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.
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...
Systems and methods for analyzing sequencing data
Bussemaker, Harmen H, Chaitanya Rastogi, and Hans Tomas Rube. 2021. “Systems and Methods for Analyzing Sequencing Data.”
Nearly supersymmetric dark atoms
Behbahani, Siavosh R, Martin Jankowiak, Tomas Rube, and Jay G Wacker. 2011. “Nearly Supersymmetric Dark Atoms”. Advances in High Energy Physics 2011.
Measuring DNA mechanics on the genome scale
Basu, Aakash, Dmitriy G Bobrovnikov, Zan Qureshi, Tunc Kayikcioglu, Thuy T M Ngo, Anand Ranjan, Sebastian Eustermann, et al. 2021. “Measuring DNA Mechanics on the Genome Scale”. Nature 589 (7842): 462–467.
Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning
Rube, Tomas, Chaitanya Rastogi, Siqian Feng, Judith F Kribelbauer, Allyson Li, Basheer Becerra, Lucas AN Melo, et al. 2022. “Prediction of Protein-Ligand Binding Affinity from Sequencing Data With Interpretable Machine Learning”. Nat. Biotechnol.