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 |