RECOMB 2008 Proceedings

Singapore, March 30 - April 2, 2008

PC Chair: Martin Vingron
Organization Committee: Limsoon Wong (chair), Agnes Ang, Lay Khim Chng, Kwok Pui Choi, Alexia Leong, Hon Wai Leong, Wai Kin Leong, Stefanie Ng, Wing-Kin Sung, Martti Tammi, Siang Yong Yap, Xin Chen, Chee Keong Kwoh, Guillaume Bourque, Alan Christoffels, Dong-Yup Lee, Gunaretnam Rajagopal
Keynote Speakers: Edison Liu, Sang Yup Lee, Andrei Lupas, Howard Cedar, Vivian Cheung, Temple F. Smith, Suzanne Cory
Website: https://recomb.org/recomb2008
Export: JSON | BibTeX

List of Publications

• Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 3-16, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_2
  • Journal: Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer. Journal of Computational Biology, 16(8): 971-987, 2009.
    • DOI: 10.1089/cmb.2009.0023
• Compost Bin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads. Sourav Chatterji, Ichitaro Yamazaki, Zhaojun Bai, Jonathan A. Eisen.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 17-28, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_3
• Reconstructing the Evolutionary History of Complex Human Gene Clusters. Yu Zhang, Giltae Song, Tomáš Vinař, Eric D. Green, Adam Siepel, Webb Miller.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 29-49, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_4
  • Journal: Evolutionary History Reconstruction for Mammalian Complex Gene Clusters. Yu Zhang, Giltae Song, Tomáš Vinař, Eric D. Green, Adam Siepel, Webb Miller. Journal of Computational Biology, 16(8): 1051-1070, 2009.
    • DOI: 10.1089/cmb.2009.0040
• Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. Paul Medvedev and Michael Brudno.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 50-64, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_5
• BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes. Tien-ho Lin, Pradipta Ray, Geir K. Sandve, Selen Uguroglu, Eric P. Xing.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 66-81, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_7
• A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors. Yanxin Shi, Itamar Simon, Tom Mitchell, Ziv Bar-Joseph.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 82-97, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_8
  • Journal: A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors. Yanxin Shi, Michael Klutstein, Itamar Simon, Tom M. Mitchell, Ziv Bar‐Joseph. Journal of Computational Biology, 16(8): 1035-1049, 2009.
    • DOI: 10.1089/cmb.2009.0024
• A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery. Raluca Gordân, Leelavati Narlikar, Alexander J. Hartemink.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 98-111, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_9
• The Statistical Power of Phylogenetic Motif Models. John Hawkins and Timothy L. Bailey.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 112-126, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_10
• Automatic Recognition of Cells (ARC) for 3D Images of C. elegans. Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart Kim, Gene Myers.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 128-139, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_12
• Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing. Ritendra Datta and Marshall Bern.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 140-153, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_13
  • Journal: Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing. Ritendra Datta, Marshall Bern. Journal of Computational Biology, 16(8): 1169-1182, 2009.
    • DOI: 10.1089/cmb.2009.0122
• A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. Yu Lin, Yantao Qiao, Shiwei Sun, Chungong Yu, Gongjin Dong, Dongbo Bu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 154-166, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_14
• A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 167-180, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_15
  • Journal: A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang. Journal of Computational Biology, 16(8): 1183-1193, 2009.
    • DOI: 10.1089/cmb.2009.0018
• De Novo Sequencing of Nonribosomal Peptides. Nuno Bandeira, Julio Ng, Dario Meluzzi, Roger G. Linington, Pieter Dorrestein, Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 181-195, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_16
  • Journal: Dereplication and de novo sequencing of nonribosomal peptides. Julio Ng, Nuno Bandeira, Wei-Ting Liu, Majid Ghassemian, Thomas L Simmons, William H Gerwick, Roger Linington, Pieter C Dorrestein, Pavel A Pevzner. Nature Methods, 6(8): 596-599, 2009.
    • DOI: 10.1038/nmeth.1350
• Protein Function Prediction Based on Patterns in Biological Networks. Mustafa Kirac and Gultekin Ozsoyoglu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 197-213, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_18
• Automatic Parameter Learning for Multiple Network Alignment. Jason Flannick, Antal Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 214-231, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_19
  • Journal: Automatic Parameter Learning for Multiple Local Network Alignment. Jason Flannick, Antal Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou. Journal of Computational Biology, 16(8): 1001-1022, 2009.
    • DOI: 10.1089/cmb.2009.0099
• An Integrative Network Approach to Map the Transcriptome to the Phenome. Michael R. Mehan, Juan Nunez-Iglesias, Mrinal Kalakrishnan, Michael S. Waterman, Xianghong Jasmine Zhou.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 232-245, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_20
  • Journal: An Integrative Network Approach to Map the Transcriptome to the Phenome. Michael R. Mehan, Juan Nunez-Iglesias, Mrinal Kalakrishnan, Michael S. Waterman, Xianghong Jasmine Zhou. Journal of Computational Biology, 16(8): 1023-1034, 2009.
    • DOI: 10.1089/cmb.2009.0037
• Fast and Accurate Alignment of Multiple Protein Networks. Maxim Kalaev, Vineet Bafna, Roded Sharan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 246-256, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_21
  • Journal: Fast and Accurate Alignment of Multiple Protein Networks. Maxim Kalaev, Vineet Bafna, Roded Sharan. Journal of Computational Biology, 16(8): 989-999, 2009.
