Bonnie Berger | Scholar Profiles and Rankings

Publications and Citation History

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Democratizing protein language models with parameter-efficient fine-tuning (journal article) Sledzieski, Samuel \| Kshirsagar, Meghana \| Baek, Minkyung \| Dodhia, Rahul \| Lavista Ferres, Juan \| Berger, Bonnie Proceedings of the National Academy of Sciences, volume 121, issue 26 (2024). 10.1073/pnas.2405840121 Cited by (1) \| Cite \| Source
Scanorama: integrating large and diverse single-cell transcriptomic datasets (journal article) Hie, Brian L. \| Kim, Soochi \| Rando, Thomas A. \| Bryson, Bryan \| Berger, Bonnie Nature Protocols (2024). 10.1038/s41596-024-00991-3 Cite \| Source
Lipophorin receptors genetically modulate neurodegeneration caused by reduction of Psn expression in the aging Drosophila brain (journal article) Kang, Jongkyun \| Zhang, Chen \| Wang, Yuhao \| Peng, Jian \| Berger, Bonnie \| Perrimon, Norbert \| Shen, Jie GENETICS, volume 226, issue 1 (2024). 10.1093/genetics/iyad202 Cite \| Source
Secure Discovery of Genetic Relatives Across Large-Scale and Distributed Genomic Datasets (book chapter) In Research in Computational Molecular Biology Hong, Matthew M. \| Froelicher, David \| Magner, Ricky \| Popic, Victoria \| Berger, Bonnie \| Cho, Hyunghoon Springer Nature Switzerland (2024) 10.1007/978-1-0716-3989-4_19 Cite \| Source
TT3D: Leveraging precomputed protein 3D sequence models to predict protein–protein interactions (journal article) Sledzieski, Samuel \| Devkota, Kapil \| Singh, Rohit \| Cowen, Lenore \| Berger, Bonnie Bioinformatics, volume 39, issue 11 (2023). 10.1093/bioinformatics/btad663 Cited by (2) \| Cite \| Source
SCA: recovering single-cell heterogeneity through information-based dimensionality reduction (journal article) DeMeo, Benjamin \| Berger, Bonnie Genome Biology, volume 24, issue 1 (2023). 10.1186/s13059-023-02998-7 Cited by (1) \| Cite \| Source
Efficient minimizer orders for large values of k using minimum decycling sets (journal article) Pellow, David \| Pu, Lianrong \| Ekim, Bariş \| Kotlar, Lior \| Berger, Bonnie \| Shamir, Ron \| Orenstein, Yaron Genome Research (2023). 10.1101/gr.277644.123 Cited by (1) \| Cite \| Source
Assessing transcriptomic reidentification risks using discriminative sequence models (journal article) Sadhuka, Shuvom \| Fridman, Daniel \| Berger, Bonnie \| Cho, Hyunghoon Genome Research (2023). 10.1101/gr.277699.123 Cite \| Source
sfkit: a web-based toolkit for secure and federated genomic analysis (journal article) Mendelsohn, Simon \| Froelicher, David \| Loginov, Denis \| Bernick, David \| Berger, Bonnie \| Cho, Hyunghoon Nucleic Acids Research, volume 51, issue W1, pages W535-W541 (2023). 10.1093/nar/gkad464 Cited by (2) \| Cite \| Source
Efficient mapping of accurate long reads in minimizer space with mapquik (journal article) Ekim, Bariş \| Sahlin, Kristoffer \| Medvedev, Paul \| Berger, Bonnie \| Chikhi, Rayan Genome Research (2023). 10.1101/gr.277679.123 Cited by (2) \| Cite \| Source
split-intein Gal4 provides intersectional genetic labeling that is repressible by Gal80 (journal article) Ewen-Campen, Ben \| Luan, Haojiang \| Xu, Jun \| Singh, Rohit \| Joshi, Neha \| Thakkar, Tanuj \| Berger, Bonnie \| White, Benjamin H. \| Perrimon, Norbert Proceedings of the National Academy of Sciences, volume 120, issue 24 (2023). 10.1073/pnas.2304730120 Cited by (8) \| Cite \| Source
