RECOMB 2014 Proceedings

Pittsburgh, PA, United States, April 2 - 5, 2014

PC Chair: Roded Sharan
Organization Committee: Panayiotis (Takis) Benos (co-chair), Russell Schwartz (co-chair)
Keynote Speakers: Ian T. Baldwin, Atul Butte, JJ Collins, Trey Ideker, Tom Mitchell, Sarah A. Tishkoff
Website: https://recomb.org/recomb2014/
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List of Publications

• Tractatus: An Exact and Subquadratic Algorithm for Inferring Identical-by-Descent Multi-shared Haplotype Tracts. Derek Aguiar, Eric Morrow, Sorin Istrail.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 1-17, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_1
• HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. Emily Berger, Deniz Yorukoglu, Jian Peng, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 18-19, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_2
  • Journal: HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data. Emily Berger, Deniz Yorukoglu, Jian Peng, Bonnie Berger. PLoS Computational Biology, 10(3): e1003502, 2014.
    • DOI: 10.1371/journal.pcbi.1003502
• Changepoint Analysis for Efficient Variant Calling. Adam Bloniarz, Ameet Talwalkar, Jonathan Terhorst, Michael I. Jordan, David Patterson, Bin Yu, Yun S. Song.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 20-34, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_3
• On the Representation of de Bruijn Graphs. Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 35-55, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_4
  • Preprint: arXiv:1401.5383
  • Journal: On the Representation of De Bruijn Graphs. Rayan Chikhi, Antoine Limasset, Shaun D. Jackman, Jared T. Simpson, Paul Medvedev. Journal of Computational Biology, 22(5): 336-352, 2015.
    • DOI: 10.1089/cmb.2014.0160
• Exact Learning of RNA Energy Parameters from Structure. Hamidreza Chitsaz and Mohammad Aminisharifabad.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 56-68, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_5
  • Journal: Exact Learning of RNA Energy Parameters From Structure. Hamidreza Chitsaz, Mohammad Aminisharifabad. Journal of Computational Biology, 22(6): 463-473, 2015.
    • DOI: 10.1089/cmb.2014.0164
• An Alignment-Free Regression Approach for Estimating Allele-Specific Expression Using RNA-Seq Data. Chen-Ping Fu, Vladimir Jojic, Leonard McMillan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 69-84, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_6
• The Generating Function Approach for Peptide Identification in Spectral Networks. Adrian Guthals, Christina Boucher, Nuno Bandeira.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 85-99, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_7
  • Journal: The Generating Function Approach for Peptide Identification in Spectral Networks. Adrian Guthals, Christina Boucher, Nuno Bandeira. Journal of Computational Biology, 22(5): 353-366, 2014.
    • DOI: 10.1089/cmb.2014.0165
• Decoding Coalescent Hidden Markov Models in Linear Time. Kelley Harris, Sara Sheehan, John A. Kamm, Yun S. Song.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 100-114, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_8
  • Preprint: arXiv:1403.0858
• AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application. Jan Hoinka, Alexey Berezhnoy, Zuben E. Sauna, Eli Gilboa, Teresa M. Przytycka.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 115-128, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_9
• Learning Sequence Determinants of Protein: Protein Interaction Specificity with Sparse Graphical Models. Hetunandan Kamisetty, Bornika Ghosh, Christopher James Langmead, Chris Bailey-Kellogg.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 129-143, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_10
  • Journal: Learning Sequence Determinants of Protein:Protein Interaction Specificity with Sparse Graphical Models. Hetunandan Kamisetty, Bornika Ghosh, Christopher J. Langmead, Chris Bailey‐Kellogg. Journal of Computational Biology, 22(6): 474-486, 2015.
    • DOI: 10.1089/cmb.2014.0289
• On Sufficient Statistics of Least-Squares Superposition of Vector Sets. Arun S. Konagurthu, Parthan Kasarapu, Lloyd Allison, James H. Collier, Arthur M. Lesk.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 144-159, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_11
  • Journal: On Sufficient Statistics of Least-Squares Superposition of Vector Sets. Arun S. Konagurthu, Parthan Kasarapu, Lloyd Allison, James H. Collier, Arthur M. Lesk. Journal of Computational Biology, 22(6): 487-497, 2015.
