Saturday, April 16
8:00 a.m. – Satellite Workshops begin at UCLA
Sunday, April 17
9:00 a.m. – On-site conference registration opens
1:30 – 4:30 p.m.- Bioinformatics Workshop
1:30 – 3:30 p.m. Mike Waterman Symposium Session 1
3:30 – 4:00 p.m. – Mike Waterman Symposium Break
4:00 – 6:00 p.m. – Mike Waterman Symposium Session 2
6:00 – 9:00 p.m. – Welcome reception at the conference venue, the Loews Santa Monica Beach hotel
Monday, April 18
8:45 – 9:00 a.m. Opening Remarks
9:00 – 10:40 a.m. [Session 1] Chair: Martin Vingron
9:00 – 10:00 a.m. KEYNOTE 1 Karen Adelman
10:00 – 10:20 a.m. PT1 Joshua Welch, Ziqing Liu, Li Wang, Junjie Liu, Paul Lerou, Jeremy Purvis, Li Qian, Alexander Hartemink and Jan Prins. SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data
10:20 – 10:40 a.m. PT2 Chenchen Zou, Yuping Zhang and Zhengqing Ouyang. Multi-track modeling for genome-scale reconstruction of 3D chromatin structure from Hi-C data
10:40 – 11:10 a.m. Coffee Break
11:10 a.m. – 12:30 p.m. [Session 2] Chair: Barbara Engelhardt
11:10 – 11: 30 a.m. PT3 Yael Steuerman and Irit Gat-Viks. Exploiting Gene-Expression Deconvolution to Probe the Genetics of the Immune System
11:30 – 11:50 a.m. PT4 Emre Sefer and Ziv Bar-Joseph. Shall we dense? Comparing design strategies for time series expression experiments
11:50 a.m. – 12:10 p.m. PT5 Chandler Zuo, Kailei Chen and Sunduz Keles. A MAD-Bayes Algorithm for State-space Inference and Clustering with Application to Querying Large Collections of ChIP-Seq Data Sets
12:10- 12:30 p.m. HIGHLIGHT 1 Adrian Sanborn, Suhas Rao, Su-Chen Huang, Neva Durand, Miriam Huntley, Andrew Jewett, Ivan Bochkov, Dharmaraj Chinnappan, Ashok Cutkosky, Jian Li, Kristopher Geeting, Andreas Gnirke, Alexandre Melnikov, Doug McKenna, Elena Stamenova, Eric Lander and Erez Aiden. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
12:30 – 2:30 p.m. Lunch Break (No Lunch Provided)
2:30- 4:10 p.m. [Session 3] Chair: Bonnie Berger
2:30 – 3:30 p.m. KEYNOTE 2 Peter Kim
3:30 – 3:50 p.m. PT6 Hao Wang, Joel McManus and Carl Kingsford. Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast
3:50- 4:10 p.m. PT7 Meghana Kshirsagar, Jaime Carbonell, Judith Klein-Seetharaman and Keerthiram Murugesan. Multitask matrix completion for learning protein interactions across diseases
4:10- 4:40 p.m. Coffee Break
4:40 – 6:30 p.m. 20th Anniversary Special Session
5:30- 6:30 p.m. [Session 4] Chair: Jadwiga Bienkowska
5:30 – 5:50 p.m. PT8 Sean Simmons, Cenk Sahinalp and Bonnie Berger. Enabling Privacy-Preserving GWAS in Heterogenous Human Populations
5:50- 6:10 p.m. PT9 Victoria Popic and Serafim Batzoglou. Efficient Privacy-Preserving Read Mapping Using Locality Sensitive Hashing and Secure Kmer Voting
6:10 – 6:30 p.m. HIGHLIGHT 2 Noah Daniels, Y. William Yu, David Christian Danko and Bonnie Berger. Entropy-Scaling Search of Massive Biological Data
7:00 – 8:30 p.m. RECOMB Dine Santa Monica Conference Dinner
Tuesday, April 19
