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
Electronic Edition (link) BibTeX
- Minghui Jiang, Binhai Zhu:
Protein Folding on the Hexagonal Lattice in the Hp Model.
19-34
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- 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
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- 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
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- Hon Wai Leong, Franco P. Preparata, Wing-Kin Sung, Hugo Willy:
Adaptive Control of Hybridization Noise in Dna Sequencing-by-hybridization.
79-98
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- Yi-Ping Phoebe Chen:
Guest Editor's Introduction: Advanced Techniques for Bioinformatics.
99-102
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- 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
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- 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
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- Tariq Riaz, Wang Yi, Kuo-Bin Li:
A Tabu Search Algorithm for Post-processing Multiple Sequence Alignment.
145-156
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- Peter L. Meintjes, Allen G. Rodrigo:
Evolution of Relative Synonymous Codon Usage in Human Immunodeficiency Virus Type-1.
157-168
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- 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
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Volume 3,
Number 2,
April 2005
- Chris H. Q. Ding, Hanchuan Peng:
Minimum Redundancy Feature Selection from Microarray Gene Expression Data.
185-206
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- Mark Cieliebak, Stephan Eidenbenz, Gerhard J. Woeginger:
Complexity and Approximability of Double Digest.
207-224
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- Jeff W. Chou, Richard S. Paules, Pierre R. Bushel:
Systematic Variation Normalization in Microarray Data to Get Gene Expression Comparison Unbiased.
225-242
Electronic Edition (link) BibTeX
- Yi Wang, Kuo-Bin Li:
Multiple Sequence Alignment Using an Exhaustive and Greedy Algorithm.
243-256
Electronic Edition (link) BibTeX
- 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
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- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- ZhenQiu Liu, Dechang Chen, Halima Bensmail, Ying Xu:
Clustering Gene Expression Data with Kernel Principal Components.
303-316
Electronic Edition (link) BibTeX
- Nadia El-Mabrouk, Mathieu Raffinot, Jean-Eudes Duchesne, Mathieu Lajoie, Nicolas Luc:
Approximate Matching of Structured Motifs in Dna Sequences.
317-342
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- Tho Hoan Pham, Kenji Satou, Tu Bao Ho:
Support Vector Machines for Prediction and Analysis of Beta and Gamma-turns in Proteins.
343-358
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- Gad Kimmel, Ron Shamir:
The Incomplete Perfect Phylogeny Haplotype Problem.
359-384
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- 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
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- 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
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- Stephen Ramsey, David Orrell, Hamid Bolouri:
Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks.
415-436
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- Stephen Ramsey, David Orrell, Hamid Bolouri:
Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks (supplementary Material).
437-454
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- 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
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- Mei Xu:
Theoretically Modeling Microarray with the Chemical Equilibrium and Thermodynamics.
477-490
Electronic Edition (link) BibTeX
- Shibaji Mukherjee, Sushmita Mitra:
Hidden Markov Models, Grammars, and Biology: a Tutorial.
491-526
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Volume 3,
Number 3,
June 2005
- Foreword.
530-550
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- 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
Electronic Edition (link) BibTeX
- Chang-Heng Chang, Li-Ching Hsieh, Ta-Yuan Chen, Hong-Da Chen, Liaofu Luo, Hoong-Chien Lee:
Shannon Information in Complete Genomes.
587-608
Electronic Edition (link) BibTeX
- Zhuozhi Wang, Kaizhong Zhang:
Multiple Rna Structure Alignment.
609-626
Electronic Edition (link) BibTeX
- Sach Mukherjee, Stephen J. Roberts:
A Theoretical Analysis of the Selection of Differentially Expressed Genes.
627-644
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- 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
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- Yinhe Cao, Wen-wen Tung, Jianbo Gao, Yan Qi:
Recurrence Time Statistics: Versatile Tools for Genomic Dna Sequence Analysis.
677-696
Electronic Edition (link) BibTeX
- Yonghua Han, Bin Ma, Kaizhong Zhang:
Spider: Software for Protein Identification from Sequence Tags with de Novo Sequencing Error.
697-716
Electronic Edition (link) BibTeX
- Orhan Çamoglu, Tolga Can, Ambuj K. Singh, Yuan-Fang Wang:
Decision Tree Based Information Integration for Automated Protein Classification.
717-742
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Mei Xu:
Erratum: Theoretically Modeling Microarray with the Chemical Equilibrium and Thermodynamics.
771
Electronic Edition (link) BibTeX
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
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- Arunkumar Chinnasamy, Wing-Kin Sung, Ankush Mittal:
Protein Structure and Fold Prediction Using Tree-augmented Naïve Bayesian Classifier.
803-820
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- Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik:
Dynamic Model-based Clustering for Time-course Gene Expression Data.
821-836
Electronic Edition (link) BibTeX
- Tianshou Zhou, Luonan Chen, Yun Tang, Xiang-Sun Zhang:
Aligning Multiple Protein Structures by Deterministic Annealing.
837-860
Electronic Edition (link) BibTeX
- Ville-Veikko Rantanen, Mats Gyllenberg, Timo Koski, Mark S. Johnson:
a Priori Contact Preferences in Molecular Recognition.