    • DOI: 10.1089/cmb.2014.0154
• IDBA-MTP: A Hybrid Meta Transcriptomic Assembler Based on Protein Information. Henry C.M. Leung, S.M. Yiu, Francis Y.L. Chin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 160-172, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_12
  • Journal: IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. Henry C. M. Leung, Siu‐Ming Yiu, Francis Y. L. Chin. Journal of Computational Biology, 22(5): 367-376, 2014.
    • DOI: 10.1089/cmb.2014.0139
• MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 173-174, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_13
  • Journal: MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu. PLoS Computational Biology, 10(3): e1003500, 2014.
    • DOI: 10.1371/journal.pcbi.1003500
• An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding. Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 175-176, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_14
  • Journal: An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding. Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford. PLoS Computational Biology, 10(3): e1003501, 2014.
    • DOI: 10.1371/journal.pcbi.1003501
• PASTA: Ultra-Large Multiple Sequence Alignment. Siavash Mirarab, Nam Nguyen, Tandy Warnow.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 177-191, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_15
  • Journal: PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. Siavash Mirarab, Nam Nguyen, Sheng Guo, Li‐San Wang, Junhyong Kim, Tandy Warnow. Journal of Computational Biology, 22(5): 377-386, 2014.
    • DOI: 10.1089/cmb.2014.0156
• Fast Flux Module Detection Using Matroid Theory. Arne C. Müller, Frank J. Bruggeman, Brett G. Olivier, Leen Stougie.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 192-206, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_16
  • Journal: Fast Flux Module Detection Using Matroid Theory. Arne C. Reimers, Frank J. Bruggeman, Brett G. Olivier, Leen Stougie. Journal of Computational Biology, 22(5): 414-424, 2015.
    • DOI: 10.1089/cmb.2014.0141
• Building a Pangenome Reference for a Population. Ngan Nguyen, Glenn Hickey, Daniel R. Zerbino, Brian Raney, Dent Earl, Joel Armstrong, David Haussler, Benedict Paten.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 207-221, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_17
  • Journal: Building a Pan-Genome Reference for a Population. Ngan Nguyen, Glenn Hickey, Daniel R. Zerbino, Brian J. Raney, Dent Earl, Joel Armstrong, W. James Kent, David Haussler, Benedict Paten. Journal of Computational Biology, 22(5): 387-401, 2015.
    • DOI: 10.1089/cmb.2014.0146
• CSAX: Characterizing Systematic Anomalies in eXpression Data. Keith Noto, Carla Brodley, Saeed Majidi, Diana W. Bianchi, Donna K. Slonim.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 222-236, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_18
  • Journal: CSAX: Characterizing Systematic Anomalies in eXpression Data. Keith Noto, Saeed Majidi, Andrea G. Edlow, Heather C. Wick, Diana W. Bianchi, Donna K. Slonim. Journal of Computational Biology, 22(5): 402-413, 2015.
    • DOI: 10.1089/cmb.2014.0155
• WHATSHAP: Haplotype Assembly for Future-Generation Sequencing Reads. Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 237-249, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_19
  • Preprint: bioRxiv 085050
  • Journal: WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth. Journal of Computational Biology, 22(6): 498-509, 2015.
    • DOI: 10.1089/cmb.2014.0157
• Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. Benjamin J. Raphael and Fabio Vandin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 250-264, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_20
  • Journal: Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. Benjamin J. Raphael, Fabio Vandin. Journal of Computational Biology, 22(6): 510-527, 2015.
    • DOI: 10.1089/cmb.2014.0161
• DIPSPADES: Assembler for Highly Polymorphic Diploid Genomes. Yana Safonova, Anton Bankevich, Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 265-279, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_21
  • Journal: dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes. Yana Safonova, Anton Bankevich, Pavel A. Pevzner. Journal of Computational Biology, 22(6): 528-545, 2015.
    • DOI: 10.1089/cmb.2014.0153
• An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes. Mingfu Shao, Yu Lin, Bernard Moret.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 280-292, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_22
  • Journal: An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes. Mingfu Shao, Yu Lin, Bernard M. E. Moret. Journal of Computational Biology, 22(5): 425-435, 2014.
