RNA in Biology, Bioengineering and Nanotechnology

October 29 - November 02, 2007

Mathematics of Molecular and Cellular Biology

Content

Overview

Organizers:

Tamar Schlick	New York University
Eric Westhof	Université de Strasbourg I (Louis Pasteur)

RNA molecules are key players in all cellular processes, from controlof gene expression to cellular differentiation. In addition, syntheticRNAs have found numerous applications in biomedicine and biomolecularengineering, such as in the design of biosensors and tools forexploring interactions in biological systems. RNA molecules are alsoconsidered in nanotechnology owing to their self-assembly properties.To advance these scientific frontiers, it is essential toquantitatively model RNA at the genomic and molecular levels usingnovel mathematical, statistical, and computational methods.The goals of our workshop are to:

Bring together researchers from the biological and mathematical sciences to explore the fundamental aspects of RNA.
Familiarize the mathematical researchers with current biological problems in the RNA field, including regulatory and catalytic RNAs, RNA folding and dynamics, and engineered RNAs.
Describe current challenges in mathematical approaches to RNA structure and function
Present advances in mathematical modeling and simulation of RNA at the genomic and molecular levels.

Schedule

Monday, October 29, 2007

10:30 am - 11:00 am	Registration and coffee	EE/CS 3-176
11:00 am - 11:15 am	Welcome to the IMA Douglas Arnold (University of Minnesota, Twin Cities)	EE/CS 3-180
11:15 am - 11:30 am	Introduction Tamar Schlick (New York University), Eric Westhof (Université de Strasbourg I (Louis Pasteur))	EE/CS 3-180
11:30 am - 12:00 pm	Computational Methods for RNA Secondary Structure Determination Michael Zuker (Rensselaer Polytechnic Institute)	EE/CS 3-180
12:05 pm - 12:35 pm	Prediction of the Secondary Structure Common to Two Sequences: Free Energy Minimization and Comparative Analysis David Mathews (University of Rochester)	EE/CS 3-180
12:35 pm - 12:50 pm	Discussions	EE/CS 3-180
12:50 pm - 2:30 pm	Lunch
2:30 pm - 3:00 pm	Analysis and Design of Nucleic Acid Devices Niles Pierce (California Institute of Technology)	EE/CS 3-180
3:05 pm - 3:20 pm	A Continuous Probabilistic Model of Local RNA 3-D Structure Jes Frellsen (University of Copenhagen)	EE/CS 3-180
3:25 pm - 3:40 pm	RNA Matrices and RNA Secondary Structures Asamoah Nkwanta (Morgan State University)	EE/CS 3-180
3:45 pm - 4:00 pm	RNA Folding During Transcriptions Facilitated by Non-native Structures Tao Pan (University of Chicago)	EE/CS 3-180
4:05 pm - 4:20 pm	Discussions	EE/CS 3-180
4:30 pm - 4:45 pm	Group Photo
5:00 pm - 6:30 pm	Reception and Poster Session	Lind 400

Tuesday, October 30, 2007

11:45 am - 12:45 pm	Coffee and Treats	Lind 400
2:00 pm - 2:30 pm	Coffee	EE/CS 3-176
2:30 pm - 3:00 pm	Analysis, Prediction, and Design of Viral RNA Secondary Structures Christine Heitsch (Georgia Institute of Technology)	EE/CS 3-180
3:05 pm - 3:35 pm	ARTS and DARTS: A Method and Database for Exploring RNA Tertiary Structures Ruth Nussinov (National Cancer Institute)	EE/CS 3-180
3:35 pm - 3:50 pm	Discussions	EE/CS 3-180
3:50 pm - 4:20 pm	Imaging RNA Structures and Folding Intermediates using Electron Cryo-Microscopy Tobin Sosnick (University of Chicago)	EE/CS 3-180
4:20 pm - 4:50 pm	Coffee	EE/CS 3-176
4:50 pm - 5:20 pm	Prediction of RNA-RNA Interactions Ivo Hofacker (Universität Wien)	EE/CS 3-180
5:20 pm - 5:35 pm	Discussions
5:35 pm - 5:50 pm	Genomic Identification of Structural RNAs using phylo-SCFGs Jakob Pedersen (University of Copenhagen)	EE/CS 3-180
5:55 pm - 6:10 pm	Locomotif: From Graphical Motif Description to RNA Motif Search Jens Reeder (Universität Bielefeld)	EE/CS 3-180
6:15 pm - 6:30 pm	Designing Structured RNA Pools for RNA inVitro Selection Hin Gan (New York University), Namhee Kim (New York University), Tamar Schlick (New York University)	EE/CS 3-180
6:30 pm - 6:45 pm	Discussions	EE/CS 3-180

