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IMA Annual Program Year Workshop

RNA in Biology, Bioengineering and Nanotechnology

October 29-November 2, 2007
Organizers:
Tamar Schlick Chemistry, Mathematics, and Computer Science, New York University
Eric Westhof Institute of Molecular and Cellular Biology, CNRS, Strasbourg

Schedule Participants Program Application Feedback
IMA Live Streaming and Webcasting Maps
Abstracts and Talk Materials Dining Guide
Videos Photo Gallery
Group Event–Guthrie Theater
Wednesday, October 31, 2007
Math Matters - U.S. Premier Screening of the film
"Achieving the Unachievable"
with the film's writer/director Jean Bergeron
Thursday, November 1, 2007
7:00 pm, Willey Hall 125 (free and open to the public)

Description:

RNA molecules are key players in all cellular processes, from control of gene expression to cellular differentiation. In addition, synthetic RNAs have found numerous applications in biomedicine and biomolecular engineering, such as in the design of biosensors and tools for exploring interactions in biological systems. RNA molecules are also considered in nanotechnology owing to their self-assembly properties. To advance these scientific frontiers, it is essential to quantitatively model RNA at the genomic and molecular levels using novel 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 | Tuesday | Wednesday | Thursday | Friday | 
  Monday, October 29
9:30a-10:00a Registration and coffee   EE/CS 3-176
10:00a-10:15a Welcome to the IMA Douglas N. Arnold (University of Minnesota) EE/CS 3-180
10:15a-10:30a Introduction Tamar Schlick (New York University), Eric Westhof (Université de Strasbourg I (Louis Pasteur)) EE/CS 3-180
10:30a-11:00a Computational methods for RNA secondary structure determination Michael Zuker (Rensselaer Polytechnic Institute) EE/CS 3-180
11:05a-11:35a Prediction of the secondary structure common to two sequences: Free energy minimization and comparative analysis David H. Mathews (University of Rochester) EE/CS 3-180
11:35a-11:50a Discussions   EE/CS 3-180
11:50a-1:30p Lunch    
1:30p-2:00p Analysis and design of nucleic acid devices Niles A. Pierce (California Institute of Technology) EE/CS 3-180
2:05p-2:20p A continuous probabilistic model of local RNA 3-D structure Jes Frellsen (University of Copenhagen) EE/CS 3-180
2:25p-2:40p RNA matrices and RNA secondary structures Asamoah Nkwanta (Morgan State University) EE/CS 3-180
2:45p-3:00p RNA folding during transcription facilitated by non-native structures Tao Pan (University of Chicago) EE/CS 3-180
3:05p-3:20p Discussions   EE/CS 3-180
3:30p-3:45p Group Photo    
4:00p-5:30p Reception and Poster Session
Lind Hall 400
Efficient parameter estimation for RNA secondary structure prediction Mirela Andronescu (University of British Columbia)
Computational comparative genomics for discovery of cis-regulatory RNAs in bacteria Walter Larry Ruzzo (University of Washington)
The Rfam database: we need you Alex Bateman (Wellcome Trust Sanger Institute)
Paul Gardner (Wellcome Trust Sanger Institute)
Utilizing the RNAJunction database for the design of RNA nanostructures Eckart Bindewald (SAIC-Frederick, Inc.)