    • DOI: 10.1089/cmb.2014.0096
• HIT’nDRIVE: Multidriver -Gene Prioritization Based on Hitting Time. Raunak Shrestha, Ermin Hodzic, Jake Yeung, Kendric Wang, Thomas Sauerwald, Phuong Dao, Shawn Anderson, Himisha Beltran, Mark A. Rubin, Colin C. Collins, Gholamreza Haffari, S. Cenk Sahinalp.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 293-306, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_23
  • Journal: HIT’nDRIVE: patient-specific multidriver gene prioritization for precision oncology. Raunak Shrestha, Ermin Hodzic, Thomas Sauerwald, Phuong Dao, Kendric Wang, Jake Yeung, Shawn Anderson, Fabio Vandin, Gholamreza Haffari, Colin C. Collins, S. Cenk Sahinalp. Genome Research, 27(9): 1573-1588, 2017.
    • DOI: 10.1101/gr.221218.117
• Modeling Mutual Exclusivity of Cancer Mutations. Ewa Szczurek and Niko Beerenwinkel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 307-308, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_24
  • Journal: Modeling Mutual Exclusivity of Cancer Mutations. Ewa Szczurek, Niko Beerenwinkel. PLoS Computational Biology, 10(3): e1003503, 2014.
    • DOI: 10.1371/journal.pcbi.1003503
• Viral Quasispecies Assembly via Maximal Clique Enumeration. Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 309-310, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_25
  • Journal: Viral Quasispecies Assembly via Maximal Clique Enumeration. Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel. PLoS Computational Biology, 10(3): e1003515, 2014.
    • DOI: 10.1371/journal.pcbi.1003515
• Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency. Hua Wang, Heng Huang, Chris Ding.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 311-325, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_26
  • Journal: Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency. Hua Wang, Heng Huang, Chris Ding. Journal of Computational Biology, 22(6): 546-562, 2015.
    • DOI: 10.1089/cmb.2014.0172
• Bayesian Multiple Protein Structure Alignment. Rui Wang and Scott C. Schmidler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 326-339, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_27
• Gene-Gene Interactions Detection Using a Two-Stage Model. Zhanyong Wang, Jae-Hoon Sul, Sagi Snir, Jose A. Lozano, Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 340-355, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_28
  • Journal: Gene–Gene Interactions Detection Using a Two-stage Model. Zhanyong Wang, Jae Hoon Sul, Sagi Snir, José A. Lozano, Eleazar Eskin. Journal of Computational Biology, 22(6): 563-576, 2015.
    • DOI: 10.1089/cmb.2014.0163
• A Geometric Clustering Algorithm and Its Applications to Structural Data. Shutan Xu, Shuxue Zou, Lincong Wang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 356-370, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_29
  • Journal: A Geometric Clustering Algorithm with Applications to Structural Data. Shutan Xu, Shuxue Zou, Lincong Wang. Journal of Computational Biology, 22(5): 436-450, 2014.
    • DOI: 10.1089/cmb.2014.0162
• A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation. Wen-Yun Yang, Farhad Hormozdiari, Eleazar Eskin, Bogdan Pasaniuc.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 371-384, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_30
  • Journal: A Spatial Haplotype Copying Model with Applications to Genotype Imputation. Wen-Yun Yang, Farhad Hormozdiari, Eleazar Eskin, Bogdan Pasaniuc. Journal of Computational Biology, 22(5): 451-462, 2014.
    • DOI: 10.1089/cmb.2014.0151
• Traversing the k-mer Landscape of NGS Read Datasets for Quality Score Sparsification. Y. William Yu, Deniz Yorukoglu, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 385-399, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_31
• Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers. Shay Zakov and Vineet Bafna.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 400-417, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_32
  • Journal: Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers. Shay Zakov, Vineet Bafna. Journal of Computational Biology, 22(6): 577-594, 2015.
    • DOI: 10.1089/cmb.2014.0166
• Reconciliation with Non-binary Gene Trees Revisited. Yu Zheng and Louxin Zhang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 418-432, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_33
• Learning Protein-DNA Interaction Landscapes by Integrating Experimental Data through Computational Models. Jianling Zhong, Todd Wasson, Alexander J. Hartemink.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 433-447, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_34
  • Journal: Learning protein–DNA interaction landscapes by integrating experimental data through computational models. Jianling Zhong, Todd Wasson, Alexander J. Hartemink. Bioinformatics, 30(20): 2868-2874, 2014.
    • DOI: 10.1093/bioinformatics/btu408
• Imputation of Quantitative Genetic Interactions in Epistatic MAPS by Interaction Propagation Matrix Completion. Marinka Žitnik and Blaž Zupan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2014. Lecture Notes in Computer Science, vol 8394, pp 448-462, Springer, Cham.
    • DOI: 10.1007/978-3-319-05269-4_35