IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 4

Volume 4, Number 1, January 2007

• Dan Gusfield:
  State of the Journal. 1
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• Dan Gusfield:
  Associate Editor Appreciation and Welcome. 2
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• Rita Casadio:
  Guest Editor's Introduction to the Special Section on Computational Biology and Bioinformatics (WABI) - Part 2. 3
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• Sèverine Bérard, Anne Bergeron, Cedric Chauve, Christophe Paul:
  Perfect Sorting by Reversals Is Not Always Difficult. 4-16
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• Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik:
  Ortholog Clustering on a Multipartite Graph. 17-27
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• Keren Lasker, Oranit Dror, Maxim Shatsky, Ruth Nussinov, Haim J. Wolfson:
  EMatch: Discovery of High Resolution Structural Homologues of Protein Domains in Intermediate Resolution Cryo-EM Maps. 28-39
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• Lipo Wang, Feng Chu, Wei Xie:
  Accurate Cancer Classification Using Expressions of Very Few Genes. 40-53
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• Degui Zhi, Uri Keich, Pavel A. Pevzner, Steffen Heber, Haixu Tang:
  Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly. 54-64
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• Rui Xu, Georgios C. Anagnostopoulos, Donald C. Wunsch:
  Multiclass Cancer Classification Using Semisupervised Ellipsoid ARTMAP and Particle Swarm Optimization with Gene Expression Data. 65-77
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• Chengbang Huang, Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, Jesús A. Izaguirre:
  Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach. 78-87
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• Jong Hyun Kim, Michael S. Waterman, Lei M. Li:
  Accuracy Assessment of Diploid Consensus Sequences. 88-97
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• Max A. Alekseyev, Pavel A. Pevzner:
  Colored de Bruijn Graphs and the Genome Halving Problem. 98-107
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• Elchanan Mossel:
  Distorted Metrics on Trees and Phylogenetic Forests. 108-116
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• Kimberly A. Aeling, Nicholas R. Steffen, Matthew Johnson, G. Wesley Hatfield, Richard H. Lathrop, Donald F. Senear:
  DNA Deformation Energy as an Indirect Recognition Mechanism in Protein-DNA Interactions. 117-125
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• Jing Yang, Sarawan Wongsa, Visakan Kadirkamanathan, Stephen A. Billings, Phillip C. Wright:
  Metabolic Flux Estimation-A Self-Adaptive Evolutionary Algorithm with Singular Value Decomposition. 126-138
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• Gang Wu, Jia-Huai You, Guohui Lin:
  Quartet-Based Phylogeny Reconstruction with Answer Set Programming. 139-152
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• Gesine Reinert, Michael S. Waterman:
  On the Length of the Longest Exact Position Match in a Random Sequence. 153-156
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• Wai-Ho Au, Keith C. C. Chan, Andrew K. C. Wong, Yang Wang:
  Correction to "Attribute Clustering for Grouping, Selection, and Classification of Gene Expression Data". 157
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Volume 4, Number 2, April 2007