    • DOI: 10.1089/cmb.2009.0136
• High-Resolution Modeling of Cellular Signaling Networks. Michael Baym, Chris Bakal, Norbert Perrimon, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 257-271, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_22
• Locating Multiple Gene Duplications through Reconciled Trees. J. Gordon Burleigh, Mukul S. Bansal, Andre Wehe, Oliver Eulenstein.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 273-284, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_24
  • Journal: Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants. J. Gordon Burleigh, Mohit Bansal, André Wehe, Oliver Eulenstein. Journal of Computational Biology, 16(8): 1071-1083, 2009.
    • DOI: 10.1089/cmb.2009.0139
• Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information. Jing Zhang, Xin Gao, Jinbo Xu, Ming Li.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 285-299, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_25
• Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins. Wei Zheng, Alan M. Friedman, Chris Bailey-Kellogg.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 300-314, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_26
  • Journal: Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins. Wei Zheng, Alan M. Friedman, Chris Bailey‐Kellogg. Journal of Computational Biology, 16(8): 1151-1168, 2009.
    • DOI: 10.1089/cmb.2009.0090
• DLIGHT Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework. Christophe Dessimoz, Daniel Margadant, Gaston H. Gonnet.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 315-330, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_27
• Computation of Median Gene Clusters. Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 331-345, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_28
  • Journal: Computation of Median Gene Clusters. Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye. Journal of Computational Biology, 16(8): 1085-1099, 2009.
    • DOI: 10.1089/cmb.2009.0098
• Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles. Igor Ulitsky, Richard M. Karp, Ron Shamir.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 347-359, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_30
• Constructing Treatment Portfolios Using Affinity Propagation. Delbert Dueck, Brendan J. Frey, Nebojsa Jojic, Vladimir Jojic, Guri Giaever, Andrew Emili, Gabe Musso, Robert Hegele.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 360-371, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_31
• Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs. Michael Sammeth, Gabriel Valiente, Roderic Guigó.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 372-395, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_32
  • Journal: Complete Alternative Splicing Events Are Bubbles in Splicing Graphs. Michael Sammeth. Journal of Computational Biology, 16(8): 1117-1140, 2009.
    • DOI: 10.1089/cmb.2009.0108
• More Efficient Algorithms for Closest String and Substring Problems. Bin Ma and Xiaoming Sun.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 396-409, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_33
  • Journal: More Efficient Algorithms for Closest String and Substring Problems. Bin Ma, Xiaoming Sun. SIAM Journal on Computing, 39(4): 1432-1443, 2009.
    • DOI: 10.1137/080739069
• Accounting for Non-genetic Factors Improves the Power of eQTL Studies. Oliver Stegle, Anitha Kannan, Richard Durbin, John Winn.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 411-422, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_35
  • Journal: A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies. Oliver Stegle, Leopold Parts, Richard Durbin, John Winn. PLoS Computational Biology, 6(5): e1000770, 2010.
    • DOI: 10.1371/journal.pcbi.1000770
• Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA. Andreas Sundquist, Eugene Fratkin, Chuong B. Do, Serafim Batzoglou.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 423-423, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_36
  • Journal: Effect of genetic divergence in identifying ancestral origin using HAPAA. Andreas Sundquist, Eugene Fratkin, Chuong B. Do, Serafim Batzoglou. Genome Research, 18(4): 676-682, 2008.
    • DOI: 10.1101/gr.072850.107
• On the Inference of Ancestries in Admixed Populations. Sriram Sankararaman, Gad Kimmel, Eran Halperin, Michael I. Jordan.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 424-433, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_37
  • Journal: On the inference of ancestries in admixed populations. Sriram Sankararaman, Gad Kimmel, Eran Halperin, Michael I. Jordan. Genome Research, 18(4): 668-675, 2008.
    • DOI: 10.1101/gr.072751.107
• Increasing Power in Association Studies by Using Linkage Disequilibrium Structure and Molecular Function as Prior Information. Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 434-434, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_38
  • Journal: Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information. Eleazar Eskin. Genome Research, 18(4): 653-660, 2008.
    • DOI: 10.1101/gr.072785.107
• Panel Construction for Mapping in Admixed Populations Via Expected Mutual Information. Sivan Bercovici, Dan Geiger, Liran Shlush, Karl Skorecki, Alan Templeton.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 435-449, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_39
  • Journal: Panel construction for mapping in admixed populations via expected mutual information. Sivan Bercovici, Dan Geiger, Liran I. Shlush, Karl Skorecki, Alan R. Templeton. Genome Research, 18(4): 661-667, 2008.
    • DOI: 10.1101/gr.073148.107
• Constructing Level-2 Phylogenetic Networks from Triplets. Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen, Teun Boekhout.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 450-462, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_40
  • Journal: Constructing Level-2 Phylogenetic Networks from Triplets. Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen, Teun Boekhout. Bioinformatics, 6(4): 667-681, 2009.
    • DOI: 10.1109/tcbb.2009.22
• Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. Rune B. Lyngsø, Yun S. Song, Jotun Hein.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955, pp 463-478, Springer, Cham.
    • DOI: 10.1007/978-3-540-78839-3_41