Riboswitches, RNA conformational switches and prokaryotic gene regulation (with Eva Freyhulta Vincent Moultonb) Peter Clote (Boston College)
Efficient algorithms for probing the RNA mutation landscape (with Waldispuehl, Devadas, Berger) Peter Clote (Boston College)
Binding of aminoglycosidic antibiotics to the oligonucleotide A-site model Maciej Dlugosz (University of Warsaw)
RNA dinucleotide step parameters Mauricio Esguerra (Rutgers University)
A continuous probabilistic model of local RNA 3-D structure Jes Frellsen (University of Copenhagen)
Designing structured RNA pools for in vitro selection of RNAs Hin Hark Gan (New York University)
Functional classification of all non-coding microbial sequences through phylogenetic profiling Daniel Gautheret (Université de Paris XI (Paris-Sud))
Multi scale simulation of RNA catalytic activity George Madalin Giambasu (University of Minnesota)
Local pairwise structural RNA alignments by pruning of the dynamical programming matrix Jan Gorodkin (University of Copenhagen)
RNA pseudoknotted secondary structure prediction using hierarchical folding Hosna Jabbari (University of British Columbia)
Determining functional conformations of two HDV III strains Wojciech (Voytek) Kasprzak (National Cancer Institute)
Finding additional functional elements in essential RNA sites: not conserved, but not unimportant Rob Knight (University of Colorado)
Annotated tertiary interaction motifs in RNA structures Christian E. Laing (New York University)
MASTR: Simultaneous multiple alignment and structure prediction of non-coding RNAs using simulated annealing Stinus Lindgreen (University of Copenhagen)
Computational models for RNA silencing pathways under time-dependent transgene transcription rates Roderick Melnik (Wilfrid Laurier University)
RNA folding during transcription facilitated by non-native structures Tao Pan (University of Chicago)
Comparative genomics beyond sequence based alignments: RNA structures in the ENCODE regions Elfar Torarinsson (University of Copenhagen)
Collective properties of evolving populations of RNA molecules Michael Stich (Instituto Nacional de Tecnica Aeroespacial)
On the design of oligos for gene synthesis Chris Thachuk (University of British Columbia)
Efficient algorithms for probing the RNA mutation landscape and prediction of deleterious mutations Jérôme Waldispühl (Massachusetts Institute of Technology)
Improved RNA gene predictions through dinucleotide controlled randomization of multiple sequence alignments Stefan Washietl (Universität Wien)
Estimating the fraction of non-coding RNAs in mammalian transcriptomes Yurong Xin (New York University)
  Tuesday, October 30
10:45a-11:45a Coffee and Treats   Lind Hall 400
1:00p-1:30p Coffee   EE/CS 3-176
1:30p-2:00p Analysis, prediction, and design of viral RNA secondary structures Christine E. Heitsch (Georgia Institute of Technology) EE/CS 3-180
2:05p-2:35p ARTS and DARTS: A method and database for exploring RNA tertiary structures Ruth Nussinov (National Cancer Institute) EE/CS 3-180
2:35p-2:50p Discussions   EE/CS 3-180
2:50p-3:20p Imaging RNA structures and folding intermediates using electron cryo-microscopy Tobin R. Sosnick (University of Chicago) EE/CS 3-180
3:20p-3:50p Coffee   EE/CS 3-176
