About our Computational Biology and Bioinformatics research group
The main focus of the Rohs lab is the understanding of molecular interactions based on three-dimensional structure.
Professor Rohs primarily accepts students from the academic programs of the QCB Department. This includes the Ph.D. Program in Computational Biology and Bioinformatics.
Professor Rohs can also advise students from the Departments of Chemistry, Physics & Astronomy, and Computer Science.
We currently work on three research topics: (1) protein-DNA binding specificity, (2) structure-based drug design, and (3) RNA structure. The primarily goal is to use three-dimensional structure and sequence to reveal readout mechanisms across multiple scales.
R. Mitra, et al.:
Geometric deep learning for interpretable prediction of protein-DNA binding specificity.
J.A. Weller, et al.:
Structure-based drug design with a deep hierarchical generative model.
J.M. Sagendorf, et al.:
Structure-based prediction of protein-nucleic acid binding using graph neural networks.
R. Mitra, et al.:
RNAscape: geometric mapping and customizable visualization of RNA structure.
J. Li, et al.:
Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers.
J. Li, et al.:
Predicting DNA structure using a deep learning method
Nat. Commun. 15, 1243 (2024)
Y. Jiang, et al.:
Probing the role of the protonation state of a minor groove linker histidine in Exd-Hox-DNA binding.
B.H. Cooper, et al.:
DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors.
T.P. Chiu, et al.:
Physicochemical models of protein-DNA binding with standard and modified base pairs.
14
Current Lab Members
13
Graduated Ph.D. Students
88
Published Peer-Reviewed Papers
2010
Est. at University of Southern California
4
Academic Department Affiliations
