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Remo Rohs

Assistant Professor of Biological Sciences, Chemistry, Physics and Astronomy and Computer Science

Contact Information
E-mail: rohs@usc.edu
Phone: (213) 740-0552
Office: RRI 404C

LINKS
Curriculum Vitae
Personal Website
 

Biographical Sketch
The main goal of my current research is to integrate two areas of studies that have developed along parallel lines, largely disconnected from each other: DNA sequence and structure. While sequence research analyzes DNA in a high-throughput manner and on a genome wide basis, structure research provides three-dimensional information on DNA and proteins at atomic resolution. My postdoctoral research provided me with an extensive training in DNA and protein-DNA structure analysis and prediction. In my own laboratory, we are currently developing new methodologies for the high-throughput prediction of DNA shape and its role in transcription factor bindding. The ability to predict DNA structure on a genomic scale will change how sequence data is analyzed.
 

Education
Ph.D. Biochemistry, Freie Universität Berlin, Germany, 2003
M.S. Physics, Humboldt Universität Berlin, Germany, 1997
 

Academic Appointment, Affiliation, and Employment History

Tenure Track Appointments
Assistant Professor (secondary), Department of Physics and Astronomy, USC Dornsife College of Letters, Arts and Sciences , 2012-  
Assistant Professor (secondary), Department of Chemistry, USC Dornsife College of Letters, Arts and Sciences, 2011-  
Assistant Professor (primary), Department of Biological Sciences, USC Dornsife College of Letters, Arts and Sciences, 2010-  
 

PostDoctoral Appointments
Associate Research Scientist, HHMI and Columbia University, New York, United States, 2009-2010  
Research Associate, HHMI and Columbia University, New York, United States, 2006-2008  
Postdoctoral Fellow, Weizmann Institute of Science, Rehovot, Israel, 2003-2005  
 

Other Employment
Ph.D. Student, Max Delbrück Center for Molecular Medicine, Berlin, Germany, 1998-2002  
Predoctoral Fellow, Institut de Biologie Physico-Chimique, Paris, France, 1997-1998  
 

Description of Research

Summary Statement of Research Interests
Professor Rohs is the Principal Investigator of a Computational Structural Biology research group. The main focus of the Rohs Lab is to further our understanding of molecular mechanisms that mediate specific interactions between nucleic acids and proteins on a structural and biophysical basis. We are working on gaining insights on the role of DNA shape in transcription factor binding on molecular and genomic scales. To achieve this goal, we are currently developing diverse computational methods to analyze the genome based on the integration of DNA sequence and shape.
 

Research Keywords
Protein-DNA readout; gene regulation; binding specificity; transcription factors; homeodomains; bHLH factors; nucleosome; Hox proteins; tumor suppressor p53; DNase I; origin recognition; SNPs; DNA shape; RNA structure; electrostatics; structure prediction; molecular simulations; genome analysis
 

Research Specialties
Computational structural biology; geometric analysis of three-dimensional structure; electrostatic analysis of molecular interactions; data mining of sequence and structure; genome-wide and high-throughput prediction of DNA shape; Monte Carlo and chain closure algorithms; molecular simulations; statistical models for transcription factor binding
 

Affiliations with Research Centers, Labs, and Other Institutions
USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Associate Member,http://uscnorriscancer.usc.edu/
 

Publications

Book Chapter
Harris, R. C., Mackoy, T., Dantas Machado, A. C., Xu, D., Rohs, R., Fenley, M. O. (2012). Opposites attract: Shape and electrostatic complementarity in protein-DNA complexes. Innovations in Biomolecular Modeling & Simulation (Vol. 2). Royal Society of Chemistry.
 

