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The Rohs Lab

Department of Quantitative and Computational Biology

University of Southern California

About

Welcome to the Rohs Lab

About our Computational Biology and Bioinformatics research group

Main Focus

The main focus of the Rohs lab is the understanding of molecular interactions based on three-dimensional structure.

Who Can Join

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.

Primary Goal

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. 

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We use a combination of different approaches to understand readout and binding mechanisms.

This includes artificial intelligence, machine learning, statistics, biophysics, molecular simulations, and wet-lab experiments such as crystallography and high-throughput sequencing."

- Remo Rohs, Ph.D. 

Selected Publications

R. Mitra, et al.:

Geometric deep learning for interpretable prediction of protein-DNA binding specificity. 

Nat. Methods 21, 1674-1683 (2024)

J.A. Weller, et al.:

Structure-based drug design with a deep hierarchical generative model.

J. Chem. Inf. Model. 64, 6450-6463 (2024)

J.M. Sagendorf, et al.:

Structure-based prediction of protein-nucleic acid binding using graph neural networks.

Biophys. Rev. 16, 297-314 (2024)

R. Mitra, et al.:

RNAscape: geometric mapping and customizable visualization of RNA structure.

Nucleic Acids Res. 52, W354-W361 (2024)

J. Li, et al.:

Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers.

Nucleic Acids Res. 52, W354-W361 (2024)

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.

Biophys. J. 123, 248-259 (2024)

B.H. Cooper, et al.:
DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors.

Nucleic Acids Res. 51, 5621-5633 (2023)

T.P. Chiu, et al.:
Physicochemical models of protein-DNA binding with standard and modified base pairs.

Proc. Natl. Acad. Sci. USA 120, e2205796120 (2023)

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Latest News

By The Numbers

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

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