3:50p-4:20p Prediction of RNA-RNA interactions Ivo L. Hofacker (Universität Wien) EE/CS 3-180
4:20p-4:35p Discussions    
4:35p-4:50p Genomic identification of structural RNAs using phylo-SCFGs Jakob Skou Pedersen (University of Copenhagen) EE/CS 3-180
4:55p-5:10p Locomotif: from graphical motif description to RNA motif search Jens Reeder (Universität Bielefeld) EE/CS 3-180
5:15p-5:30p Designing structured RNA Pools for RNA in vitro selection Hin Hark Gan (New York University), Namhee Kim (New York University), Tamar Schlick (New York University) EE/CS 3-180
5:30p-5:45p Discussions   EE/CS 3-180
  Wednesday, October 31
9:30a-10:00a Coffee   EE/CS 3-176
10:00a-10:30a Theory and application of a novel RNA folding approach based on nucleotide cyclic motifs Francois Major (University of Montreal) EE/CS 3-180
10:35a-11:05a Structure-neutral RNA substitutions from 3D structure alignments and 3D motif search Neocles B. Leontis (Bowling Green State University) EE/CS 3-180
11:05a-11:20a Discussions   EE/CS 3-180
11:20a-11:50a Coffee   EE/CS 3-176
11:50a-12:20p Using RNA 3D structure data in SCFG/MRF models to do sequence alignment and motif inference Craig L. Zirbel (Bowling Green State University) EE/CS 3-180
12:25p-12:40p Feynman diagrams, RNA folding, and the transition polynomial Yongwu Rong (George Washington University) EE/CS 3-180
12:45p-1:00p 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) EE/CS 3-180
1:05p-1:20p Architecture and reactivity of RNA Eric Westhof (Université de Strasbourg I (Louis Pasteur)) EE/CS 3-180
1:20p-1:30p Discussions   EE/CS 3-180
7:00p-9:00p Group Event Guthrie Theater   818 South 2nd Street, Minneapolis 
  Thursday, November 1
10:45a-11:45a Coffee and Treats   Lind Hall 400
1:00p-1:30p Coffee   EE/CS 3-176
1:30p-2:00p How RNA tells right from wrong: base pairs, tertiary interactions, and counterions in RNA folding Sarah Woodson (Johns Hopkins University) EE/CS 3-180
2:05p-2:35p Structure, dynamics and catalytic mechanisms of two ribozymes David M.J. Lilley (University of Dundee) EE/CS 3-180
2:35p-2:50p Discussions   EE/CS 3-180
2:50p-3:20p Coffee   EE/CS 3-176
3:20p-3:50p A topological classification of RNA folds Henri Orland (Commissariat à l'Énergie Atomique Saclay (CEA)) EE/CS 3-180
3:55p-4:25p Exploring the energy landscape of RNA Devarajan Thirumalai (University of Maryland) EE/CS 3-180
4:30p-5:00p RNA / RNP synthetic biology Tan Inoue (Kyoto University) EE/CS 3-180
5:00p-6:30p Math Matters public lecture reception   Lind Hall 400
7:00p-8:15p Math Matters public lecture: U.S. premier screening of the film "Achieving the unachievable" with the film's writer/director Jean Bergeron (Alpha-Zoulou Films) Willey Hall 125 (free and open to the public) 
  Friday, November 2
9:30a-10:00a Coffee    
10:00a-10:30a Computational approaches to RNA nanodesign Bruce A. Shapiro (National Cancer Institute) EE/CS 3-180
10:35a-11:05a RNA tertiary structure as a proto-language for nano-construction Luc Jaeger (University of California) EE/CS 3-180
11:05a-11:20a Discussions   EE/CS 3-180
11:20a-11:30a Concluding remarks Tamar Schlick (New York University), Eric Westhof (Université de Strasbourg I (Louis Pasteur)) EE/CS 3-180

