MCB Faculty


Remo Rohs

Associate Professor of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science

Contact Information
E-mail: rohs@usc.edu
Phone: (213) 740-0552
Office: RRI 413H

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

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

  • 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
    • Tangprasertchai, N. S., Zhang, X., Ding, Y., Tham, K., Rohs, R., Haworth, I. S., Qin, P. Z. (2015). An integrated spin-labeling/computational-modeling approach for mapping global structures of nucleic acids. Methods in Enzymology (Vol. 564). pp. 427-453. Elsevier. PubMed Web Address
    • 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
    • Chiu, T., Comoglio, F., Zhou, T., Yang, L., Paro, R., Rohs, R. (2015). DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding. Bioinformatics. Vol. in press
    • Zentner, G. E., Kasinathan, S., Xin, B., Rohs, R., Henikoff, S. (2015). ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo. Nat. Commun.. Vol. 6, pp. 8733. PubMed Web Address
    • Dror, I., Golan, T., Levy, C., Rohs, R., Mandel-Gutfreund, Y. (2015). A widespread role of the motif environment in transcription factor binding across diverse protein families. Genome Res.. Vol. 25, pp. 1268-1280. PubMed Web Address
    • Deng, Z., Wang, Q., Liu, Z., Zhang, M., Dantas Machado, A. C., Chiu, T. P., Feng, C., Zhang, Q., Yu, L., Qi, L., Zheng, J., Wang, X., Huo, X., Qi, X., Li, X., Wu, W., Rohs, R., Li, Y., Chen, Z. (2015). Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator. Nat. Commun.. Vol. 6, pp. 7642. PubMed Web Address
    • Rohs, R., Dantas Machado, A. C., Yang, L. (2015). Exposing the secrets of sex determination. Nat. Struct. Mol. Biol.. Vol. 22 (6), pp. 437-438. PubMed Web Address
    • Abe, N., Dror, I., Yang, L., Slattery, M., Zhou, T., Bussemaker, H. J., Rohs, R., Mann, R. S. (2015). Deconvolving the recognition of DNA shape from sequence. Cell. Vol. 161 (2), pp. 307-18. PubMed Web Address
    • Zhou, T., Shen, N., Yang, L., Abe, N., Horton, J., Mann, R. S., Bussemaker, H. J., Gordân, R., Rohs, R. (2015). Quantitative modeling of transcription factor binding specificities using DNA shape. Proc. Natl. Acad. Sci. U S A. Vol. 112 (15), pp. 4654-9. PubMed Web Address
    • Comoglio, F., Schlumpf, T., Schmid, V., Rohs, R., Beisel, C., Paro, R. (2015). High-resolution profiling of Drosophila replication start sites reveals a DNA shape and chromatin signature of metazoan origins. Cell Rep.. Vol. 11 (5), pp. 821-834. PubMed Web Address
    • Levo, M., Zalckvar, E., Sharon, E., Dantas, A. C., Kalma, Y., Lotam-Pompan, M., Weinberger, A., Yakhini, Z., Rohs, R., Segal, E. (2015). Unraveling determinants of transcription factor binding outside the core binding site. Genome Res.. Vol. 25 (7), pp. 1018-29. PubMed Web Address
    • Hadžic, T., Park, D., Abruzzi, K. C., Yang, L., Trigg, J. S., Rohs, R., Rosbash, M., Taghert, P. H. (2015). Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED. Nucleic Acids Res.. Vol. 43 (4), pp. 2199-215. PubMed Web Address
    • Chiu, T. P., Yang, L., Zhou, T., Main, B. J., Parker, S. C., Nuzhdin, S. V., Tullius, T. D., Rohs, R. (2015). GBshape: a genome browser database for DNA shape annotations. Nucleic Acids Research. Vol. 43 (Database issue), pp. D103-9. PubMed Web Address
    • Dantas Machado, A. C., Zhou, T., Rao, S., Goel, P., Rastogi, C., Lazarovici, A., Bussemaker, H. J., Rohs, R. (2014). Evolving insights on how cytosine methylation affects protein-DNA binding. Brief. Funct. Genomics. Vol. 14 (1), pp. 61-73. PubMed Web Address
    • Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., Rohs, R. (2014). Absence of a simple code: how transcription factors read the genome. Trends Biochem. Sci.. Vol. 39, pp. 381-399. PubMed Web Address
    • Barozzi, I., Simonatto, M., Bonifacio, S., Yang, L., Rohs, R., Ghisletti, S., Rohs, R., Ghisletti, S., Natoli, G. (2014). Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers. Mol. Cell. Vol. 54 (5), pp. 844-857. PubMed Web Address
    • Zhang, X., Dantas Machado, A. C., Ding, Y., Chen, Y., Lu, Y., Tham, K. W., Chen, L., Rohs, R., Qin, P. Z. (2014). Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling. Nucleic Acids Res.. Vol. 42, pp. 2789-2797.
    • Dror, I., Zhou, T., Mandel-Gutfreund, Y., Rohs, R. (2014). Covariation between homeodomain transcription factors and the shape of their DNA binding sites. Nucleic Acids Res.. Vol. 42, pp. 430-441. PubMed Web Address
    • Yang, L., Zhou, T., Dror, I., Mathelier, A., Wasserman, W. W., Gordân, R., Rohs, R. (2014). TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res.. Vol. 42, pp. D148-D155. 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
    • Gordân, 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). Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen. Cell Rep.. Vol. 3, pp. 1117-1127. PubMed Web Address
    • 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
    • Rohs, R., Sklenar, H., Shakked, Z. (2005). Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites. Structure (London, England : 1993). Vol. 13 (10), pp. 1499-509. PubMed Web Address
    • Rohs, R., Sklenar, H. (2004). Methylene blue binding to DNA with alternating AT base sequence: Minor groove binding is favored over intercalation. J. Biomol. Struct. Dyn.. Vol. 21, pp. 699-711. PubMed Web Address
    • Rohs, R. (2001). Methylene blue binding to DNA with alternating GC base sequence: Continuum treatment of salt effects. Indian. J. Biochem. Biophys.. Vol. 38, pp. 1-6. PubMed Web Address
    • Rohs, R., Sklenar, H., Lavery, R., Röder, B. (2000). Methylene blue binding to DNA with alternating GC base sequence: A modeling study. J. Am. Chem. Soc.. Vol. 122, pp. 2860-2866. http://pubs.acs.org/doi/full/10.1021/ja992966k?prevSearch=%2528Rohs%2529%2BNOT%2B%255Batype%253A%2Bad%255D%2BNOT%2B%255Batype%253A%2Bacs-toc%255D&searchHistoryKey=
    • Rohs, R., Etchebest, C., Lavery, R. (1999). Unraveling proteins: A molecular mechanics study. Biophys. J.. Vol. 76, pp. 2760-2768. PubMed Web Address

