Jose Manuel Barraza
PhD
TODO
Publications within the group (3)
Do protein representations encode variant function? Diagnosing residue-level protein attributions via embedding-space gradients / bioRxiv / '26
Introduces IGLOO, a diagnostic framework that evaluates whether residue-level embedding gradients from protein language models faithfully capture functional importance against synthetic and experimental fitness landscapes.
Rana A. Barghout, Shengqing Wu, William Chau, José Manuel Barraza-Chavez, Paola Driza, Radhakrishnan Mahadevan, Benjamin Sanchez-Lengeling
TubercuProbe: A cross-attention graph-sequence model for cross-species chemoproteomic discovery in Mycobacterium tuberculosis / bioRxiv / '26
Pairs a GINE molecular graph encoder with frozen ESM-C protein language model embeddings via cross-attention to predict covalent target engagement across pathogen proteomes with few-shot transfer.
Abhiram Chalamalasetty, Adesh Rohan Mishra, Fleur M. Ferguson, Benjamin Sanchez-Lengeling, José Manuel Barraza-Chavez, Adrian Jinich
Graph Data Modeling: Molecules, Proteins, & Chemical Processes / ACS In Focus / '25
A foundational pedagogical text and monograph introducing structural, geometric, and kinetic graph neural networks for molecules, macromolecular proteins, and complex biological pathways.
José Manuel Barraza-Chavez, Rana A. Barghout, Ricardo Almada-Monter, Adrian Jinich, Radhakrishnan Mahadevan, Benjamin Sanchez-Lengeling