12. RECOMB 2008: Singapore

• Temple F. Smith:
  Computational Biology: Its Challenges Past, Present, and Future. 1-2
  
• Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer:
  Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. 3-16
  
• Sourav Chatterji, Ichitaro Yamazaki, Zhaojun Bai, Jonathan A. Eisen:
  CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads. 17-28
  
• Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller:
  Reconstructing the Evolutionary History of Complex Human Gene Clusters. 29-49
  
• Paul Medvedev, Michael Brudno:
  Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. 50-64
  
• Howard Cedar:
  Orchestration of DNA Methylation. 65
  
• Tien-ho Lin, Pradipta Ray, Geir Kjetil Sandve, Selen Uguroglu, Eric P. Xing:
  BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes. 66-81
  
• Yanxin Shi, Itamar Simon, Tom Mitchell, Ziv Bar-Joseph:
  A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors. 82-97
  
• Raluca Gordân, Leelavati Narlikar, Alexander J. Hartemink:
  A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery. 98-111
  
• John Hawkins, Timothy L. Bailey:
  The Statistical Power of Phylogenetic Motif Models. 112-126
  
• Edison T. Liu:
  Transcriptional Regulation and Cancer Genomics. 127
  
• Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart K. Kim, Gene Myers:
  Automatic Recognition of Cells (ARC) for 3D Images of C. elegans. 128-139
  
• Ritendra Datta, Marshall W. Bern:
  Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing. 140-153
  
• Yu Lin, Yantao Qiao, Shiwei Sun, Chungong Yu, Gongjin Dong, Dongbo Bu:
  A Fragmentation Event Model for Peptide Identification by Mass Spectrometry. 154-166
  
• Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang:
  A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. 167-180
  
• Nuno Bandeira, Julio Ng, Dario Meluzzi, Roger G. Linington, Pieter C. Dorrestein, Pavel A. Pevzner:
  De Novo Sequencing of Nonribosomal Peptides. 181-195
  
• Sang Yup Lee:
  Systems Metabolic Engineering. 196
  
• Mustafa Kirac, Gultekin Özsoyoglu:
  Protein Function Prediction Based on Patterns in Biological Networks. 197-213
  
• Jason Flannick, Antal F. Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou:
  Automatic Parameter Learning for Multiple Network Alignment. 214-231
  
• Michael R. Mehan, Juan Nunez-Iglesias, Mrinal Kalakrishnan, Michael S. Waterman, Xianghong Jasmine Zhou:
  An Integrative Network Approach to Map the Transcriptome to the Phenome. 232-245
  
• Maxim Kalaev, Vineet Bafna, Roded Sharan:
  Fast and Accurate Alignment of Multiple Protein Networks. 246-256
  
• Michael Baym, Chris Bakal, Norbert Perrimon, Bonnie Berger:
  High-Resolution Modeling of Cellular Signaling Networks. 257-271
  
• Andrei N. Lupas:
  At the Origin of Life: How Did Folded Proteins Evolve? 272
  
• J. Gordon Burleigh, Mukul S. Bansal, André Wehe, Oliver Eulenstein:
  Locating Multiple Gene Duplications through Reconciled Trees. 273-284
  
• Jing Zhang, Xin Gao, Jinbo Xu, Ming Li:
  Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information. 285-299
  
• Wei Zheng, Alan M. Friedman, Chris Bailey-Kellogg:
  Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins. 300-314
  
• Christophe Dessimoz, Daniel Margadant, Gaston H. Gonnet:
  DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework. 315-330
  
• Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye:
  Computation of Median Gene Clusters. 331-345
  
• Suzanne Cory:
  BCL-2: From Translocation to Therapy. 346
  
• Igor Ulitsky, Richard M. Karp, Ron Shamir:
  Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles. 347-359
  
• Delbert Dueck, Brendan J. Frey, Nebojsa Jojic, Vladimir Jojic, Guri Giaever, Andrew Emili, Gabe Musso, Robert Hegele:
  Constructing Treatment Portfolios Using Affinity Propagation. 360-371
  
• Michael Sammeth, Gabriel Valiente, Roderic Guigó:
  Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs. 372-395
  
• Bin Ma, Xiaoming Sun:
  More Efficient Algorithms for Closest String and Substring Problems. 396-409
  
• Denis Smirnov, Vivian G. Cheung:
  Disruption of a Transcriptional Regulatory Pathway Contributes to Phenotypes in Carriers of Ataxia Telangiectasia. 410
  
• Oliver Stegle, Anitha Kannan, Richard Durbin, John M. Winn:
  Accounting for Non-genetic Factors Improves the Power of eQTL Studies. 411-422
  
• Andreas Sundquist, Eugene Fratkin, Chuong B. Do, Serafim Batzoglou:
  Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA. 423
  
• Sriram Sankararaman, Gad Kimmel, Eran Halperin, Michael I. Jordan:
  On the Inference of Ancestries in Admixed Populations. 424-433
  
• Eleazar Eskin:
  Increasing Power in Association Studies by Using Linkage Disequilibrium Structure and Molecular Function as Prior Information. 434
  
• Sivan Bercovici, Dan Geiger, Liran Shlush, Karl Skorecki, Alan Templeton:
  Panel Construction for Mapping in Admixed Populations Via Expected Mutual Information. 435-449
  
• Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen, Teun Boekhout:
  Constructing Level-2 Phylogenetic Networks from Triplets. 450-462
  
• Rune B. Lyngsø, Yun S. Song, Jotun Hein:
  Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony. 463-477
  

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