Journal of Bioinformatics and Computational Biology, Volume 4

Volume 4, Number 1, February 2006

• Editorial. 3-18
  
• 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
  
• Henry C. M. Leung, Francis Y. L. Chin:
  Algorithms for Challenging Motif Problems. 43-58
  
• Ying-Jun He, Trinh N. D. Huynh, Jesper Jansson, Wing-Kin Sung:
  Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets. 59-74
  
• 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
  
• Lei Huang, Yang Dai:
  Direct Prediction of T-cell Epitopes Using Support Vector Machines with Novel Sequence Encoding Schemes. 93-108
  
• Emily W. Xu, Paul Kearney, Daniel G. Brown:
  The Use of Functional Domains to Improve Transmembrane Protein Topology Prediction. 109-124
  
• Jian Liu, Bin Ma, Ming Li:
  Prima: Peptide Robust Identification from Ms/ms Spectra. 125-138
  
• 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
  
• Naomi L. Haworth, Lina L. Feng, Merridee A. Wouters:
  High Torsional Energy Disulfides: Relationship between Cross-strand Disulfides and Right-handed Staples. 155-168
  
• 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

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

• Anantharaman Kalyanaraman, Srinivas Aluru:
  Efficient Algorithms and Software for Detection of Full-length Ltr Retrotransposons. 197-216
  
• Xutao Deng, Huimin Geng, Hesham H. Ali:
  Joint Learning of Gene Functions - a Bayesian Network Model Approach. 217-240
  
• Tu Minh Phuong, Zhen Lin, Russ B. Altman:
  Choosing Snps Using Feature Selection. 241-258
  
• 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
  
• Sun-Yuan Kung, Man-Wai Mak, Ilias Tagkopoulos:
  Symmetric and Asymmetric Multi-modality Biclustering Analysis for Microarray Data Matrix. 275-298
  
• Tobias P. Mann, Richard Humbert, John A. Stamatoyannopoulos, William Stafford Noble:
  Automated Validation of Polymerase Chain Reaction Amplicon Melting Curves. 299-316
  
• Zhong Chen, Ying Xu:
  Structure Prediction of Helical Transmembrane Proteins at Two Length Scales. 317-334
  
• 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
  

• 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
  
• Oxana V. Galzitskaya, Sergiy O. Garbuzynskiy, Michail Yu. Lobanov:
  Is It Possible to Predict Amyloidogenic Regions from Sequence Alone? 373-388
  
• 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
  
• Yvonne Y. Li, Steven J. M. Jones, Artem Cherkasov:
  Selective Targeting of Indel-inferred Differences in Spatial Structures of Homologous Proteins. 403-414
  
• 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
  
• Irina I. Abnizova, Alistair G. Rust, Mark Robinson, Rene te Boekhorst, Walter R. Gilks:
  Transcription Binding Site Prediction Using Markov Models. 425-442
  
• 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
  
• 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
  
• 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
  
• Björn Olsson, Barbara Gawronska, Björn Erlendsson:
  Deriving Pathway Maps from Automated Text Analysis Using a Grammar-based Approach. 483-502
  
• Daisuke Tominaga, Paul Horton:
  Inference of Scale-free Networks from Gene Expression Time Series. 503-514
  
• 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
  
• Yuriy L. Orlov, Rene te Boekhorst, Irina I. Abnizova:
  Statistical Measures of the Structure of Genomic Sequences: Entropy, Complexity, and Position Information. 523-536
  
• Mireille Régnier, Mathias Vandenbogaert:
  Comparison of Statistical Significance Criteria. 537-552
  
• Gregory Kucherov, Laurent Noé, Mikhail A. Roytberg:
  A Unifying Framework for Seed Sensitivity and its Application to Subset Seeds. 553-570
  
• Simon B. Kogan:
  Decomposition of Overlapping Patterns by Cumulative Local Cross-correlation. 571-588
  
• 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
  
• Natalya S. Bogatyreva, Alexei V. Finkelstein, Oxana V. Galzitskaya:
  Trend of Amino Acid Composition of Proteins of Different Taxa. 597-608
  
• 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

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

Volume 4, Number 4, August 2006

• Alexander Seliverstov, Vassily A. Lyubetsky:
  Translation Regulation of Intron-containing Genes in Chloroplasts. 783-792
  
• Yuhua Duan, Boojala V. B. Reddy, Yiannis N. Kaznessis:
  Residue Conservation Information for Generating near-native Structures in Protein-protein Docking. 793-806
  
• Ho-Leung Chan, Jesper Jansson, Tak Wah Lam, Siu-Ming Yiu:
  Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix. 807-832
  
• 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
  
• Sergey I. Rogov, Kuvat T. Momynaliev, Vadim M. Govorun:
  Coexpressionfinder: a New Algorithm for Finding Groups of Coexpressed Genes. 853-864
  
• 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
  
• 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
  
• Haifeng Li, Xin Chen, Keshu Zhang, Tao Jiang:
  A General Framework for Biclustering Gene Expression Data. 911-993
  

Volume 4, Number 5, October 2006

• Zhipeng Cai, Maysam Heydari, Guohui Lin:
  Iterated Local Least Squares Microarray Missing Value Imputation. 935-958
  
• Chenhong Zhang, Mikelis G. Bickis, Fang-Xiang Wu, Anthony J. Kusalik:
  Optimally-connected Hidden Markov Models for Predicting Mhc-binding Peptides. 959-980
  
• 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
  
• Victor Olman, Chindo Hicks, Peng Wang, Ying Xu:
  Gene Expression Data Analysis in Subtypes of Ovarian Cancer Using Covariance Analysis. 999-1014
  
• Xiu-Feng Wan, Guohui Lin, Dong Xu:
  Rnall: an Efficient Algorithm for Predicting Rna Local Secondary Structural Landscape in Genomes. 1015-1032
  
• 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
  
• Xing Qiu, Andrei Yakovlev:
  Some Comments on Instability of False Discovery Rate Estimation. 1057-1068
  
• 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
  
• Hirokazu Anai, Shigeo Orii, Katsuhisa Horimoto:
  Symbolic-numeric Estimation of Parameters in Biochemical Models by Quantifier Elimination. 1097-1118
  
• 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

• Liangjiang Wang, Susan J. Brown:
  Prediction of Dna-binding Residues from Sequence Features. 1141-1158
  
• 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
  
• Jian Guo, Xian Pu, Yuanlie Lin, Howard Leung:
  Protein Subcellular Localization Based on Psi-blast and Machine Learning. 1181-1196
  
• Zeyar Aung, Kian-Lee Tan:
  Matalign: Precise Protein Structure Comparison by Matrix Alignment. 1197-1216
  
• Timur S. Shakuov:
  The Comparison of Three Methods for Chromosomal Abnormality Detection. 1217-1226
  
• William J. Heuett, Hong Qian:
  Combining Flux and Energy Balance Analysis to Model Large-scale Biochemical Networks. 1227-1244
  
• 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
  
• 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
  
• Ching-Tai Chen, Hsin-Nan Lin, Ting-Yi Sung, Wen-Lian Hsu:
  Hyplosp: a Knowledge-based Approach to Protein Local Structure Prediction. 1287-1308
  
• Arvind Gupta, Ján Manuch, Xiaohong Zhao, Ladislav Stacho:
  Characterization of the Existence of Galled-tree Networks. 1309-1328
  
• Ket Fah Chong, Kang Ning, Hon Wai Leong, Pavel A. Pevzner:
  Modeling and Characterization of Multi-charge Mass Spectra for Peptide Sequencing. 1329-1352
  

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