Volume 4, Number 1, February 2006

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  Editorial. 3-18
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  K. C. Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, Tatsuya Akutsu: Protein Threading with Profiles and Distance Constraints Using Clique Based Algorithms. 19-42
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  Henry C. M. Leung, Francis Y. L. Chin: Algorithms for Challenging Motif Problems. 43-58
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  Ying-Jun He, Trinh N. D. Huynh, Jesper Jansson, Wing-Kin Sung: Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets. 59-74
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  Tun-Wen Pai, Bo-Han Su, Pei-Chih Wu, Margaret Dah-Tsyr Chang, Hao-Teng Chang, Tan-Chi Fan, Shi-Hwei Liu: Unique Peptide Identification of Rnasea Superfamily Sequences Based on Reinforced Merging Algorithms. 75-92
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  Lei Huang, Yang Dai: Direct Prediction of T-cell Epitopes Using Support Vector Machines with Novel Sequence Encoding Schemes. 93-108
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  Emily W. Xu, Paul Kearney, Daniel G. Brown: The Use of Functional Domains to Improve Transmembrane Protein Topology Prediction. 109-124
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  Jian Liu, Bin Ma, Ming Li: Prima: Peptide Robust Identification from Ms/ms Spectra. 125-138
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  Hiroshi Matsuno, Shin-Ichi T. Inouye, Yasuki Okitsu, Yasushi Fujii, Satoru Miyano: A New Regulatory Interaction Suggested by Simulations for Circadian Genetic Control Mechanism in Mammals. 139-154
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  Naomi L. Haworth, Lina L. Feng, Merridee A. Wouters: High Torsional Energy Disulfides: Relationship between Cross-strand Disulfides and Right-handed Staples. 155-168
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  Eli Kaminuma, Naohiko Heida, Takeshi Yoshizumi, Miki Nakazawa, Minami Matsui, Tetsuro Toyoda: Erratum: "In Silico Phenotypic Screening Method of Mutants Based on Statistical Modeling of Genetically Mixed Samples". 169

Volume 4, Number 2, April 2006

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  Gregory Kucherov, Andrey A. Mironov, Mikhail A. Roytberg: An Overview of the Algorithmic Session of MCCMB'05.

Selected Papers from CSB2005

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  Anantharaman Kalyanaraman, Srinivas Aluru: Efficient Algorithms and Software for Detection of Full-length Ltr Retrotransposons. 197-216
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  Xutao Deng, Huimin Geng, Hesham H. Ali: Joint Learning of Gene Functions - a Bayesian Network Model Approach. 217-240
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  Tu Minh Phuong, Zhen Lin, Russ B. Altman: Choosing Snps Using Feature Selection. 241-258
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  Anya Tsalenko, Roded Sharan, Vessela N. Kristensen, Hege Edvardsen, Anne-Lise Børresen-Dale, Amir Ben-Dor, Zohar Yakhini: Analysis of Snp-expression Association Matrices. 259-274
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  Sun-Yuan Kung, Man-Wai Mak, Ilias Tagkopoulos: Symmetric and Asymmetric Multi-modality Biclustering Analysis for Microarray Data Matrix. 275-298
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  Tobias P. Mann, Richard Humbert, John A. Stamatoyannopoulos, William Stafford Noble: Automated Validation of Polymerase Chain Reaction Amplicon Melting Curves. 299-316
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  Zhong Chen, Ying Xu: Structure Prediction of Helical Transmembrane Proteins at Two Length Scales. 317-334
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  Tarek S. Najdi, Chin-Rang Yang, Bruce E. Shapiro, G. Wesley Hatfield, Eric Mjolsness: Application of a Generalized Mwc Model for the Mathematical Simulation of Metabolic Pathways Regulated by Allosteric Enzymes. 335-356

