DIMACS Conference on Effects of Genome Structure and Sequence on the Generation of Variation and Evolution

August 9 - 11, 2011
CoRE Auditorium, CoRE Building, Rutgers University

Lynn Caporale, Conference Chair
Stephen Benkovic, Pennsylvania State University
Giorgio Bernardi, Stazione Zoologica Anton Dohrn
Gyan Bhanot, Institute for Advanced Studies, Princeton
Laura Landweber, Princeton University
Nancy Maizels, University of Washington School of Medicine
Richard Moxon, Oxford University
Advisory committee:
Guna Rajagopal, The Cancer Institute of NJ (CINJ)
Fred Roberts, DIMACS, Rutgers University
Presented under the auspices of the DIMACS/BioMaPS/MB Center Special Focus on Information Processing in Biology.

Workshop Program:

Monday, August 8, 2011

 6:00 -  8:00pm  Reception at Panico's Restaurant
                 103 Church Street
                 New Brunswick, NJ

                 Panico's is within walking distance of the Heldrich Hotel.  
                 Here are directions

Tuesday, August 9, 2011

 7:45          Poster setup

 8:15 -  9:00  Registration and Breakfast
 9:00 -  9:30  Conference Overview Lynn Caporale

 9:30 -  9:45  Special Guest: Evelyn Witkin
               A brief look back

Session I: DNA Sequence, Structure and Replication
               Session Chair: Thomas Kunkel

10:00 - 10:30  Balancing eukaryotic replication asymmetry with replication fidelity   
               Thomas Kunkel, Laboratory of Molecular Genetics and Laboratory of Structural Biology

10:30 - 11:00  DNA sequence context-dependent mutations               
               Jan Drake, National Institute of Environmental Health Sciences

11:00 - 11:30  Break 

11:30 - 12:00  Sequence-context dependence of DNA conformation
               Victor Zhurkin, National Cancer Institute, NIH 

12:00 - 12:30  Structural Transitions in Superhelically stressed DNA               
               Craig Benham, University of California at Davis

12:30 -  1:20  Lunch

Session II: Selection for Rapid Generation of Diversity
               Session Chair: Richard Moxon

 1:20 -  1:30  Welcoming Remarks
               Rebecca Wright, DIMACS Deputy Director
 1:30 -  2:00  Indirect selection of local mutation rates
               David King, Southern Illinois University - Carbondale

 2:00 -  2:30  Rapid Generation of Diversity in Bacterial Contingency Genes
               Richard Moxon, University of Oxford

 2:30 -  3:00  Phenotypic variation due to Tandem Repeats in Mammals
               John "Trey" Fondon, University of Texas

 3:00 -  3:30  Break

 3:30 -  4:00  Determinants of repeat instability and genome evolution
               David Mittelman, Virginia Bioinformatics Institute	

 4:00 -  4:30  Adaptive Evolution via Repeated Deletions in a Vertebrate Enhancer
               Kathy Xie, Stanford University School of Medicine

 5:00 -  5:30  Exogenes: accelerated evolution of venom peptides from cone snails and other venomous molluscs
               Baldomero Olivera, University of Utah

 5:30          Poster session and buffet dinner

Wednesday, August 10, 2011

 8:30 -  9:00  Breakfast and Registration

Session III: Inducible focused variation
               Session Chair: Nancy Maizels

 9:00 -  9:30  DNA structure and regulated region-directed recombination 
               Nancy Maizels, University of Washington

 9:30 - 10:00  Balance between error-free and error-prone DNA repair in the immunoglobulin loci
               Patricia Gearhart, National Institute on Aging, NIH

10:00 - 10:30  Evolution of active deamination of DNA and RNA
               Silvestro Conticello, Core Research Laboratory, Istituto Toscano Tumori, Firenze

10:30 - 11:00  Break

11:00 - 11:30  The mechanisms underlying mutagenesis in E. coli,
               the p53 tumor suppressor gene, and somatic hypermutation
               Barbara Wright, The University of Montana

11:30 - 12:00  The three dimensional spatial organization of the Igh locus directs class switch recombination
               Amy Kenter, University of Illinois College of Medicine, Chicago

12:00 - 12:30  Distribution and Mechanisms of Meiotic Recombination
               Liisa Kauppi, Memorial Sloan-Kettering Cancer Center

12:30 -  1:30  Lunch

Session IV: Genetic variation under stress and other signals
               Session Chair: Nancy Craig

 1:30 -  2:00  Control and function of translesion DNA polymerases
               Graham Walker, Massachusetts Institute of Technology

 2:00 -  2:30  Environmental Regulation of Switching rates in Phase Variable Pathogens and Commensal Bacteria
               Chris Bayliss, University of Leicester

 2:30 -  3:00  DNA double-strand-breaks localize stress-induced mutagenesis in the E. coli genome
               Susan Rosenberg, Baylor College of Medicine

 3:00 -  3:30  Break

 3:30 -  4:00  Initiation of stress-induced mutagenesis and nonhomologous recombination through transcriptional RNA/DNA hybrid molecules
               Phil Hastings

 4:00 -  4:30  Metabolite-dependent alteration of RNA folding, splicing and function
               Narasimhan Sudarsan, Yale University

 4:30 -  5:00  Knowing where transposons go and why
               Nancy Craig, Johns Hopkins University School of Medicine

 5:30          Poster Session and Buffet Dinner

Thursday, August 11, 2011
 8:30 -  9:00  Breakfast and Registration

Session V:  Protocols
               Session Chair: Laura Landweber

 9:00 -  9:30  Protocols, from the Internet to the Genome 
               John Doyle, California Institute of Technology

 9:30 - 10:00  Integrons: Frameworks for information sharing
               Ruth Hall, The University of Sydney

10:00 - 10:30  Materials and methods in the generation of immune diversity in invertebrates
               L. Courtney Smith, George Washington University

10:30 - 11:00  Break

11:00 - 11:30  Generation of variation in trypanosomes
               David Barry, Wellcome Trust Centre for Molecular Parisitology, Glasgow, Scotland, UK 

11:30 - 12:00  RNA-mediated epigenetic inheritance in Oxytricha
               Laura Landweber, Princeton University

12:00 - 12:30  Cryptogenes and RNA Editing
               Ruslan Aphasizhev, University of California, Irvine

12:30  - 1:30  Lunch

Session VI: Evolution, of Genomes and Tumors
               Session Chair: Baldomero Olivera

 1:30 -  2:00  Multiple levels of meaning in DNA sequences? and one more
               Ed Trifonov, University of Haifa

 2:00 -  2:30  Sites of genetic instability in mitosis and cancer
               Ann Casper, Eastern Michigan University

 2:30 -  3:00  Dissecting homologous recombination outcomes: A critical role for noncrossovers in genomic diversity
               Francesca Cole, Memorial Sloan-Kettering Cancer Center 

 3:00 -  3:30  Break

 3:30 -  4:00  Transposable elements in Human Germline Genetic Variation and Cancer
               Kathleen H. Burns, Johns Hopkins University School of Medicine

 4:00 -  4:30  Genome organization and evolution in vertebrates
               Giorgio Bernardi, Rome University

 4:30 -  5:00  Cancer, Evolving
               Lawrence Loeb, University of Washington

If you would like to contribute a poster, please send title/abstract to Nicole Clark at nicolec at dimacs.rutgers.edu no later than June 1, 2011. You will be notified of acceptance of your poster as soon as possible after you submit it.

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Document last modified on August 10, 2011.