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Topological Structures in Computational Biology
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Gunnar Carlsson | |
Christine Heitsch | Georgia Institute of Technology |
Susan Holmes | Stanford University |
Konstantin Mischaikow | Rutgers, The State University Of New Jersey |
Phenomena surrounding and arising from the topological features of nucleic acids and the metric geometry of proteins form the basis of many fundamental questions in molecular biology. The tools of low-dimensional topology and knot theory have been highly visible in providing descriptions of phenomena associated with supercoiling, knotting, and catenation in DNA and RNA strands. Many other challenges in biology demand the qualitative tools that topology provides. Questions in protein structure determination and structural biology require deciphering the connection between local geometric properties and global topological features such as folding patterns. Furthermore, there has been recent fascinating work on understanding the broader biological impact and consequences of topological features of macromolecules. At a higher level of abstraction, there is a developing body of work on applying topological ideas to the study of the properties of gene regulation networks and protein interaction graphs, much of which implicates topological methods. The mathematics of genomic data is under intense development that would benefit from qualitative, robust tools.
Although there has been rapid uptake of certain topological ideas in the biological community [for instance the work on linking numbers and writhe in DNA strands], an increase in the breadth and depth of this interaction necessitates a mixing of research communities that this workshop will provide.
8:00 am - 8:45 am | Registration | Keller 3-176 | |
8:45 am - 9:00 am | Welcome | Keller 3-180 | |
9:00 am - 9:50 am | Visualizing and Exploring Molecular Simulation Data via Energy Landscape Metaphor Yusu Wang [The Ohio State University] | Keller 3-180 | |
9:50 am - 10:15 am | Break | Keller 3-176 | |
10:15 am - 11:05 am | The Topology of Evolution Raul Rabadan [Columbia University] | Keller 3-180 | |
11:05 am - 11:30 am | Break | Keller 3-176 | |
11:30 am - 12:20 pm | Statistics on Deformations in Computational Anatomy: Geometric Structures and Topological Questions Xavier Pennec [Institut National de Recherche en Informatique Automatique [INRIA]] | Keller 3-180 | |
12:20 pm - 2:00 pm | Lunch | ||
2:00 pm - 2:50 pm | RNA Folding: From Random Matrix Theory to Structure Prediction Algorithms Henri Orland [Commissariat à l'Énergie Atomique [CEA]] | Keller 3-180 | |
2:50 pm - 3:15 pm | Break | Keller 3-176 | |
3:15 pm - 4:05 pm | Spaces of Shapes: Creating Moduli Spaces of Chemical Compounds for Drug Discovery Anthony Bak [Ayasdi, Inc.] | Keller 3-180 | |
4:05 pm - 5:00 pm | Discussion | Keller 3-180 | |
6:00 pm - 8:00 am | Social Event - Republic Restaurant |
8:30 am - 9:00 am | Coffee | Keller 3-176 | |
9:00 am - 9:50 am | Topological Symmetries of Molecules Erica Flapan [Pomona College] | Keller 3-180 | |
9:50 am - 10:15 am | Break | Keller 3-176 | |
10:15 am - 11:05 am | Topological RNA Structures Christian Reidys [Syddansk Universitet [University of Southern Denmark]] | Keller 3-180 | |
11:05 am - 11:10 am | Group Photo | Keller 3-180 | |
11:10 am - 11:30 am | Break | Keller 3-176 | |
11:30 am - 12:20 pm | Applications of TDA to the Understanding of Disease and Drug Discovery Pek Lum [Ayasdi, Inc.] | Keller 3-180 | |
12:20 pm - 2:00 pm | Lunch | ||
2:00 pm - 2:50 pm | A Topological Model of the Hippocampal Spatial Map Yuri Dabaghian [Rice University] | Keller 3-180 | |
2:50 pm - 3:15 pm | Break | Keller 3-176 | |
3:15 pm - 4:05 pm | RNA Profiling: A Combinatorial Approach to Denoising Secondary Structure Prediction Christine Heitsch [Georgia Institute of Technology] | Keller 3-180 | |
4:05 pm - 6:00 pm | Reception and Poster Session | Lind 400 |
8:30 am - 9:00 am | Coffee | Keller 3-176 | |
9:00 am - 9:50 am | Topological Structures of Ensemble Neuronal Codes in the Rat Hippocampus Zhe [Sage] Chen [Massachusetts Institute of Technology] | Keller 3-180 | |
9:50 am - 10:15 am | Break | Keller 3-176 | |
10:15 am - 11:05 am | Knots and Links in Circular DNA Molecules Alexander Vologodskii [New York University] | Keller 3-180 | |
11:05 am - 11:30 am | Break | Keller 3-176 | |
11:30 am - 12:20 pm | Topological Tools for Detecting Hidden Geometric Structure in Neural Data Carina Curto [University of Nebraska] | Keller 3-180 | |
12:20 pm - 2:00 pm | Lunch | ||
2:00 pm - 2:50 pm | Knotted DNA: Mathematical Models and Biological Consequences Dorothy Buck [Imperial College London] | Keller 3-180 | |
