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Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|August 20, 2005
Wrap-and-Pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoilsMatthew Menke, Jonathan King, Bonnie Berger, et al.IEEE Transactions on Information Theory|July 14, 2021
Levenshtein Distance, Sequence Comparison and Biological Database SearchBonnie Berger, Michael S Waterman, Yun William YuF1000Research|July 18, 2017
2017 Outstanding Contributions to ISCB Award: Fran LewitterChristiana N Fogg, Diane E Kovats, Bonnie BergerF1000Research|July 18, 2017
2017 ISCB Overton Prize: Christoph BockChristiana N Fogg, Diane E Kovats, Bonnie BergerPlos Computational Biology|August 9, 2008
Efficient algorithms for probing the RNA mutation landscapeJérôme Waldispühl, Srinivas Devadas, Bonnie Berger, et al.Proceedings of the National Academy of Sciences of the United States of America|August 19, 2025
Sparse autoencoders uncover biologically interpretable features in protein language model representationsOnkar Gujral, Mihir Bafna, Eric Alm, et al.Proceedings of the National Academy of Sciences of the United States of America|August 24, 2010
Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3'UTRsMichael Schnall-Levin, Yong Zhao, Norbert Perrimon, et al.Bioinformatics (Oxford, England)|December 21, 2019
Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activationLuke A D Hutchison, Bonnie Berger, Isaac S KohaneCell Systems|May 16, 2024
Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factorsRohit Singh, Alexander P Wu, Anish Mudide, et al.Biorxiv : the Preprint Server for Biology|March 27, 2026
Evolutionary dynamics under phenotypic uncertaintyVaibhav Mohanty, Anna Sappington, Eugene I Shakhnovich, et al.Pageof 24