USC.edu

Remo Rohs

Professor of Quantitative and Computational Biology, Chemistry, Physics and Astronomy and Computer Science
Email rohs@usc.edu Office RRI 413H Office Phone (213) 740-0552

Research & Practice Areas

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

Center, Institute & Lab Affiliations

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

Biography

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

  • Other Degree Business, Columbia University, New York, USA, 2009
  • Ph.D. Biochemistry, Freie Universität Berlin, Germany, 2003
  • M.S. Physics, Humboldt Universität Berlin, Germany, 1997

  • Tenure Track Appointments

    • Chair, Department of Quantitative and Computational Biology, University of Southern California, 01/2021 –
    • Section Head, Quantitative and Computational Biology, University of Southern California, 08/2018 – 12/2020
    • Full Professor (with Tenure) of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, 08/2016 –
    • Vice Chair, Department of Biological Sciences, University of Southern California, 08/2016 – 08/2019
    • Head, Program in Computational Biology and Bioinformatics, University of Southern California, 07/2016 – 08/2018
    • Associate Professor (with Tenure) of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, 01/2016 – 08/2016
    • Assistant Professor of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, 08/2010 – 01/2016

    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

  • 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

  • Book Chapters

    • 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

    • Jiang, Y., Chiu, T. P., Mitra, R., Rohs, R. (2024). Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding. Biophysical journal. Vol. 123 (2), pp. 248-259. PubMed Web Address
    • Li, Y., Cooper, B. H., Liu, Y., Wu, D., Zhang, X., Rohs, R., Qin, P. Z. (2023). CRISPR-Cas9 Activities with Truncated 16-Nucleotide RNA Guides Are Tuned by Target Duplex Stability Beyond the RNA/DNA Hybrid. Biochemistry. Vol. 62 (17), pp. 2541-2548. PubMed Web Address
    • Cooper, B. H., Dantas, A. C., Gan, Y., Aparicio, O. M., Rohs, R. (2023). DNA binding specificity of all four Saccharomyces cerevisiae forkhead transcription factors. Nucleic acids research. Vol. 51 (11), pp. 5621-5633. PubMed Web Address
    • Chiu, T. P., Rao, S., Rohs, R. (2023). Physicochemical models of protein-DNA binding with standard and modified base pairs. Proceedings of the National Academy of Sciences of the United States of America. Vol. 120 (4), pp. e2205796120. PubMed Web Address
    • Cooper, B. H., Chiu, T. P., Rohs, R. (2022). Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics. Bioinformatics (Oxford, England). Vol. 38 (22), pp. 5121-5123. PubMed Web Address
    • Chiu, T. P., Li, J., Jiang, Y., Rohs, R. (2022). It is in the flanks: Conformational flexibility of transcription factor binding sites. Biophysical journal. Vol. 121 (20), pp. 3765-3767. PubMed Web Address
    • Oberbeckmann, E., Krietenstein, N., Niebauer, V., Wang, Y., Schall, K., Moldt, M., Straub, T., Rohs, R., Hopfner, K., Korber, P., Eustermann, S. (2021). Genome information processing by the INO80 chromatin remodeler positions nucleosomes. Nat Coomun. Vol. 12 (1), pp. 3231. PubMed Web Address
    • Lee, C. S., Cheung, M. F., Li, J., Zhao, Y., Lam, W. H., Ho, V., Rohs, R., Zhao, Y., Leung, D., Tye, B. K. (2021). Humanizing the yeast origin recognition complex. Nat Commun. Vol. 12 (1), pp. 33. PubMed Web Address
    • Le Poul, Y., Xin, Y., Ling, L., Mühling, B., Jaenichen, R., Hörl, D., Bunk, D., Harz, H., Leonhardt, H., Wang, Y., Osipova, E., Museridze, M., Dharmadhikari, D., Murphy, E., Rohs, R., Preibisch, S., Prud’homme, B., Gompel, N. (2020). Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer. Sci Adv. Vol. 6 (49), pp. eabe2955. PubMed Web Address
    • Lara-Gonzalez, S., Dantas, A. C., Rao, S., Napoli, A. A., Birktoft, J., Di, R., Rohs, R., Lawson, C. L. (2020). The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element. Biochemistry. Vol. 59 (48), pp. 4523-4532. PubMed Web Address
    • Lara-Gonzalez, S., Dantas Machado, A. C., Rao, S., Napoli, A. A., Birktoft, J., Di Felice, R., Rohs, R., Lawson, C. L. (2020). The RNA polymerase alpha subunit recognizes the DNA shape of the upstream promoter element. Biochemistry. Vol. 59 (48), pp. 4523-4532. PubMed Web Address
    • Dantas Machado, A. C., Cooper, B. H., Lei, X., Di Felice, R., Chen, L., Rohs, R. (2020). Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout. Nucleic Acids Research. Vol. 48 (15), pp. 8529-8544. PubMed Web Address
