Search

Search results

40 results found

Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning

Publication: Journal Article

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

Publication: Journal Article

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

Publication: Journal Article

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

Publication: Journal Article

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

Page

Rube Lab

Moitrish joins the lab

News: January 01, 2024

We would like to welcome Applied Math graduate student Moitrish to the lab!

Teaching

Page

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...

AsCas12a ultra nuclease facilitates the rapid generation of therapeutic cell medicines

Publication: Journal Article

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.

A unified approach for quantifying and interpreting DNA shape readout by transcription factors

Publication: Journal Article

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.