NOTE : All WABI technical sessions will take place in Room 235.
The keynotes and other plenary events will take place in Room 236.

Thursday, September 10

07:00-08:15 Continental breakfast

08:15-08:30 Opening remarks

08:30-09:30 Keynote: From Meaningful use to Precision Medicine: Lessons Learned
Douglas B. Fridsma, President and Chief Executive Officer of American Medical Informatics Association

009:30-10:00 Break

10:00-12:00 WABI Session 1: Phylogenetics and Association Studies
Session Chair: Jens Stoye (Room 235)

10:00-10:30 Ademir Hujdurovic, Ursa Kacar, Martin Milanic, Bernard Ries and Alexandru I. Tomescu.
Finding a perfect phylogeny from mixed tumor samples

10:30-11:00 Jun Zhou, Yu Lin, Vaibhav Rajan, William Hoskins and Jijun Tang.
Maximum parsimony analysis of gene copy number changes in tumor phylogenetics

11:00-11:30 Yaron Margalit, Yael Baran and Eran Halperin.
Multiple-Ancestor Localization for Recently Admixed Individuals

11:30-12:00 Dan Gusfield and Rasmus Nielsen.
Association Mapping for Compound Heterozygous Traits Using Phenotypic Distance and Integer Programming

12:00-13:30 Lunch

13:30-15:30 WABI Session 2: RNA Structure
Session Chair: Michal Ziv-Ulkerson (Room 235)

13:30-14:00 Yelena Frid and Dan Gusfield.
A Sparsified Four-Russians algorithm for RNA folding.

14:00-14:30 Sebastian Will and Hosna Jabbari.
Sparse RNA folding revisited: space-efficient minimum free energy prediction

14:30-15:00 Peter Clote.
Network properties of the ensemble of RNA structures

15:00-15:30 Yaron Orenstein and Bonnie Berger.
Efficient design of compact unstructured RNA libraries covering all k-mers

15:30-16:00 Break

16:00-18:00 SIGBio General Meeting

18:00-20:00 Poster Reception
Friday, September 11

07:00-08:30 Breakfast

08:30-09:30 Keynote: Computational biology in the 21st century: Algorithms that scale
Bonnie Berger, Professor of Applied Math and Computer Science at MIT, and head of the Computation and Biology group at MIT's Computer Science and AI Lab

09:30-10:00 Break

10:00-12:00 WABI Session 3: Network Analysis
Session Chair: Dan Gusfield (Room 235)

10:00-10:30 Rui Henriques and Sara C. Madeira.
BicNET: Efficient Biclustering of Biological Networks to Unravel Non-Trivial Modules

10:30-11:00 Yihan Sun, Joseph Crawford, Jie Tang and Tijana Milenkovic.
Simultaneous Optimization of Both Node and Edge Conservation in Network Alignment via WAVE

11:00-11:30 Todd A. Gibson and Debra Goldberg.
The Topological Profile of a Model of Protein Network Evolution Can Direct Model Improvement

11:30-12:00 Ilan Smoly, Amir Carmel, Yonat Shemer-Avni, Esti Yeger-Lotem and Michal Ziv-Ukelson.
Algorithms for Regular Tree Grammar search and their application to mining human-viral infection patterns

12:00-13:30 Lunch; Women in Bioinformatics panel.

13:30-15:30 WABI Session 4: High-Throughput Sequencing
Session Chair: Mihai Pop (Room 235)

13:30-14:00 Denisa Duma, Francesca Cordero, Marco Beccuti, Gianfranco Ciardo, Timothy Close and Stefano Lonardi.
Scrible: Ultra-Accurate Error-Correction of Pooled Sequenced Reads

14:00-14:30 Giles Miclotte, Mahdi Heydari, Piet Demeester, Pieter Audenaert and Jan Fostier.
Jabba: Hybrid Error Correction for Long Sequencing Reads using Maximal Exact Matches

14:30-15:00 Kristoffer Sahlin, Rayan Chikhi and Lars Arvestad.
Genome scaffolding with PE-contaminated mate-pair libraries

15:00-15:30 Emre Sefer and Carl Kingsford.
Nonparametric Modeling of Topological Domain Formation From Epigenetic Data

15:30-16:00 Break

16:00-18:00 WABI Session 5: Comparative Genomics and Classification
Session Chair: Paola Bonizzoni (Room 235)

16:00-16:30 Krister Swenson and Mathieu Blanchette.
Models and Algorithms for Genome Rearrangement with Positional Constraints

16:30-17:00 Roberto Grossi, Costas Iliopoulos, Robert Mercas, Nadia Pisanti, Solon Pissis, Ahmad Retha and Fatima Vayani.
Circular Sequence Comparison with q-grams

17:00-17:30 Rachid Ounit and Stefano Lonardi.
Higher classification accuracy of short metagenomic reads by discriminative spaced k-mers

18:30-20:30 Banquet
Saturday, September 12

07:00-08:30 Breakfast

08:30-09:30 Keynote: What is a gene? How and why computer science helps in answering this Question?
Paola Bonizzoni, Professor of Computer Science at the Università di Milano-Bicocca

09:30-10:00 Break

10:00-12:00 WABI Session 6: Phylogenetics
Session Chair: Bernard Moret (Room 235)

10:00-10:30 Manuel Lafond and Nadia El-Mabrouk.
Orthology relation and Gene Tree correction: Complexity results

10:30-11:00 Benjamin Drinkwater and Michael Charleston.
A sub-quadratic time and space complexity solution for the dated tree reconciliation problem for select tree topologies

11:00-11:30 Poly Hannah Da Silva, Simone Dantas, Chunfang Zheng and David Sankoff.
Graph-theoretic modelling of the domain chaining problem

11:30-12:00 Zhong Sichen, Lu Zhao, Yan Liang, Mohammadzaman Zamani, Rob Patro, Rezaul Chowdhury, Esther Arkin, Joseph Mitchell and Steven Skiena.
Optimizing Read Reversal for Sequence Compression (Extended Abstract)

12:00-13:30 Lunch

13:30-14:30 WABI Session 7: High-Throughput Sequencing
Session Chair: Helene Touzet (Room 235)

13:30-14:00 Gaetan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, Raluca Uricaru and Guillaume Rizk.
Reference-free compression of high throughput sequencing data with a probabilistic de Bruijn graph

14:00-14:30 Guillaume Holley, Roland Wittler and Jens Stoye.
Bloom Filter Trie -- a data structure for pan-genome storage