9:00 – 11:00 a.m. [Session 5] Chair: Carl Kingsford
9:00 – 10:00 a.m. KEYNOTE 3 Teresa Przytycka
10:00 – 10:20 a.m. PT10 Tommy Hansen and Fabio Vandin. Finding Mutated Subnetworks Associated with Survival Time in Cancer
10:20 – 10:40 a.m. PT11 Simona Cristea, Jack Kuipers and Niko Beerenwinkel. pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and their Dependencies in Tumor Progression
10:40 – 11:00 a.m. PT12 Mohammed El-Kebir, Gryte Satas, Layla Oesper and Ben Raphael. Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing
11:00- 11:30 a.m. Coffee Break
11:30 a.m. – 12:30 p.m. [Session 6] Chair: Ben Raphael
11:30 – 11:50 a.m. PT13 Katharina Jahn, Jack Kuipers and Niko Beerenwinkel. Tree inference for single-cell data
11:50 – 12:10 p.m. PT14 Nilgun Donmez, Salem Malikic, Alexander Wyatt, Colin Collins, Martin Gleave and Cenk Sahinalp. Clonality inference from single tumor samples using low coverage sequence data
12:10 a.m. – 12:30 p.m. HIGHLIGHT 3 Allison Tegge, Nicholas Sharp and T. M. Murali. XTalk: a Path-Based Approach for Identifying Crosstalk between Signaling Pathways
12:30 – 2:30 p.m. Lunch Break (No Lunch Provided)
2:30- 4:10 p.m. [Session 7] Chair: Mona Singh
2:30 – 3:30 p.m. KEYNOTE 4 Leonid Kruglyak
3:30 – 3:50 p.m. PT15 Nicolo Fusi and Jennifer Listgarten. Leveraging Non-Linear Genetic Effects on Functional Traits for GWAS
3:50 – 4:10 p.m. PT16 Phuong Dao, Jan Hoinka, Yijie Wang, Mayumi Takahashi, Jiehua Zhou, Fabrizio Costa, John Rossi, John Burnett, Rolf Backofen and Teresa Przytycka. AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments
4:10 – 5:30 p.m. Poster Session + Refreshments
5:30 – Free evening / sightseeing
Wednesday, April 20
9:00 – 11:00 a.m. [Session 8] Chair: Fengzhu Sun
9:00 – 10:00 a.m. KEYNOTE 5: Rob Knight
10:00 – 10:20 a.m. PT17 Yuqing Yang, Ning Chen and Ting Chen. mLDM: a Statistical Model for Sparse Microbial Association Discovery
10:20 – 10:40 a.m. PT18 Yunan Luo, Jianyang Zeng, Bonnie Berger and Jian Peng. Low-density locality-sensitive hashing boosts metagenomic binning
10:40 – 11:00 a.m. P19 Ahmed Sobih, Alexandru I. Tomescu and Veli Mäkinen. MetaFlow: Metagenomic profiling based on whole-genome coverage analysis with min-cost flows
11:00 – 11:30 a.m. Coffee Break
11:30 – 12:30 p.m. [Session 9] Chair: Cenk Sahinalp
11:30 – 11:50 a.m. PT20 Sergey Nurk, Dmitry Meleshko and Pavel Pevzner. metaSPAdes: a new versatile de novo metagenomics assembler
11:50 a.m. – 12:10 p.m. PT21 Shashank Singh, Sabrina Rashid, Saket Navlakha and Ziv Bar-Joseph. Distributed Gradient Descent in Bacterial Food Search
12:10 p.m. – 12:30 p.m. HIGHLIGHT 4 Volodymyr Kuleshov, Chao Jiang, Wenyu Zhou, Fereshteh Jahanbani, Serafim Batzoglou and Michael Snyder. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome
12:30 – 2:30 p.m. Lunch Break (No Lunch Provided)
2:30- 4:10 p.m. [Session 10] Chair: Russell Schwartz
2:30 – 3:30 p.m. KEYNOTE 6: Phil Bradley
