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AsCas12a ultra nuclease facilitates the rapid generation of therapeutic cell medicines

Publication: Journal Article

Zhang, Liyang, John A Zuris, Ramya Viswanathan, Jasmine N Edelstein, Rolf Turk, Bernice Thommandru, Tomas Rube, et al. 2021. “AsCas12a Ultra Nuclease Facilitates the Rapid Generation of Therapeutic Cell Medicines”. Nat. Commun. 12 (1): 4500.

Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer

Publication: Journal Article

Bell, Robert J A, Tomas Rube, Alex Kreig, Andrew Mancini, Shaun D Fouse, Raman P Nagarajan, Serah Choi, et al. 2015. “Cancer. The Transcription Factor GABP Selectively Binds and Activates the Mutant TERT Promoter in Cancer”. Science 348 (6238): 1036–1039.

Categorical spectral analysis of periodicity in nucleosomal DNA

Publication: Journal Article

Jin, Hu, Tomas Rube, and Jun S Song. 2016. “Categorical Spectral Analysis of Periodicity in Nucleosomal DNA”. Nucleic Acids Res. 44 (5): 2047–2057.

SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site

Publication: Journal Article

Zhang, Liyang, Gabriella D Martini, Tomas Rube, Judith F Kribelbauer, Chaitanya Rastogi, Vincent D FitzPatrick, Jon C Houtman, Harmen J Bussemaker, and Miles A Pufall. 2018. “SelexGLM Differentiates Androgen and Glucocorticoid Receptor DNA-Binding Preference over an Extended Binding Site”. Genome Res. 28 (1): 111–121.

N= 8 Supergravity 4-point amplitudes

Publication: Journal Article

Kallosh, Renata, Ching Hua Lee, and Tomas Rube. 2009. “N= 8 Supergravity 4-Point Amplitudes”. Journal of High Energy Physics 2009 (02): 050.

Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors

Publication: Journal Article

Feng, Siqian, Chaitanya Rastogi, Ryan E Loker, William J Glassford, Tomas Rube, Harmen J Bussemaker, and Richard S Mann. 2022. “Transcription Factor Paralogs Orchestrate Alternative Gene Regulatory Networks by Context-Dependent Cooperation With Multiple Cofactors”. BioRxiv.

Chaotic inflation and supersymmetry breaking

Publication: Journal Article

Kallosh, Renata, Andrei Linde, Keith A Olive, and Tomas Rube. 2011. “Chaotic Inflation and Supersymmetry Breaking”. Physical Review D 84 (8): 083519.

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. Forthcoming. “Accurate Sequence-to-Affinity Models for SH2 Domains from Multi-Round Peptide Binding Assays Coupled With Free-Energy Regression”. BioRxiv, Forthcoming.

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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.