Selected Papers from MCCMB2005

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  Anna Karyagina, Anna S. Ershova, Mikhail Titov, Ivan Olovnikov, Evgeniy Aksianov, Alexandra Ryazanova, Elena Kubareva, Sergei A. Spirin, Andrei Alexeevski: Analysis of Conserved Hydrophobic Cores in Proteins and Supramolecular Complexes. 357-372
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  Oxana V. Galzitskaya, Sergiy O. Garbuzynskiy, Michail Yu. Lobanov: Is It Possible to Predict Amyloidogenic Regions from Sequence Alone? 373-388
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  Elena Svirshchevskaya, Ludmila Alekseeva, Alexei Marchenko, Sergei Benevolenskii, Valentina M. Berzhec, Alexei Nekrasov: Selection of Cryptic B-cell Epitopes Using Informational Analysis of Protein Sequenses. 389-402
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  Yvonne Y. Li, Steven J. M. Jones, Artem Cherkasov: Selective Targeting of Indel-inferred Differences in Spatial Structures of Homologous Proteins. 403-414
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  Oleg V. Koliasnikov, Miroslav O. Kiral, Vitaly G. Grigorenko, Alexey M. Egorov: Antibody Cdr H3 Modeling Rules: Extension for the Case of Absence of Arg H94 and Asp H101. 415-424
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  Irina I. Abnizova, Alistair G. Rust, Mark Robinson, Rene te Boekhorst, Walter R. Gilks: Transcription Binding Site Prediction Using Markov Models. 425-442
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  Olga N. Ozoline, Alexander A. Deev: Predicting Antisense Rnas in the Genomes of escherichia Coli and salmonella Typhimurium Using Promoter-search Algorithm Platprom. 443-454
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  Anatoly A. Sorokin, Alexander A. Osypov, Timur R. Dzhelyadin, Petr M. Beskaravainy, Svetlana G. Kamzolova: Electrostatic Properties of Promoter Recognized by e. Coli Rna Polymerase Esigma⁷⁰. 455-468
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  Natalia Polouliakh, Tohru Natsume, Hajime Harada, Wataru Fujibuchi, Paul Horton: Comparative Genomic Analysis of Transcription Regulation Elements Involved in Human Map Kinase G-protein Coupling Pathway. 469-482
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  Björn Olsson, Barbara Gawronska, Björn Erlendsson: Deriving Pathway Maps from Automated Text Analysis Using a Grammar-based Approach. 483-502
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  Daisuke Tominaga, Paul Horton: Inference of Scale-free Networks from Gene Expression Time Series. 503-514
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  Dmitry Klimov, Mikhail Skoblov, Andrei Ryazantzev, Tatiana Tiazhelova, Ancha V. Baranova: in Silico Search for Natural Antisense Transcripts Reveals their Differential Expression in Human Tumors. 515-522
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  Yuriy L. Orlov, Rene te Boekhorst, Irina I. Abnizova: Statistical Measures of the Structure of Genomic Sequences: Entropy, Complexity, and Position Information. 523-536
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  Mireille Régnier, Mathias Vandenbogaert: Comparison of Statistical Significance Criteria. 537-552
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  Gregory Kucherov, Laurent Noé, Mikhail A. Roytberg: A Unifying Framework for Seed Sensitivity and its Application to Subset Seeds. 553-570
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  Simon B. Kogan: Decomposition of Overlapping Patterns by Cumulative Local Cross-correlation. 571-588
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  Ludmila V. Danilova, Dmitri D. Pervouchine, Alexander V. Favorov, Andrey A. Mironov: Rnakinetics: a Web Server that Models Secondary Structure Kinetics of an Elongating RNA. 589-596
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  Natalya S. Bogatyreva, Alexei V. Finkelstein, Oxana V. Galzitskaya: Trend of Amino Acid Composition of Proteins of Different Taxa. 597-608
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  Swetlana Nikolajewa, Maik Friedel, Andreas Beyer, Thomas Wilhelm: The New Classification Scheme of the Genetic Code, its Early Evolution, and Trna Usage. 609-620

Volume 4, Number 3, June 2006

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  Tatsuya Sekiguchi, Masahiro Okamoto: Winbest-kit: Windows-based Biochemical Reaction Simulator for Metabolic Pathways. 621-638
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  Eleazar Eskin, Roded Sharan, Eran Halperin: A Note on Phasing Long Genomic Regions Using Local Haplotype Predictions. 639-648
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  Kana Shimizu, Jun Adachi, Yoichi Muraoka: Angle: a Sequencing Errors Resistant Program for Predicting Protein Coding Regions in Unfinished Cdna. 649-664
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  Simeone Marino, Eberhard O. Voit: An Automated Procedure for the Extraction of Metabolic Network Information from Time Series Data. 665-692
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  Xinan Yang, Stefan Bentink, Stefanie Scheid, Rainer Spang: Similarities of Ordered Gene Lists. 693-708
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  Bin Ma, Lieyu Wu, Kaizhong Zhang: Improving the Sensitivity and Specificity of Protein Homology Search by Incorporating Predicted Secondary Structures. 709-720
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  Leonid Chindelevitch, Zhentao Li, Eric Blais, Mathieu Blanchette: On the Inference of Parsimonious Indel Evolutionary Scenarios. 721-744
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  H. X. Li, Shitong Wang, Yu Xiu: Applying Robust Directional Similarity Based Clustering Approach Rdsc to Classification of Gene Expression Data. 745-768
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  Xin Liu, Wei-Mou Zheng: An Amino Acid Substitution Matrix for Protein Conformation Identification. 769-782