861-890
Electronic Edition (link) BibTeX
- T. 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
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- Lixia Jin, Huanwen Tang, Weiwu Fang:
Prediction of Protein Subcellular Locations Using a New Measure of Information Discrepancy.
915-928
Electronic Edition (link) BibTeX
- Laurent Bianchetti, Julie Dawn Thompson, Odile Lecompte, Frédéric Plewniak, Olivier Poch:
Valid: Validation of Protein Sequence Quality Based on Multiple Alignment Data.
929-948
Electronic Edition (link) BibTeX
- Rongxiang Liu, Pankaj Agarwal:
Computational Identification of Transcription Factors Involved in Early Cellular Response to a Stimulus.
949-964
Electronic Edition (link) BibTeX
- Matthias E. Futschik, Bronwyn Carlisle:
Noise-robust Soft Clustering of Gene Expression Time-course Data.
965-988
Electronic Edition (link) BibTeX
- Xu Guo, Wei Pan:
Using Weighted Permutation Scores to Detect Differential Gene Expression with Microarray Data.
989-1006
Electronic Edition (link) BibTeX
- Anna V. Gerasimova, Mikhail S. Gelfand:
Evolution of the Nadr Regulon in Enterobacteriaceae.
1007-1019
Electronic Edition (link) BibTeX
Volume 3,
Number 5,
October 2005
- Ao Yuan, Guanjie Chen, Charles Rotimi, George E. Bonney:
A Statistical Framework for Haplotype Block Inference.
1021-1038
Electronic Edition (link) BibTeX
- Lusheng Wang, Liang Dong:
Randomized Algorithms for Motif Detection.
1039-1052
Electronic Edition (link) BibTeX
- Sanghamitra Bandyopadhyay, Angshuman Bagchi, Ujjwal Maulik:
Active Site Driven Ligand Design: an Evolutionary Approach.
1053-1070
Electronic Edition (link) BibTeX
- Satoshi Niijima, Satoru Kuhara:
Multiclass Molecular Cancer Classification by Kernel Subspace Methods with Effective Kernel Parameter Selection.
1071-1088
Electronic Edition (link) BibTeX
- Tie-Fei Liu, Wing-Kin Sung, Yi Li, Jian-Jun Liu, Ankush Mittal, Pei-lin Mao:
Effective Algorithms for Tag Snp Selection.
1089-1106
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Boojala V. B. Reddy, Yiannis N. Kaznessis:
A Quantitative Analysis of Interfacial Amino Acid Conservation in Protein-protein Hetero Complexes.
1137-1150
Electronic Edition (link) BibTeX
- Hongzhi Li, Yaoqi Zhou:
Fold Helical Proteins by Energy Minimization in Dihedral Space and a Dfire-based Statistical Energy Function.
1151-1170
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Enrico Capobianco:
Mining Time-dependent Gene Features.
1191-1206
Electronic Edition (link) BibTeX
- Guanglan Zhang, Asif M. Khan, Kellathur N. Srinivasan, J. Thomas August, Vladimir Brusic:
Neural Models for Predicting Viral Vaccine Targets.
1207-1226
Electronic Edition (link) BibTeX
- Zeke S. H. Chan, Nikola K. Kasabov, Lesley Collins:
A Hybrid Genetic Algorithm and Expectation Maximization Method for Global Gene Trajectory Clustering.
1227-1242
Electronic Edition (link) BibTeX
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
Electronic Edition (link) BibTeX
- Shihong Mao, Guozhu Dong:
Discovery of Highly Differentiative Gene Groups from Microarray Gene Expression Data Using the Gene Club Approach.
1263-1280
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
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- Feng Cui, Robert L. Jernigan, Zhijun Wu:
Refinement of Nmr-determined Protein Structures with Database Derived Distance Constraints.
1315-1330
Electronic Edition (link) BibTeX
- Guohui Lin, Theodore Tegos, Zhi-Zhong Chen:
Heuristic Search in Constrained Bipartite Matching with Applications to Protein Nmr Backbone Resonance Assignment.
1331-1350
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Guanghua Xiao, Wei Pan:
Gene Function Prediction by a Combined Analysis of Gene Expression Data and Protein-protein Interaction Data.
1371-1390
Electronic Edition (link) BibTeX
- Lu-Yong Wang:
Covariation Analysis of Local Amino Acid Sequences in Recurrent Protein Local Structures.
1391-1410
Electronic Edition (link) BibTeX
- Eugene Novikov, Emmanuel Barillot:
A Robust Algorithm for Ratio Estimation in Two-color Microarray Experiments.
1411-1428
Electronic Edition (link) BibTeX
- Manuel Gil, Christophe Dessimoz, Gaston H. Gonnet:
A Dimensionless Fit Measure for Phylogenetic Distance Trees.
1429-1440
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- Steinar Thorvaldsen:
A Tutorial on Markov Models Based on Mendel's Classical Experiments.
1441-1460
Electronic Edition (link) BibTeX
Copyright © Sun May 17 00:06:50 2009
by Michael Ley (ley@uni-trier.de)