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Francisco Melo Ledermann
Profesor Titular
Facultad de Ciencias Biológicas
Pontificia Universidad Católica de Chile
Tiene el agrado de invitarle al Seminario “Integrating Genomics and Structural Biology Reveals Mechanisms of Gene Regulation”, que será dictado por el Dr. Remo Rohs, Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, y que se realizará el jueves 28 de septiembre a las 12:30 pm en el Auditorio Abate Molina de la Facultad de Ciencias Biológicas de la Pontificia Universidad Católica de Chile (Avda. Portugal 49). Se adjunta el resumen de la presentación, así como también una breve descripción del curriculum del Dr. Rohs. Al final del seminario se servirán pizzas y bebidas para que los asistentes puedan compartir un momento entre ellos y discutir con el Dr. Rohs.
Santiago, septiembre de 2017.
Integrating Genomics and Structural Biology Reveals Mechanisms of Gene Regulation
Dr. Remo Rohs
Molecular and Computational Biology Program
Department of Biological Sciences
University of Southern California
United States
Our current knowledge of genome function is the result of sequence-based data in the form of one-dimensional strings of letters. However, DNA-binding proteins recognize the double helix as a three-dimensional object. Therefore, an understanding of transcription factor (TF) binding specificity must ultimately include DNA shape. The sequence-structure relationship in DNA is highly degenerate, and different nucleotide sequences can give rise to the same structure, while single nucleotide sequence variants sometimes change DNA shape over a region of several base pairs. DNA methylation is another way of altering DNA shape. To explore these effects on a genomic scale, we developed methods for the high-throughput prediction of DNA shape features. We used these structural features to augment nucleotide sequence in binding specificity models derived from statistical machine learning approaches and learned DNA binding specificity models from high-throughput binding assays. Based on data for many TFs from diverse protein families, we demonstrated that shape-augmented models are generally more efficient than existing sequence-based models in terms of accuracy, number of features, and computation time. Our models provide information on the importance of specific DNA sequence and shape features and thus reveal TF family-specific readout mechanisms and better explain why a given TF binds to a specific genomic target site. 
Dr. Remo Rohs Biosketch
Remo Rohs received his M.Sc. in Physics and Ph.D. in Biochemistry in Berlin, Germany. He trained as a Postdoc at the Weizmann Institute of Science in Israel with Zippora Shakked and at Columbia University with Barry Honig. Rohs assumed a Faculty position at the University of Southern California as Assistant Professor of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science in 2010. He was promoted to the rank of Associate Professor with tenure in January 2016, and to the rank of Full Professor in August 2016. Rohs is currently the Vice Chair of the Department of Biological Sciences and Head of the Computational Biology and Bioinformatics Section at the University of Southern California.