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IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 4
Volume 4, Number 1, January 2007
- Dan Gusfield:
State of the Journal. 1 - Dan Gusfield:
Associate Editor Appreciation and Welcome. 2 - Rita Casadio:
Guest Editor's Introduction to the Special Section on Computational Biology and Bioinformatics (WABI) - Part 2. 3 - Sèverine Bérard, Anne Bergeron, Cédric Chauve
, Christophe Paul
Perfect Sorting by Reversals Is Not Always Difficult. 4-16 - Akshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik:
Ortholog Clustering on a Multipartite Graph. 17-27 - Keren Lasker, Oranit Dror, Maxim Shatsky, Ruth Nussinov
EMatch: Discovery of High Resolution Structural Homologues of Protein Domains in Intermediate Resolution Cryo-EM Maps. 28-39 - Lipo Wang, Feng Chu, Wei Xie:
Accurate Cancer Classification Using Expressions of Very Few Genes. 40-53 - Degui Zhi, Uri Keich
Correcting Base-Assignment Errors in Repeat Regions of Shotgun Assembly. 54-64 - 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 - Chengbang Huang, Faruck Morcos
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach. 78-87 - Jong Hyun Kim, Michael S. Waterman, Lei M. Li:
Accuracy Assessment of Diploid Consensus Sequences. 88-97 - Max A. Alekseyev
Colored de Bruijn Graphs and the Genome Halving Problem. 98-107 - Elchanan Mossel
Distorted Metrics on Trees and Phylogenetic Forests. 108-116 - 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 - Jing Yang, Sarawan Wongsa, Visakan Kadirkamanathan
Metabolic Flux Estimation-A Self-Adaptive Evolutionary Algorithm with Singular Value Decomposition. 126-138 - Gang Wu, Jia-Huai You, Guohui Lin:
Quartet-Based Phylogeny Reconstruction with Answer Set Programming. 139-152 - Gesine Reinert
On the Length of the Longest Exact Position Match in a Random Sequence. 153-156 - 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
Volume 4, Number 2, April 2007
- Jagath C. Rajapakse
Guest Editors' Introduction to the Special Section: Computational Intelligence Approaches in Computational Biology and Bioinformatics. 161-162 - Haiying Wang
Poisson-Based Self-Organizing Feature Maps and Hierarchical Clustering for Serial Analysis of Gene Expression Data. 163-175 - Ozy Sjahputera, James M. Keller, J. Wade Davis, Kristen H. Taylor
Relational Analysis of CpG Islands Methylation and Gene Expression in Human Lymphomas Using Possibilistic C-Means Clustering and Modified Cluster Fuzzy Density. 176-189 - Yijuan Lu, Qi Tian, Feng Liu, Maribel Sanchez, Yufeng Wang
Interactive Semisupervised Learning for Microarray Analysis. 190-203 - Boaz Lerner, Josepha Yeshaya, Lev Koushnir:
On the Classification of a Small Imbalanced Cytogenetic Image Database. 204-215 - Christian Igel, Tobias Glasmachers, Britta Mersch, Nico Pfeifer
Gradient-Based Optimization of Kernel-Target Alignment for Sequence Kernels Applied to Bacterial Gene Start Detection. 216-226 - Hasan Ogul, Ü. Erkan Mumcuoglu:
Subcellular Localization Prediction with New Protein Encoding Schemes. 227-232 - Wenyuan Li, Ying Liu, Hung-Chung Huang, Yanxiong Peng, Yongjing Lin, Wee Keong Ng
Dynamical Systems for Discovering Protein Complexes and Functional Modules from Biological Networks. 233-250 - Xiaohua Hu, Daniel Duanqing Wu:
Data Mining and Predictive Modeling of Biomolecular Network from Biomedical Literature Databases. 251-263 - Ferrante Neri
An Adaptive Multimeme Algorithm for Designing HIV Multidrug Therapies. 264-278 - Julia Handl, Douglas B. Kell
Multiobjective Optimization in Bioinformatics and Computational Biology. 279-292 - Gianluca Bontempi
A Blocking Strategy to Improve Gene Selection for Classification of Gene Expression Data. 293-300 - Yoan Diekmann
Evolution under Reversals: Parsimony and Conservation of Common Intervals. 301-309 - Nils Weskamp, Eyke Hüllermeier, Daniel Kuhn, Gerhard Klebe:
Multiple Graph Alignment for the Structural Analysis of Protein Active Sites. 310-320
Volume 4, Number 3, July 2007
- Dan Gusfield:
Associate Editor Appreciation and Welcome. 321 - Krzysztof Fujarewicz
Adjoint Systems for Models of Cell Signaling Pathways and their Application to Parameter Fitting. 322-335 - Xiang Wan, Guohui Lin:
CISA: Combined NMR Resonance Connectivity Information Determination and Sequential Assignment. 336-348 - Michael Cameron, Hugh E. Williams:
Comparing Compressed Sequences for Faster Nucleotide BLAST Searches. 349-364 - Yuchun Tang, Yan-Qing Zhang, Zhen Huang:
Development of Two-Stage SVM-RFE Gene Selection Strategy for Microarray Expression Data Analysis. 365-381 - Lydia Ng, Sayan D. Pathak, Chihchau Kuan, Christopher Lau, Hong-wei Dong, Andrew Sodt, Chinh Dang, Brian B. Avants
Neuroinformatics for Genome-Wide 3-D Gene Expression Mapping in the Mouse Brain. 382-393 - C. Thach Nguyen, Nguyen Bao Nguyen, Wing-Kin Sung
Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem. 394-402 - Michael A. Lones
Regulatory Motif Discovery Using a Population Clustering Evolutionary Algorithm. 403-414 - Andy M. Yip, Michael K. Ng
Strategies for Identifying Statistically Significant Dense Regions in Microarray Data. 415-429 - Kuo-ching Liang, Xiaodong Wang, Dimitris Anastassiou:
Bayesian Basecalling for DNA Sequence Analysis Using Hidden Markov Models. 430-440 - Trias Thireou
Bidirectional Long Short-Term Memory Networks for Predicting the Subcellular Localization of Eukaryotic Proteins. 441-446 - Gergely Korodi, Ioan Tabus
Compression of Annotated Nucleotide Sequences. 447-457 - Magnus Bordewich
Computing the Hybridization Number of Two Phylogenetic Trees Is Fixed-Parameter Tractable. 458-466 - Di Huang, Tommy W. S. Chow:
Effective Gene Selection Method With Small Sample Sets Using Gradient-Based and Point Injection Techniques. 467-475 - David Hecht
High-Throughput Ligand Screening via Preclustering and Evolved Neural Networks. 476-484 - Runxuan Zhang
Multicategory Classification Using An Extreme Learning Machine for Microarray Gene Expression Cancer Diagnosis. 485-495 - Louxin Zhang:
Superiority of Spaced Seeds for Homology Search. 496-505 - Frederick A. Matsen IV:
Optimization Over a Class of Tree Shape Statistics. 506-512
Volume 4, Number 4, October 2007
- Ion I. Mandoiu
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 513-514 - Chunfang Zheng, Qian Zhu, David Sankoff:
Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis. 515-522 - Guillaume Blin, Cédric Chauve, Guillaume Fertin, Romeo Rizzi, Stéphane Vialette:
Comparing Genomes with Duplications: A Computational Complexity Point of View. 523-534 - Paola Bonizzoni
Exemplar Longest Common Subsequence. 535-543 - Jaime I. Dávila
Fast and Practical Algorithms for Planted (l, d) Motif Search. 544-552 - Adrian Schneider, Gaston H. Gonnet, Gina Cannarozzi
SynPAM-A Distance Measure Based on Synonymous Codon Substitutions. 553-560 - 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 - Jinmiao Chen, Narendra S. Chaudhari
Cascaded Bidirectional Recurrent Neural Networks for Protein Secondary Structure Prediction. 572-582 - Huilin Xiong, Ya Zhang, Xue-wen Chen:
Data-Dependent Kernel Machines for Microarray Data Classification. 583-595 - Shahar Michal, Tor Ivry, Omer Cohen, Moshe Sipper
Finding a Common Motif of RNA Sequences Using Genetic Programming: The GeRNAMo System. 596-610 - Tara McIntosh, Sanjay Chawla:
High Confidence Rule Mining for Microarray Analysis. 611-623 - Ignacio Ponzoni
Inferring Adaptive Regulation Thresholds and Association Rules from Gene Expression Data through Combinatorial Optimization Learning. 624-634 - Nasimul Noman
Inferring Gene Regulatory Networks using Differential Evolution with Local Search Heuristics. 634-647 - Shinn-Ying Ho
An Intelligent Two-Stage Evolutionary Algorithm for Dynamic Pathway Identification From Gene Expression Profiles. 648-704 - Sergey Bereg, Yuanyi Zhang:
Phylogenetic Networks Based on the Molecular Clock Hypothesis. 661-667 - Jacek Blazewicz
Simplified Partial Digest Problem: Enumerative and Dynamic Programming Algorithms. 668-680 - Rui Xu, Donald C. Wunsch II, Ronald Frank:
Inference of Genetic Regulatory Networks with Recurrent Neural Network Models Using Particle Swarm Optimization. 681-692 - Phaedra Agius, Barry Kreiswirth, Steve Naidich, Kristin P. Bennett:
Typing Staphylococcus aureus Using the spa Gene and Novel Distance Measures. 693-704
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