IMA Workshop: RNA in Biology, Bioengineering and Nanotechnology, October 29-November 2, 2007

Mathematics of Molecular and Cellular Biology

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, 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, Berkeley)

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, Santa Barbara)

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	School of Mathematics	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, Berkeley
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 Biochemistry	University of California, Santa Barbara
Peter Clote		Boston College
Anne E. Condon	Department of Computer Science	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		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 D. 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, Santa Barbara
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 Biochemistry	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 Silva Lopez	Department of Chemistry	University of Minnesota
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
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	Department of Electrical Engineering	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 M. 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	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 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 Department	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	Mathematics 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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IMA Annual Program Year Workshop

RNA in Biology, Bioengineering and Nanotechnology

LIST OF CONFIRMED PARTICIPANTS