Saturday, April 11

16:00- Registration opens in Sofitel Victoria Warsaw hotel lobby
18:00-21:00 Welcome reception at the conference venue, the Sofitel Victoria Warsaw hotel, "Opera" Room

Sunday, April 12

08:45-09:00 Opening Remarks
09:00-10:00 KEYNOTE Michael Levitt Birth and future of multiscale modeling of macromolecules Introduction by Michael Waterman
10:00-10:40 Session 1. Chair: Rolf Backofen
10:00-10:20 Ilan Ben-Bassat and Benny Chor. CRISPR detection from very short reads using partial overlap graph
10:20-10:40 Rasmus Fonseca, Henry van den Bedem and Julie Bernauer. KGSrna: Efficient 3D kinematics-based sampling for nucleic acids
10:40-11:10 Coffee break
11:10-12:30 Session 2 (structure, part 1). Chair: Marek Cieplak
11:10-11:30 Mark Hallen and Bruce Donald. COMETS (Constrained Optimization of Multistate Energies by Tree Search): A provable and efficient algorithm to optimize binding affinity and specificity with respect to sequence
11:30-11:50 Naama Amir, Dan Cohen and Haim J. Wolfson. DockStar: A novel ILP based integrative method for structural modelling of multimolecular protein complexes
11:50-12:10 Jianzhu Ma, Sheng Wang, Zhiyong Wang and Jinbo Xu. Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning
12:10-12:30 Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong and Jianyang Zeng. Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data
12:30-13:30 Lunch
13:30-14:30 KEYNOTE Bonnie Berger Computational biology in the 21st century: Algorithms that scale Introduction by Mona Singh
14:30-15:10 Session 3 (alignment free methods). Chair: Knut Reinert
14:30-14:50 Srinivas Aluru, Alberto Apostolico and Sharma V. Thankachan. Efficient Alignment Free Sequence Comparison with Bounded Mismatches
14:50-15:10 Highlight Rob Patro, Stephen Mount and Carl Kingsford.  Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
15:10-15:40 Coffee break
15:40-17:00 Session 4 (sequence analysis). Chair: Ron Shamir
15:40-16:00 Nam-Phuong Nguyen, Siavash Mirarab, Keerthana Kumar and Tandy Warnow. Ultra-large alignments using ensembles of Hidden Markov Models
16:00-16:20 Leena Salmela, Kristoffer Sahlin, Veli Mäkinen and Alexandru Tomescu. Gap Filling as Exact Path Length Problem
16:20-16:40 Alex Bishara, Yuling Liu, Dorna Kashef-Haghighi, Ziming Weng, Daniel Newburger, Robert West, Arend Sidow and Serafim Batzoglou.Read Clouds Uncover Variation in Complex Regions of the Human Genome
16:40-17:00 Igor Mandric and Alex Zelikovsky. ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching
17:30-19:00 Poster session sponsored by University of Pittsburgh
20:30-22:30 Social dinner at the new Library of the University of Warsaw

 Monday, April 13

09:00-10:00 KEYNOTE M. Madan Babu The contribution of intrinsically disordered regions to protein function, cellular complexity and human diseases Introduction by Michal Linial
10:00-10:40 Session 5 (chromatin structure). Chair: Bartek Wilczyński
10:00-10:20 Emre Sefer, Geet Duggal and Carl Kingsford. Deconvolution Of Ensemble Chromatin Interaction Data Reveals The Latent Mixing Structures In Cell Subpopulations
10:20-10:40 Highlight Alon Diament, Ron Y. Pinter and Tamir Tuller.  Three Dimensional Eukaryotic Genomic Organization is Strongly Correlated with Codon Usage Expression and Function
10:40-11:10 Coffee break
11:10-12:30 Session 6 (population). Chair: Jens Lagergren
11:10-11:30 Emily Berger, Deniz Yorukoglu and Bonnie Berger. HapTree-X: An integrative Bayesian framework for haplotype reconstruction from transcriptome and genome sequencing data
11:30-11:50 Shuo Yang, Shai Carmi and Itsik Pe'er. Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs
11:50-12:10 Laxmi Parida, Deniz Yorukoglu, Filippo Utro, Anna Paola Carrieri, Saugata Basu and David Kuhn. Topological Signatures for Population Admixture
12:10-12:30 Jong Wha Joo, Eun Yong Kang, Elin Org, Nick Furlotte, Brian Parks, Aldons Lusis and Eleazar Eskin. Efficient and accurate multiple-phenotype regression method for high dimensional data considering population structure
12:30-13:30 Lunch
13:30-14:10 Session 7. Chair: Roded Sharan
13:30-13:50 Roy Ronen, Glenn Tesler, Ali Akbari, Shay Zakov, Noah A. Rosenberg and Vineet Bafna. Haplotype Allele Frequency (HAF) Score: Predicting Carriers of Ongoing Selective Sweeps Without Knowledge of the Adaptive Allele
13:50-14:10 Maja Temerinac-Ott, Armaghan W. Naik and Robert F. Murphy. Deciding when to stop: Efficient experimentation to learn to predict drug-target interactions
14:10-15:30 KEYNOTE Wacław Szybalski Memorial Lecture dedicated to Stanislaw Ulam of the Polish School of Mathematics,  Lwów, Poland and the film    The Essence of Life (directed by Anna Ferens). Introduction by Teresa Przytycka. This event is kindly sponsored by BIOGEN
 15:30-19:00 Free time / Sightseeing

