The paper develops a cysteine-free UTag system for live-cell single-mRNA translation tracking, showing improved thermostability and performance comparable to existing systems.

bioRxiv · May 7, 2026 · PreprintBiophysics

AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications

Gabriel Galindo, Daiki Maejima, Jacob DeRoo, Scott R. Burlingham, Gretchen M. Fixen, Tatsuya Morisaki, Hallie P. Febvre, Ryan Hasbrook, Ning Zhao, Soham Ghosh, E. Handly Mayton, Christopher Davis Snow, Brian J. Geiss, Yasuyuki Ohkawa, Yuko Sato, , Timothy J. Stasevich

This paper presents an AI-driven method to convert antibody sequences into functional intrabodies, successfully converting 19 out of 26 sequences, including those targeting histone modifications.

Science Advances · Jan 2, 2026Peer-reviewedCell Biology

Identification of potential riboswitch elements in Homo Sapiens mRNA 5'UTR sequences using Positive-Unlabeled Machine learning

William Raymond, Jacob DeRoo, Brian E. Munsky

The paper uses positive-unlabeled machine learning to identify potential riboswitch elements in human mRNA 5'UTR sequences by comparing them to known riboswitch sequences.

PLoS ONE · Apr 24, 2025Peer-reviewedBioinformatics

PAbFold: Linear Antibody Epitope Prediction using AlphaFold2

Jacob DeRoo, James S. Terry, Ning Zhao, Timothy J. Stasevich, Christopher Davis Snow, Brian J. Geiss

PAbFold predicts linear antibody epitopes using AlphaFold2 by modeling antibody-antigen complexes, showing accuracy on known targets and validating on a novel anti-SARS-CoV-2 antibody.

bioRxiv · Apr 19, 2024 · PreprintMolecular Biology