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Accurate sequence-to-affinity models for SH2 domains from multi-round peptide binding assays coupled with free-energy regression

Publication: Journal Article

Gagoski, Dejan, Tomas Rube, Chaitanya Rastogi, Lucas AN Melo, Xiaoting Li, Rashmi Voleti, Neel H. Shah, and Harmen J. Bussemaker. 2025. “Accurate Sequence-to-Affinity Models for SH2 Domains from Multi-Round Peptide Binding Assays Coupled With Free-Energy Regression”. BioRxiv 34 (11).

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H. Tomas Rube Assistant Professor, Department of Applied Mathematics Starting July 2022, H. Tomas Rube is an assistant professor in Applied Mathematics at University of California, Merced. With an undergraduate degree in engineering physics and a PhD in theoretical physics, Tomas’ research lies at...

A unified approach for quantifying and interpreting DNA shape readout by transcription factors

Publication: Journal Article

Rube, Tomas, Chaitanya Rastogi, Judith F Kribelbauer, and Harmen J Bussemaker. 2018. “A Unified Approach for Quantifying and Interpreting DNA Shape Readout by Transcription Factors”. Mol. Syst. Biol. 14 (2): e7902.

Accurate and sensitive quantification of protein-DNA binding affinity

Publication: Journal Article

Rastogi, Chaitanya, Tomas Rube, Judith F Kribelbauer, Justin Crocker, Ryan E Loker, Gabriella D Martini, Oleg Laptenko, et al. 2018. “Accurate and Sensitive Quantification of Protein-DNA Binding Affinity”. Proc. Natl. Acad. Sci. U. S. A. 115 (16): E3692–E3701.

The simplicity of perfect atoms: degeneracies in supersymmetric hydrogen

Publication: Journal Article

Rube, Tomas, and Jay G Wacker. 2011. “The Simplicity of Perfect Atoms: Degeneracies in Supersymmetric Hydrogen”. Journal of Mathematical Physics 52 (6): 062102.

Rube Lab Founded

News: July 01, 2022

Tomas joins the Applied Mathematics Department at the University of California, Merced as an Assistant Professor.

Shahram Joins Lab

News: September 01, 2023

We would like to welcome Applied Math graduate student Shahram to the lab!

Research

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Our current research spans three areas: Accelerating proteomics research using compressed sensing - Protein-protein interactions (PPIS) are important in governing numerous processes like development and the onset of pathological conditions such as cancer and neurodegenerative disease. PPIs form...

Pooled IP-MS NSF grant funded

News: July 31, 2025

Our collaborative project with the Jovanovic Lab at Columbia University was funded by the NSF.

SPRINT-MS: A high-throughput platform for identifying protein-protein interactions using pooled IP-MS and sparse signal recovery

Publication: Journal Article

Street, Lena A., Moitrish Majumdar, Katherine L. Rothamel, Esin Gogus, Gloria Brar, Gene W. Yeo, Tomas Rube, and Marko Jovanovic. Submitted. “SPRINT-MS: A High-Throughput Platform for Identifying Protein-Protein Interactions Using Pooled IP-MS and Sparse Signal Recovery”. BioRxiv, Submitted.