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
Website: https://recomb.org/recomb2012/
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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
  • Journal: Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models. Jesse M. Rodriguez, Sivan Bercovici, Megan Elmore, Serafim Batzoglou. Journal of Computational Biology, 20(3): 199-211, 2013.
    • DOI: 10.1089/cmb.2012.0088
• 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
  • Journal: Charge Group Partitioning in Biomolecular Simulation. Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau. Journal of Computational Biology, 20(3): 188-198, 2013.
    • DOI: 10.1089/cmb.2012.0239
• 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
  • Journal: Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment. John Kececioglu, Dan DeBlasio. Journal of Computational Biology, 20(4): 259-279, 2013.
    • DOI: 10.1089/cmb.2013.0007
• 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
  • Preprint: arXiv:1111.7243
  • Journal: Quantifying the Dynamics of Coupled Networks of Switches and Oscillators. Matthew R. Francis, Elana J. Fertig. PLoS ONE, 7(1): e29497, 2012.
    • DOI: 10.1371/journal.pone.0029497
• 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
  • Journal: lobSTR: A short tandem repeat profiler for personal genomes. Melissa Gymrek, David E. Golan, Saharon Rosset, Yaniv Erlich. Genome Research, 22(6): 1154-1162, 2012.
    • DOI: 10.1101/gr.135780.111
• 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
  • Journal: Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data. Dan He, Buhm Han, Eleazar Eskin. Journal of Computational Biology, 20(2): 80-92, 2013.
    • DOI: 10.1089/cmb.2012.0091
• 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
  • Journal: Ballast : A Ball-based Algorithm for Structural Motifs. Lu He, Fabio Vandin, Gopal Pandurangan, Chris Bailey‐Kellogg. Journal of Computational Biology, 20(2): 137-151, 2013.
    • DOI: 10.1089/cmb.2012.0246
• 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
  • Journal: Ancestral Genome Organization: An Alignment Approach. Patrick Holloway, Krister M. Swenson, David H. Ardell, Nadia El-Mabrouk. Journal of Computational Biology, 20(4): 280-295, 2013.
    • DOI: 10.1089/cmb.2012.0292
• 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
  • Journal: LoopWeaver: Loop Modeling by the Weighted Scaling of Verified Proteins. Daniel G. Holtby, Shuai Cheng Li, Ming Li. Journal of Computational Biology, 20(3): 212-223, 2013.
    • DOI: 10.1089/cmb.2012.0078
• 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
  • Journal: 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. Journal of Computational Biology, 20(3): 167-187, 2013.
    • DOI: 10.1089/cmb.2012.0230
• 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
  • Journal: Combinatorics of the Breakage-Fusion-Bridge Mechanism. Marcus Kinsella, Vineet Bafna. Journal of Computational Biology, 19(6): 662-678, 2012.
    • DOI: 10.1089/cmb.2012.0020
• 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
  • Journal: TrueSight: a new algorithm for splice junction detection using RNA-seq. Yang Li, Hongmei Li‐Byarlay, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma. Nucleic Acids Research, 41(4): e51, 2012.
    • DOI: 10.1093/nar/gks1311
• 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
  • Journal: Synthetic Sequence Design for Signal Location Search. Yaw-Ling Lin, Charles B. Ward, Steven Skiena. Algorithmica, 67(3): 368-383, 2013.
    • DOI: 10.1007/s00453-013-9760-9
• 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
  • Journal: nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing. Andrew McPherson, Chunxiao Wu, Alexander W. Wyatt, Sohrab P. Shah, Colin C. Collins, S. Cenk Sahinalp. Genome Research, 22(11): 2250-2261, 2012.
    • DOI: 10.1101/gr.136572.111
• 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
  • Journal: Structure-Guided Deimmunization of Therapeutic Proteins. Andrew S. Parker, Yoonjoo Choi, Karl E. Griswold, Chris Bailey‐Kellogg. Journal of Computational Biology, 20(2): 152-165, 2013.
    • DOI: 10.1089/cmb.2012.0251
• 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
  • Journal: Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. Son Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, Max A. Alekseyev. Journal of Computational Biology, 20(4): 359-371, 2012.
    • DOI: 10.1089/cmb.2012.0098
• 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
  • Journal: Finding Maximum Colorful Subtrees in Practice. Imran Rauf, Florian Rasche, François Nicolas, Sebastian Böcker. Journal of Computational Biology, 20(4): 311-321, 2013.
    • DOI: 10.1089/cmb.2012.0083
• 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
  • Preprint: arXiv:1206.3520
• 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
  • Journal: RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks. Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon. Bioinformatics, 28(16): 2129-2136, 2012.
    • DOI: 10.1093/bioinformatics/bts341
• 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
• 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
  • Journal: Reconstructing Boolean models of signaling. Roded Sharan and Richard M. Karp. Journal of Computational Biology, 20(3):249-57, 2013.
    • DOI: 10.1089/cmb.2012.0241
• 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
  • Journal: Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads. Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng, Fengzhu Sun. Journal of Computational Biology, 20(2): 64-79, 2013.
    • DOI: 10.1089/cmb.2012.0228
• 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
  • Journal: Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. Nurcan Tunçbağ, Alfredo Braunstein, Andrea Pagnani, Shao‐shan Carol Huang, Jennifer Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel. Journal of Computational Biology, 20(2): 124-136, 2013.
    • DOI: 10.1089/cmb.2012.0092
• 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
  • Journal: Function–Function Correlated Multi-label Protein Function Prediction over Interaction Networks. Hua Wang, Heng Huang, Chris Ding. Journal of Computational Biology, 20(4): 322-343, 2013.
    • DOI: 10.1089/cmb.2012.0272
• 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
  • Journal: Predicting Protein–Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization. Hua Wang, Heng Huang, Chris Ding, Feiping Nie. Journal of Computational Biology, 20(4): 344-358, 2013.
    • DOI: 10.1089/cmb.2012.0273
• 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
  • Journal: CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping. Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin, Eleazar Eskin. Journal of Computational Biology, 20(3): 224-236, 2013.
    • DOI: 10.1089/cmb.2012.0258
• 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
  • Journal: Structure-based whole-genome realignment reveals many novel noncoding RNAs. Sebastian Will, Michael Yu, Bonnie Berger. Genome Research, 23(6): 1018-1027, 2013.
    • DOI: 10.1101/gr.137091.111
• 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
  • Journal: Probabilistic Inference of Viral Quasispecies Subject to Recombination. Armin Töpfer, Osvaldo Zagordi, Sandhya Prabhakaran, Volker Röth, Eran Halperin, Niko Beerenwinkel. Journal of Computational Biology, 20(2): 113-123, 2013.
    • DOI: 10.1089/cmb.2012.0232
• 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
  • Journal: Simultaneously Learning DNA Motif Along with Its Position and Sequence Rank Preferences Through Expectation Maximization Algorithm. Zhizhuo Zhang, Cheng Chang, Willy Hugo, Edwin Cheung, Wing‐Kin Sung. Journal of Computational Biology, 20(3): 237-248, 2013.
    • DOI: 10.1089/cmb.2012.0233