Systems and methods for analyzing sequencing data
Bussemaker, Harmen H, Chaitanya Rastogi, and Hans Tomas Rube. 2021. “Systems and Methods for Analyzing Sequencing Data.”
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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.
Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA
Kim, Minji, Alex Kreig, Chun-Ying Lee, Tomas Rube, Jacob Calvert, Jun S Song, and Sua Myong. 2016. “Quantitative Analysis and Prediction of G-Quadruplex Forming Sequences in Double-Stranded DNA”. Nucleic Acids Res. 44 (10): 4807–4817.
Sequence features accurately predict genome-wide MeCP2 binding in vivo
Rube, Tomas, Wooje Lee, Miroslav Hejna, Huaiyang Chen, Dag H Yasui, John F Hess, Janine M LaSalle, Jun S Song, and Qizhi Gong. 2016. “Sequence Features Accurately Predict Genome-Wide MeCP2 Binding in Vivo”. Nat. Commun. 7 (1): 11025.
Context-dependent gene regulation by homeodomain transcription factor complexes revealed by shape-readout deficient proteins
Kribelbauer, Judith F, Ryan E Loker, Siqian Feng, Chaitanya Rastogi, Namiko Abe, Tomas Rube, Harmen J Bussemaker, and Richard S Mann. 2020. “Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins”. Mol. Cell 78 (1): 152–167.e11.
Publications
Moitrish joins the lab
We would like to welcome Applied Math graduate student Moitrish to the lab!
AsCas12a ultra nuclease facilitates the rapid generation of therapeutic cell medicines
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.