3:30 – 3:50 p.m. PT22 Mark Hallen, Jonathan Jou and Bruce Donald. LUTE (Local Unpruned Tuple Expansion): Accurate continuously flexible protein design with general energy functions and rigid-rotamer-like efficiency
3:50- 4:10 p.m. HIGHLIGHT 5 Tianyin Zhou, Ning Shen, Lin Yang, Namiko Abe, John Horton, Richard Mann, Harmen Bussemaker, Raluca Gordan and Remo Rohs. Quantitative modeling of transcription factor binding specificities using DNA shape
4:10- 4:40 p.m. Coffee Break
4:40- 5:30 p.m. [Session 11] Chair: Jennifer Lisgarten
4:40 – 5:00 PT23 John Wiedenhoeft, Eric Brugel and Alexander Schliep. Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression
5:00 – 5:20 PT24 Yu Lin, Max W. Shen, Jeffrey Yuan and Pavel Pevzner. Assembly of Long Error-Prone Reads Using de Bruijn Graphs
5:20 – 6:00 Business meeting
6:00 – 7:00 Poster Session + Refreshments
Thursday, April 21
9:00 – 11:00 a.m. [Session 12] Chair: Can Alkan
9:00 – 9:20 PT25 Yang Li, Shiguo Zhou, David Schwartz and Jian Ma. Allele-Specific Quantification of Structural Variations in Cancer Genomes
9:20 – 9:40 PT26 Alexandru I. Tomescu and Paul Medvedev. Safe and complete contig assembly via omnitigs
9:40- 10:00 PT27 Alexander Artyomenko, Nicholas Wu, Serghei Mangul, Eleazar Eskin, Ren Sun and Alex Zelikovsky. Long single-molecule reads can resolve the complexity of the Influenza virus composed of rare, closely related mutant variants
10:00 – 10:20 a.m. PT28 Kristoffer Sahlin, Mattias Frånberg and Lars Arvestad. Structural variation detection with read pair information — An improved null-hypothesis reduces bias
10:20 – 10:40 a.m. PT29 David Pellow, Darya Filippova and Carl Kingsford. Improving Bloom filter performance on sequence data using k-mer Bloom filters
10:40 – 11:00 a.m. HIGHLIGHT 6 Shrutii Sarda and Sridhar Hannenhalli. High-Throughput Identification of Cis-Regulatory Rewiring Events in Yeast
11:00 – 11:30 Coffee Break
11:30 – 12:30 p.m. [Session 13] Chair: Maga Rowicka
11:30 – 11:50 a.m. PT30 Mingfu Shao and Bernard Moret. On Computing Pairwise Breakpoint Distances
11:50 a.m. – 12:10 p.m. PT31 Luis Antonio B. Kowada, Daniel Doerr, Simone Dantas and Jens Stoye. New Genome Similarity Measures based on Conserved Gene Adjacencies
12:10 – 12:30 p.m. PT32 Constantinos Tsirogiannis and Brody Sandel. Fast Phylogenetic Biodiversity Computations Under a Non-Uniform Random Distribution
12:30 – 2:00 p.m. Lunch Break (No Lunch Provided)
2:00- 3:30 p.m. [Session 14] Chair: Bernard Moret
2:00 – 2:20 PT33 Andreas Dwi Maryanto Gunawan, Bhaskar Dasgupta and Louxin Zhang. Locating a Tree in a Reticulation-Visible Network in Cubic Time
2:20- 2:40 PT34 Somaye Hashemifar, Qixing Huang and Jinbo Xu. Joint alignment of multiple protein-protein interaction networks via convex optimization
2:40- 3:00 PT35 Xiuli Ma, Guangyu Zhou, Jingjing Wang, Jian Peng and Jiawei Han. Complexes Detection in Biological Networks via Diversified Dense Subgraphs Mining
3:00 – 3:30 p.m. Award ceremony and closing remarks