Rules of Protein-DNA Recognition: Computational and Experimental Advances (15w5167)

Arriving in Oaxaca, Mexico Sunday, June 21 and departing Friday June 26, 2015


(Columbia University)

(University of Southern California)


This workshop will focus on recent progress in understanding structural and energetic mechanisms that enable DNA-binding proteins (such as transcription factors) to bind their cognate genomic sites with high affinity and specificity. The main purpose of the workshop is to bring together researchers with diverse approaches and perspectives to studying protein-DNA recognition, not just experimental versus computational but also different approaches within each of those areas. The goal will be to obtain a better understanding of how transcription factors achieve specificity and how specificity can be modeled and predicted. A second goal is to improve the methods for the design of proteins with novel DNA-binding interfaces and specificities. Advances in understanding the rules of protein-DNA recognition will lead to better understanding of such fundamental biological processes such as DNA replication and transcription, with numerous future applications in biotechnology and medicine. Recent breakthroughs in developing high-throughput experimental techniques make the development of novel mathematical and computational frameworks for analyzing protein-DNA interaction data a high priority. This workshop will help fulfill this urgent need.

The organizer, Dr. Harmen Bussemaker, is an Associate Professor in the Department of Biological Sciences and the Department of Systems Biology at Columbia University. He is widely known for his pioneering computational work aimed at understanding gene regulatory networks based on the integration of genome sequence, transcription factor binding, and gene expression data. His credentials include a Lenfest Distinguished Columbia Faculty Award and a John Simon Guggenheim Foundation Fellowship. His laboratory is funded by the National Institutes of Health.

The co-organizer, Dr. Remo Rohs, is an Assistant Professor in the Molecular and Computational Biology Program of the Department of Biological Sciences at the University of Southern California, Los Angeles. His work established DNA shape readout as a source of transcription factor binding specificity in genome analysis. Dr. Rohs developed computational tools for the high-throughput prediction of DNA shape on a genomic scale. He was awarded an Alfred P. Sloan Research Fellowship in 2013, and his laboratory is funded by the National Institutes of Health.

The confirmed participants include prominent experimental biophysicists and biologists who are the forefront of the field, as well as mathematicians and physicists whose main focus is on mathematical modeling of protein-DNA interactions. We have taken special care to include a significant number of promising young scientists.

One of the main goals for this meeting is to facilitate free exchange of ideas and foster new collaborations, both formal and informal. We believe that BIRS, with its common areas and a beautiful location, will provide an ideal setting for these activities. A similar workshop in the summer of 2013 was hugely successful and the overwhelming consensus was to continue this dialog every two years. The 2015 organizer, who was an attendant at the 2013 meeting, is aware of at least six new collaborations that were initiated as a direct result of the 2013 BIRS meeting. Given its success, the overall agenda and goals for the proposed 2015 meeting will follow closely from the one in 2013. Rather than presenting experiments and modeling in separate sessions, we will mix experimental and theoretical presentations within a given lecture block whenever possible. Because many invited attendees have both experimental and theoretical/computational components in their labs, they will be encouraged to cover recent advances using both approaches in their talks. We will stress the desire for informal presentations and discussions of unpublished data, to maximize the immediate influence that the meeting has on how the field will evolve.

For the structured part of the meeting, we plan to adopt a format in which 30-minute talks (+10 min for questions) will be scheduled in groups of three or four. Every invited participant will be encouraged to give a talk, though it will not be mandatory. Each group of talks will be followed by a tea/coffee break during which the participants will have a chance to discuss the latest lectures in more detail. We will also schedule time for round-table discussions and thematic focus groups that could be devoted to some of the more technical aspects of experiments and mathematical models. Furthermore, we are planning on starting off the workshop with a longer opening lecture (50 min + 10 min for questions), which will set the stage for the entire meeting by providing an overview of the main issues in the field.