Journal of Bioinformatics and Computational Biology, Volume 3

Volume 3, Number 1, February 2005

• Francis Y. L. Chin, N. L. Ho, Tak Wah Lam, Prudence W. H. Wong:
  Efficient Constrained Multiple Sequence Alignment with Performance Guarantee. 1-18
  
• Minghui Jiang, Binhai Zhu:
  Protein Folding on the Hexagonal Lattice in the Hp Model. 19-34
  
• Kang Peng, Slobodan Vucetic, Predrag Radivojac, Celeste J. Brown, A. Keith Dunker, Zoran Obradovic:
  Optimizing Long Intrinsic Disorder Predictors with Protein Evolutionary Information. 35-60
  
• Jeong Ho Chang, Kyu Baek Hwang, Sok June Oh, Byoung-Tak Zhang:
  Bayesian Network Learning with Feature Abstraction for Gene-drug Dependency Analysis. 61-78
  
• Hon Wai Leong, Franco P. Preparata, Wing-Kin Sung, Hugo Willy:
  Adaptive Control of Hybridization Noise in Dna Sequencing-by-hybridization. 79-98
  
• Yi-Ping Phoebe Chen:
  Guest Editor's Introduction: Advanced Techniques for Bioinformatics. 99-102
  
• K. C. Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Tatsuya Akutsu:
  Protein Side-chain Packing Problem: a Maximum Edge-weight Clique Algorithmic Approach. 103-126
  
• Ihsan A. Shehadi, Alexej Abyzov, Alper Uzun, Ying Wei, Leonel F. Murga, Valentin A. Ilyin, Mary Jo Ondrechen:
  Active Site Prediction for Comparative Model Structures with Thematics. 127-144
  
• Tariq Riaz, Wang Yi, Kuo-Bin Li:
  A Tabu Search Algorithm for Post-processing Multiple Sequence Alignment. 145-156
  
• Peter L. Meintjes, Allen G. Rodrigo:
  Evolution of Relative Synonymous Codon Usage in Human Immunodeficiency Virus Type-1. 157-168
  
• Akinori Sarai, Jorg Siebers, Samuel Selvaraj, M. Michael Gromiha, Hidetoshi Kono:
  Integration of Bioinformatics and Computational Biology to Understand Protein-dna Recognition Mechanism. 169-183
  

Volume 3, Number 2, April 2005

• Chris H. Q. Ding, Hanchuan Peng:
  Minimum Redundancy Feature Selection from Microarray Gene Expression Data. 185-206
  
• Mark Cieliebak, Stephan Eidenbenz, Gerhard J. Woeginger:
  Complexity and Approximability of Double Digest. 207-224
  
• Jeff W. Chou, Richard S. Paules, Pierre R. Bushel:
  Systematic Variation Normalization in Microarray Data to Get Gene Expression Comparison Unbiased. 225-242
  
• Yi Wang, Kuo-Bin Li:
  Multiple Sequence Alignment Using an Exhaustive and Greedy Algorithm. 243-256
  
• Shih-Huang Chan, Li-Ju Chen, Nan-Hwa Chow, Hsiao-Sheng Liu:
  An Ancova Approach to Normalize Microarray Data, and its Performance to Existing Methods. 257-268
  
• Kevin Gale, Houyuan Jiang, Mark Westcott:
  An Optimization Method for the Identification of Minimal Sets of Discriminating Gene Markers: Application to Cultivar Identification in Wheat. 269-280
  
• Patrick C. H. Ma, Keith C. C. Chan, David K. Y. Chiu:
  Clustering and re-clustering for Pattern Discovery in Gene Expression Data. 281-302
  
• ZhenQiu Liu, Dechang Chen, Halima Bensmail, Ying Xu:
  Clustering Gene Expression Data with Kernel Principal Components. 303-316
  
• Nadia El-Mabrouk, Mathieu Raffinot, Jean-Eudes Duchesne, Mathieu Lajoie, Nicolas Luc:
  Approximate Matching of Structured Motifs in Dna Sequences. 317-342
  
• Tho Hoan Pham, Kenji Satou, Tu Bao Ho:
  Support Vector Machines for Prediction and Analysis of Beta and Gamma-turns in Proteins. 343-358
  
• Gad Kimmel, Ron Shamir:
  The Incomplete Perfect Phylogeny Haplotype Problem. 359-384
  
• Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, Luonan Chen:
  Exploring Protein's Optimal Hp Configurations by Self-organizing Mapping. 385-400
  
• Eli Kaminuma, Naohiko Heida, Yuko Tsumoto, Miki Nakazawa, Nobuharu Goto, Akihiko Konagaya, Minami Matsui, Tetsuro Toyoda:
  Three-dimensional Definition of Leaf Morphological Traits of arabidopsis in Silico Phenotypic Analysis. 401-414
  
