Multiple Sequence Alignment - IPAM

Multiple Sequence Alignment

January 12 - 16, 2015

Schedule

All times in this Schedule are Pacific Time (PT)

Monday, January 12, 2015

Morning Session

08:00-08:50
Check-In/Light Breakfast (Hosted by IPAM)
08:50-09:00
Welcome and Opening Remarks
09:00-09:40
Tandy Warnow (University of Illinois at Urbana-Champaign)
Overview
10:00-10:15
Break
10:15-10:55
Martin Weigt (Université de Paris VI (Pierre et Marie Curie))
Coevolutionary modeling of protein sequences: Inference of 3D structure and mutational landscapes
11:15-11:30
Break
11:30-12:10
Alexandre Bouchard-Cote (University of British Columbia)
MSA using Divide-and-Conquer Sequential Monte Carlo

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:10
Cedric Notredame (Center for Genomic Regulation)
Grabbing High Hanging Fruits From the Tree Of Life
15:30-16:00
Break
16:00-16:40
Participants: Open Problems and Computational or Scientific Challenges
17:00-18:30
Poster Session & Reception (Hosted by IPAM)

Tuesday, January 13, 2015

Morning Session

08:00-09:00
Check-In/Breakfast (Hosted by IPAM)
09:00-09:40
Sebastien Roch (University of Wisconsin-Madison)
A survey of theoretical results on the TKF model
10:00-10:15
Break
10:15-10:55
Steven Evans (University of California, Berkeley (UC Berkeley))
Recovering a tree from the lengths of random subtrees
11:15-11:30
Break
11:30-12:10
Ari Loytynoja (University of Helsinki)
Phylogeny-aware alignment with sequence graphs

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:10
Mark Ragan (University of Queensland)
Phylogenetics without multiple sequence alignment
15:30-16:00
Break
16:00-17:00
Short talks by Participants

Wednesday, January 14, 2015

Morning Session

08:00-09:00
Check-In/Breakfast (Hosted by IPAM)
09:00-09:40
Nick Grishin (UT Southwestern Medical School)
Pushing the limits of sequence profile similarity search and alignment
10:00-10:15
Break
10:15-10:55
Noah Daniels (Massachusetts Institute of Technology)
Structure-based multiple sequence alignments
11:15-11:30
Break
11:30-12:10
Olivier Lichtarge (Baylor College of Medicine)
Evolution versus disease: the calculus of life

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:10
Jinbo Xu (Toyota Technological Institute at Chicago )
Graphical models of multiple protein sequence alignment
15:30-16:00
Break
16:00-16:40
Patricia Babbitt (University of California, San Francisco (UCSF))
Back to the Beginning: Which sequences to align?

Thursday, January 15, 2015

Morning Session

08:00-09:00
Check-In/Breakfast (Hosted by IPAM)
09:00-09:40
Jim Leebens-Mack (University of Georgia)
Plant gene family circumscription, multiples sequence alignment and phylogenomic analysis
10:00-10:15
Break
10:15-10:55
Siavash Mir arabbaygi (University of California, San Diego (UCSD))
Co-estimation of sequence alignments and trees
11:15-11:30
Break
11:30-12:10
Nam-phuong Nguyen (University of Illinois at Urbana-Champaign)
New HMM-based Methods in Sequence Alignment, Phylogenetics, and Metagenomics

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:10
Elena Rivas (Howard Hughes Medical Institute)
Parameterizing sequence alignment with an explicit evolutionary model reduces homologous overextension artifacts
15:30-16:00
Break
16:00-17:00
Short talks by Participants

Friday, January 16, 2015

Morning Session

08:00-09:00
Check-In/Breakfast (Hosted by IPAM)
09:00-09:40
Scott Schmidler (Duke University)
The Cutoff Phenomenon in Evolutionary Models for Sequence Alignment
10:00-10:15
Break
10:15-10:55
Benjamin Redelings (Duke University)
Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection
11:15-11:30
Break
11:30-12:10
Adam Godzik (Sanford-Burnham Medical Research Institute)
Analysis and multiple alignments of periodic proteins

Afternoon Session

12:30-14:30
Lunch (on your own)
14:30-15:10
Jian Peng (University of Illinois at Urbana-Champaign)
Distances between protein sequence alignments
15:30-16:30
Open Problems and Discussion
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