Volume 4, Number 4, August 2006

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  Alexander Seliverstov, Vassily A. Lyubetsky: Translation Regulation of Intron-containing Genes in Chloroplasts. 783-792
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  Yuhua Duan, Boojala V. B. Reddy, Yiannis N. Kaznessis: Residue Conservation Information for Generating near-native Structures in Protein-protein Docking. 793-806
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  Ho-Leung Chan, Jesper Jansson, Tak Wah Lam, Siu-Ming Yiu: Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix. 807-832
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  Corneliu Henegar, Raffaella Cancello, Sophie Rome, Hubert Vidal, Karine Clément, Jean-Daniel Zucker: Clustering Biological Annotations and Gene Expression Data to Identify Putatively Co-regulated Biological Processes. 833-852
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  Sergey I. Rogov, Kuvat T. Momynaliev, Vadim M. Govorun: Coexpressionfinder: a New Algorithm for Finding Groups of Coexpressed Genes. 853-864
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  L. N. Drozdov-Tikhomirov, G. I. Scurida, A. V. Davidov, A. A. Alexandrov, R. A. Zvyagilskaya: Mathematical Modeling of Living Cell Metabolism Using the Method of Steady-state Stoichiometric Flux Balance. 865-886
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  A. A. Novikov, A. S. Taisova, Z. G. Fetisova: Optimal Spectral Coordination of Subantennae in Natural Antennae as an Efficient Strategy for Light Harvesting in Photosynthesis. 887-910
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  Haifeng Li, Xin Chen, Keshu Zhang, Tao Jiang: A General Framework for Biclustering Gene Expression Data. 911-993

Volume 4, Number 5, October 2006

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  Zhipeng Cai, Maysam Heydari, Guohui Lin: Iterated Local Least Squares Microarray Missing Value Imputation. 935-958
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  Chenhong Zhang, Mikelis G. Bickis, Fang-Xiang Wu, Anthony J. Kusalik: Optimally-connected Hidden Markov Models for Predicting Mhc-binding Peptides. 959-980
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  Galina Yu. Kovaleva, Georgii A. Bazykin, Michael Brudno, Mikhail S. Gelfand: Comparative Genomics of Transcriptional Regulation in Yeasts and its Application to Identification of a Candidate Alpha-isopropylmalate Transporter. 981-998
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  Victor Olman, Chindo Hicks, Peng Wang, Ying Xu: Gene Expression Data Analysis in Subtypes of Ovarian Cancer Using Covariance Analysis. 999-1014
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  Xiu-Feng Wan, Guohui Lin, Dong Xu: Rnall: an Efficient Algorithm for Predicting Rna Local Secondary Structural Landscape in Genomes. 1015-1032
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  Nataliya S. Sadovskaya, Roman A. Sutormin, Mikhail S. Gelfand: Recognition of Transmembrane Segments in Proteins: Review and Consistency-based Benchmarking of Internet Servers. 1033-1056
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  Xing Qiu, Andrei Yakovlev: Some Comments on Instability of False Discovery Rate Estimation. 1057-1068
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  Sarah Cohen Boulakia, Susan B. Davidson, Christine Froidevaux, Zoé Lacroix, Maria-Esther Vidal: Path-based Systems to Guide Scientists in the Maze of Biological Data Sources. 1069-1096
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  Hirokazu Anai, Shigeo Orii, Katsuhisa Horimoto: Symbolic-numeric Estimation of Parameters in Biochemical Models by Quantifier Elimination. 1097-1118
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  Chen Li, Shunichi Suzuki, Qi-Wei Ge, Mitsuru Nakata, Hiroshi Matsuno, Satoru Miyano: Structural Modeling and Analysis of Signaling Pathways Based on Petri Nets. 1119-1140

Volume 4, Number 6, December 2006

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  Liangjiang Wang, Susan J. Brown: Prediction of Dna-binding Residues from Sequence Features. 1141-1158
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  Jung Hun Oh, Animesh Nandi, Prem Gurnani, Lynne Knowles, John Schorge, Kevin P. Rosenblatt, Jean X. Gao: Proteomic Biomarker Identification for Diagnosis of Early Relapse in Ovarian Cancer. 1159-1180
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  Jian Guo, Xian Pu, Yuanlie Lin, Howard Leung: Protein Subcellular Localization Based on Psi-blast and Machine Learning. 1181-1196
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  Zeyar Aung, Kian-Lee Tan: Matalign: Precise Protein Structure Comparison by Matrix Alignment. 1197-1216
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  Timur S. Shakuov: The Comparison of Three Methods for Chromosomal Abnormality Detection. 1217-1226
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  William J. Heuett, Hong Qian: Combining Flux and Energy Balance Analysis to Model Large-scale Biochemical Networks. 1227-1244
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  Gek Huey Chua, Arun Krishnan, Kuo-Bin Li, Masaru Tomita: Multiresolution Analysis Uncovers Hidden Conservation of Properties in Structurally and Functionally Similar Proteins. 1245-1268
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  Michael K. Ng, Eric S. Fung, Yiu-Fai Lee, Wai-Ki Ching: A Recursive Method for Solving Haplotype Frequencies with Application to Genetics. 1269-1286
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  Ching-Tai Chen, Hsin-Nan Lin, Ting-Yi Sung, Wen-Lian Hsu: Hyplosp: a Knowledge-based Approach to Protein Local Structure Prediction. 1287-1308
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  Arvind Gupta, Ján Manuch, Xiaohong Zhao, Ladislav Stacho: Characterization of the Existence of Galled-tree Networks. 1309-1328
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  Ket Fah Chong, Kang Ning, Hon Wai Leong, Pavel A. Pevzner: Modeling and Characterization of Multi-charge Mass Spectra for Peptide Sequencing. 1329-1352