    • Lei, X., Zhao, J., Sagendorf, J. M., Rajashekar, N., Xu, J., Dantas Machado, A. C., Sen, C., Rohs, R., Feng, P., Chen, L. (2020). Crystal structures of ternary complexes of MEF2 and NKX2-5 bound to DNA reveal a disease related protein-protein interaction interface. Journal of Molecular Biology. Vol. 432 (19), pp. 5499-5508. PubMed Web Address
    • Wu, X., Cao, B., Aquino, P., Chiu, T. P., Chen, C., Jiang, S., Deng, Z., Chen, S., Rohs, R., Wang, L., Galagan, J. E., Dedon, P. C. (2020). Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria. Proceedings of the National Academy Sciences U S A. Vol. 117 (25), pp. 14322-14330. PubMed Web Address
    • Kribelbauer, J. F., Lu, X. J., Rohs, R., Mann, R. S., Bussemaker, H. J. (2020). Towards a mechanistic understanding of DNA methylation readout by transcription factors. Journal of Molecular Biology. Vol. 432 (6), pp. 1801-1815. PubMed Web Address
    • Kribelbauer, J. F., Lu, X. J., Rohs, R., Mann, R. S., Bussemaker, H. J. (2020). Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors. Journal of molecular biology. Vol. 432 (6), pp. 1801-1815. PubMed Web Address
    • Sagendorf, J. M., Markarian, N., Berman, H. M., Rohs, R. (2020). DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes. Nucleic Acids Research. Vol. 48 (D1), pp. D277-D287. PubMed Web Address
    • Chiu, T. P., Xin, B., Markarian, N., Wang, Y., Rohs, R. (2020). TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Research. Vol. 48 (D1), pp. D246-D255. PubMed Web Address
    • Wang, X., Zhou, T., Wunderlich, Z., Maurano, M. T., DePace, A. H., Nuzhdin, S. V., Rohs, R. (2018). Analysis of genetic variation indicates DNA shape involvement in purifying selection. Molecular Biology and Evolution. Vol. 35 (8), pp. 1958-1967. PubMed Web Address
    • Xin, B., Rohs, R. (2018). Relationship between histone modifications and transcription factor binding is protein family specific. Genome Research. Vol. 28, pp. 321-333. PubMed Web Address
    • Rao, S., Chiu, T. P., Kribelbauer, J. F., Mann, R. S., Bussemaker, H. J., Rohs, R. (2018). Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding. Epigenetics & Chromatin. Vol. 11 (1), pp. 6. PubMed Web Address
    • Li, R. Y., Di Felice, R., Rohs, R., Lidar, D. A. (2018). Quantum annealing versus classical machine learning applied to a simplified computational biology problem. npj Quantum Information. Vol. 4, pp. 14. Nature Partner Journals Web Address
    • Azad, R. N., Zafiropoulos, D., Ober, D., Jiang, Y., Chiu, T. P., Sagendorf, J. M., Rohs, R., Tullius, T. D. (2018). Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations. Nucleic Acids Research. Vol. 46 (5), pp. 2636-2647. PubMed Web Address
    • Li, J., Sagendorf, J. M., Chiu, T. P., Pasi, M., Perez, A., Rohs, R. (2017). Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding. Nucleic Acids Research. Vol. 45 (22), pp. 12877-12887. PubMed Web Address
    • Chiu, T. P., Rao, S., Mann, R. S., Honig, B., Rohs, R. (2017). Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding. Nucleic Acids Research. Vol. 45 (21), pp. 12565-12576. PubMed Web Address
    • Li, J., Dantas Machado, A. C., Guo, M., Sagendorf, J. M., Zhou, Z., Jiang, L., Chen, X., Wu, D., Qu, L., Chen, Z., Chen, L., Rohs, R., Chen, Y. (2017). Structure of the forkhead domain of FOXA2 bound to a complete DNA consensus site. Biochemistry. Vol. 56, pp. 3745-3753. PubMed Web Address
    • Ma, W., Yang, L., Rohs, R., Noble, W. S. (2017). DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding. Bioinformatics. Vol. 33, pp. 3003-3010. PubMed Web Address
    • Sagendorf, J. M., Berman, H. M., Rohs, R. (2017). DNAproDB: an interactive tool for structural analysis of DNA-protein complexes. Nucleic Acids Research. Vol. 45, pp. W89-W97. PubMed Web Address
    • Tangprasertchai, N. S., Di Felice, R., Zhang, X., Slaymaker, I. M., Vazquez Reyes, C., Jiang, W., Rohs, R., Qin, P. Z. (2017). CRISPR-Cas9 mediated DNA unwinding detected using site-directed spin labeling. ACS Chemical Biology. Vol. 12, pp. 1489-1493. PubMed Web Address
    • Yang, L., Orenstein, Y., Jolma, A., Yin, Y., Taipale, J., Shamir, R., Rohs, R. (2017). Transcription factor family-specific DNA shape readout revealed by quantitative specificity models. Molecular Systems Biology. Vol. 13 (2), pp. 910. PubMed Web Address