Wednesday, October 31, 2007

10:30 am - 11:00 am	Coffee	EE/CS 3-176
11:00 am - 11:30 am	Theory and Application of a Novel RNA Folding Approach Based on Nucleotide Cyclic Motifs Francois Major (University of Montreal)	EE/CS 3-180
11:35 am - 12:05 pm	Structure-neutral RNA Substitutions from 3D Structure Alignments and 3D Motif Search Neocles Leontis (Bowling Green State University)	EE/CS 3-180
12:05 pm - 12:20 pm	Discussions	EE/CS 3-180
12:20 pm - 12:50 pm	Coffee	EE/CS 3-176
12:50 pm - 1:20 pm	Using RNA 3D Structure Data in SCFG/MRF Models to do Sequence Alignment and Motif Inference Craig Zirbel (Bowling Green State University)	EE/CS 3-180
1:25 pm - 1:40 pm	Feynman Diagrams, RNA Folding, and the Transition Polynomial Yongwu Rong (George Washington University)	EE/CS 3-180
1:45 pm - 2:00 pm	Ultraconserved Nonsense: Pervasive Unproductive Splicing of SR Proteins Associated with Exceptionally Conserved DNA Elements -- A Bizarre Prevalent Mode of Gene Regulation Steven Brenner (University of California, Berkeley)	EE/CS 3-180
2:05 pm - 2:20 pm	Architecture and Reactivity of RNA Eric Westhof (Université de Strasbourg I (Louis Pasteur))	EE/CS 3-180
2:20 pm - 2:30 pm	Discussions	EE/CS 3-180
8:00 pm - 10:00 pm	Group Event Guthrie Theater

Thursday, November 01, 2007

11:45 am - 12:45 pm	Coffee and Treats	Lind 400
2:00 pm - 2:30 pm	Coffee	EE/CS 3-176
2:30 pm - 3:00 pm	How RNA Tells Right from Wrong: Base Pairs, Tertiary Interactions, and Counterions in RNA Folding Sarah Woodson (Johns Hopkins University)	EE/CS 3-180
3:05 pm - 3:35 pm	Structure, Dynamics and Catalytic Mechanisms of Two Ribozymes David Lilley (University of Dundee)	EE/CS 3-180
3:35 pm - 3:50 pm	Discussions	EE/CS 3-180
3:50 pm - 4:20 pm	Coffee	EE/CS 3-176
4:20 pm - 4:50 pm	A Topological Classification of RNA Folds Henri Orland (Commissariat à l'Énergie Atomique (CEA))	EE/CS 3-180
4:55 pm - 5:25 pm	Exploring the Energy Landscape of RNA Devarajan Thirumalai (University of Maryland)	EE/CS 3-180
5:30 pm - 6:00 pm	RNA / RNP Synthetic Biology Tan Inoue (Kyoto University)	EE/CS 3-180
6:00 pm - 7:30 pm	Math Matters Public Lecture Reception	Lind 400
8:00 pm - 9:15 pm	Math Matters Public Lecture: U.S. Premier Screening of the Film Achieving the Unachievable with the film's writer/director Jean Bergeron

Friday, November 02, 2007

10:30 am - 11:00 am	Coffee
11:00 am - 11:30 am	Computational Approaches to RNA Nanodesign Bruce Shapiro (National Cancer Institute)	EE/CS 3-180
11:35 am - 12:05 pm	RNA Tertiary Structure as a Proto-language for Nano-construction Luc Jaeger (University of California)	EE/CS 3-180
12:05 pm - 12:20 pm	Discussions	EE/CS 3-180
12:20 pm - 12:30 pm	Concluding remarks Tamar Schlick (New York University), Eric Westhof (Université de Strasbourg I (Louis Pasteur))	EE/CS 3-180

