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Search Publications by: Olga Vasilyeva (Assoc)

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Displaying 1 - 8 of 8

GROQ-seq Datasets Across Transcription Factors (LacI, RamR, VanR), T7 RNA Polymerase and TEV Protease

April 19, 2026
Author(s)
Aviv Spinner, Shwetha Sreenivasan, James McLellan, Svetlana Ikonomova, Dana Cortade, Simon d'Oelsnitz, Kristen Sheldon, Olga Vasilyeva, Nina Alperovich, Anjali Chadha, Lily Nematollahi, Andi Dhroso, Zach Sisson, Corey Hudson, Erika DeBenedictis, Peter Kelly, Amanda Reider Apel, David Ross, Catherine Baranowski
Predicting any protein's function from its sequence alone would be a significant breakthrough in molecular biology. Although machine learning approaches have sought to tackle this, their limited generalizability reflects the absence of sufficiently large

Mapping the phenotypic landscape of a transcriptional repressor using Deep Mutational Scanning and Growth-based Quantitative Sequencing

December 2, 2025
Author(s)
Zachary Jansen, Xuan Le, Qiyao Wei, Devon Kulhanek, Nina Alperovich, Olga Vasilyeva, Andrew Gilmour, David Ross, Ross Thyer
CymR is a TetR-family transcriptional repressor that recognizes a well-defined operator sequence in the promoter PcymRC. The native ligand cuminic acid and a series of structurally related aromatic acids can bind at an allosteric site and induce a

Experimental Evaluation of AI-Driven Protein Design Risks Using Safe Biological Proxies

June 20, 2025
Author(s)
Svetlana Ikonomova, Bruce Wittmann, Fernanda Piorino Macruz de Oliveira, David Ross, Samuel Schaffter, Olga Vasilyeva, Elizabeth Strychalski, Eric Horvitz, James Diggans, Sheng Lin-Gibson, Geoffrey Taghon
Advances in machine learning are providing new abilities for engineering biology, promising leaps forward with beneficial applications. At the same time, these advances raise concerns about biosecurity. Recently, Wittmann et al. described an in silico

Using enantioselective biosensors to evolve asymmetric biocatalysts

January 30, 2025
Author(s)
d'Oelsnitz Simon, Wantae Kim, Haley Hardtke, Svetlana Ikonomova, Nina Alperovich, Olga Vasilyeva, Michael James, Eric Zigon, Charlie Johnson, Andrew Ellington, Quincey Justman, Michael Springer, Jessie Zhang, Pamela Silver, David Ross
Biocatalysts are championed for their exquisite stereochemistry, but slow chromatographic separations necessary to measure enantiomeric excess can bottleneck their development. Prokaryotic transcription factors can address this limitation by transducing

Method for reproducible automated bacterial cell culture and measurement

August 8, 2022
Author(s)
David Ross, Peter Tonner, Olga Vasilyeva
Microbial cell culture is one of the most commonly performed protocols for synthetic biology, and laboratories are increasingly using 96-well plates and laboratory automation systems for cell culture. Here we describe a method for reproducible microbial

The genotype-phenotype landscape of an allosteric protein

December 16, 2021
Author(s)
Drew S. Tack, Peter Tonner, Abe Pressman, Nathanael Olson, Eugenia Romantseva, Nina Alperovich, Olga Vasilyeva, David Ross, Sasha F. Levy
Allostery is a fundamental biophysical mechanism where the activity of a biomolecule is regulated by the binding of a ligand. Despite playing a central role in many biological processes, a quantitative understanding of allostery is lacking. To
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