Tuesday, April 14

09:00-10:00 KEYNOTE Bas van Steensel Mapping genome – nuclear lamina interactions in single cells Introduction by Martin Vingron
10:00-10:40 Session 8 (gene regulation). Chair: Fabio Vandin
10:00-10:20 Yifeng Li, Chih-Yu Chen and Wyeth Wasserman. Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters
10:20-10:40 Highlight James Zou, Christoph Lippert, David Heckerman, Martin Aryee and Jennifer Listgarten.  Epigenome-wide association studies without the need for cell-type composition
10:40-11:10 Coffee break
11:10-12:30 Session 9 (cancer). Chair: Cenk Sahinalp
11:10-11:30 Andrew McPherson, Andrew Roth, Cedric Chauve and Cenk Sahinalp. Joint inference of genome structure and content in heterogeneous tumor samples
11:30-11:50 Mark Leiserson, Hsin-Ta Wu, Fabio Vandin and Benjamin Raphael. CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer
11:50-12:10 Fabio Vandin, Ben Raphael and Eli Upfal. On the Sample Complexity of Cancer Pathways Identification
12:10-12:30 Highlight Mark Leiserson, Fabio Vandin, Hsin-Ta Wu, Jason Dobson, Jonathan Eldridge, Jacob Thomas, Alexandra Papoutsaki, Younhun Kim, Beifang Niu, Michael McLellan, Michael Lawrence, Abel Gonzalez-Perez, David Tamborero, Yuwei Cheng, Gregory Ryslik, Nuria Lopez-Bigas, Gad Getz, Li Ding and Benjamin Raphael.  Pan-Cancer Network Analysis Identifies Combinations of Rare Somatic Mutations across Pathways and Protein Complexes
12:30-13:30 Lunch
13:30-14:50 Session 10 (structure, part 2). Chair: Sorin Istrail
13:30-13:50 Stefano Bonissone and Pavel Pevzner. Immunoglobulin classification using the colored antibody graph
13:50-14:10 Jonathan D Jou, Swati Jain, Ivelin Georgiev and Bruce R Donald. BWM*: A Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design
14:10-14:30 Yichao Zhou, Yuexin Wu and Jianyang Zeng. Computational Protein Design Using AND/OR Branch-and-Bound Search
14:30-14:50 Sumudu Leelananda, Robert Jernigan and Andrzej Kloczkowski. Exploration of Designability of Proteins Using Graph Features of Contact Maps: Beyond Lattice Models
14:50-15:20 Coffee break
15:20-16:40 Session 11 (networks). Chair: Ben Raphael
15:20-15:40 Arnon Mazza, Allon Wagner, Eytan Ruppin and Roded Sharan. Functional alignment of metabolic networks
15:40-16:00 Hyunghoon Cho, Bonnie Berger and Jian Peng. Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks
16:00-16:20 Surojit Biswas, Meredith McDonald, Jeffery Dangl and Vladimir Jojic. Learning microbial interaction networks from metagenomic count data
16:20-16:40 Highlight Bo Wang, Aziz Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains and Anna Goldenberg. Similarity Network Fusion for aggregating data types on a genomic scale
16:50-17:20 Business Meeting
17:30-19:00 Poster session sponsored by National Science Foundation

 Wednesday, April 15

09:00-10:00 KEYNOTE M. Magda Konarska Analysis of spliceosome function: from the mechanisms of catalysis to interconnections within global networks of gene expression Introduction by Jerzy Tiuryn
10:00-10:40 Session 12 (splicing). Chair: Vineet Bafna
10:00-10:20 Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert and Gunnar W. Klau. CIDANE: Comprehensive isoform discovery and abundance estimation
10:20-10:40 Highlight Hui Yuan Xiong, Babak Alipanahi, Leo Lee, Hannes Bretschneider, Daniele Merico, Ryan Yuen, Yimin Hua, Serge Gueroussov, Hamed Najafabadi, Tim Hughes, Quaid Morris, Yoseph Barash, Adrian Krainer, Nebojsa Jojic, Stephen Scherer, Benjamin Blencowe and Brendan Frey.  The human splicing code reveals new insights into the genetic determinants of disease
10:40-11:10 Coffee break
11:10-12:30 Session 13 (evolutionary trees). Chair: Russell Schwartz
11:10-11:30 Kai Dührkop and Sebastian Böcker. Fragmentation trees reloaded
11:30-11:50 Mingfu Shao and Bernard Moret. A Fast and Exact Algorithm for the Exemplar Breakpoint Distance
11:50-12:10 Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stephane Vialette and Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time
12:10-12:30 Highlight Siavash Mirarab, Md. Shamsuzzoha Bayzid, Bastien Boussau and Tandy Warnow. Statistical binning enables an accurate coalescent-based estimation of the avian tree
12:30-13:30 Lunch
13:30-14:50 Session 14 (association analysis). Chair: Anna Gambin
13:30-13:50 Roni Wilentzik and Irit Gat-Viks. A novel probabilistic methodology for eQTL analysis of signaling networks
13:50-14:10 Seunghak Lee, Aurelie Lozano, Prabhanjan Kambadur and Eric Xing. An Efficient Nonlinear Regression Approach for Genome-Wide Detection of Marginal and Interacting Genetic Variations
14:10-14:30 David Manescu and Uri Keich. A symmetric length-aware enrichment
14:30-15:00 Award Ceremony and closing remarks