Participants

Name	Department	Affiliation
Mirela Andronescu	Department of Computer Science	University of British Columbia
Douglas Arnold	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
F. Javier Arsuaga	Department of Mathematics	San Francisco State University
Rolf Backofen	Institute of Computer Science	Albert-Ludwigs-Universität Freiburg
Nina Barnett		University of Minnesota, Twin Cities
Alex Bateman		Wellcome Trust Sanger Institute
Daniel Bates	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Peter Bates	Department of Mathematics	Michigan State University
John Baxter	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Yermal Bhat	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Eckart Bindewald	Center for Cancer Research Nanobiology Program	SAIC-Frederick, Inc.
Michael Bon	Service de Physique Theorique	Commissariat à l'Énergie Atomique (CEA)-Centre d'Études Nucléaires de Saclay (CENS)
Steven Brenner	Department of Plant and Microbial Biology	University of California, Berkeley
Anke Busch	Bioinformatics Group	Albert-Ludwigs-Universität Freiburg
Carme Calderer	School of Mathematics	University of Minnesota, Twin Cities
Hannah Callender	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
David Case	Department of Molecular Biology	Scripps Research Institute
Shi-Jie Chen	Department of Physics	University of Missouri
Arkadiusz Chworos	Department of Chemistry and Biochemistry	University of California
Peter Clote		Boston College
Anne Condon		University of Wisconsin, Madison
Ludovica Cotta-Ramusino	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Irma Cruz-White	Department of Mathematics and Natural Sciences	Chipola College
Isabel Darcy	Department of Mathematics	The University of Iowa
Kaushik Dayal	Department of Aerospace Engineering and Mechanics	University of Minnesota, Twin Cities
Maciej Dlugosz	Interdisciplinary Centre for Mathematical, , and Computational Modeling	University of Warsaw
Mauricio Esguerra	Chemistry and Chemical Biology	Rutgers, The State University Of New Jersey
Marcia Fenley	Institute of Molecular Biophysics	Florida State University
Jes Frellsen	Department of Molecular Biology	University of Copenhagen
Hin Gan	Department of Chemistry	New York University
Paul Gardner	Rfam Group	Wellcome Trust Sanger Institute
Daniel Gautheret	Institut de Génétique et Microbiologie	Université de Paris XI (Paris-Sud)
Zhumur Ghosh	Computational Biology Group	Indian Association for the Cultivation of Science (IACS)
George Giambasu	Department of Chemistry	University of Minnesota, Twin Cities
Haipeng Gong		University of Chicago
Jan Gorodkin	Division of Genetics and Bioinformatics, IBHV	University of Copenhagen
Jason Gower	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Christine Heitsch	School of Mathematics	Georgia Institute of Technology
Hugh Heldenbrand		University of Minnesota, Twin Cities
Milena Hering	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Peter Hinow	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Ivo Hofacker	Institut für Theoretische Chemie	Universität Wien
Mihaela Iftime	Massachusetts College of Pharmacy and Health Sciences	Boston University
Tan Inoue	Department of Chemistry	Kyoto University
Hosna Jabbari	Department of Computer Science	University of British Columbia
Luc Jaeger	Department of Chemistry and Biochemistry	University of California
Richard James	Department of Aerospace Engineering and Mechanics	University of Minnesota, Twin Cities
Tiefeng Jiang	School of Statistics	University of Minnesota, Twin Cities
Wojciech (Voytek) Kasprzak	Nanobiology Program / Basic Research Program	National Cancer Institute
Abdelouahab Kenoufi	Institute of Physics	Universität Basel
Namhee Kim	Department of Chemistry	New York University
Soojeong Kim	Department of Mathematics	The University of Iowa
Rob Knight	Department of Chemistry and Biochemistry	University of Colorado
Debra Knisley	Department of Mathematics	East Tennessee State University
Erick kuechler		University of Minnesota, Twin Cities
Christian Laing	Department of Mathematics, Chemistry	New York University
Chang Lee	Department of Mathematical Sciences	Worcester Polytechnic Institute
Hyunju Lee	Chemistry Department	University of Minnesota, Twin Cities
Tai-Sing Lee	Department of Computer Science	Carnegie-Mellon University
Neocles Leontis	Department of Chemistry	Bowling Green State University
Anton Leykin	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
David Lilley	The Nucleic Acid Structure Research Group	University of Dundee
Stinus Lindgreen	Bioinformatics Centre	University of Copenhagen
Carlos Lopez		University of Minnesota, Twin Cities
Andy Lorenz	Department of Biology	Boston College
Roger Lui	Department of Mathematical Sciences	Worcester Polytechnic Institute
Laura Lurati	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Maciej Maciejczyk	Department of Chemistry	Cornell University
Francois Major	Departement d'Informatique et de Recherche Operationnelle	University of Montreal
