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

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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• 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