RECOMB 2012 Proceedings

Barcelona, Spain, April 21-24, 2012

PC Chair: Benny Chor
Organization Committee: Rodric Guigo (chair), Josep F Abril, Francisco Cámara, Eduardo Eyras, Pedro Ferreira, Toni Gabaldón, Cédric Notredame, Gabriel Valiente, Blanka Wysocka
Keynote Speakers: Richard Durbin, Eileen Furlong, Thomas Gingeras, Alfonso Valencia, Ada E. Yonath

List of Publications

• Protein Structure by Semidefinite Facial Reduction. Babak Alipanahi, Nathan Krislock, Ali Ghodsi, Henry Wolkowicz, Logan Donaldson, Ming Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 1-11, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_1
• Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models. Sivan Bercovici, Jesse M. Rodriguez, Megan Elmore, Serafim Batzoglou.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 12-28, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_2
• Charge Group Partitioning in Biomolecular Simulation. Stefan Canzar, Mohammed El-Kebir, Rene Pool, Khaled Elbassioni, Alpesh K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 29-43, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_3
• Increased Methylation Variation in Epigenetic Domains across Cancer Types. Hector Corrada Bravo.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 44-44, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_4
• Estimating the Accuracy of Multiple Alignments and its Use in Parameter Advising. Dan F. DeBlasio, Travis J. Wheeler, John D. Kececioglu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 45-59, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_5
• Quantifying the Dynamics of Coupled Networks of Switches and Oscillators. Matthew R. Francis and Elana J. Fertig.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 60-61, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_6
• lobSTR: A Short Tandem Repeat Profiler for Personal Genomes. Melissa Gymrek, David Golan, Saharon Rosset, Yaniv Erlich.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 62-63, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_7
• Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data. Dan He, Buhm Han, Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 64-78, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_8
• BALLAST: A Ball-Based Algorithm for Structural Motifs. Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey-Kellogg.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 79-93, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_9
• Evolution of Genome Organization by Duplication and Loss: An Alignment Approach. Patrick Holloway, Krister Swenson, David Ardell, Nadia El-Mabrouk.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 94-112, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_10
• LoopWeaver Loop Modeling by the Weighted Scaling of Verified Proteins. Daniel Holtby, Shuai Cheng Li, Ming Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 113-126, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_11
• A Robust Method for Transcript Quantification with RNA-seq Data. Yan Huang, Yin Hu, Corbin D. Jones, James N. MacLeod, Derek Y. Chiang, Yufeng Liu, Jan F. Prins, Jinze Liu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 127-147, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_12
• Modeling the Breakage-Fusion-Bridge Mechanism: Combinatorics and Cancer Genomics. Marcus Kinsella and Vineet Bafna.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 148-162, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_13
• TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq. Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 163-164, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_14
• Synthetic Sequence Design for Signal Location Search. Yaw-Ling Lin, Charles Ward, Steven Skiena.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 165-179, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_15
• The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation. Marc A. Marti-Renom.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 180-180, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_16
• Discovery of Complex Genomic Rearrangements in Cancer Using High-Throughput Sequencing. Andrew McPherson, Chunxiao Wu, Alexander Wyatt, Sohrab Shah, Colin Collins, S. Cenk Sahinalp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 181-182, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_17
• Network-Based Prediction and Analysis of HIV Dependency Factors. T.M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, Michael G. Katze.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 183-183, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_18
• Structure-Guided Deimmunization of Therapeutic Proteins. Andrew S. Parker, Karl E. Griswold, Chris Bailey-Kellogg.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 184-198, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_19
• Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures. Dmitri Pervouchine, Ekaterina Khrameeva, Marina Pichugina, Olexii Nikolaienko, Mikhail Gelfand, Petr Rubtsov, Andrei Mironov.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 199-199, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_20
• Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. Son K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, Max A. Alekseyev.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 200-212, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_21
• Finding Maximum Colorful Subtrees in Practice. Imran Rauf, Florian Rasche, François Nicolas, Sebastian Böcker.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 213-223, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_22
• Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis. Sebastien Roch and Sagi Snir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 224-238, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_23
• RESQUE: Network Reduction Using Semi-Markov Random Walk Scores for Efficient Querying of Biological Networks. Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 239-240, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_24
• Detecting SNP-Induced Structural Changes in RNA: Application to Disease Studies. Raheleh Salari, Chava Kimchi-Sarfaty, Michael M. Gottesman, Teresa M. Przytycka.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 241-243, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_25
• A Model for Biased Fractionation after Whole Genome Duplication. David Sankoff, Chunfang Zheng, Baoyong Wang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 244-244, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_26
• Exact Pattern Matching for RNA Structure Ensembles. Christina Schmiedl, Mathias Möhl, Steffen Heyne, Mika Amit, Gad M. Landau, Sebastian Will, Rolf Backofen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 245-260, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_27
• Reconstructing Boolean Models of Signaling. Roded Sharan and Richard M. Karp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 261-271, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_28
• Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads: Extended Abstract. Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng, Fengzhu Sun.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 272-285, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_29
• Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer. Rory Stark.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 286-286, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_30
• Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 287-301, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_31
• Function-Function Correlated Multi-Label Protein Function Prediction over Interaction Networks. Hua Wang, Heng Huang, Chris Ding.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 302-313, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_32
• Predicting Protein-Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization. Hua Wang, Heng Huang, Chris Ding, Feiping Nie.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 314-325, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_33
• CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping. Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin, Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 326-340, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_34
• Structure-Based Whole Genome Realignment Reveals Many Novel Non-coding RNAs. Sebastian Will, Michael Yu, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 341-341, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_35
• Probabilistic Inference of Viral Quasispecies Subject to Recombination. Osvaldo Zagordi, Armin Töpfer, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 342-354, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_36
• Simultaneously Learning DNA Motif along with Its Position and Sequence Rank Preferences through EM Algorithm. ZhiZhuo Zhang, Cheng Wei Chang, Willy Hugo, Edwin Cheung, Wing-Kin Sung.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2012. Lecture Notes in Computer Science, vol 7262, pp 355-370, Springer, Cham.
    • DOI: 10.1007/978-3-642-29627-7_37