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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 (courtesy), Department of Computer Science, USC Viterbi School of Engineering, 2013-  
Assistant Professor (courtesy), Department of Physics & Astronomy, USC Dornsife College of Letters, Arts & Sciences, 2012-  
Assistant Professor (courtesy), Department of Chemistry, USC Dornsife College of Letters, Arts & Sciences, 2011-  
Assistant Professor (primary), Department of Biological Sciences, USC Dornsife College of Letters, Arts & 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

The Rohs lab is a computational biology group that integrates genomics and structural biology to discover unknown molecular mechanisms underlying gene regulation, using bioinformatics analyses of high-throughput sequencing and DNA methylation data of whole genomes.
 

Research Keywords

Protein-DNA readout; gene regulation; transcription factor binding specificity; DNA shape; genome analysis
 

Research Specialties

Computational structural biology; statistical machine learning; high-throughput prediction of DNA shape; genome-wide analysis of sequence and structure; Monte Carlo simulation; electrostatics
 

Affiliations with Research Centers, Labs, and Other Institutions

USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Member
 

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

Yang, L., Zhou, T., Dror, I., Mathelier, A., Wasserman, W. W., Gordan, R., Rohs, R. (2013). TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res.. Vol. Epub 2013 Nov 7 PubMed Web Address
Dror, I., Zhou, T., Mandel-Gutfreund, Y., Rohs, R. (2013). Covariation between homeodomain transcription factors and the shape of their DNA binding sites. Nucleic Acids Res.. Vol. Epub 2013 Sep 27 PubMed Web Address
Chen, Y., Zhang, X., Dantas Machado, A. C., Ding, Y., Chen, Z., Qin, P. Z., Rohs, R., Chen, L. (2013). Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion. Nucleic Acids Res.. Vol. 41, pp. 8368-8376.
Eldar, A., Rozenberg, H., Diskin-Posner, Y., Rohs, R., Shakked, Z. (2013). Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions. Nucleic Acids Res.. Vol. 41, pp. 8748-8759. PubMed Web Address
Hancock, S. P., Ghane, T., Cascio, D., Rohs, R., Di Felice, R., Johnson, R. C. (2013). Control of DNA minor groove width and Fis protein binding by the purine 2-amino group. Nucleics Acids Res.. Vol. 41, pp. 6750-6760. PubMed Web Address
Zhou, T., Yang, L., Lu, Y., Dror, I., Dantas Machado, A. C., Ghane, T., Di Felice, R., Rohs, R. (2013). DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale. Nucleic Acids Res.. Vol. 41, pp. W56-W62. PubMed Web Address
Gordan, R., Shen, N., Dror, I., Zhou, T., Horton, J., Rohs, R., Bulyk, M. L. (2013). Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape. Cell Rep.. Vol. 3, pp. 1093-1104. PubMed Web Address
Lazarovici, A., Zhou, T., Shafer, A., Dantas Machado, A. C., Riley, T. R., Sandstrom, R., Sabo, P. J., Lu, Y., Rohs, R., Stamatoyannopoulos, J. A., Bussemaker, H. J. (2013). Probing DNA shape and methylation state on a genomic scale with DNase I. Proc. Natl. Acad. Sci. U S A. Vol. 110, pp. 6376-6381. PubMed Web Address
Chang, Y. P., Xu, M., Dantas Machado, A. C., Yu, X. J., Rohs, R., Chen, X. S. (2013). Origin DNA recognition by the SV40 large tumor antigen: Insights into the mechanism of initiator assembly. Cell Rep.. Vol. 3, pp. 1117-1127. 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
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
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
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
 

Honors and Awards

Sloan Research Fellowship Recipient, Received Alfred P. Sloan Research Fellowship Award, 2013-  
Gordân et al. Cell Rep. paper received a RECOMB/ISCB Top-10 Paper Award for being one of the ten most influential publications in the fields of regulatory and systems genomics, 2012-2013   
Lazarovici et al. PNAS paper received a RECOMB/ISCB Top-10 Paper Award for being one of the ten most influential publications in the fields of regulatory and systems genomics, 2012-2013   
Yang et al. Nucleic Acids Res. paper was selected as NAR Breakthrough Article for its originality, significance, and scientific impact, 2012-2013   
Slattery et al. Cell paper received the RECOMB/ISCB Top-10 Paper Award for being one of the ten most influential publications in the fields of systems biology and regulatory genomics, 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, Biannual Conversations 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 Association for the Advancement of Science (AAAS), 2013-  
American Chemical Society (ACS), 2012-  
International Society for Computational Biology (ISCB), 2012-  
 

Review Panels

Israel Science Foundation, Review of research grant proposals, 2012-  
Howard Hughes Medical Institute, HHMI fellowship review panel, 2011-  

Other Service to the Profession

Member, Academic Advisory Board, zSpace, Inc., Sunnyvale, California, 2012-  
Faculty Member, Faculty of 1000 in Biology (Structural Biology, Section Structure: Transcription and Translation), 2011-  
Member, Poster Awards Committee of The Protein Society, International Conference on Biomolecular Forms and Functions, Bangalore, India, 2013  
Program Committee Member, 21st Annual International Conference on Intelligent Systems in Molecular Biology (ISMB)/12th European Conference on Computational Biology (ECCB), Berlin, Germany, 2013  
 
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