18th Annual International Conference on Research in Computational Molecular Biology
Pittsburgh, Pennsylvania
April 2-5, 2014
RECOMB 2014 PROGRAM
The conference proceedings (Lecture Notes in Computer Science Volume 8394, 2014) are now online. Attendees will receive printed and electronic copies of the proceedings.
April 2, April 3, April 4, April 5.
Tuesday, April 1 (Pittsburgh Athletic Association) | |
18:00-21:00 | Opening Night Reception |
Wednesday, April 2 (Alumni Hall) | |
8:45-9:00 | Opening Remarks and Welcome by Subra Suresh, President, Carnegie Mellon University |
9:00-10:40 | Session 1. Chair: Russell Schwartz, Carnegie Mellon University |
9:00-10:00 | KEYNOTE: James Collins. Synthetic Biology and Biocomputation: Life Redesigned |
10:00-10:20 | Armin Töpfer, Tobias Marschall, Rowena Bull, Fabio Luciani, Alexander Schönhuth and Niko Beerenwinkel. Viral quasispecies assembly via maximal clique enumerationion |
10:20-10:40 | Henry C.M. Leung, S.M. Yiu and Francis Chin. IDBA-MTP: A Hybrid MetaTranscriptomic Assembler Based on Protein Information |
10:40-11:10 | BREAK |
11:10-12:10 | Session 2. Chair: Michael Waterman, University of Southern California |
11:10-11:30 | Rayan Chikhi, Antoine Limasset, Shaun Jackman and Jared Simpson and Paul Medvedev. On the representation of de Bruijn graphs |
11:30-11:50 | Yana Safonova, Anton Bankevich and Pavel Pevzner. DipSPAdes: Assembler for Highly Polymorphic Diploid Genomes |
11:50-12:10 | HIGHLIGHT: Noam Kaplan and Job Dekker. High-throughput genome scaffolding from in vivo DNA interaction frequency |
12:10-13:30 | LUNCH |
13:30-15:10 | Session 3. Chair: Ron Shamir, Tel Aviv University |
13:30-13:50 | Jianzhu Ma, Sheng Wang and Jinbo Xu. MRFalign: Protein Homology Detection through Alignment of Markov Random Fields |
13:50-14:10 | Siavash Mirarab, Nam-Phuong Nguyen and Tandy Warnow. PASTA: ultra-large multiple sequence alignment |
14:10-15:10 | PANEL: Publication policies in RECOMB Moderator: Ron Shamir, Tel Aviv University Confirmed Participants: Irit Gat-Viks, Tel Aviv University Carl Kingsford, Carnegie Mellon University Teresa Przytycka, NIH Martin Vingron, MPI Berlin |
15:10-15:40 | BREAK |
15:40-17:00 | Session 4. Chair: Tandy Warnow, University of Texas, Austin |
15:40-16:00 | Mingfu Shao, Yu Lin and Bernard Moret. An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes |
16:00-16:20 | Yu Zheng and Louxin Zhang. Reconciliation with Non-binary Gene Trees Revisited |
16:20-16:40 | Ngan Nguyen, Glenn Hickey, Daniel Zerbino, Brian Raney, Dent Earl, Joel Armstrong, David Haussler and Benedict Paten. Building a Pangenome Reference for a Population |
16:40-17:00 | HIGHLIGHT: John A. Capra, Maureen Stolzer, Dannie Durand and Katherine S. Pollard. How old is my gene? |
17:00 | Free afternoon |
Thursday, April 3 (William Pitt Union) | |
9:00-10:00 | Session 5. Chair: Sorin Istail, Brown University |
9:00-9:20 | Emily Berger, Deniz Yorukoglu and Bonnie Berger. HapTree: A novel Bayesian framework for single individual polyplotyping using NGS data |
9:20-9:40 | Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar Klau and Alexander Schönhuth. WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads |
