Volume 3, Number 1, January 2006

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  Dan Gusfield: State of the Journal. 1
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  John A. Berger, Sampsa Hautaniemi, Sanjit K. Mitra, Jaakko Astola: Jointly Analyzing Gene Expression and Copy Number Data in Breast Cancer Using Data Reduction Models. 2-16
• 
  Rafael Sebastián, María Elena Díaz, Guillermo Ayala, Kresimir Letinic, Jose Moncho-Bogani, Derek Toomre: Spatio-Temporal Analysis of Constitutive Exocytosis in Epithelial Cells. 17-32
• 
  Eli Hershkovitz, Guillermo Sapiro, Allen Tannenbaum, Loren Dean Williams: Statistical Analysis of RNA Backbone. 33-46
• 
  Zaher Dawy, Bernhard Goebel, Joachim Hagenauer, Christophe Andreoli, Thomas Meitinger, Jakob C. Mueller: Gene Mapping and Marker Clustering Using Shannon's Mutual Information. 47-56
• 
  John K. Goutsias: A Hidden Markov Model for Transcriptional Regulation in Single Cells. 57-71
• 
  Luis Rueda, Vidya Vidyadharan: A Hill-Climbing Approach for Automatic Gridding of cDNA Microarray Images. 72-83
• 
  Charles Semple, Mike A. Steel: Unicyclic Networks: Compatibility and Enumeration. 84-91
• 
  Sébastien Roch: A Short Proof that Phylogenetic Tree Reconstruction by Maximum Likelihood Is Hard. 92-94

Volume 3, Number 2, April-June 2006

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  Dan Gusfield: Introduction of New Associate Editors. 97

• 
  Wei Chu, Zoubin Ghahramani, Alexei A. Podtelezhnikov, David L. Wild: Bayesian Segmental Models with Multiple Sequence Alignment Profiles for Protein Secondary Structure and Contact Map Prediction. 98-113
• 
  Samuel A. Danziger, Sanjay Joshua Swamidass, Jue Zeng, Lawrence R. Dearth, Qiang Lu, Jonathan H. Chen, Jianlin Cheng, Vinh P. Hoang, Hiroto Saigo, Ray Luo, Pierre Baldi, Rainer K. Brachmann, Richard H. Lathrop: Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants. 114-125
• 
  Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie-France Sagot: An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences. 126-140
• 
  Daniel G. Brown, Ian M. Harrower: Integer Programming Approaches to Haplotype Inference by Pure Parsimony. 141-154
• 
  Marc Vass, Clifford A. Shaffer, Naren Ramakrishnan, Layne T. Watson, John J. Tyson: The JigCell Model Builder: A Spreadsheet Interface for Creating Biochemical Reaction Network Models. 155-164
• 
  Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael Sanderson: Minimum-Flip Supertrees: Complexity and Algorithms. 165-173
• 
  Petteri Sevon, Hannu Toivonen, Vesa Ollikainen: TreeDT: Tree Pattern Mining for Gene Mapping. 174-185

• 
  Yun S. Song: A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree. 186-191

Volume 3, Number 3, July-September 2006

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  Petros Daras, Dimitrios Zarpalas, Apostolos Axenopoulos, Dimitrios Tzovaras, Michael G. Strintzis: Three-Dimensional Shape-Structure Comparison Method for Protein Classification. 193-207
• 
  Weichuan Yu, Xiaoye Li, Junfeng Liu, Baolin Wu, Kenneth R. Williams, Hongyu Zhao: Multiple Peak Alignment in Sequential Data Analysis: A Scale-Space-Based Approach. 208-219
• 
  Osman Abul, Reda Alhajj, Faruk Polat: A Powerful Approach for Effective Finding of Significantly Differentially Expressed Genes. 220-231
• 
  Radhakrishnan Nagarajan, Meenakshi Upreti: Correlation Statistics for cDNA Microarray Image Analysis. 232-238
• 
  Yun S. Song, Rune B. Lyngsø, Jotun Hein: Counting All Possible Ancestral Configurations of Sample Sequences in Population Genetics. 239-251
• 
  Matti Pirinen, Dario Gasbarra: Finding Consistent Gene Transmission Patterns on Large and Complex Pedigrees. 252-262
• 
  Mihail Popescu, James M. Keller, Joyce A. Mitchell: Fuzzy Measures on the Gene Ontology for Gene Product Similarity. 263-274
• 
  Matthias Bernt, Daniel Merkle, Martin Middendorf: Genome Rearrangement Based on Reversals that Preserve Conserved Intervals. 275-288
• 
  Vincent Berry, François Nicolas: Improved Parameterized Complexity of the Maximum Agreement Subtree and Maximum Compatible Tree Problems. 289-302
• 
  Roded Sharan, Bjarni V. Halldórsson, Sorin Istrail: Islands of Tractability for Parsimony Haplotyping. 303-311
• 
  Chaolin Zhang, Xuesong Lu, Xuegong Zhang: Significance of Gene Ranking for Classification of Microarray Samples. 312-320

Volume 3, Number 4, October-December 2006

• 
  Rita Casadio: Guest Editor's Introduction to the Special Issue on Computational Biology and Bioinformatics -- Part 1. 321-322
• 
  Sagi Snir, Satish Rao: Using Max Cut to Enhance Rooted Trees Consistency. 323-333
• 
  Ganeshkumar Ganapathy, Barbara Goodson, Robert K. Jansen, Hai-Son Le, Vijaya Ramachandran, Tandy Warnow: Pattern Identification in Biogeography. 334-346
• 
  Sebastian Wernicke: Efficient Detection of Network Motifs. 347-359
• 
  Vincent Lacroix, Cristina G. Fernandes, Marie-France Sagot: Motif Search in Graphs: Application to Metabolic Networks. 360-368
• 
  Isaac Elias, Tzvika Hartman: A 1.375-Approximation Algorithm for Sorting by Transpositions. 369-379
• 
  Anthony Labarre: New Bounds and Tractable Instances for the Transposition Distance. 380-394
• 
  Michael Sammeth, Jens Stoye: Comparing Tandem Repeats with Duplications and Excisions of Variable Degree. 395-407
• 
  Yonatan Bilu, Pankaj K. Agarwal, Rachel Kolodny: Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons. 408-422
• 
  Yinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai: Efficient Parameterized Algorithms for Biopolymer Structure-Sequence Alignment. 423-432

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