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ORCIDJournal of Bioinformatics and Computational Biology, Volume 3
Volume 3, Number 1, February 2005
- Francis Y. L. Chin, Ngai Lam 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 J. 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, Bhartendu Nath 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, Chris Maliepaard, Hetty C. Van Den Broeck, Rudolf W. Kessler, Marcel A. J. Toonen, Hilko 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, Jianjun 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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