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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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.
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.
Boosting genome editing efficiency in human cells and plants with novel LbCas12a variants.
Zhang, L, G Li, Y Zhang, Y Cheng, N Roberts, SE Glenn, D DeZwaan-McCabe, et al. 2023. “Boosting Genome Editing Efficiency in Human Cells and Plants With Novel LbCas12a Variants.”. Europe PMC.
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.
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.
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.
Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors
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
Kallosh, Renata, Andrei Linde, Keith A Olive, and Tomas Rube. 2011. “Chaotic Inflation and Supersymmetry Breaking”. Physical Review D 84 (8): 083519.