2:50 pm - 3:15 pm | Break | Keller 3-176 | |
3:15 pm - 4:00 pm | Discussion | Keller 3-180 | |
8:00 pm - 9:00 pm | Informal Social Event |
8:30 am - 9:00 am | Coffee | Keller 3-176 | |
9:00 am - 9:50 am | Structure of the Afferent Terminals in Terminal Ganglion of a Cricket and Persistent Homology Tomas Gedeon [Montana State University] | Keller 3-180 | |
9:50 am - 10:15 am | Break | Keller 3-176 | |
10:15 am - 11:05 am | Unlinking DNA Replication Links by Xer Recombination Mariel Vazquez [San Francisco State University] | Keller 3-180 | |
11:05 am - 11:30 am | Break | Keller 3-176 | |
11:30 am - 12:20 pm | Multiscale Multiphysics and Multidomain Models for Biomolecules Guowei Wei [Michigan State University] | Keller 3-180 | |
12:20 pm - 2:00 pm | Lunch | ||
2:00 pm - 2:50 pm | High-Performance, High-Throughput Approaches to Computational Chemistry Julie Mitchell [University of Wisconsin, Madison] | Keller 3-180 | |
2:50 pm - 3:15 pm | Break | Keller 3-176 | |
3:15 pm - 4:05 pm | The Topology of Fragile X David Romano [Stanford University] | Keller 3-180 | |
4:05 pm - 5:00 pm | Discussion | Keller 3-180 | |
8:00 pm - 9:00 pm | Informal Social Event |
8:30 am - 9:00 am | Coffee | Keller 3-176 | |
9:00 am - 9:50 am | Unraveling the Topology of Biological Data From Multiple Viewpoints Monica Nicolau [Stanford University] | Keller 3-180 | |
9:50 am - 10:15 am | Break | Keller 3-176 | |
10:15 am - 11:05 am | Detecting Morse Decompositions of the Global Attractor of Regulatory Networks by Time Series Data Hiroshi Kokubu [Kyoto University] | Keller 3-180 | |
11:05 am - 11:30 am | Break | Keller 3-176 | |
11:30 am - 12:30 pm | Discussion | Keller 3-180 |
Henry Adams | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
Leyda Almodovar | Department of Mathematics | The University of Iowa |
Douglas Arnold | School of Mathematics | University of Minnesota, Twin Cities |
F. Javier Arsuaga | Department of Mathematics | San Francisco State University |
Nils Baas | Department of Mathematical Sciences | Norwegian University of Science and Technology [NTNU] |
Anthony Bak | Department of Mathematics | Ayasdi, Inc. |
Greg Bell | Department of Mathematics and Statistics | University of North Carolina, Greensboro |
Nitsan Ben-Gal | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
Jesse Berwald | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
Andrew Blumberg | Department of Mathematics | The University of Texas at Austin |
Dorothy Buck | Department of Mathematics | Imperial College London |
Yiqing Cai | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
Luiz Miguel Camargo | Center for Proteomic Chemistry | Novartis Institute for Biomedical Research |
Gunnar Carlsson | Department of Mathematics | Stanford University |
Zhe [Sage] Chen | Department of Brain and Cognitive Sciences | Massachusetts Institute of Technology |
Alhaji Cherif | Mathematical Institute | University of Oxford |
Marla Cheston | Department of Biomedical Engineering | University of Saskatchewan |
Eungchun Cho | Department of Mathematics | Kentucky State University |
Frederick Cohen | Department of Mathematics | University of Rochester |
Brian Cruz | Department of Mathematics | University of California, Berkeley |
Carina Curto | Department of Mathematics | University of Nebraska |
Yuri Dabaghian | Department of Computational & Applied Mathematics | Rice University |
Isabel Darcy | Department of Mathematics | The University of Iowa |
Elizabeth Denne | Department of Mathematics | Washington and Lee University |
Vin de Silva | Department of Mathematics and Computer Science | Pomona College |
Satyan Devadoss | Department of Mathematics | Williams College |
Alicia Dickenstein | Departamento de Matemática, FCEN | University of Buenos Aires |
Kevin Emmett | Department of Physics | Columbia University |
Saba Emrani | Department of Electrical and Computer Engineering | North Carolina State University |
Adam Ferguson | Department of Neurological Surgery | University of California, San Francisco |
Erica Flapan | Department of Mathematics | Pomona College |
Juraj Foldes | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
Tomas Gedeon | Department of Mathematics | Montana State University |
Chad Giusti | Department of Mathematics | University of Nebraska |
Hong Guo | Department of Mathematics | San Francisco State University |
Marshall Hampton | Department of Mathematics & Statistics | University of Minnesota, Twin Cities |
Joel Hass | Department of Mathematics | University of California |
Christine Heitsch | School of Mathematics | Georgia Institute of Technology |
Annette Honken | Department of Mathematics | The University of Iowa |
Michele Intermont | Department of Mathematics | Kalamazoo College |
Nataša Jonoska | Department of Mathematics | University of South Florida |
