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Cell Systems|December 25, 2017
Enhancing Evolutionary Couplings with Deep Convolutional Neural NetworksYang Liu, Perry Palmedo, Qing Ye, et al.
Nature Communications|August 29, 2025
Unveiling causal regulatory mechanisms through cell-state parallaxAlexander P Wu, Rohit Singh, Christopher A Walsh, et al.
Genome Biology|January 11, 2023
Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharingHaris Smajlović, Ariya Shajii, Bonnie Berger, et al.
Bioinformatics (Oxford, England)|October 28, 2023
TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactionsSamuel Sledzieski, Kapil Devkota, Rohit Singh, et al.
Proceedings of the National Academy of Sciences of the United States of America|June 8, 2023
Contrastive learning in protein language space predicts interactions between drugs and protein targetsRohit Singh, Samuel Sledzieski, Bryan Bryson, et al.
Biorxiv : the Preprint Server for Biology|June 22, 2026
Promera: a unified model for biomolecular structure prediction, filtering, and designBowen Jing, Mihir Bafna, Daniel Diaz, et al.
Genome Biology|February 2, 2012
MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosisLeonid Chindelevitch, Sarah Stanley, Deborah Hung, et al.
Bioinformatics (Oxford, England)|September 20, 2013
Optimizing a global alignment of protein interaction networksLeonid Chindelevitch, Cheng-Yu Ma, Chung-Shou Liao, et al.
Genome Research|July 3, 2023
Efficient mapping of accurate long reads in minimizer space with mapquikBariş Ekim, Kristoffer Sahlin, Paul Medvedev, et al.
Bioinformatics (Oxford, England)|March 13, 2012
SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zoneNoah M Daniels, Raghavendra Hosur, Bonnie Berger, et al.
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