Sergio E. Mares
Computational Biology Ph.D. Candidate at UC Berkeley

I am an AI Engineer III at AbbVie. I recently graduated with my Computational Biology Ph.D. from UC Berkeley. I developed models to understand the pMHC interaction. My work covers everything from finetuning models to generating synthetic data for benchmarking on OOD samples.


In Summer 2026 I worked at Adimab, where I built machine learning models for TCR cross-reactivity, using inverse folding models to probe the tolerated peptide neighborhood underlying pMHC-TCR recognition.


In Summer 2025 I interned at Ultima Genomics, where I integrated a DNA sequence simulation into the production sequencing pipeline (reducing reagent use by 50%) and built a scalable single-cell ATAC-seq processing pipeline handling up to 100M cells end-to-end.

Sergio E. Mares
Inverse folding peptides sampled over a pMHC-TCR energy landscape
Sergio E. Mares, Brian Petersen, Kyle Barlow
Adimab, 2026
We sample peptides from four inverse folding models across 43 pMHC-TCR crystal structures and score them for predicted presentation and structural compatibility. Rather than recovering the native peptide or ranking binding strength, the models sample the sequence space compatible with the structural context — a probe of the tolerated neighborhood that drives cross-reactivity in TCR-based therapies.
Masked-language modeling per residue on a MART-1 peptide with ESM: confident anchors P2 and P-omega, near-uniform elsewhere
Sergio E. Mares, Ariel Espinoza, Nilah M. Ioannidis
Machine Learning in Computational Biology (MLCB), 2025
We test whether domain-specific continued pre-training of protein language models is beneficial for pMHC-I binding affinity prediction. Starting from ESM Cambrian (300M parameters), we perform masked-language modeling on HLA-associated peptides and fine-tune for quantitative IC50 binding affinity prediction.
RFdiffusion generating pMHC-I peptide backbones in the MHC groove, colored by AF2 confidence
Sergio E. Mares, Ariel Espinoza, Nilah M. Ioannidis
ICML Gen AI and Biology Workshop, 2025
We introduce a structure-guided benchmark of pMHC-I peptides designed using diffusion models conditioned on crystal structure interaction distances, spanning twenty high-priority HLA alleles.
Calcium signaling protein structure
Biraj B. Kayastha, A. Kubo, J. Burch-Konda, R. L. Dohmen, J. L. McCoy, R. R. Rogers, Sergio E. Mares, J. Bevere, A. Huckaby, W. Witt, S. Peng, B. Chaudhary, S. Mohanty, M. Barbier, G. Cook, J. Deng, M. Patrauchan
Nature Scientific Reports, 2022
We study the putative Ca²+-binding protein EfhP (PA4107) and CalC as proteins involved in the calcium network, elucidating the mechanisms of bacterial Ca²+ signaling in Pseudomonas aeruginosa.
Baculovirus invadosome dynamics
Domokos I. Lauko, Taro Ohkawa, Sergio E. Mares, Matthew D. Welch
Molecular Biology of the Cell, 2021
We investigate how AcMNPV protein actin rearrangement inducing factor-1 (Arif-1) induces the formation of cortical concentrations of polymerized actin (ventral aggregates) in cultured insect cells.
Pseudomonas aeruginosa
Sergio E. Mares, M. King, A. Kubo, A. Khavov, E. Lutter, N. Youssef, M. Patrauchan
Journal of Microbiology, 2020
We study the conservation of carP sequence and its occurrence in diverse phylogenetic groups, finding that carP and its two paralogues are primarily present in P. aeruginosa and belong to the core genome, demonstrating potential as a biomarker.
Myxococcota swarming
Chelsea L. Murphy, R. Yang, T. Decker, C. Cavalliere, V. Andreev, N. Bircher, J. Cornell, R. Dohmen, C. J. Pratt, A. Grinnell, J. Higgs, C. Jett, E. Gillett, R. Khadka, Sergio E. Mares, C. Meili, J. Liu, H. Mukhtar, Mostafa S. Elshahed, Noha H. Youssef
Environmental Microbiology, 2021
Detailed analysis of 13 distinct pathways crucial to predation and cellular differentiation reveals severely curtailed machineries, proposing that these represent a niche adaptation strategy that evolved circa 500 million years ago.
Molecular Modeling and Simulation
Molecular Modeling and Simulation: An Interdisciplinary Guide
Tamar Schlick
Finished
Pedro Páramo
Pedro Páramo
Juan Rulfo
Currently Reading
On the Origin of Species
On the Origin of Species
Charles Darwin
Currently Reading
Structural Bioinformatics
Structural Bioinformatics
Philip E. Bourne & Helge Weissig
Currently Reading
Soviet Middlegame Technique
Soviet Middlegame Technique
Peter Romanovsky
Currently Reading
Miles de millones
Miles de millones
Carl Sagan
Currently Reading
Cien años de soledad
Cien años de soledad
Gabriel García Márquez
Currently Reading
♘ Chess
I've been playing chess since I moved to the US. I mainly play rapid and blitz on Lichess. Feel free to challenge me!
💻 Open Source
Building tools at the intersection of ML and biology. Check out my projects on GitHub.