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    Journal: IEEE/ACM Trans. Comput. Biology Bioinform.

    Volume 3, Issue 4

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

    Volume 3, Issue 3

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

    Volume 3, Issue 2

    97 -- 0Dan Gusfield. Introduction of New Associate Editors
    98 -- 113Wei Chu, Zoubin Ghahramani, Alexei Podtelezhnikov, David L. Wild. Bayesian Segmental Models with Multiple Sequence Alignment Profiles for Protein Secondary Structure and Contact Map Prediction
    114 -- 125Samuel 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
    126 -- 140Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie-France Sagot. An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences
    141 -- 154Daniel G. Brown, Ian M. Harrower. Integer Programming Approaches to Haplotype Inference by Pure Parsimony
    155 -- 164Marc 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
    165 -- 173Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael Sanderson. Minimum-Flip Supertrees: Complexity and Algorithms
    174 -- 185Petteri Sevon, Hannu Toivonen, Vesa Ollikainen. TreeDT: Tree Pattern Mining for Gene Mapping
    186 -- 191Yun S. Song. A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree

    Volume 3, Issue 1

    1 -- 0Dan Gusfield. State of the Journal
    2 -- 16John A. Berger, Sampsa Hautaniemi, Sanjit K. Mitra, Jaakko Astola. Jointly Analyzing Gene Expression and Copy Number Data in Breast Cancer Using Data Reduction Models
    17 -- 32Rafael Sebastian, María Elena Díaz, Guillermo Ayala, Kresimir Letinic, Jose Moncho-Bogani, Derek Toomre. Spatio-Temporal Analysis of Constitutive Exocytosis in Epithelial Cells
    33 -- 46Eli Hershkovitz, Guillermo Sapiro, Allen Tannenbaum, Loren Dean Williams. Statistical Analysis of RNA Backbone
    47 -- 56Zaher Dawy, Bernhard Goebel, Joachim Hagenauer, Christophe Andreoli, Thomas Meitinger, Jakob C. Mueller. Gene Mapping and Marker Clustering Using Shannon s Mutual Information
    57 -- 71John K. Goutsias. A Hidden Markov Model for Transcriptional Regulation in Single Cells
    72 -- 83Luis Rueda, Vidya Vidyadharan. A Hill-Climbing Approach for Automatic Gridding of cDNA Microarray Images
    84 -- 91Charles Semple, Mike A. Steel. Unicyclic Networks: Compatibility and Enumeration
    92 -- 94Sébastien Roch. A Short Proof that Phylogenetic Tree Reconstruction by Maximum Likelihood Is Hard
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