Alexander Derry
Overview
Explore the profile of Alexander Derry including associated specialties, affiliations and a list of published articles.
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Articles
10
Citations
182
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0
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Recent Articles
1.
Hayes T, Rao R, Akin H, Sofroniew N, Oktay D, Lin Z, et al.
Science
. 2025 Jan;
387(6736):850-858.
PMID: 39818825
More than 3 billion years of evolution have produced an image of biology encoded into the space of natural proteins. Here, we show that language models trained at scale on...
2.
Machiraju G, Derry A, Desai A, Guha N, Karimi A, Zou J, et al.
ArXiv
. 2024 Jul;
PMID: 38947933
Feature attribution, the ability to localize regions of the input data that are relevant for classification, is an important capability for ML models in scientific and biomedical domains. Current methods...
3.
Derry A, Altman R
bioRxiv
. 2023 Oct;
PMID: 37905033
The rapid expansion of protein sequence and structure databases has resulted in a significant number of proteins with ambiguous or unknown function. While advances in machine learning techniques hold great...
4.
Derry A, Krzywinski M, Altman N
Nat Methods
. 2023 Aug;
20(9):1269-1270.
PMID: 37580560
No abstract available.
5.
Derry A, Krzywinski M, Altman N
Nat Methods
. 2023 Jan;
20(2):165-167.
PMID: 36627451
No abstract available.
6.
Derry A, Altman R
Protein Sci
. 2022 Dec;
32(2):e4541.
PMID: 36519247
The identification and characterization of the structural sites which contribute to protein function are crucial for understanding biological mechanisms, evaluating disease risk, and developing targeted therapies. However, the quantity of...
7.
Anand N, Eguchi R, Mathews I, Perez C, Derry A, Altman R, et al.
Nat Commun
. 2022 Feb;
13(1):746.
PMID: 35136054
The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. Here,...
8.
Derry A, Carpenter K, Altman R
Pac Symp Biocomput
. 2021 Dec;
27:10-21.
PMID: 34890132
The three-dimensional structures of proteins are crucial for understanding their molecular mechanisms and interactions. Machine learning algorithms that are able to learn accurate representations of protein structures are therefore poised...
9.
Rensi S, Keys A, Lo Y, Derry A, McInnes G, Liu T, et al.
ChemRxiv
. 2020 Jun;
PMID: 32511288
The most rapid path to discovering treatment options for the novel coronavirus SARS-CoV-2 is to find existing medications that are active against the virus. We have focused on identifying repurposing...
10.
Sosa D, Derry A, Guo M, Wei E, Brinton C, Altman R
Pac Symp Biocomput
. 2019 Dec;
25:463-474.
PMID: 31797619
Millions of Americans are affected by rare diseases, many of which have poor survival rates. However, the small market size of individual rare diseases, combined with the time and capital...