Regina Barzilay
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Explore the profile of Regina Barzilay including associated specialties, affiliations and a list of published articles.
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60
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2673
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Recent Articles
1.
Wohlwend J, Nathan A, Shalon N, Crain C, Tano-Menka R, Goldberg B, et al.
Nat Mach Intell
. 2025 Feb;
7(2):232-243.
PMID: 40008296
Accurate in silico determination of CD8 T cell epitopes would greatly enhance T cell-based vaccine development, but current prediction models are not reliably successful. Here, motivated by recent successes applying...
2.
Kilgore H, Chinn I, Mikhael P, Mitnikov I, Van Dongen C, Zylberberg G, et al.
Science
. 2025 Feb;
387(6738):1095-1101.
PMID: 39913643
Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. In this study, we demonstrate that proteins with...
3.
Wohlwend J, Corso G, Passaro S, Reveiz M, Leidal K, Swiderski W, et al.
bioRxiv
. 2024 Nov;
PMID: 39605745
Understanding biomolecular interactions is fundamental to advancing fields like drug discovery and protein design. In this paper, we introduce Boltz-1, an open-source deep learning model incorporating innovations in model architecture,...
4.
Fan V, Qian Y, Wang A, Wang A, Coley C, Barzilay R
J Chem Inf Model
. 2024 Jul;
64(14):5521-5534.
PMID: 38950894
Information extraction from chemistry literature is vital for constructing up-to-date reaction databases for data-driven chemistry. Complete extraction requires combining information across text, tables, and figures, whereas prior work has mainly...
5.
Campbell A, Yim J, Barzilay R, Rainforth T, Jaakkola T
ArXiv
. 2024 Jun;
PMID: 38883240
Combining discrete and continuous data is an important capability for generative models. We present Discrete Flow Models (DFMs), a new flow-based model of discrete data that provides the missing link...
6.
Stark H, Jing B, Wang C, Corso G, Berger B, Barzilay R, et al.
ArXiv
. 2024 Jun;
PMID: 38855543
Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this...
7.
Kilgore H, Chinn I, Mikhael P, Mitnikov I, Van Dongen C, Zylberberg G, et al.
bioRxiv
. 2024 Apr;
PMID: 38659952
Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must efficiently assemble. Here, we demonstrate that proteins with shared...
8.
Corso G, Deng A, Fry B, Polizzi N, Barzilay R, Jaakkola T
ArXiv
. 2024 Mar;
PMID: 38463508
Accurate blind docking has the potential to lead to new biological breakthroughs, but for this promise to be realized, docking methods must generalize well across the proteome. Existing benchmarks, however,...
9.
Yim J, Campbell A, Mathieu E, Foong A, Gastegger M, Jimenez-Luna J, et al.
ArXiv
. 2024 Jan;
PMID: 38259348
Protein design often begins with the knowledge of a desired function from a motif which motif-scaffolding aims to construct a functional protein around. Recently, generative models have achieved breakthrough success...
10.
Koscher B, Canty R, McDonald M, Greenman K, McGill C, Bilodeau C, et al.
Science
. 2023 Dec;
382(6677):eadi1407.
PMID: 38127734
A closed-loop, autonomous molecular discovery platform driven by integrated machine learning tools was developed to accelerate the design of molecules with desired properties. We demonstrated two case studies on dye-like...