• Jagath C. Rajapakse, Yan-Qing Zhang, Gary B. Fogel:
  Guest Editors' Introduction to the Special Section: Computational Intelligence Approaches in Computational Biology and Bioinformatics. 161-162
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• Haiying Wang, Huiru Zheng, Francisco Azuaje:
  Poisson-Based Self-Organizing Feature Maps and Hierarchical Clustering for Serial Analysis of Gene Expression Data. 163-175
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• Ozy Sjahputera, James M. Keller, J. Wade Davis, Kristen H. Taylor, Farahnaz Rahmatpanah, Huidong Shi, Derek Anderson, Samuel Blisard, Robert H. Luke III, Mihail Popescu, Gerald C. Arthur, Charles William Caldwell:
  Relational Analysis of CpG Islands Methylation and Gene Expression in Human Lymphomas Using Possibilistic C-Means Clustering and Modified Cluster Fuzzy Density. 176-189
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• Yijuan Lu, Qi Tian, Feng Liu, Maribel Sanchez, Yufeng Wang:
  Interactive Semisupervised Learning for Microarray Analysis. 190-203
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• Boaz Lerner, Josepha Yeshaya, Lev Koushnir:
  On the Classification of a Small Imbalanced Cytogenetic Image Database. 204-215
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• Christian Igel, Tobias Glasmachers, Britta Mersch, Nico Pfeifer, Peter Meinicke:
  Gradient-Based Optimization of Kernel-Target Alignment for Sequence Kernels Applied to Bacterial Gene Start Detection. 216-226
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• Hasan Ogul, Erkan U. Mumcuoglu:
  Subcellular Localization Prediction with New Protein Encoding Schemes. 227-232
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• Wenyuan Li, Ying Liu, Hung-Chung Huang, Yanxiong Peng, Yongjing Lin, Wee Keong Ng, Kok-Leong Ong:
  Dynamical Systems for Discovering Protein Complexes and Functional Modules from Biological Networks. 233-250
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• Xiaohua Hu, Daniel Duanqing Wu:
  Data Mining and Predictive Modeling of Biomolecular Network from Biomedical Literature Databases. 251-263
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• Ferrante Neri, Jari Toivanen, Giuseppe Leonardo Cascella, Yew-Soon Ong:
  An Adaptive Multimeme Algorithm for Designing HIV Multidrug Therapies. 264-278
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• Julia Handl, Douglas B. Kell, Joshua D. Knowles:
  Multiobjective Optimization in Bioinformatics and Computational Biology. 279-292
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• Gianluca Bontempi:
  A Blocking Strategy to Improve Gene Selection for Classification of Gene Expression Data. 293-300
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• Yoan Diekmann, Marie-France Sagot, Eric Tannier:
  Evolution under Reversals: Parsimony and Conservation of Common Intervals. 301-309
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• Nils Weskamp, Eyke Hüllermeier, Daniel Kuhn, Gerhard Klebe:
  Multiple Graph Alignment for the Structural Analysis of Protein Active Sites. 310-320
  Electronic Edition (ACM DL) BibTeX

Volume 4, Number 3, July 2007

• Dan Gusfield:
  Associate Editor Appreciation and Welcome. 321
  Electronic Edition (ACM DL) BibTeX
• Krzysztof Fujarewicz, Marek Kimmel, Tomasz Lipniacki, Andrzej Swierniak:
  Adjoint Systems for Models of Cell Signaling Pathways and their Application to Parameter Fitting. 322-335
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• Xiang Wan, Guohui Lin:
  CISA: Combined NMR Resonance Connectivity Information Determination and Sequential Assignment. 336-348
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• Michael Cameron, Hugh E. Williams:
  Comparing Compressed Sequences for Faster Nucleotide BLAST Searches. 349-364
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• Yuchun Tang, Yan-Qing Zhang, Zhen Huang:
  Development of Two-Stage SVM-RFE Gene Selection Strategy for Microarray Expression Data Analysis. 365-381
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• Lydia Ng, Sayan D. Pathak, Chihchau Kuan, Christopher Lau, Hong-wei Dong, Andrew Sodt, Chinh Dang, Brian B. Avants, Paul A. Yushkevich, James C. Gee, David R. Haynor, Ed Lein, Allan Jones, Michael Hawrylycz:
  Neuroinformatics for Genome-Wide 3-D Gene Expression Mapping in the Mouse Brain. 382-393
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• C. Thach Nguyen, Nguyen Bao Nguyen, Wing-Kin Sung, Louxin Zhang:
  Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem. 394-402
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• Michael Lones, Andy Tyrrell:
  Regulatory Motif Discovery Using a Population Clustering Evolutionary Algorithm. 403-414
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• Andy M. Yip, Michael K. Ng, Edmond HaoCun Wu, Tony F. Chan:
  Strategies for Identifying Statistically Significant Dense Regions in Microarray Data. 415-429
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• Kuo-ching Liang, Xiaodong Wang, Dimitris Anastassiou:
  Bayesian Basecalling for DNA Sequence Analysis Using Hidden Markov Models. 430-440
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• Trias Thireou, Martin Reczko:
  Bidirectional Long Short-Term Memory Networks for Predicting the Subcellular Localization of Eukaryotic Proteins. 441-446
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• Gergely Korodi, Ioan Tabus:
  Compression of Annotated Nucleotide Sequences. 447-457
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• Magnus Bordewich, Charles Semple:
  Computing the Hybridization Number of Two Phylogenetic Trees Is Fixed-Parameter Tractable. 458-466
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• D. Huang, Tommy W. S. Chow:
  Effective Gene Selection Method With Small Sample Sets Using Gradient-Based and Point Injection Techniques. 467-475
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• David Hecht, Gary B. Fogel:
  High-Throughput Ligand Screening via Preclustering and Evolved Neural Networks. 476-484
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• Runxuan Zhang, Guang-Bin Huang, N. Sundararajan, P. Saratchandran:
  Multicategory Classification Using An Extreme Learning Machine for Microarray Gene Expression Cancer Diagnosis. 485-495
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• Louxin Zhang:
  Superiority of Spaced Seeds for Homology Search. 496-505
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• Frederick A. Matsen III:
  Optimization Over a Class of Tree Shape Statistics. 506-512
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Volume 4, Number 4, October 2007

