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...
SH2 preprint out
The preprint " Accurate sequence-to-affinity models for SH2 domains from multi-round peptide binding assays coupled with free-energy regression" is out on bioRxiv.
Shahram and Moitrish present their work at AM Retreat
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.
Systems and methods for analyzing sequencing data
Bussemaker, Harmen H, Chaitanya Rastogi, and Hans Tomas Rube. 2021. “Systems and Methods for Analyzing Sequencing Data.”