9:40-10:00 | HIGHLIGHT: Mohamed Aziz Mezlini, Eric J. M. Smith, Marc Fiume, Orion Buske, Gleb L. Savich, Sohrab Shah, Sam Aparicio, Derek Chiang, Anna Goldenberg and Michael Brudno. iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data |
10:00-10:30 | BREAK |
10:30-12:10 | Session 6. Chair: Bonnie Berger, Massachusetts Institute of Technology |
10:30-11:30 | KEYNOTE: Ian Baldwin. Using our biological legacy before it's lost; melding computational and natural history approaches to provide economic arguments for conservation |
11:30-11:50 | Rui Wang and Scott Schmidler. Bayesian Multiple Protein Structure Alignment |
11:50-12:10 | Shutan Xu, Shuxue Zou and Lincong Wang. A geometric clustering algorithm and its applications to structural data |
12:10-14:30 | LUNCH + ISCB POSTER SESSION |
14:30-16:10 | Session 7. Chair: Takis Benos, University of Pittsburgh |
14:30-15:30 | KEYNOTE: Atul Butte. Translating a trillion points of data into therapies, diagnostics, and new insights into disease |
15:30-15:50 | Shay Zakov and Vineet Bafna. Reconstructing Breakage Fusion Bridge architectures using noisy copy numbers |
15:50-16:10 | Arun Konagurthu, Parthan Kasarapu, Lloyd Allison, James Collier and Arthur Lesk. On sufficient statistics of least-squares superposition of vector sets |
16:10-16:30 | BREAK |
16:30-17:30 | Session 8. Chair: S. Cenk Sahinalp, Simon Fraser University |
16:30-16:50 | Adam Bloniarz, Ameet Talwalkar, Jonathan Terhorst, Michael Jordan, David Patterson, Bin Yu and Yun Song. Changepoint Analysis for Efficient Variant Calling |
16:50-17:10 | Y. William Yu, Deniz Yorukoglu and Bonnie Berger. Traversing the k-mer landscape of NGS read datasets for quality score sparsification |
17:10-17:30 | Chen-Ping Fu, Vladimir Jojic and Leonard Mcmillan. An Alignment-Free Regression Approach for Estimating Allele-Specific Expression using RNA-Seq Data |
18:00-22:00 | Conference Banquet - Carnegie Museums |
Friday, April 4 (William Pitt Union) | |
9:00-10:00 | Session 9. Chair: Ziv Bar-Joseph, Carnegie Mellon University |
9:00-9:20 | Arne Reimers, Frank Bruggeman, Brett Olivier and Leen Stougie. Fast Flux Module Detection using Matroid Theory |
9:20-9:40 | Shaun Mahony, Matthew Edwards, Esteban Mazzoni, Richard Sherwood, Akshay Kakumanu, Carolyn Morrison, Hynek Wichterle and David Gifford. An integrated model of multiple-condition ChIP-seq data reveals predeterminants of Cdx2 binding |
9:40-10:00 | Jianling Zhong, Todd Wasson and Alexander Hartemink. Learning protein-DNA interaction landscapes by integrating experimental data through computational models |
10:00-10:30 | BREAK |
10:30-12:10 | Session 10. Chair: Carl Kingsford, Carnegie Mellon University |
10:30-11:30 | KEYNOTE: Tom Mitchell. How the Brain Represents the Meaning of Language |
11:30-11:50 | Hetu Kamisetty, Bornika Ghosh, Christopher James Langmead and Chris Bailey-Kellogg. Learning Sequence Determinants of Protein:protein Interaction Specificity with Sparse Graphical Models |
11:50-12:10 | HIGHLIGHT: Irit Gat-Viks, Nicolas Chevrier, Roni Wilentzik, Thomas Eisenhaure, Raktima Raychowdhury, Yael Steuerman, Nir Hacohen, Ido Amit and Aviv Regev. Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli |
12:10-13:30 | LUNCH |
13:30-15:10 | Session 11. Chair: Serafim Batzoglou, Stanford University |
13:30-14:30 | KEYNOTE: Trey Ideker. Network-based stratification of tumor mutations |