    Honors and Awards

    • Sloan Research Fellowship Recipient, Alfred P. Sloan Research Fellowship, 2013-  
    • American Chemical Society OpenEye Outstanding Junior Faculty Award in Computational Chemistry presented at the ACS Spring 2016 National Meeting, San Diego, CA, 2015-2016   
    • Abe et al. Cell paper received a RECOMB/ISCB Top-Paper Award for being one of the ten most influential publications in the fields of regulatory and systems genomics, 2014-2015   
    • Zhou et al. PNAS paper received a RECOMB/ISCB Top-Paper Award for being one of the ten most influential publications in the fields of regulatory and systems genomics, 2014-2015   
    • Barozzi et al. Mol. Cell 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, 2013-2014   
    • Yang et al. Nucleic Acids Res. 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, 2013-2014   
    • 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   
    • 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   
    • 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
    • Chair, High-performance computing committee, Computational Biology and Bioinformatics section, University of Southern California, 2015-  
    • Member, Advisory Board, Women in Science and Engineering (WiSE) Program, University of Southern California, 2015-  
    • Member, Building committee, Ray R. Irani Hall, Molecular and Computational Biology section University of Southern California, 2015-  
    • Chair, Space committee, Computational Biology and Bioinformatics section, University of Southern California, 2014-  
    • Member, Retreat committee, Molecular and Computational Biology section, University of Southern California, 2014-  
    • 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-  
    • Member, Self-study subcommittee "undergraduate programs", Department of Biological Sciences, University of Southern California, 2015  
    • Member, Self-study steering/"uber" committee, Department of Biological Sciences, University of Southern California, 2015  

    Service to the Profession


    Conferences Organized
    • Member Organizing Committee, Biannual Conversations on Biomolecular Structure and Dynamics, Albany, New York, United States, 2010-  
    • Co-organizer, Workshop "Rules of protein-DNA recognition: computational and experimental advances", funded by Banff International Research Station for Mathematical , Casa Matemática Oaxaca, Mexico, 2015  

    Editorships and Editorial Boards
    • Guest Editor, PLoS Comput. Biol., 2011-  
    • Associate Editor, BMC Bioinformatics, 2010-  
    • Editorial Board Member, J. Biomol. Struct. Dyn., 2010-  

    Professional Memberships
    • American Society for Cell Biology (ASCB), 2015-  
    • American Association for the Advancement of Science (AAAS), 2013-  
    • American Chemical Society (ACS), 2012-  
    • International Society for Computational Biology (ISCB), 2012-  

    Review Panels
    • Human Frontiers Science Program, HFSP fellowship reviewer, 2015-  
    • National Institutes of Health, Ad hoc member GCAT study section, 2014-  
    • National Science Foundation, Ad hoc reviewer CAREER awards, 2014-  
    • Israel Science Foundation, Review of research grant proposals, 2012-  
    • Howard Hughes Medical Institute, HHMI fellowship review panel, 2011-  

    Other Service to the Profession
    • Faculty Member, Faculty of 1000 in Biology (Structural Biology, Section Structure: Transcription and Translation), 2011-  
    • Member, Academic Advisory Board, zSpace, Inc., Sunnyvale, California, 2012-2014  
    • Program Committee Member, 21st Annual International Conference on Intelligent Systems in Molecular Biology (ISMB)/12th European Conference on Computational Biology (ECCB), Berlin, Germany, 2013  




  • Department of Biological Sciences
  • University of Southern California
  • Allan Hancock Foundation Building
  • Los Angeles, CA 90089-0371