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.
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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.
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Rube Lab
Moitrish joins the lab
We would like to welcome Applied Math graduate student Moitrish to the lab!
Teaching
Fall Semester 2022 - MATH 180 - Modern Applied Statistics Fall Semester 2023 - MATH 180 - Modern Applied Statistics Spring Semester 2024 - MATH 32 - Probability and Statistics Fall Semester 2024 - MATH 180 - Applied Statistics and Machine Learning Spring Semester 2025 - MATH 280 - Mathematical and...