Bibekanand Mallick	Computational Biology Group	Indian Association for the Cultivation of Science (IACS)
David Mathews	Department of Biochemistry and Molecular Biophysics	University of Rochester
Roderick Melnik	CRC in Mathematical Modeling	Wilfrid Laurier University
Ezra Miller	School of Mathematics	University of Minnesota, Twin Cities
Maria Giovanna Mora	Department of Mathematics	International School for Advanced Studies (SISSA/ISAS)
Alejandro Morales Valencia	Department of Computational Sciences	University of Guadalajara
Junalyn Navarra-Madsen	Department of Mathematics and Computer Science	Texas Woman's University
Timothy Newman	Department of Physics	Arizona State University
Olalla Nieto Faza	Department of Chemistry	University of Minnesota, Twin Cities
Asamoah Nkwanta	Department of Mathematics	Morgan State University
Ruth Nussinov	Computational Structural Biology Group	National Cancer Institute
Duane Nykamp	School of Mathematics	University of Minnesota, Twin Cities
Wilma Olson	Department of Chemistry and Chemical Biology	Rutgers, The State University of New Jersey
Henri Orland	Institut de Physique Theorique	Commissariat à l'Énergie Atomique (CEA)
Hans Othmer	Department of Mathematics	University of Minnesota, Twin Cities
Tao Pan	Department of Biochemistry and Molecular Biology	University of Chicago
Jakob Pedersen	The Bioinformatics Center/Department of Molecular Biology	University of Copenhagen
Niles Pierce	Department of Applied and Computational Mathematics	California Institute of Technology
Yann Ponty	Department of Biology	Boston College
Eric Rawdon	Department of Mathematics	University of St. Thomas
Jens Reeder	Technische Fakultät	Universität Bielefeld
Yongwu Rong	Department of Mathematics	George Washington University
Ioulia Rouzina	Biochemistry, Molecular Biology and Biophysics	University of Minnesota, Twin Cities
Walter Ruzzo	Department of Computer Science and Engineering	University of Washington
Tamar Schlick	Courant Institute of Mathematical Sciences	New York University
Deena Schmidt	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Hullas Sehcal	Department of Electrical Engineering	University of Minnesota, Twin Cities
Chehrzad Shakiban	Institute of Mathematics and its Applications	University of Minnesota, Twin Cities
Bruce Shapiro	CCR Nanobiology Program/NCI - Frederick	National Cancer Institute
Tobin Sosnick	Department of Biochemistry and Molecular Biology	University of Chicago
Andrew Stein	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Michael Stich		Instituto Nacional de Tecnica Aeroespacial
Andrew Stuart	Mathematics Institute	University of Warwick
De Witt Sumners		Florida State University
Vladimir Sverak	School of Mathematics	University of Minnesota, Twin Cities
David Swigon	Department of Mathematics	University of Pittsburgh
Berhanu Tameru	Center for Computational Epidemiology, Bioinformatics & Risk Analysis (CCEBRA)	Tuskegee University
Chris Thachuk	Department of Computer Science	University of British Columbia
Devarajan Thirumalai	Department of Chemistry and Biochemistry	University of Maryland
Madhan Tirumalai	Department of Biology and Biochemistry	University of Houston
Elfar Torarinsson	Division of Genetics and Bioinformatics, IBHV	University of Copenhagen
Erkan Tüzel	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Tanya Vassilevska	Center for Applied Scientific Computing	Lawrence Livermore National Laboratory
Mariel Vazquez	Department of Mathematics	San Francisco State University
Jérôme Waldispühl	Department of Applied Mathematics	Massachusetts Institute of Technology
Haiyan Wang	Department of Mathematical Sciences and Applied Computing	Arizona State University
Zhian Wang	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Stefan Washietl	Institute of Theoretical Chemistry and Structural biology	Universität Wien
Eric Westhof	Institut de biologie moleculaire et cellulaire du CNRS	Université de Strasbourg I (Louis Pasteur)
Sebastian Will	Institute of Computer Science	Albert-Ludwigs-Universität Freiburg
Sarah Woodson	Department of Biophysics	Johns Hopkins University
Zhijun Wu	Department of Mathematics	Iowa State University
Yurong Xin	Computational Bilogy, Chemistry & Biomathematics	New York University
Yi Xing	Department of Internal Medicine & Biomedical Engineering	The University of Iowa
Yanji Xu		Minnesota Supercomputing Institute
Chuan Xue	Department of Mathematics	University of Minnesota, Twin Cities
Masoud Yari	Department of Mathematics	Indiana University
Darrin York	Department of Chemistry	University of Minnesota, Twin Cities
Hongchao Zhang	Institute for Mathematics and its Applications	University of Minnesota, Twin Cities
Zhichuan Zhang	Department of Computer Science	University of British Columbia
Likun Zheng		University of Minnesota, Twin Cities
Craig Zirbel	Department of Mathematics & Statistics	Bowling Green State University
Michael Zuker	Department of Mathematical Sciences	Rensselaer Polytechnic Institute