Journal Article
Dantas Machado, A. C., Saleebyan, S. B., Holmes, B. T., Karelina, M., Tam, J., Kim, S. Y., Kim, K. H., Dror, I., Hodis, E., Martz, E., Compeau, P. A., Rohs, R. (2012). Proteopedia: 3D visualization and annotation of transcription factor-DNA readout modes. Biochemistry and Molecular Biology Education. Vol. 40 (6), pp. 400-401. PubMed Web Address
Chen, Y., Bates, D. L., Dey, R., Chen, P. H., Dantas Machado, A. C., Laird-Offringa, I. A., Rohs, R., Chen, L. (2012). DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation. Cell Reports. Vol. 2, pp. 1197-1206. PubMed Web Address
Bishop, E. P., Rohs, R., Parker, S. C., West, S. M., Liu, P., Mann, R. S., Honig, B., Tullius, T. D. (2011). A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chemical Biology. Vol. 6 (12), pp. 1314-1320. PubMed Web Address
Slattery, M., Riley, T., Liu, P., Abe, N., Gomez-Alcala, P., Dror, I., Zhou, T., Rohs, R., Honig, B., Bussemaker, H. J., Mann, R. S. (2011). Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell. Vol. 147 (6), pp. 1270-1282. PubMed Web Address
Honig, B., Rohs, R. (2011). Biophysics: Flipping Watson and Crick. Nature. Vol. 470, pp. 472-473. PubMed Web Address
Rohs, R., Jin, X., West, S. M., Joshi, R., Honig, B., Mann, R. S. (2010). Origins of specificity in protein-DNA recognition. Annu. Rev. Biochem.. Vol. 79, pp. 233-269. PubMed Web Address
West, S. M., Rohs, R., Mann, R. S., Honig, B. (2010). Electrostatic interactions between arginines and the minor groove in the nucleosome. J. Biomol. Struct. Dyn.. Vol. 27, pp. 861-866. PubMed Web Address
Kitayner, M., Rozenberg, H., Rohs, R., Suad, O., Rabinovich, D., Honig, B., Shakked, Z. (2010). Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. Nat. Struct. Mol. Biol.. Vol. 17, pp. 423-429. PubMed Web Address
Rohs, R., West, S. M., Sosinsky, A., Liu, P., Mann, R. S., Honig, B. (2009). The role of DNA shape in protein-DNA recognition. Nature. Vol. 461, pp. 1248-1253. PubMed Web Address
Rohs, R., West, S. M., Liu, P., Honig, B. (2009). Nuance in the double-helix and its role in protein-DNA recognition. Current opinion in structural biology. Vol. 19 (2), pp. 171-7. PubMed Web Address
Joshi, R., Passner, J. M., Rohs, R., Jain, R., Sosinsky, A., Crickmore, M. A., Jacob, V., Aggarwal, A. K., Honig, B., Mann, R. S. (2007). Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell. Vol. 131, pp. 530-543. PubMed Web Address
Sklenar, H., Wüstner, D., Rohs, R. (2006). Using internal and collective variables in Monte Carlo simulations of nucleic acid structures: Chain breakage/closure algorithm and associated Jacobians. J. Comput. Chem.. Vol. 27, pp. 309-315. PubMed Web Address
Rohs, R., Bloch, I., Sklenar, H., Shakked, Z. (2005). Molecular flexibility in ab initio drug docking to DNA: Binding-site and binding-mode transitions in all-atom Monte Carlo simulations. Nucleic Acids Res.. Vol. 33, pp. 7048-7057. PubMed Web Address
Rohs, R., Sklenar, H., Shakked, Z. (2005). Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2 protein-DNA binding sites. Structure. Vol. 13, pp. 1499-1509. PubMed Web Address
 

Honors and Awards
Publication selected by RECOMB and ISMB as one of the 10 most influential papers of 2011 in the fields of systems biology and regulatory genomics, 2011-2012   
Received Certificate of Appreciation from LCUSD Governing Board for dedication to students of La Cañada High School, 2011-2012   
Selected by GenomeWeb as one of their 6 Annual Young Investigators, 2011-2012   
 

Service to the University

Committees
Member, Screening Committee, Ph.D. Program in Computational Biology and Bioinformatics, University of Southern California, 2011-  
Member, Admissions Committee, Ph.D. Program in Computational Biology and Bioinformatics, University of Southern California, 2010-  
 

Other Service to the University
Initiated and organized lecture featuring 2009 Chemistry Nobel Laureate Professor Ada Yonath, 2011-2012   
 

Service to the Profession

Conferences Organized
Member Organizing Committee, 17th Conversation on Biomolecular Structure and Dynamics, Albany, New York, United States, 2010-  
 

Editorships and Editorial Boards
Associate Editor, BMC Bioinformatics, 2010-  
Editorial Board Member, J. Biomol. Struct. Dyn., 2010-  
 

Professional Memberships
American Chemical Society (ACS), 2012-  
International Society for Computational Biology (ISCB), 2012-  
 

Review Panels
Howard Hughes Medical Institute, HHMI Review Panel, 2011-2012   

Other Service to the Profession
Faculty Member, Faculty of 1000 in Biology (Structural Biology, Section Structure: Transcription and Translation), 2011-  
 
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