• Stephen Ramsey, David Orrell, Hamid Bolouri:
  Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks. 415-436
  
• Stephen Ramsey, David Orrell, Hamid Bolouri:
  Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks (supplementary Material). 437-454
  
• Tema Fridman, Jane Razumovskaya, Nathan Verberkmoes, Gregory B. Hurst, Vladimir Protopopescu, Ying Xu:
  The Probability Distribution for a Random Match between an Experimental-theoretical Spectral Pair in Tandem Mass Spectrometry. 455-476
  
• Mei Xu:
  Theoretically Modeling Microarray with the Chemical Equilibrium and Thermodynamics. 477-490
  
• Shibaji Mukherjee, Sushmita Mitra:
  Hidden Markov Models, Grammars, and Biology: a Tutorial. 491-526
  

Volume 3, Number 3, June 2005

• Foreword. 530-550
  
• Sarah E. Boyd, Robert N. Pike, George B. Rudy, James C. Whisstock, Maria J. García de la Banda:
  Pops: a Computational Tool for Modeling and Predicting Protease Specificity. 551-586
  
• Chang-Heng Chang, Li-Ching Hsieh, Ta-Yuan Chen, Hong-Da Chen, Liaofu Luo, Hoong-Chien Lee:
  Shannon Information in Complete Genomes. 587-608
  
• Zhuozhi Wang, Kaizhong Zhang:
  Multiple Rna Structure Alignment. 609-626
  
• Sach Mukherjee, Stephen J. Roberts:
  A Theoretical Analysis of the Selection of Differentially Expressed Genes. 627-644
  
• Kreshna Gopal, Tod D. Romo, James C. Sacchettini, Thomas R. Ioerger:
  Determining Relevant Features to Recognize Electron Density Patterns in X-ray Protein Crystallography. 645-676
  
• Yinhe Cao, Wen-wen Tung, Jianbo Gao, Yan Qi:
  Recurrence Time Statistics: Versatile Tools for Genomic Dna Sequence Analysis. 677-696
  
• Yonghua Han, Bin Ma, Kaizhong Zhang:
  Spider: Software for Protein Identification from Sequence Tags with de Novo Sequencing Error. 697-716
  
• Orhan Çamoglu, Tolga Can, Ambuj K. Singh, Yuan-Fang Wang:
  Decision Tree Based Information Integration for Automated Protein Classification. 717-742
  
• Raf M. Podowski, John G. Cleary, Nicholas T. Goncharoff, Gregory Amoutzias, William S. Hayes:
  Suregene, a Scalable System for Automated Term Disambiguation of Gene and Protein Names. 743-770
  
• Mei Xu:
  Erratum: Theoretically Modeling Microarray with the Chemical Equilibrium and Thermodynamics. 771
  

Volume 3, Number 4, August 2005

• Feroz Khan, Shipra Agarwal, B. N. Mishra:
  Genome Wide Identification of Dna Binding Motifs of Nodd-factor in Sinorhizobium Meliloti and Mesorhizobium Loti. 773-802
  
• Arunkumar Chinnasamy, Wing-Kin Sung, Ankush Mittal:
  Protein Structure and Fold Prediction Using Tree-augmented Naïve Bayesian Classifier. 803-820
  
• Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik:
  Dynamic Model-based Clustering for Time-course Gene Expression Data. 821-836
  
• Tianshou Zhou, Luonan Chen, Yun Tang, Xiang-Sun Zhang:
  Aligning Multiple Protein Structures by Deterministic Annealing. 837-860
  
• Ville-Veikko Rantanen, Mats Gyllenberg, Timo Koski, Mark S. Johnson:
  a Priori Contact Preferences in Molecular Recognition. 861-890
  
• Theo H. Reijmers, C. Maliepaard, H. C. Van Den Broeck, R. W. Kessler, M. A. J. Toonen, H. Van Der Voet:
  Integrated Statistical Analysis of Cdna Microarray and Nir Spectroscopic Data Applied to a Hemp Dataset. 891-914
  
• Lixia Jin, Huanwen Tang, Weiwu Fang:
  Prediction of Protein Subcellular Locations Using a New Measure of Information Discrepancy. 915-928
  
• Laurent Bianchetti, Julie Dawn Thompson, Odile Lecompte, Frédéric Plewniak, Olivier Poch:
  Valid: Validation of Protein Sequence Quality Based on Multiple Alignment Data. 929-948
  
• Rongxiang Liu, Pankaj Agarwal:
  Computational Identification of Transcription Factors Involved in Early Cellular Response to a Stimulus. 949-964
  
• Matthias E. Futschik, Bronwyn Carlisle:
  Noise-robust Soft Clustering of Gene Expression Time-course Data. 965-988
  
• Xu Guo, Wei Pan:
  Using Weighted Permutation Scores to Detect Differential Gene Expression with Microarray Data. 989-1006
  
