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Carlos L. Araya
Researcher at Stanford University
Publications - 26
Citations - 3002
Carlos L. Araya is an academic researcher from Stanford University. The author has contributed to research in topics: Gene & Genome. The author has an hindex of 16, co-authored 25 publications receiving 2329 citations. Previous affiliations of Carlos L. Araya include University of Washington.
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Journal ArticleDOI
High-resolution mapping of protein sequence-function relationships
Douglas M. Fowler,Carlos L. Araya,Sarel J. Fleishman,Elizabeth H. Kellogg,Jason J. Stephany,Jason J. Stephany,David Baker,David Baker,Stanley Fields,Stanley Fields +9 more
TL;DR: This work tracked the performance of >600,000 variants of a human WW domain after three and six rounds of selection by phage display for binding to its peptide ligand, providing a general means for understanding how protein function relates to sequence.
Posted Content
Captum: A unified and generic model interpretability library for PyTorch.
Narine Kokhlikyan,Vivek Miglani,Miguel Martin,Edward Wang,Bilal Alsallakh,Jonathan Reynolds,Alexander Melnikov,Natalia Kliushkina,Carlos L. Araya,Siqi Yan,Orion Reblitz-Richardson +10 more
TL;DR: An interactive visualization tool called Captum Insights that is built on top of Captum library and allows sample-based model debugging and visualization using feature importance metrics and is designed for easy understanding and use.
Journal ArticleDOI
Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens
David W. Morgens,Michael Wainberg,Evan A. Boyle,Oana Ursu,Carlos L. Araya,C. Kimberly Tsui,Michael S. Haney,Gaelen T. Hess,Kyuho Han,Edwin E. Jeng,Amy Li,Michael Snyder,William J. Greenleaf,Anshul Kundaje,Michael C. Bassik +14 more
TL;DR: A CRISPR-Cas9 library with 10 variable-length guides per gene and thousands of negative controls targeting non-functional, non-genic regions (termed safe-targeting guides) has excellent performance in identifying genes affecting growth and sensitivity to the ricin toxin.
Journal ArticleDOI
A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function
TL;DR: Measure the ability of 47,000 variants of a WW domain to bind to a peptide ligand and use these functional measurements to identify stabilizing mutations without directly assaying stability, rooted in the well-established concept that protein function is closely related to stability.
Journal ArticleDOI
Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes.
Jason D. Buenrostro,Carlos L. Araya,Lauren M. Chircus,Curtis J. Layton,Howard Y. Chang,Michael Snyder,William J. Greenleaf +6 more
TL;DR: This work repurposes a high-throughput sequencing instrument to quantitatively measure binding and dissociation of a fluorescently labeled protein to >107 RNA targets generated on a flow cell surface by in situ transcription and intermolecular tethering of RNA to DNA.