LIST OF CONFIRMED PARTICIPANTS

Name Department Affiliation
Mirela Andronescu Department of Computer Science University of British Columbia
Douglas N. Arnold Institute for Mathematics and its Applications University of Minnesota
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
Alex Bateman   Wellcome Trust Sanger Institute
Daniel J. Bates Institute for Mathematics and its Applications University of Minnesota
Peter W. Bates Department of Mathematics Michigan State University
John Baxter Institute for Mathematics and its Applications University of Minnesota
Yermal Sujeet Bhat Institute for Mathematics and its Applications University of Minnesota
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
Anke Busch Bioinformatics Group Albert-Ludwigs-Universität Freiburg
Maria-Carme T. Calderer School of Mathematics University of Minnesota
Hannah Callender Institute for Mathematics and its Applications University of Minnesota
David Case Department of Molecular Biology Scripps Research Institute
Shi-Jie Chen Department of Physics University of Missouri
Arkadiusz Chworos Department of Chemistry and Bio-Chemistry University of California
Peter Clote   Boston College
Anne E. Condon   University of Wisconsin
Ludovica Cecilia Cotta-Ramusino Institute for Mathematics and its Applications University of Minnesota
Irma Cruz-White Department of Mathematics and Natural Sciences Chipola College
Isabel K. Darcy Department of Mathematics University of Iowa
Kaushik Dayal Department of Aerospace Engineering and Mechanics University of Minnesota
Maciej Dlugosz Interdisciplinary Centre for Mathematical and Computational Modeling University of Warsaw
Mauricio Esguerra Chemistry and Chemical Biology Rutgers University
Marcia O. Fenley Department of Physics Florida State University
Jes Frellsen Department of Molecular Biology University of Copenhagen
Hin Hark 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 Madalin Giambasu Department of Chemistry University of Minnesota
Haipeng Gong BMB University of Chicago
Jan Gorodkin Division of Genetics and Bioinformatics, IBHV University of Copenhagen
Jason E. Gower Institute for Mathematics and its Applications University of Minnesota
Christine E. Heitsch School of Mathematics Georgia Institute of Technology
Hugh Heldenbrand Chemistry Department University of Minnesota
Milena Hering Institute for Mathematics and its Applications University of Minnesota
Peter Hinow Institute for Mathematics and its Applications University of Minnesota
Ivo L. Hofacker Institut für Theoretische Chemie Universität Wien
Mihaela Iftime   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 Bio-Chemistry University of California
Richard D. James Department of Aerospace Engineering and Mechanics University of Minnesota
Tiefeng Jiang Department of Statistics University of Minnesota
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 University of Iowa
Rob Knight Department of Chemistry and Bio-Chemistry University of Colorado
Debra Knisley Department of Mathematics East Tennessee State University
Erick kuechler Chemistry Department University of Minnesota
Christian E. Laing Department of Mathematics, Chemistry New York University
Chang Hyeong Lee Department of Mathematical Sciences Worcester Polytechnic Institute
Hyunju Lee Chemistry Department University of Minnesota
Tai-Sing Lee Department of Computer Science Carnegie Mellon University
Neocles B. Leontis Department of Chemistry Bowling Green State University
Anton Leykin Institute for Mathematics and its Applications University of Minnesota
David M.J. Lilley The Nucleic Acid Structure Research Group University of Dundee
Stinus Lindgreen Bioinformatics Centre University of Copenhagen
Carlos Siva Lopez Chemistry Department University of Minnesota
Andy Lorenz Department of Biology Boston College
Roger Y. Lui Department of Mathematical Sciences Worcester Polytechnic Institute
Laura Lurati Institute for Mathematics and its Applications University of Minnesota
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 H. 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
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
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
Wilma K. Olson Department of Chemistry and Chemical Biology Rutgers University
Henri Orland Service de Physique Theorique Commissariat à l'Énergie Atomique Saclay (CEA)
Hans G. Othmer Department of Mathematics University of Minnesota
Tao Pan Department of Biochemistry and Molecular Biology University of Chicago
Jakob Skou Pedersen The Bioinformatics Center/Department of Molecular Biology University of Copenhagen
Niles A. Pierce Department of Applied and Computational Mathematics California Institute of Technology
Yann Ponty Department of Biology Boston College
Eric J. 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
Walter Larry 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
Hullas Sehcal Electrical Engeneering University of Minnesota
Chehrzad Shakiban Institute of Mathematics and its Application University of Minnesota
Bruce A. Shapiro CCR Nanobiology Program/NCI - Frederick National Cancer Institute
Tobin R. Sosnick Department of Biochemistry and Molecular Biology University of Chicago
Andrew Stein Institute for Mathematics and its Applications University of Minnesota
Michael Stich   Instituto Nacional de Tecnica Aeroespacial
Andrew M. Stuart Mathematics Institute University of Warwick
De Witt L. Sumners Department of Mathematics Florida State University
Vladimir Sverak School of Mathematics University of Minnesota
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 Chemistry and Biochemistry University of Maryland
Madhan Tirumalai Department of Biology and Biochemistry University of Houston
Elfar Torarinsson Division of Genetics and Bioinformatics, IBHV and Center for Bioinformatics University of Copenhagen
Erkan Tüzel Institute for Mathematics and its Applications University of Minnesota
Tanya Vassilevska Center for Applied Scientific Computing Lawrence Livermore National Laboratory
Mariel Vazquez Department of Mathematics San Francisco State University
Jérôme Waldispühl Applied Mathematics & CSAIL 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
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 University of Iowa
Yanji Xu   Minnesota Supercomputing Institute
Chuan Xue Department of Mathematics University of Minnesota
Masoud Yari Department of Mathematics Indiana University
Darrin M. York Department of Chemistry University of Minnesota
Hongchao Zhang Institute for Mathematics and its Applications University of Minnesota
Zhichuan Zhang Computer Science Department University of British Columbia
Likun Zheng Math Department University of Minnesota
Craig L. Zirbel Department of Mathematics and Statistics Bowling Green State University
Michael Zuker Department of Mathematical Sciences Rensselaer Polytechnic Institute

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