14:30-14:50 | Wen-Yun Yang, Farhad Hormozdiari, Eleazar Eskin and Bogdan Pasaniuc. A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation |
14:50-15:10 | Derek Aguiar, Eric Morrow and Sorin Istrail. Tractatus: an exact and subquadratic algorithm for inferring identity-by-descent multi-shared haplotype tracts |
15:10-15:40 | BREAK |
15:40-17:00 | Session 12. Chair: Vineet Bafna, University of California, San Diego |
15:40-16:00 | Zhanyong Wang, Jae-Hoon Sul, Sagi Snir, Jose A. Lozano and Eleazar Eskin. Gene-Gene Interactions Detection Using A Two-stage Model |
16:00-16:20 | Kelley Harris, Sara Sheehan, John Kamm and Yun S. Song. Decoding Coalescent Hidden Markov Models in Linear Time |
16:20-16:40 | Adrian Guthals, Christina Boucher and Nuno Bandeira. The generating function approach for peptide identification in spectral networks |
16:40-17:00 | HIGHLIGHT: Joseph Paulson, O Colin Stine, Hector Corrada Bravo and Mihai Pop. Differential abundance analysis for microbial marker-gene surveys |
17:00-17:30 | Business Meeting |
17:30-19:00 | REFRESHMENTS + NSF POSTER SESSION |
Saturday, April 5 (William Pitt Union) | |
9:00-10:00 | Session 13. Chair: Martin Vingron, MPI Berlin |
9:00-9:20 | Raunak Shrestha, Ermin Hodzic, Jake Yeung, Kendric Wang, Thomas Sauerwald, Phuong Dao, Shawn Anderson, Himisha Beltran, Mark A. Rubin, Colin Collins, Gholamreza Haffari and S. Cenk Sahinalp. HIT.nDRIVE: Multi-Driver Gene Prioritization based on Hitting Time |
9:20-9:40 | Jan Hoinka, Alexey Berezhnoy, Zuben E. Sauna, Eli Gilboa and Teresa Przytycka. AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from its Application |
9:40-10:00 | HIGHLIGHT: Soheil Feizi, Daniel Marbach, Muriel Medard and Manolis Kellis. Network deconvolution as a general method to distinguish direct dependencies in networks |
10:00-10:30 | BREAK |
10:30-12:10 | Session 14. Chair: Roded Sharan, Tel Aviv University |
10:30-11:30 | KEYNOTE: Sarah Tishkoff. African Evolutionary Genomics: Implications for human origins and adaptation |
11:30-11:50 | Ewa Szczurek and Niko Beerenwinkel. Modeling mutual exclusivity of cancer mutations |
11:50-12:10 | Ben Raphael and Fabio Vandin. Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data |
12:10-13:30 | LUNCH |
13:30-14:30 | Session 15. Chair: Teresa Przytycka, NIH |
13:30-13:50 | Keith Noto, Carla Brodley, Saeed Majidi, Diana Bianchi and Donna Slonim. CSAX: Characterizing Systematic Anomalies in eXpression Data |
13:50-14:10 | Hua Wang, Heng Huang and Chris Ding. Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency |
14:10-14:30 | HIGHLIGHT: Julia Lasserre, Ho-Ryun Chung and Martin Vingron. Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks |
14:30-15:00 | BREAK |
15:00-16:00 | Session 16. Chair: Lenore Cowen, Tufts University |
15:00-15:20 | Marinka Zitnik and Blaz Zupan. Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion |
15:20-15:40 | Hamidreza Chitsaz and Mohammad Aminisharifabad. Exact Learning of RNA Energy Parameters From Structure |
15:40-16:00 | HIGHLIGHT: Raluca Gordan, Ning Shen, Iris Dror, Tianyin Zhou, John Horton, Remo Rohs and Martha Bulyk. Genomic Regions Flanking E-Box Binding Sites Influence DNA Binding Specificity of bHLH Transcription Factors through DNA Shape |
16:00-16:30 | Award ceremony and closing remarks |
16:30 | Conference Adjourns |