18th Annual International Conference on Research in Computational Molecular Biology
Pittsburgh, Pennsylvania
April 2-5, 2014


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)

18:00-21:00Opening Night Reception

Wednesday, April 2 (Alumni Hall)

8:45-9:00Opening 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
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

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