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ORCIDJournal 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 S. 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 N. 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 V. 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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