Bonnie Berger

Affiliations: 
1992- Mathematics Massachusetts Institute of Technology, Cambridge, MA, United States 
Area:
Theoretical Computer Science, Computational Biological Modeling, Computational Biology
Website:
https://math.mit.edu/directory/profile.html?pid=20
Google:
""Bonnie Anne Berger MIT""
Bio:

https://scholar.google.com/citations?user=bYjKaowAAAAJ&hl=en
https://people.csail.mit.edu/silvio/CV.pdf

Parents

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Silvio Micali grad student 1990 MIT (Computer Science Tree)
 (Using Randomness to Design Efficient Deterministic Algorithms)

Children

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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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Battistella E, Maheshwari A, Ekim B, et al. (2025) ralphi: a deep reinforcement learning framework for haplotype assembly. Biorxiv : the Preprint Server For Biology
Singh M, Sahinalp C, Zeng J, et al. (2024) How has the AI boom impacted algorithmic biology? Cell Systems. 15: 483-487
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
Berger B, Yu YW. (2022) Navigating bottlenecks and trade-offs in genomic data analysis. Nature Reviews. Genetics
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
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
Ekim B, Berger B, Orenstein Y. (2020) A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005- ). 12074: 37-53
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
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