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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.

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.

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.

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.

Rube, Tomas, Chaitanya Rastogi, Judith F Kribelbauer, and Harmen J Bussemaker. 2018. “A unified approach for quantifying and interpreting DNA shape readout by transcription factors”. Mol. Syst. Biol. 14 (2): e7902.

Rastogi, Chaitanya, Tomas Rube, Judith F Kribelbauer, Justin Crocker, Ryan E Loker, Gabriella D Martini, Oleg Laptenko, et al. 2018. “Accurate and sensitive quantification of protein-DNA binding affinity”. Proc. Natl. Acad. Sci. U. S. A. 115 (16): E3692–E3701.

Rube, Tomas, and Jay G Wacker. 2011. “The simplicity of perfect atoms: degeneracies in supersymmetric hydrogen”. Journal of Mathematical Physics 52 (6): 062102.