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Bussemaker, Harmen H, Chaitanya Rastogi, and Hans Tomas Rube. 2021. “Systems and Methods for Analyzing Sequencing Data.”

Behbahani, Siavosh R, Martin Jankowiak, Tomas Rube, and Jay G Wacker. 2011. “Nearly Supersymmetric Dark Atoms”. Advances in High Energy Physics 2011.

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.

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.