakhia, Gill Bejerano, William J. Dally |
| 2018 | ASPLOS | Darwin: A Genomics Co-processor Provides up to 15, 000X Acceleration on Long Read Assembly. | Yatish Turakhia, Gill Bejerano, William J. Dally |
| 2004 | ISMB | Into the heart of darkness: large-scale clustering of human non-coding DNA. | Gill Bejerano, David Haussler, Mathieu Blanchette |
| 2003 | RECOMB | Efficient exact value computation and applications to biosequence analysis. | Gill Bejerano |
| 2002 | ICML | Discriminative Feature Selection via Multiclass Variable Memory Markov Model. | Noam Slonim, Gill Bejerano, Shai Fine, Naftali Tishby |
| 2001 | ICML | Unsupervised Sequence Segmentation by a Mixture of Switching Variable Memory Markov Sources. | Yevgeny Seldin, Gill Bejerano, Naftali Tishby |
| 2001 | WABI | A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites. | Yoseph Barash, Gill Bejerano, Nir Friedman |
| 2000 | RECOMB | Optimal amnesic probabilistic automata or how to learn and classify proteins in linear time and space. | Alberto Apostolico, Gill Bejerano |
| 1999 | RECOMB | Modeling protein families using probabilistic suffix trees. | Gill Bejerano, Golan Yona |