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IMA Annual Program Year Workshop
RNA in Biology, Bioengineering and Nanotechnology
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 |
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
Download full schedule »| Monday | Tuesday | Wednesday | Thursday | Friday | | |||
|---|---|---|---|
| Monday October 29, 2007 | |||
| 10:30am-11:00am | Registration and coffee | EE/CS 3-176 | |
| 11:00am-11:15am | Welcome to the IMA | Douglas Arnold (University of Minnesota, Twin Cities) | EE/CS 3-180 |
| 11:15am-11:30am | Introduction | Tamar Schlick (New York University) Eric Westhof (Université de Strasbourg I (Louis Pasteur)) | EE/CS 3-180 |
| 11:30am-12:00pm | Computational methods for RNA secondary structure determination | Michael Zuker (Rensselaer Polytechnic Institute) | EE/CS 3-180 |
| 12:05pm-12:35pm | Prediction of the secondary structure common to two sequences: Free energy minimization and comparative analysis | David Mathews (University of Rochester) | EE/CS 3-180 |
| 12:35pm-12:50pm | Discussions | EE/CS 3-180 | |
| 12:50pm-2:30pm | Lunch | ||
| 2:30pm-3:00pm | Analysis and design of nucleic acid devices | Niles Pierce (California Institute of Technology) | EE/CS 3-180 |
| 3:05pm-3:20pm | A continuous probabilistic model of local RNA 3-D structure | Jes Frellsen (University of Copenhagen) | EE/CS 3-180 |
| 3:25pm-3:40pm | RNA matrices and RNA secondary structures | Asamoah Nkwanta (Morgan State University) | EE/CS 3-180 |
| 3:45pm-4:00pm | RNA folding during transcription facilitated by non-native structures | Tao Pan (University of Chicago) | EE/CS 3-180 |
| 4:05pm-4:20pm | Discussions | EE/CS 3-180 | |
| 4:30pm-4:45pm | Group Photo | ||
| 5:00pm-6:30pm | Reception and Poster SessionLind Hall 400 | ||
| Tuesday October 30, 2007 | |||
| 11:45am-12:45pm | Coffee and Treats | Lind Hall 400 | |
| 2:00pm-2:30pm | Coffee | EE/CS 3-176 | |
| 2:30pm-3:00pm | Analysis, prediction, and design of viral RNA secondary structures | Christine Heitsch (Georgia Institute of Technology) | EE/CS 3-180 |
| 3:05pm-3:35pm | ARTS and DARTS: A method and database for exploring RNA tertiary structures | Ruth Nussinov (National Cancer Institute) | EE/CS 3-180 |
| 3:35pm-3:50pm | Discussions | EE/CS 3-180 | |
| 3:50pm-4:20pm | Imaging RNA structures and folding intermediates using electron cryo-microscopy | Tobin Sosnick (University of Chicago) | EE/CS 3-180 |
| 4:20pm-4:50pm | Coffee | EE/CS 3-176 | |
| 4:50pm-5:20pm | Prediction of RNA-RNA interactions | Ivo Hofacker (Universität Wien) | EE/CS 3-180 |
| 5:20pm-5:35pm | Discussions | ||
| 5:35pm-5:50pm | Genomic identification of structural RNAs using phylo-SCFGs | Jakob Pedersen (University of Copenhagen) | EE/CS 3-180 |
| 5:55pm-6:10pm | Locomotif: from graphical motif description to RNA motif search | Jens Reeder (Universität Bielefeld) | EE/CS 3-180 |
| 6:15pm-6:30pm | Designing structured RNA Pools for RNA in vitro selection | Hin Gan (New York University) Namhee Kim (New York University) Tamar Schlick (New York University) | EE/CS 3-180 |
| 6:30pm-6:45pm | Discussions | EE/CS 3-180 | |
| Wednesday October 31, 2007 | |||
| 10:30am-11:00am | Coffee | EE/CS 3-176 | |
| 11:00am-11:30am | Theory and application of a novel RNA folding approach based on nucleotide cyclic motifs | Francois Major (University of Montreal) | EE/CS 3-180 |
| 11:35am-12:05pm | Structure-neutral RNA substitutions from 3D structure alignments and 3D motif search | Neocles Leontis (Bowling Green State University) | EE/CS 3-180 |
| 12:05pm-12:20pm | Discussions | EE/CS 3-180 | |
| 12:20pm-12:50pm | Coffee | EE/CS 3-176 | |
| 12:50pm-1:20pm | 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 |
| 1:25pm-1:40pm | Feynman diagrams, RNA folding, and the transition polynomial | Yongwu Rong (George Washington University) | EE/CS 3-180 |
| 1:45pm-2:00pm | 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 |
| 2:05pm-2:20pm | Architecture and reactivity of RNA | Eric Westhof (Université de Strasbourg I (Louis Pasteur)) | EE/CS 3-180 |
| 2:20pm-2:30pm | Discussions | EE/CS 3-180 | |
| 8:00pm-10:00pm | Group Event Guthrie Theater | 818 South 2nd Street, Minneapolis | |
| Thursday November 01, 2007 | |||
| 11:45am-12:45pm | Coffee and Treats | Lind Hall 400 | |
| 2:00pm-2:30pm | Coffee | EE/CS 3-176 | |
| 2:30pm-3:00pm | How RNA tells right from wrong: base pairs, tertiary interactions, and counterions in RNA folding | Sarah Woodson (Johns Hopkins University) | EE/CS 3-180 |
| 3:05pm-3:35pm | Structure, dynamics and catalytic mechanisms of two ribozymes | David Lilley (University of Dundee) | EE/CS 3-180 |
| 3:35pm-3:50pm | Discussions | EE/CS 3-180 | |
| 3:50pm-4:20pm | Coffee | EE/CS 3-176 | |
| 4:20pm-4:50pm | A topological classification of RNA folds | Henri Orland (Commissariat à l'Énergie Atomique Saclay (CEA)) | EE/CS 3-180 |
| 4:55pm-5:25pm | Exploring the energy landscape of RNA | Devarajan Thirumalai (University of Maryland) | EE/CS 3-180 |
| 5:30pm-6:00pm | RNA / RNP synthetic biology | Tan Inoue (Kyoto University) | EE/CS 3-180 |
| 6:00pm-7:30pm | Math Matters public lecture reception | Lind Hall 400 | |
| 8:00pm-9:15pm | Math Matters public lecture: U.S. premier screening of the film "Achieving the unachievable" with the film's writer/director | Jean Bergeron | Willey Hall 125 (free and open to the public) |
| Friday November 02, 2007 | |||
| 10:30am-11:00am | Coffee | ||
| 11:00am-11:30am | Computational approaches to RNA nanodesign | Bruce Shapiro (National Cancer Institute) | EE/CS 3-180 |
| 11:35am-12:05pm | RNA tertiary structure as a proto-language for nano-construction | Luc Jaeger (University of California, Santa Barbara) | EE/CS 3-180 |
| 12:05pm-12:20pm | Discussions | EE/CS 3-180 | |
| 12:20pm-12:30pm | 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, Santa Barbara |
| Peter Clote | Boston College | |
| Anne Condon | Department of Computer Science | 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, Santa Barbara |
| 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 Saclay (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 |
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