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Research in Computational Molecular Biology

12th Annual International Conference, RECOMB 2008, Singapore, March 30 - April 2, 2008. Proceedings

  • Editors
  • Martin Vingron
  • Limsoon Wong
Conference proceedings RECOMB 2008

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4955)

Also part of the Lecture Notes in Bioinformatics book sub series (LNBI, volume 4955)

Table of contents

  1. Front Matter
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  2. Computational Biology: Its Challenges Past, Present, and Future
    Temple F. Smith
    Pages 1-2
  3. Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast
    Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer
    Pages 3-16
  4. CompostBin: A DNA Composition-Based Algorithm for Binning Environmental Shotgun Reads
    Sourav Chatterji, Ichitaro Yamazaki, Zhaojun Bai, Jonathan A. Eisen
    Pages 17-28
  5. Reconstructing the Evolutionary History of Complex Human Gene Clusters
    Yu Zhang, Giltae Song, Tomáš Vinař, Eric D. Green, Adam Siepel, Webb Miller
    Pages 29-49
  6. Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads
    Paul Medvedev, Michael Brudno
    Pages 50-64
  7. Orchestration of DNA Methylation
    Howard Cedar
    Pages 65-65
  8. 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
    Pages 66-81
  9. A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors
    Yanxin Shi, Itamar Simon, Tom Mitchell, Ziv Bar-Joseph
    Pages 82-97
  10. A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery
    Raluca Gordân, Leelavati Narlikar, Alexander J. Hartemink
    Pages 98-111
  11. The Statistical Power of Phylogenetic Motif Models
    John Hawkins, Timothy L. Bailey
    Pages 112-126
  12. Transcriptional Regulation and Cancer Genomics
    Edison Liu
    Pages 127-127
  13. Automatic Recognition of Cells (ARC) for 3D Images of C. elegans
    Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart Kim, Gene Myers
    Pages 128-139
  14. Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing
    Ritendra Datta, Marshall Bern
    Pages 140-153
  15. A Fragmentation Event Model for Peptide Identification by Mass Spectrometry
    Yu Lin, Yantao Qiao, Shiwei Sun, Chungong Yu, Gongjin Dong, Dongbo Bu
    Pages 154-166
  16. A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics
    Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang
    Pages 167-180
  17. De Novo Sequencing of Nonribosomal Peptides
    Nuno Bandeira, Julio Ng, Dario Meluzzi, Roger G. Linington, Pieter Dorrestein, Pavel A. Pevzner
    Pages 181-195
  18. Systems Metabolic Engineering
    Sang Yup Lee
    Pages 196-196
  19. Protein Function Prediction Based on Patterns in Biological Networks
    Mustafa Kirac, Gultekin Ozsoyoglu
    Pages 197-213
  20. Automatic Parameter Learning for Multiple Network Alignment
    Jason Flannick, Antal Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou
    Pages 214-231
  21. 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
    Pages 232-245
  22. Fast and Accurate Alignment of Multiple Protein Networks
    Maxim Kalaev, Vineet Bafna, Roded Sharan
    Pages 246-256
  23. High-Resolution Modeling of Cellular Signaling Networks
    Michael Baym, Chris Bakal, Norbert Perrimon, Bonnie Berger
    Pages 257-271
  24. At the Origin of Life: How Did Folded Proteins Evolve?
    Andrei Lupas
    Pages 272-272
  25. Locating Multiple Gene Duplications through Reconciled Trees
    J. Gordon Burleigh, Mukul S. Bansal, Andre Wehe, Oliver Eulenstein
    Pages 273-284
  26. Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information
    Jing Zhang, Xin Gao, Jinbo Xu, Ming Li
    Pages 285-299
  27. Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins
    Wei Zheng, Alan M. Friedman, Chris Bailey-Kellogg
    Pages 300-314
  28. DLIGHT – Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework
    Christophe Dessimoz, Daniel Margadant, Gaston H. Gonnet
    Pages 315-330
  29. Computation of Median Gene Clusters
    Sebastian Böcker, Katharina Jahn, Julia Mixtacki, Jens Stoye
    Pages 331-345
  30. BCL-2: From Translocation to Therapy
    Suzanne Cory
    Pages 346-346
  31. Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles
    Igor Ulitsky, Richard M. Karp, Ron Shamir
    Pages 347-359
  32. Constructing Treatment Portfolios Using Affinity Propagation
    Delbert Dueck, Brendan J. Frey, Nebojsa Jojic, Vladimir Jojic, Guri Giaever, Andrew Emili et al.
    Pages 360-371
  33. Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs
    Michael Sammeth, Gabriel Valiente, Roderic Guigó
    Pages 372-395
  34. More Efficient Algorithms for Closest String and Substring Problems
    Bin Ma, Xiaoming Sun
    Pages 396-409
  35. Disruption of a Transcriptional Regulatory Pathway Contributes to Phenotypes in Carriers of Ataxia Telangiectasia
    Denis Smirnov, Vivian G. Cheung
    Pages 410-410
  36. Accounting for Non-genetic Factors Improves the Power of eQTL Studies
    Oliver Stegle, Anitha Kannan, Richard Durbin, John Winn
    Pages 411-422
  37. Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA
    Andreas Sundquist, Eugene Fratkin, Chuong B. Do, Serafim Batzoglou
    Pages 423-423
  38. On the Inference of Ancestries in Admixed Populations
    Sriram Sankararaman, Gad Kimmel, Eran Halperin, Michael I. Jordan
    Pages 424-433
  39. Increasing Power in Association Studies by Using Linkage Disequilibrium Structure and Molecular Function as Prior Information
    Eleazar Eskin
    Pages 434-434
  40. Panel Construction for Mapping in Admixed Populations Via Expected Mutual Information
    Sivan Bercovici, Dan Geiger, Liran Shlush, Karl Skorecki, Alan Templeton
    Pages 435-449
  41. Constructing Level-2 Phylogenetic Networks from Triplets
    Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen, Teun Boekhout
    Pages 450-462
  42. Accurate Computation of Likelihoods in the Coalescent with Recombination Via Parsimony
    Rune B. Lyngsø, Yun S. Song, Jotun Hein
    Pages 463-477
  43. Back Matter
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About these proceedings

Keywords

DNA sequence motifs algorithm algorithms bioinformatics computational biology computational proteomics comutational molecular biology feature extraction gene transfer genome genome data analysis genome signatures optimization origin of life sequence analysis

Bibliographic information

  • DOI https://doi.org/10.1007/978-3-540-78839-3
  • Copyright Information Springer-Verlag Berlin Heidelberg 2008
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Computer Science
  • Print ISBN 978-3-540-78838-6
  • Online ISBN 978-3-540-78839-3
  • Series Print ISSN 0302-9743
  • Series Online ISSN 1611-3349
  • Buy this book on publisher's site