Contrastive learning in protein language space predicts interactions between drugs and protein targets (journal article) Singh, Rohit \| Sledzieski, Samuel \| Bryson, Bryan \| Cowen, Lenore \| Berger, Bonnie Proceedings of the National Academy of Sciences, volume 120, issue 24 (2023). 10.1073/pnas.2220778120 Cited by (31) \| Cite \| Source
Scalable and Privacy-Preserving Federated Principal Component Analysis (conference) Froelicher, David \| Cho, Hyunghoon \| Edupalli, Manaswitha \| Sa Sousa, Joao \| Bossuat, Jean-Philippe \| Pyrgelis, Apostolos \| Troncoso-Pastoriza, Juan R. \| Berger, Bonnie \| Hubaux, Jean-Pierre 2023 IEEE Symposium on Security and Privacy (SP) (2023) San Francisco, CA, USA 10.1109/SP46215.2023.10179350 Cited by (4) \| Cite \| Source
Navigating bottlenecks and trade-offs in genomic data analysis (journal article) Berger, Bonnie \| Yu, Yun William Nature Reviews Genetics, volume 24, issue 4, pages 235-250 (2023). 10.1038/s41576-022-00551-z Cited by (9) \| Cite \| Source
Codon: A Compiler for High-Performance Pythonic Applications and DSLs (conference) Shajii, Ariya \| Ramirez, Gabriel \| Smajlović, Haris \| Ray, Jessica \| Berger, Bonnie \| Amarasinghe, Saman \| Numanagić, Ibrahim CC '23: 32nd ACM SIGPLAN International Conference on Compiler Construction (2023) Montréal QC Canada 10.1145/3578360.3580275 Cited by (6) \| Cite \| Source
Sequre: a high-performance framework for secure multiparty computation enables biomedical data sharing (journal article) Smajlović, Haris \| Shajii, Ariya \| Berger, Bonnie \| Cho, Hyunghoon \| Numanagić, Ibrahim Genome Biology, volume 24, issue 1 (2023). 10.1186/s13059-022-02841-5 Cited by (7) \| Cite \| Source
virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2 (journal article) Zaman, Sumaira \| Sledzieski, Samuel \| Berger, Bonnie \| Wu, Yi-Chieh \| Bansal, Mukul S. Journal of Computational Biology, volume 30, issue 1, pages 3-20 (2023). 10.1089/cmb.2021.0507 Cited by (2) \| Cite \| Source
Uncovering structural ensembles from single-particle cryo-EM data using cryoDRGN (journal article) Kinman, Laurel F. \| Powell, Barrett M. \| Zhong, Ellen D. \| Berger, Bonnie \| Davis, Joseph H. Nature Protocols (2022). 10.1038/s41596-022-00763-x Cited by (6) \| Cite \| Source
Genome-wide mapping of somatic mutation rates uncovers drivers of cancer (journal article) Sherman, Maxwell A. \| Yaari, Adam U. \| Priebe, Oliver \| Dietlein, Felix \| Loh, Po-Ru \| Berger, Bonnie Nature Biotechnology, volume 40, issue 11, pages 1634-1643 (2022). 10.1038/s41587-022-01353-8 Cited by (18) \| Cite \| Source
Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis) (journal article) Jaiswal, Swati \| Nyquist, Sarah K. \| Boyce, Shayla \| Jivanjee, Tasneem \| Ibrahim, Samira \| Bromley, Joshua D. \| Gatter, G. James \| Gideon, Hannah \| Patel, Kush \| Ganchua, Sharie Keanne \| ... \| Behar, Samuel M. BMC Genomics, volume 23, issue 1 (2022). 10.1186/s12864-022-08867-0 Cited by (3) \| Cite \| Source

Title	Investigators	Year	Expiration	Amount
The Nineteenth International Conference on Research in Computational Molecular Biology (RECOMB 2015)	Berger, Bonnie	02-01-2015	01-31-2016	$12,000
Career: Probabilistic Methods and Algorithms to Solve Protein Folding Problems	Berger, Bonnie	07-01-1995	08-31-1999	$124,582