Bonnie Berger
Affiliations: | 1992- | Mathematics | Massachusetts Institute of Technology, Cambridge, MA, United States |
Area:
Theoretical Computer Science, Computational Biological Modeling, Computational BiologyWebsite:
https://math.mit.edu/directory/profile.html?pid=20Google:
""Bonnie Anne Berger MIT""Bio:
https://scholar.google.com/citations?user=bYjKaowAAAAJ&hl=en
https://people.csail.mit.edu/silvio/CV.pdf
Parents
Sign in to add mentor| Silvio Micali | grad student | 1990 | MIT (Computer Science Tree) | |
| (Using Randomness to Design Efficient Deterministic Algorithms) | ||||
Children
Sign in to add trainee| Lisa C. Tucker-Kellogg | research assistant | 1991-1993 | (Neurotree) |
| Michael Baym | grad student | ||
| Baris Ekim | grad student | MIT | |
| Russell Schwartz | grad student | MIT | |
| Mona Singh | grad student | 1990-1995 | MIT (Computer Science Tree) |
| Lior Pachter | grad student | 1994-1999 | MIT (Evolution Tree) |
| Manolis Kellis | grad student | 2000-2003 | MIT |
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Publications
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| Sledzieski S, Devkota K, Singh R, et al. (2023) TT3D: Leveraging Pre-Computed Protein 3D Sequence Models to Predict Protein-Protein Interactions. Bioinformatics (Oxford, England) |
| Pellow D, Pu L, Ekim B, et al. (2023) Efficient minimizer orders for large values of using minimum decycling sets. Genome Research |
| Ekim B, Sahlin K, Medvedev P, et al. (2023) Efficient mapping of accurate long reads in minimizer space with mapquik. Genome Research |
| Singh R, Sledzieski S, Bryson B, et al. (2023) Contrastive learning in protein language space predicts interactions between drugs and protein targets. Proceedings of the National Academy of Sciences of the United States of America. 120: e2220778120 |
| Kumar L, Brenner N, Sledzieski S, et al. (2023) Transfer of knowledge from model organisms to evolutionarily distant non-model organisms: The coral Pocillopora damicornis membrane signaling receptome. Plos One. 18: e0270965 |
| Zaman S, Sledzieski S, Berger B, et al. (2022) virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology |
| Singh R, Devkota K, Sledzieski S, et al. (2022) Topsy-Turvy: integrating a global view into sequence-based PPI prediction. Bioinformatics (Oxford, England). 38: i264-i272 |
| Sledzieski S, Singh R, Cowen L, et al. (2021) D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions. Cell Systems |
| Ekim B, Berger B, Chikhi R. (2021) Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer. Cell Systems |
| Berger E, Yorukoglu D, Zhang L, et al. (2020) Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets. Nature Communications. 11: 4662 |