• Anna V. Gerasimova, Mikhail S. Gelfand:
  Evolution of the Nadr Regulon in Enterobacteriaceae. 1007-1019
  

Volume 3, Number 5, October 2005

• Ao Yuan, Guanjie Chen, Charles Rotimi, George E. Bonney:
  A Statistical Framework for Haplotype Block Inference. 1021-1038
  
• Lusheng Wang, Liang Dong:
  Randomized Algorithms for Motif Detection. 1039-1052
  
• Sanghamitra Bandyopadhyay, Angshuman Bagchi, Ujjwal Maulik:
  Active Site Driven Ligand Design: an Evolutionary Approach. 1053-1070
  
• Satoshi Niijima, Satoru Kuhara:
  Multiclass Molecular Cancer Classification by Kernel Subspace Methods with Effective Kernel Parameter Selection. 1071-1088
  
• Tie-Fei Liu, Wing-Kin Sung, Yi Li, Jian-Jun Liu, Ankush Mittal, Pei-lin Mao:
  Effective Algorithms for Tag Snp Selection. 1089-1106
  
• Liang Goh, Nikola K. Kasabov:
  An Integrated Feature Selection and Classification Method to Select Minimum Number of Variables on the Case Study of Gene Expression Data. 1107-1136
  
• Boojala V. B. Reddy, Yiannis N. Kaznessis:
  A Quantitative Analysis of Interfacial Amino Acid Conservation in Protein-protein Hetero Complexes. 1137-1150
  
• Hongzhi Li, Yaoqi Zhou:
  Fold Helical Proteins by Energy Minimization in Dihedral Space and a Dfire-based Statistical Energy Function. 1151-1170
  
• Rainer Breitling, Pawel Herzyk:
  Rank-based Methods as a Non-parametric Alternative of the T-statistic for the Analysis of Biological Microarray Data. 1171-1190
  
• Enrico Capobianco:
  Mining Time-dependent Gene Features. 1191-1206
  
• Guanglan Zhang, Asif M. Khan, Kellathur N. Srinivasan, J. Thomas August, Vladimir Brusic:
  Neural Models for Predicting Viral Vaccine Targets. 1207-1226
  
• Zeke S. H. Chan, Nikola K. Kasabov, Lesley Collins:
  A Hybrid Genetic Algorithm and Expectation Maximization Method for Global Gene Trajectory Clustering. 1227-1242
  

Volume 3, Number 6, December 2005

• Angelika Longacre, L. Ridgway Scott, Jerrold S. Levine:
  Linear Independence of Pairwise Comparisons of Dna Microarray Data. 1243-1262
  
• Shihong Mao, Guozhu Dong:
  Discovery of Highly Differentiative Gene Groups from Microarray Gene Expression Data Using the Gene Club Approach. 1263-1280
  
• Eli Kaminuma, Naohiko Heida, Takeshi Yoshizumi, Miki Nakazawa, Minami Matsui, Tetsuro Toyoda:
  in Silico Phenotypic Screening Method of Mutants Based on Statistical Modeling of Genetically Mixed Samples. 1281-1294
  
• Yoshinori Tamada, Hideo Bannai, Seiya Imoto, Toshiaki Katayama, Minoru Kanehisa, Satoru Miyano:
  Utilizing Evolutionary Information and Gene Expression Data for Estimating Gene Networks with Bayesian Network Models. 1295-1314
  
• Feng Cui, Robert L. Jernigan, Zhijun Wu:
  Refinement of Nmr-determined Protein Structures with Database Derived Distance Constraints. 1315-1330
  
• Guohui Lin, Theodore Tegos, Zhi-Zhong Chen:
  Heuristic Search in Constrained Bipartite Matching with Applications to Protein Nmr Backbone Resonance Assignment. 1331-1350
  
• Lei Ye, Huajun Chen, Ting Liu, Zhaohui Wu, Jingyuan Li, Ruhong Zhou:
  A Wavelet Approach for the Analysis of Folding Trajectory of Protein Trp-cage. 1351-1370
  
• Guanghua Xiao, Wei Pan:
  Gene Function Prediction by a Combined Analysis of Gene Expression Data and Protein-protein Interaction Data. 1371-1390
  
• Lu-Yong Wang:
  Covariation Analysis of Local Amino Acid Sequences in Recurrent Protein Local Structures. 1391-1410
  
• Eugene Novikov, Emmanuel Barillot:
  A Robust Algorithm for Ratio Estimation in Two-color Microarray Experiments. 1411-1428
  
• Manuel Gil, Christophe Dessimoz, Gaston H. Gonnet:
  A Dimensionless Fit Measure for Phylogenetic Distance Trees. 1429-1440
  
• Steinar Thorvaldsen:
  A Tutorial on Markov Models Based on Mendel's Classical Experiments. 1441-1460
  

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