• Ion I. Mandoiu, Yi Pan, Alexander Zelikovsky:
  Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 513-514
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• Chunfang Zheng, Qian Zhu, David Sankoff:
  Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis. 515-522
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• Guillaume Blin, Cedric Chauve, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette:
  Comparing Genomes with Duplications: A Computational Complexity Point of View. 523-534
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• Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Raffaella Rizzi, Stéphane Vialette:
  Exemplar Longest Common Subsequence. 535-543
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• Jaime Davila, Sudha Balla, Sanguthevar Rajasekaran:
  Fast and Practical Algorithms for Planted (l, d) Motif Search. 544-552
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• Adrian Schneider, Gaston H. Gonnet, Gina Cannarozzi:
  SynPAM-A Distance Measure Based on Synonymous Codon Substitutions. 553-560
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• Srinath Sridhar, Kedar Dhamdhere, Guy E. Blelloch, Eran Halperin, R. Ravi, Russell Schwartz:
  Algorithms for Efficient Near-Perfect Phylogenetic Tree Reconstruction in Theory and Practice. 561-571
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• Jinmiao Chen, Narendra S. Chaudhari:
  Cascaded Bidirectional Recurrent Neural Networks for Protein Secondary Structure Prediction. 572-582
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• Huilin Xiong, Ya Zhang, Xue-wen Chen:
  Data-Dependent Kernel Machines for Microarray Data Classification. 583-595
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• Shahar Michal, Tor Ivry, Omer Cohen, Moshe Sipper, Danny Barash:
  Finding a Common Motif of RNA Sequences Using Genetic Programming: The GeRNAMo System. 596-610
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• Tara McIntosh, Sanjay Chawla:
  High Confidence Rule Mining for Microarray Analysis. 611-623
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• Ignacio Ponzoni, Francisco Azuaje, Juan Augusto, David Glass:
  Inferring Adaptive Regulation Thresholds and Association Rules from Gene Expression Data through Combinatorial Optimization Learning. 624-634
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• Nasimul Noman, Hitoshi Iba:
  Inferring Gene Regulatory Networks using Differential Evolution with Local Search Heuristics. 634-647
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• Shinn-Ying Ho, Chih-Hung Hsieh, Fu-Chieh Yu, Hui-Ling Huang:
  An Intelligent Two-Stage Evolutionary Algorithm for Dynamic Pathway Identification From Gene Expression Profiles. 648-704
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• Sergey Bereg, Yuanyi Zhang:
  Phylogenetic Networks Based on the Molecular Clock Hypothesis. 661-667
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• Jacek Blazewicz, Edmund K. Burke, Marta Kasprzak, Alexandr Kovalev, Mikhail Y. Kovalyov:
  Simplified Partial Digest Problem: Enumerative and Dynamic Programming Algorithms. 668-680
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• Rui Xu, Donald C. Wunsch II, Ronald Frank:
  Inference of Genetic Regulatory Networks with Recurrent Neural Network Models Using Particle Swarm Optimization. 681-692
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• Phaedra Agius, Barry Kreiswirth, Steve Naidich, Kristin Bennett:
  Typing Staphylococcus aureus Using the spa Gene and Novel Distance Measures. 693-704
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