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Schedule and Presentations

Multiple Sequence Alignment

January 12 - 16, 2015

Organizing Committee | Scientific Overview | Speaker List

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Organizing Committee

Jim Leebens-Mack (University of Georgia)
Sebastien Roch (University of Wisconsin-Madison, Mathematics)
Tandy Warnow (University of Texas at Austin, Computer Sciences)

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Scientific Overview

In multiple sequence alignment (MSA), a set of nucleotide or amino-acid sequences are "aligned" through the addition of spaces or rearrangement of individual sequences. A gap in the alignment indicates a possible loss or gain of an element and rearrangements account for inversions or translocations (particularly important for genome alignments); thus evolutionary inference of the insertion and deletion, translocation and inversion processes is inherent in MSA. In addition, MSA estimation is closely tied to phylogenetic estimation – a mathematically rich area with connections to probability theory, geometry, algebra, and graph theory. MSA estimation also informs protein function and structure prediction, and thus has strong connections to structural biology. However, these disciplines approach MSA estimation very differently. As a result, a variety of techniques have been explored, including combinatorial optimization, biophysical models of protein structure, machine learning, and probabilistic models of evolution.

Despite the importance of MSA estimation and active research, many challenges persist. The research community is addressing these through improved mathematical formalization of MSA estimation; development of sophisticated and biologically meaningful models of sequence evolution that include insertions, deletions, and rearrangements; and design of new methods that have good mathematical properties and empirical performance for large datasets. This workshop will engage researchers from different fields, including mathematicians, statisticians, evolutionary biologists, structural biologists, and computer scientists, with the aim of integrating diverse viewpoints, improving mathematical foundations, and developing new and more powerful methods for estimating MSAs.

This workshop will include a poster session; a request for posters will be sent to registered participants in advance of the workshop.

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Confirmed Speakers

Maria Anisimova (Swiss Federal Institute of Technology of Zurich)
Patsy Babbitt (University of California, San Francisco (UCSF))
Alexandre Bouchard-Cote (University of British Columbia)
Lenore Cowen (Tufts University)
Aaron Darling (University of Technology, Sydney)
Charlotte Deane (University of Oxford)
Roland Dunbrack (Fox Chase Cancer Center)
Steve Evans (University of California, Berkeley (UC Berkeley))
Adam Godzik (Sanford-Burnham Medical Research Institute)
Nick Goldman (EMBL-EBI)
Nick Grishin (UT Southwestern Medical School)
Jotun Hein (University of Oxford)
Jim Leebens-Mack (University of Georgia)
Olivier Lichtarge (Baylor College of Medicine)
Ari Loytynoja (University of Helsinki)
Cedric Notredame (Center for Genomic Regulation)
Mark Ragan (University of Queensland)
Benjamin Redelings (Duke University)
Elena Rivas (Howard Hughes Medical Institute)
Sebastien Roch (University of Wisconsin-Madison)
Scott Schmidler (Duke University)
Kimmen Sjolander (University of California, Berkeley (UC Berkeley))
Tandy Warnow (University of Texas at Austin)
Jinbo Xu (Toyota Technological Institute at Chicago )

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An application/registration form is available at:


The application form is for those requesting financial support to attend the workshop. We urge you to apply as early as possible. Applications received by Monday, November 17, 2014 will receive fullest consideration. Letters of reference may be sent to the address or email address below. Successful applicants will be notified as soon as funding decisions are made. If you do not need or want to apply for funding, you may simply register. IPAM will close registration if we reach capacity; for this reason, we encourage you to register early.

We have funding especially to support the attendance of recent PhD's, graduate students, and researchers in the early stages of their career; however, mathematicians and scientists at all levels who are interested in this area are encouraged to apply for funding. Encouraging the careers of women and minority mathematicians and scientists is an important component of IPAM's mission and we welcome their applications.

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Contact Us:

Institute for Pure and Applied Mathematics (IPAM)
Attn: MSA2015
460 Portola Plaza
Los Angeles CA 90095-7121
Phone: 310 825-4755
Fax: 310 825-4756
Website: http://www.ipam.ucla.edu/programs/msa2015/

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