List of papers accepted to WABI 2004:
<ol>
<li>Solving the protein threading problem by lagrangian relaxation<br>Stefan Balev 


<li>Protein-Protein Interfaces: Recognition of Similar Spatial and Chemical Organizations<br>Alexandra Shulman-Peleg, Shira Mintz, Ruth  Nussinov, Haim Wolfson 


<li>A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals<br>Tzvika Hartman, Roded Sharan 


<li>The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics<br>Brona Brejova, Daniel G. Brown, Tomas Vinar 


<li>Multiple vector seeds for protein alignment<br>Daniel Brown 


<li>Approximation Algorithms for the Selection of Robust Tag SNPs<br>Yao-Ting Huang, Kui Zhang, Ting Chen, Kun-Mao Chao 


<li>Adding Hidden Nodes to Gene Networks.<br>Tamir  Tuller, Benny Chor 


<li>Algorithms for finding maximal-scoring segment sets<br>Miklos Csuros 


<li>Integrating Sample-driven and Pattern-driven Approaches in Motif Finding<br>Sing-Hoi Sze, Songjian Lu, Jianer Chen 


<li>A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns<br>Jens  Gramm 


<li>Finding Optimal Pairs of Patterns<br>Hideo Bannai, Heikki Hyyro, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano 


<li>Gapped Local Similarity Search with Provable Guarantees<br>Manikandan Narayanan, Richard Karp 


<li>Novel tree edit operations for RNA secondary structure comparison<br>Julien  Allali, Marie-France Sagot 


<li>Joint Analysis of DNA Copy Numbers and Expression Levels<br>Doron Lipson, Amir Ben-Dor, Elinor Dehan, Zohar Yakhini 


<li>Finding missing patterns<br>Shunsuke Inenaga, Teemu Kivioja, Veli Mäkinen 


<li>Fast Hare: a Fast Heuristic for Single Individual SNP Haplotype Reconstruction<br>Alessandro Panconesi, Mauro Sozio 


<li>A Faster and More Space-Efficient Algorithm for Inferring Arc-Annotations of RNA Sequences through Alignment<br>Jesper Jansson, See-Kiong Ng, Wing-Kin Sung, Willy Hugo 


<li>The Minisatellite Transformation Problem  Revisited: A Run   Length Encoded Approach<br>Behshad  Behzadi, Jean-Marc Steyaert 


<li>ATDD: An Algorithmic Tool for Domain Discovery in Protein Sequences<br>Stanislav Angelov, Sanjeev Khanna, Li Li, Fernando Pereira 


<li>New Algorithms for Multiple DNA Sequence Alignment<br>Daniel G. Brown, Alexander K. Hudek 


<li>A faster reliable algorithm to estimate the p-value of the multinomial llr statistic<br>Uri Keich, Niranjan Nagarajan 


<li>Linear Reduction for Haplotype Inference<br>Jingwu  He, Alex Zelikovsky 


<li>Chaining algorithms for alignment of draft sequence<br>Michael Brudno, Mukund  Sundararajanan, Serafim Batzoglou 


<li>A new integer programming formulation for the pure parsimony problem in haplotype analysis<br>Daniel Brown, Ian Harrower 


<li>Sorting By Reversals with Common Intervals<br>Figeac Martin, Varre Jean-Stephane 


<li>Online Consensus and Agreement of Phylogenetic Trees<br>Tanya Y. Berger-Wolf 


<li>Relation of residues in the variable region of 16S rDNA sequences and their relevance to genus-specificity<br>Maciej Liskiewicz, Hemant Purohit, Dhananjay Raje 


<li>Supervised learning-aided optimization of expert-driven functional protein sequence annotation<br>Lev Soinov, Alexander Kanapin, Misha Kapushesky 


<li>Reconstructing Ancestral Gene Orders Using Conserved Intervals<br>Anne Bergeron, Mathieu Blanchette, Annie Chateau, Cedric Chauve 


<li>Sequence database compression for peptide identification from tandem mass spectra<br>Nathan Edwards, Ross Lippert 


<li>Topological Rearrangements and Local Search Method for Tandem Duplication Trees<br>Denis BERTRAND, Olivier GASCUEL 


<li>Local Search Heuristic for Rigid Protein Docking<br>Vicky Choi, Pankaj Agarwal, Herbert Edelsbrunner, Johannes Rudolph 


<li>Monotone Scoring of Patterns with Mismatches<br>Alberto Apostolico, Cinzia Pizzi 


<li>Suboptimal local alignments across multiple scoring schemes<br>Morris Michael, Christoph Dieterich, Jens Stoye 


<li>Phylogenetic Super-Networks from Partial Trees<br>Daniel Huson, Tobias Dezulian, Tobias Klöpper, Mike Steel 


<li>Translation Initiation Sites Prediction with mixture Gaussian models<br>Guoliang Li, Tze-Yun Leong, Louxin Zhang 


<li>Phylogeny by Hybridization<br>Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev  Khanna, Junhyong Kim, Li-San Wang 


<li>Reversing Gene Erosion--Reconstructing Ancestral Bacterial Genomes from Gene-Content and Gene Order Data<br>Joel V. Earnest-DeYoung, Emmanuelle Lerat, Bernard M.E. Moret 


<li>Searching for Regulatory Elements of Alternative Splicing Events Using Ph ylogenetic Footprinting<br>Daichi Shigemizu, Osamu Maruyama 
</ol>