Rohs, Remo - University of Southern California, USC - Department of Biological Sciences

个人简介

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

研究领域

The main focus of our Computational Structural Biology research group is the integration of two fields of research: genomics and structural biology. Our primary goal is to reveal yet unknown molecular mechanisms underlying gene regulation using bioinformatics analyses of high-throughput sequencing and DNA methylation data of whole genomes.

近期论文

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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. 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. 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. 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