    • Schwörer, S., Becker, F., Feller, C., Baig, A. H., Köber, U., Henze, H., Kraus, J. M., Xin, B., Lechel, A., Lipka, D. B., Varghese, C. S., Schmidt, M., Rohs, R., Aebersold, R., Medina, K. L., Kestler, H. A., Neri, F., von Maltzahn, J., Tümpel, S., Rudolph, K. L. (2016). Epigenetic stress responses induce muscle stem-cell ageing by Hoxa9 developmental signals. Nature. Vol. 540 (7633), pp. 428-432. PubMed Web Address
    • Schöne, S., Jurk, M., Helabad, M. B., Dror, I., Lebars, I., Kieffer, B., Imhof, P., Rohs, R., Vingron, M., Thomas-Chollier, M., Meijsing, S. H. (2016). Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity. Nature Communications. Vol. 7, pp. 12621. PubMed Web Address
    • Mathelier, A., Xin, B., Chiu, T. P., Yang, L., Rohs, R., Wasserman, W. W. (2016). DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo. Cell systems. Vol. 3 (3), pp. 278-286.e4. PubMed Web Address
    • Mathelier, A., Xin, B., Chiu, T. P., Yang, L., Rohs, R., Wasserman, W. W. (2016). DNA shape features improve transcription factor binding site predictions in vivo. Cell Systems. Vol. 3 (3), pp. 278-286. PubMed Web Address
    • Kuzu, G., Kaye, E. G., Chery, J., Siggers, T., Yang, L., Dobson, J. R., Boor, S., Bliss, J., Liu, W., Jogl, G., Rohs, R., Singh, N. D., Bulyk, M. L., Larschan, E., Tolstorukov, M. Y. (2016). Expansion of GA dinucleotide repeats increases the density of CLAMP binding sites on the X-chromosome to promote Drosophila dosage compensation. PLOS Genetics. Vol. 12 (7), pp. e1006120. PubMed Web Address
    • Dror, I., Rohs, R., Mandel-Gutfreund, Y. (2016). How motif environment influences transcription factor search dynamics: Finding a needle in a haystack. BioEssays. Vol. 38, pp. 605-612. PubMed Web Address
    • Chiu, T. P., Comoglio, F., Zhou, T., Yang, L., Paro, R., Rohs, R. (2016). DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding. Bioinformatics. Vol. 32, pp. 1211-1213. PubMed Web Address
    • 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. Nature Communications. 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 Research. 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. Nature Communications. Vol. 6, pp. 7642. PubMed Web Address
    • Rohs, R., Dantas Machado, A. C., Yang, L. (2015). Exposing the secrets of sex determination. Nature Structural and Molecular Biology. 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. Proceedings of the National Academy of Sciences 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 Reports. 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 Research. 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 Research. 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, 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. Briefings in Functional 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 in Biochemical Sciences. 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. Molecular 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 Research. 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 Research. 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 Research. 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 Research. 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 Research. 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 Research. 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 Research. 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 Reports. 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. Proceedings of the National Academy of Sciences 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 Reports. 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. Annual Reviews in Biochemistry. 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. Journal of Biomolecular Structure and Dynamics. 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. Nature Structural and Molecular Biology. 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. Journal of Computational Chemistry. 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 Research. 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-DNA binding sites. Structure. 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. Journal of Biomolecular Structure and Dynamics. 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 Journal of Biochemistry and Biophysics. 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. Journal of the American Chemical Society. Vol. 122, pp. 2860-2866.
    • Rohs, R., Etchebest, C., Lavery, R. (1999). Unraveling proteins: A molecular mechanics study. Biophysical Journal. Vol. 76, pp. 2760-2768. PubMed Web Address

