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Cell Systems|August 24, 2018
Statistical Binning for Barcoded Reads Improves Downstream AnalysesAriya Shajii, Ibrahim Numanagić, Christopher Whelan, et al.
Nucleic Acids Research|June 18, 2009
RNAmutants: a web server to explore the mutational landscape of RNA secondary structuresJerome Waldispühl, Srinivas Devadas, Bonnie Berger, et al.
Plos Computational Biology|March 29, 2014
HapTree: a novel Bayesian framework for single individual polyplotyping using NGS dataEmily Berger, Deniz Yorukoglu, Jian Peng, et al.
Arxiv|October 14, 2024
Generative Modeling of Molecular Dynamics TrajectoriesBowen Jing, Hannes Stärk, Tommi Jaakkola, et al.
F1000Research|July 18, 2017
2017 ISCB Accomplishment by a Senior Scientist Award: Pavel PevznerChristiana N Fogg, Diane E Kovats, Bonnie Berger
Cell Systems|September 18, 2021
D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactionsSamuel Sledzieski, Rohit Singh, Lenore Cowen, et al.
Nature Communications|January 7, 2026
Learning the language of protein-protein interactionsVarun Ullanat, Bowen Jing, Samuel Sledzieski, et al.
Biorxiv : the Preprint Server for Biology|April 1, 2025
Learning the language of protein-protein interactionsVarun Ullanat, Bowen Jing, Samuel Sledzieski, et al.
Genome Research|August 4, 2023
Assessing transcriptomic reidentification risks using discriminative sequence modelsShuvom Sadhuka, Daniel Fridman, Bonnie Berger, et al.
Genome Research|February 11, 2010
Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screenOaz Nir, Chris Bakal, Norbert Perrimon, et al.
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