Mateusz Juda | Department of Computational Mathematics | Jagiellonian University |
Kaushik Kalyanaraman | Department of Computer Science | University of Illinois at Urbana-Champaign |
Xingye Kan | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
Irina Kogan | Department of Mathematics | North Carolina State University |
Hiroshi Kokubu | Department of Mathematics | Kyoto University |
Woong Kook | Department of Mathematical Sciences | Seoul National University |
Hamid Krim | ECE | North Carolina State University |
Bala Krishnamoorthy | Department of Mathematics | Washington State University |
Reinhard Laubenbacher | Center for Quantitative Medicine | University of Connecticut Health Center |
Tyler Lawson | School of Mathematics | University of Minnesota, Twin Cities |
Michael Lesnick | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
Ryan Lewis | Institute for Computational and Mathematical Engineering | Stanford University |
Hongxia Li | University of Minnesota, Twin Cities | |
Ji Li | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
Longfei Li | Department of Mathematical Sciences | University of Delaware |
Pek Lum | Data Science | Ayasdi, Inc. |
Michael Mandell | Department of Mathematics | Indiana University |
Alexander Manta | MantaMatics UG [haftungsbeschränkt] | |
Yi Mao | Department of Microbiology | Boston University |
Facundo Mémoli | Department of Mathematics | The Ohio State University |
Konstantin Mischaikow | Department of Mathematics | Rutgers, The State University Of New Jersey |
Julie Mitchell | Departments of Mathematics and Biochemistry | University of Wisconsin, Madison |
Dmitriy Morozov | Computer and Data Sciences - Visualization Group | Lawrence Berkeley Laboratory |
Elizabeth Munch | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
David Murrugarra | Department of Mathematics | Georgia Institute of Technology |
Linda Ness | Applied Research | Applied Communication Sciences [ACS] |
Monica Nicolau | Department of Mathematics | Stanford University |
Asamoah Nkwanta | Department of Mathematics | Morgan State University |
João Miguel Nogueira | Department of Mathematics | University of Coimbra |
Carl Olimb | Department of Mathematics and Computer Science | Southwest Minnesota State University |
Henri Orland | Institut de Physique Theorique | Commissariat à l'Énergie Atomique [CEA] |
Megan Owen | David R. Cheriton School of Computer Science | University of Waterloo |
Amit Patel | Institute for Advanced Study | |
Xavier Pennec | Asclepios Team | Institut National de Recherche en Informatique Automatique [INRIA] |
Jose Perea | Department of Mathematics | Duke University |
Thomas Peters | Department of Computer Science | University of Connecticut |
Peter Polacik | School of Mathematics | University of Minnesota, Twin Cities |
Svetlana Poznanovikj | Department of Mathematical Sciences | Clemson University |
Raul Rabadan | Department of Biomedical Informatics | Columbia University |
Martin Raussen | Department of Mathematical Sciences | Aalborg University |
Christian Reidys | Department of Mathematics and Computer Science | Syddansk Universitet [University of Southern Denmark] |
Weiqing Ren | Department of Mathematics | National University of Singapore |
David Romano | Department of Psychiatry and Behavioral Sciences | Stanford University |
Daniel Rosenbloom | Program for Evolutionary Dynamics | Harvard University |
Mark Schubel | Department of Physics | University of Illinois at Urbana-Champaign |
Benjamin Schweinhart | Department of Mathematics | Princeton University |
Christine Soteros | Department of Mathematics & Statistics | University of Saskatchewan |
Krystal Taylor | University of Minnesota, Twin Cities | |
Mimi Tsuruga | Department of Mathematics | Technische Universität Berlin |
Mariel Vazquez | Department of Mathematics | San Francisco State University |
Mikael Vejdemo-Johansson | Computer Vision and Active Perception Lab | Royal Institute of Technology [KTH] |
Alexander Vologodskii | Department of Chemistry | New York University |
Bao Wang | Department of Mathematics | Michigan State University |
Ke Wang | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
Yusu Wang | Department of Computer Science and Engineering | The Ohio State University |
Guowei Wei | Department of Mathematics | Michigan State University |
Craig Westerland | School of Mathematics | University of Minnesota, Twin Cities |
Matthew Wright | Institute for Mathematics and its Applications | University of Minnesota, Twin Cities |
Kelin Xia | Department of Mathematics | Michigan State University |
Melissa Yeung | Department of Mathematics | California Institute of Technology |
Lori Ziegelmeier | Department of Mathematics | Macalester College |