Quantifying the role of steric constraints in nucleosome positioning
Rube, Tomas, and Jun S Song. 2014. “Quantifying the role of steric constraints in nucleosome positioning”. Nucleic Acids Res. 42 (4): 2147–2158.
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Understanding TERT promoter mutations: A common path to immortality
Bell, Robert J A, Tomas Rube, Ana Xavier-Magalhães, Bruno M Costa, Andrew Mancini, Jun S Song, and Joseph F Costello. 2016. “Understanding TERT promoter mutations: A common path to immortality”. Mol. Cancer Res. 14 (4): 315–323.
Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes
Zhang, Liyang, Tomas Rube, Christopher A Vakulskas, Mark A Behlke, Harmen J Bussemaker, and Miles A Pufall. 2020. “Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes”. Nucleic Acids Res. 48 (9): 5037–5053.
Lab News
ProBound published
The paper Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning was published in Nature Biotechnology.
Methods
This page contains a list of computational methods and resources that we have developed. Please do not hessitate to contact us if you have any problems or questions. ProBound - A software that analyzes sequencing data from randomized binding assays in order to learn energetic models of sequence...
N= 8 Supergravity 4-point amplitudes
Kallosh, Renata, Ching Hua Lee, and Tomas Rube. 2009. “N= 8 Supergravity 4-point amplitudes”. Journal of High Energy Physics 2009 (02): 050.
SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site
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.
Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer
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
Jin, Hu, Tomas Rube, and Jun S Song. 2016. “Categorical spectral analysis of periodicity in nucleosomal DNA”. Nucleic Acids Res. 44 (5): 2047–2057.