List of papers accepted to WABI 2004:
  1. Solving the protein threading problem by lagrangian relaxation
    Stefan Balev
  2. Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations
    Alexandra Shulman-Peleg, Shira Mintz, Ruth Nussinov, Haim Wolfson
  3. A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals
    Tzvika Hartman, Roded Sharan
  4. The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics
    Brona Brejova, Daniel G. Brown, Tomas Vinar
  5. Multiple vector seeds for protein alignment
    Daniel Brown
  6. Approximation Algorithms for the Selection of Robust Tag SNPs
    Yao-Ting Huang, Kui Zhang, Ting Chen, Kun-Mao Chao
  7. Adding Hidden Nodes to Gene Networks.
    Tamir Tuller, Benny Chor
  8. Algorithms for finding maximal-scoring segment sets
    Miklos Csuros
  9. Integrating Sample-driven and Pattern-driven Approaches in Motif Finding
    Sing-Hoi Sze, Songjian Lu, Jianer Chen
  10. A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns
    Jens Gramm
  11. Finding Optimal Pairs of Patterns
    Hideo Bannai, Heikki Hyyro, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano
  12. Gapped Local Similarity Search with Provable Guarantees
    Manikandan Narayanan, Richard Karp
  13. Novel tree edit operations for RNA secondary structure comparison
    Julien Allali, Marie-France Sagot
  14. Joint Analysis of DNA Copy Numbers and Expression Levels
    Doron Lipson, Amir Ben-Dor, Elinor Dehan, Zohar Yakhini
  15. Finding missing patterns
    Shunsuke Inenaga, Teemu Kivioja, Veli Mäkinen
  16. Fast Hare: a Fast Heuristic for Single Individual SNP Haplotype Reconstruction
    Alessandro Panconesi, Mauro Sozio
  17. A Faster and More Space-Efficient Algorithm for Inferring Arc-Annotations of RNA Sequences through Alignment
    Jesper Jansson, See-Kiong Ng, Wing-Kin Sung, Willy Hugo
  18. The Minisatellite Transformation Problem Revisited: A Run Length Encoded Approach
    Behshad Behzadi, Jean-Marc Steyaert
  19. ATDD: An Algorithmic Tool for Domain Discovery in Protein Sequences
    Stanislav Angelov, Sanjeev Khanna, Li Li, Fernando Pereira
  20. New Algorithms for Multiple DNA Sequence Alignment
    Daniel G. Brown, Alexander K. Hudek
  21. A faster reliable algorithm to estimate the p-value of the multinomial llr statistic
    Uri Keich, Niranjan Nagarajan
  22. Linear Reduction for Haplotype Inference
    Jingwu He, Alex Zelikovsky
  23. Chaining algorithms for alignment of draft sequence
    Michael Brudno, Mukund Sundararajanan, Serafim Batzoglou
  24. A new integer programming formulation for the pure parsimony problem in haplotype analysis
    Daniel Brown, Ian Harrower
  25. Sorting By Reversals with Common Intervals
    Figeac Martin, Varre Jean-Stephane
  26. Online Consensus and Agreement of Phylogenetic Trees
    Tanya Y. Berger-Wolf
  27. Relation of residues in the variable region of 16S rDNA sequences and their relevance to genus-specificity
    Maciej Liskiewicz, Hemant Purohit, Dhananjay Raje
  28. Supervised learning-aided optimization of expert-driven functional protein sequence annotation
    Lev Soinov, Alexander Kanapin, Misha Kapushesky
  29. Reconstructing Ancestral Gene Orders Using Conserved Intervals
    Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cedric Chauve
  30. Sequence database compression for peptide identification from tandem mass spectra
    Nathan Edwards, Ross Lippert
  31. Topological Rearrangements and Local Search Method for Tandem Duplication Trees
    Denis BERTRAND, Olivier GASCUEL
  32. Local Search Heuristic for Rigid Protein Docking
    Vicky Choi, Pankaj Agarwal, Herbert Edelsbrunner, Johannes Rudolph
  33. Monotone Scoring of Patterns with Mismatches
    Alberto Apostolico, Cinzia Pizzi
  34. Suboptimal local alignments across multiple scoring schemes
    Morris Michael, Christoph Dieterich, Jens Stoye
  35. Phylogenetic Super-Networks from Partial Trees
    Daniel Huson, Tobias Dezulian, Tobias Klöpper, Mike Steel
  36. Translation Initiation Sites Prediction with mixture Gaussian models
    Guoliang Li, Tze-Yun Leong, Louxin Zhang
  37. Phylogeny by Hybridization
    Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim, Li-San Wang
  38. Reversing Gene Erosion--Reconstructing Ancestral Bacterial Genomes from Gene-Content and Gene Order Data
    Joel V. Earnest-DeYoung, Emmanuelle Lerat, Bernard M.E. Moret
  39. Searching for Regulatory Elements of Alternative Splicing Events Using Ph ylogenetic Footprinting
    Daichi Shigemizu, Osamu Maruyama