Participant Testimonials

Jun 16 - Jun 21, 2013

For a person like me who is trying to choose his field of research for future, it was a great conference to start with. I learnt a lot, interacted with masters of the field and got inputs for my SSL(Sequence Specificity Landscape) program. After seeing everyone's interest in the field and towards my work, I am now excited to continue working on this project and improve my programs so that it can be helpful for analysis for other people too. I new about research of few people who presented, by this meeting I was able to clear my doubts by asking them. Also learnt about research of lot of other people in the area, which is equally exciting and challenging. This conference has filled in me the interest to work on research, specially in the area of DNA-Protein interaction.

Devesh Bhimsaria Student
Department of Biochemistry, University of Wisconsin

Thank you very much for hosting the workshop on Rules of protein-DNA recognition. The meeting was spectacular! Very high quality talks, all highly related to my research, and also very inspiring. Alexandre Morozov and Gary Stormo did a great job putting together such an excellent scientific program. It was great to have, in the same room, so many professors who have pioneered the computational models and the experimental techniques I am currently using in my research, and the discussion times allowed me to better understand the details of each model/method, as well as compare and contrast the various existing technologies. In addition, several collaborations were initiated during this workshop. Remo Rohs, Matt Slattery and myself are going to write a review on the topic. David Lukatsky and I have already exchanged data and results, and we are now talking about writing a paper together. Alex Morozov and I have started a new collaboration - we are now trying to use his thermodynamic models on some of the data I am generating in my lab, and we have already discussed some ideas for future projects. I expect that other discussions during the meeting will also turn into collaborations later on. So, in conclusion, the workshop has helped me a lot in my research, both in terms of immediate effects, as well as inspiration for future research directions. Thank you again for making this workshop possible!

Raluca Gordan Institute for Genome Sciences and Policy, Duke University

Looking over my notes virtually all talks provided me with a new valuable nugget of information. However for my work directly, several talks had a significant impact: Phil Bradley & Carlos Comacho: Provided computational support for the idea that water plays a consistent, potentially (structurally) predictable role in forming protein-DNA interfaces. Phil's ideas that there are solvent 'rotamers' will greatly assist in efficient prediction of hydration schemes. Carlo's finding that differential solvation of a particular protein-DNA contact in different protein or DNA sequence contexts provides a potential (and likely correct) explanation for 'non-linear' effects of substitution mutations on protein-nucleic acid complex affinity. Tali Haran: Injected a note of function and reminded us that binding protein concentration and not just sequence, are important elements when considering functional binding site occupancy. Scot Wolfe: For illustrating his method for selecting not only preferred DNA sequence, but protein sequence outside of the interface region. Aseem Ansari: While not earth shattering, the sequence preference 'landscapes' will provide novices in the field with an easy to read way to identify interesting features of selected sequences. The practical outcomes via new methods to be employed and collaborations was almost as valuable as the ideas. Collaborations: Phil Bradley and I will begin a collaboration on large scale prediction of protein-DNA interactions in bacteriophage repressor proteins. This effort will have a significant impact on testing hypotheses related to how toxin-encoding bacteriophages have evolved to have a 'hair-trigger' induction mechanism-a feature that may lead to their increase virulence. We sent the first set of 'test' data to him today! New methods: Having failed at using purified chimeric transcription factors to identify cooperative changes in preferred binding site motifs, the information on bacterial one-hybrid obtained from Scot Wolfe's and Marcus Noyes' talks and informal interactions with them have emboldened us to try this route. We ordered the oligos and DNA yesterday. We hope that experiment will be complete by the next meeting!!

Gerald Koudelka Professor and Chair
Department of Biological Sciences, University at Buffalo (SUNY)

This was an extremely productive meeting for me. It gave me a chance to see how my research projects might fit into the goals of the protein-nucleotide world. I met many people whose papers I had cited but had never crossed paths with before. I discussed potential collaborations with other participants, based on both published and unpublished work. Attending with a close colleague and collaborator, the meeting helped us put our upcoming paper into the context of the state of the field. It has also been very helpful in our thinking about future projects and an upcoming proposal.

Julie Mitchell Mathematics and Biochemistry, University of Wisconsin - Madison

The meeting was a great way to learn about new tools, their power, and their potential pitfalls. I will include what I've learned in my teaching next year. I also got a chance to network with several people I might collaborate with in the future, and to spend some focused time with a current collaborator from a different institution. Also, we really really really appreciated how helpful BIRS was when we were marooned in Banff. My extra time there was very productive.

Phoebe Rice Biochem & Mol Biol, University of Chicago

This was a wonderful meeting. I like this kind of small meeting focused on specific topic rather than large conferences, especially in this perfect environment. In spite of the small meeting, there was a good mixture of presentations from different backgrounds. I listened to all the talks, and all of them were interesting and useful to my research. I was impressed by the progress of this field, especially new experimental methods and new tools to analyze them. This meeting helped me to expand the scope of protein-DNA recognition. I could meet many new people and the discussion was very stimulating. All the talks and discussions were inspiring and lead to new insight into the mechanism of protein-DNA recognition. This meeting also provide me a possibility to collaborate with some researchers.

Akinori Sarai Professor
Kyushu Institute of Technology, Kyushu Institute of Technology

The BIRS workshop on protein-DNA interactions was really superb. It brought together people working on a common topic, protein-DNA interactions, with a variety of experimental and computational approaches. Although I had previously read papers by most of the participants I had only met about half of them. The talks generated several new ideas that we will test and possibly some new collaborations. It definitely will have an impact on our research directions.

Gary Stormo Professor
Department of Genetics, Washington University in St. Louis School of Medicine

The range of topics related to protein-DNA recognition that was the highlight of the meeting. The opportunity to hear both experimental and computational approaches related to protein-DNA recognition provided the opportunity to expand my perception of the key questions that remained in the field, and the suite of approaches that are being used to achieve greater understanding of the biological questions that still remain. The meeting also provided a great opportunity to strengthen interactions between my laboratory and the Stormo and Noyes laboratory. In addition, new potential collaborations were defined with the Hughes lab on protein DNA-binding specificity and the Bondos lab on artificial homeodomain recognition. Opportunities to discuss science over meals were particularly valuable with both theoretical and experimental approaches being weighed for particular questions. Alex Morozov and Carlos Camacho provided very valuable critiques of an idea that my lab will pursue on homeodomain evolution that will affect the planned direction of these studies. This was by far the most valuable meeting in this field that I have attended.

Scot Wolfe associate professor
Program in Gene Function and Expression, UMass Medical School