Multiple Sequence Alignment

January 12 - 16, 2015

Schedule

All times in this Schedule are Pacific Time (PT)

Monday, January 12, 2015

Morning Session
8:00 - 8:50 Check-In/Light Breakfast (Hosted by IPAM)
8:50 - 9:00 Welcome and Opening Remarks
9:00 - 9:40
Tandy Warnow (University of Illinois at Urbana-Champaign)

Overview
PDF Presentation
10:00 - 10:15 Break
10:15 - 10:55
11:15 - 11:30 Break
11:30 - 12:10
Alexandre Bouchard-Cote (University of British Columbia)

MSA using Divide-and-Conquer Sequential Monte Carlo

12:30 - 2:30 Lunch (on your own)

Afternoon Session
2:30 - 3:10
Cedric Notredame (Center for Genomic Regulation)

Grabbing High Hanging Fruits From the Tree Of Life

3:30 - 4:00 Break
4:00 - 4:40 Participants: Open Problems and Computational or Scientific Challenges
5:00 - 6:30 Poster Session & Reception (Hosted by IPAM)

Tuesday, January 13, 2015

Morning Session
8:00 - 9:00 Check-In/Breakfast (Hosted by IPAM)
9:00 - 9:40
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

12:30 - 2:30 Lunch (on your own)

Afternoon Session
2:30 - 3:10
Mark Ragan (University of Queensland)

Phylogenetics without multiple sequence alignment
PDF Presentation
Presentation (PowerPoint File)
3:30 - 4:00 Break
4:00 - 5:00 Short talks by Participants

Wednesday, January 14, 2015

Morning Session
8:00 - 9:00 Check-In/Breakfast (Hosted by IPAM)
9:00 - 9:40
10:00 - 10:15 Break
10:15 - 10:55
Noah Daniels (Massachusetts Institute of Technology)

Structure-based multiple sequence alignments
PDF Presentation
11:15 - 11:30 Break
11:30 - 12:10
Olivier Lichtarge (Baylor College of Medicine)

Evolution versus disease: the calculus of life
PDF Presentation
12:30 - 2:30 Lunch (on your own)

Afternoon Session
2:30 - 3:10
Jinbo Xu (Toyota Technological Institute at Chicago )

Graphical models of multiple protein sequence alignment
Presentation (PowerPoint File)
3:30 - 4:00 Break
4:00 - 4:40
Patricia Babbitt (University of California, San Francisco (UCSF))

Back to the Beginning: Which sequences to align?
PDF Presentation

Thursday, January 15, 2015

Morning Session
8:00 - 9:00 Check-In/Breakfast (Hosted by IPAM)
9:00 - 9:40
Jim Leebens-Mack (University of Georgia)

Plant gene family circumscription, multiples sequence alignment and phylogenomic analysis
Presentation (PowerPoint File)
10:00 - 10:15 Break
10:15 - 10:55
Siavash Mir arabbaygi (University of Texas at Austin)

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
Presentation (PowerPoint File)
12:30 - 2:30 Lunch (on your own)

Afternoon Session
2:30 - 3:10
3:30 - 4:00 Break
4:00 - 5:00 Short talks by Participants

Friday, January 16, 2015

Morning Session
8:00 - 9:00 Check-In/Breakfast (Hosted by IPAM)
9:00 - 9:40
10:00 - 10:15 Break
10:15 - 10:55
11:15 - 11:30 Break
11:30 - 12:10
Adam Godzik (Sanford-Burnham Medical Research Institute)

Analysis and multiple alignments of periodic proteins

12:30 - 2:30 Lunch (on your own)

Afternoon Session
2:30 - 3:10
Jian Peng (University of Illinois at Urbana-Champaign)

Distances between protein sequence alignments

3:30 - 4:30 Open Problems and Discussion