    Proceedings

    • Chu, C., Li, Z., Xin, B., Peng, F., Liu, C., Rohs, R., Luo, Q., Zhou, J. (2018). Deep graph embedding for ranking optimization in E-commerce. pp. 2007-2015. Proc ACM Int Conf Inf Knowl Manag. PubMed Web Address
    • Sloan Research Fellowship Recipient, Alfred P. Sloan Research Fellowship, 2013 – 2017
    • Yang et al. Mol. Syst. Biol. 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, 2016-2017
    • American Chemical Society OpenEye Outstanding Junior Faculty Award in Computational Chemistry presented at the ACS Spring 2016 National Meeting, San Diego, CA, 2015-2016
    • Dror et al. Genome Res. 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, 2015-2016
    • USC Mentoring Award in the category “Mentoring of Graduate Students”, 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

  • Administrative Appointments

    • Chair, 08/16/2021 – 08/15/2024
    • Interim Chair, 01/01/2021 – 08/15/2021
    • Section Head, 08/16/2018 – 12/31/2020
    • Vice Chair, 08/16/2017 – 08/15/2019
    • Vice Chair, 08/16/2016 – 08/15/2017

    Committees

    • Chair, Quantitative Biology (QBIO) Executive Committee, University of Southern California, 2016 –
    • Chair, Biological Sciences Curriculum Committee, University of Southern California, 2016 –
    • Member, Chemistry/Biology Interface Training Grant Executive Committee, University of Southern California, 2016 –
    • 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, Data Advisory Group, Michelson Center for Convergent Biosciences, University of Southern California, 2016-2017
    • Member, Science & Engineering Curriculum Committee, University of Southern California, 2016-2017
    • Member, Computational Biology Faculty Search Committee, University of Southern California, 2016-2017
    • Member, Theoretical Biophysics Faculty Search Committee, University of Southern California, 2016-2017
    • Member, Screening Committee, Ph.D. Program in Computational Biology and Bioinformatics, University of Southern California, 2011 – 2016
    • Member, Admissions Committee, Ph.D. Program in Computational Biology and Bioinformatics, University of Southern California, 2010 – 2016
    • Chair, High-performance computing committee, Computational Biology and Bioinformatics section, University of Southern California, 2015-2016
    • Member, Self-study subcommittee “undergraduate programs”, Department of Biological Sciences, University of Southern California, 2015-2016
    • Member, Self-study steering/”uber” committee, Department of Biological Sciences, University of Southern California, 2015-2016

  • 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 Association for the Advancement of Science (AAAS), 2013 –
    • American Chemical Society (ACS), 2012 –
    • International Society for Computational Biology (ISCB), 2012 –

    Review Panels

    • 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 –
    • Human Frontiers Science Program, HFSP fellowship reviewer, 2015-2016
    • Howard Hughes Medical Institute, HHMI fellowship review panel, 2011 – 2015

    Other Service to the Profession

    • Faculty Member, Faculty of 1000 in Biology (Structural Biology, Section Structure: Transcription and Translation), 2011 – 2015
    • 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
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