Program

Monday August 27
08:00 - 08:45	Registration
08:45 - 09:00	Introductory Remarks
Assembly (Chair: Alexander Kulikov)
09:00 - 09:45	SPAdes: a New Genome Assembly Algorithm and its Applications to Single-Cell Sequencing	Sergey Nikolenko	Invited
09:45 - 10:00	De Bruijn Superwalk with Multiplicities Problem	Paul Medvedev	Open Problem
10:00 - 10:15	Mate-pair consistency and Generating Problems	Son Pham	Open Problem
10:15 - 10:45	Coffee Break
Genome Rearrangements (Chair: Kira Vyatkina)
10:45 - 11:30	Genome rearrangements: when intuition fails	Max Alekseyev	Invited
11:30 - 12:15	The combinatorics of the breakage fusion bridge and its application to cancer genomics	Vineet Bafna	Invited
12:15 - 13:30	Lunch (included)
Phylogenetic Trees (Chair: Kira Vyatkina)
13:30 - 14:15	Following Dobzhansky: Extending The Reach of Phylogenies	Bernard Moret	Invited
14:15 - 14:30	Algorithms for constructing k-articulated network: a more powerful classification of phylogenetic networks	S.M. Yiu	Open Problem
14:30 - 14:45	Phylogenetic tree reconstruction with protein linkage	Francis Chin	Open Problem
14:45 - 15:00	Reconciliation of Gene and Species Trees with Polytomies	Yu Zheng	Research Abstract
15:00 - 15:30	Coffee Break
Alignment (Chair: Max Alekseyev)
15:30 - 16:15	Alignment-Free Local Sequence Comparison: Statistics and Algorithms	Michael Waterman	Invited
16:15 - 16:30	Alignment Plots: Local Sequence Comparison in Sliding Windows	Alexander Tiskin	Research Abstract

Tuesday August 28
Systems Biology (Chair: Paul Medvedev)
09:00 - 09:45	Three Optimization Problems in Molecular Biology and Genetics	Richard Karp	Invited
09:45 - 10:30	Dissecting inner structure in disease regulatory networks using differential co-expression	Ron Shamir	Invited
10:30 - 11:00	Coffee Break
11:00 - 11:15	Metabolic stories: uncovering all possible scenarios for interpreting metabolomics data	Paulo Vieira Milreu	Open Problem
Genetics / Statistics (Chair: Nikolay Vyahhi)
11:15 - 12:00	The Linkage Disequilibrium Measures Unification Problem	Sorin Istrail	Invited
12:00 - 12:15	Reconstructing Pedigrees from Data	Bonnie Kirkpatrick	Open Problem
12:15 - 12:30	Analysis of single-cell RNA-seq data using probabilistic mixture models	Peter Kharchenko	Research Abstract
12:30 - 14:00	Lunch (on your own)
Sequencing (Chair: Nikolay Vyahhi)
14:00 - 14:45	Efficient communication and storage vs. accurate variant calls in high throughput sequencing: two sides of the same coin	Cenk Sahinalp	Invited
14:45 - 15:45	Coffee Break
Posters
14:45 - 15:45	The problems of reconciling gene and species trees, mapping a gene tree into a species tree and gene tree inference	Konstantin Gorbunov	Open Problem
	Finding a Combinatorially Optimal Model for RNA Folding Pathways	Bonnie Kirkpatrick	Open Problem
	Non-Identifiable Pedigrees and a Bayesian Solution	Bonnie Kirkpatrick	Research Abstract
	Open Problems in Metagenomics	Gabriel Valiente	Open Problem
Panel
15:45 - 16:45	Discussion panel on problem formulation
19:45	Jazz Boat

Wednesday August 29
Systems Biology (Chair: Sergey Nurk)
09:00 - 09:45	Lasting relations	Marie-France Sagot	Invited
Mass Spectrometry (Chair: Sergey Nurk)
09:45 - 10:30	Sequencing antibiotics: bioinformatics meets nuclear physics	Pavel Pevzner	Invited
10:30 - 11:00	Coffee Break
11:00 - 11:15	Combinatorial problems for SNP and mutation discovery using base-specific cleavage and mass spectrometry	Xin Chen	Open Problem
Evolution (Chair: Alla Lapidus)
11:15 - 12:00	Evolution of bacterial genomes	Mikhail Gelfand	Invited
12:00 - 12:45	A Moving Landscape for Comparative Genomics in Mammals	Steve O'Brien	Invited
12:45 - 13:00	Concluding remarks
13:00	Lunch (on your own)

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