Volume 4,
Number 1,
February 2006
- Editorial.
3-18
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- Bahadur K. C. Dukka, 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
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Volume 4,
Number 2,
April 2006
Selected Papers from CSB2005
- 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 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
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Selected Papers from MCCMB2005
- Anna Karyagina, Anna Ershova, Mikhail Titov, Ivan Olovnikov, Evgeniy Aksianov, Alexandra Ryazanova, Elena Kubareva, Sergei 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, Alexandr 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 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
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Volume 4,
Number 3,
June 2006
- 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
Electronic Edition (link) BibTeX
- Simeone Marino, Eberhard O. Voit:
An Automated Procedure for the Extraction of Metabolic Network Information from Time Series Data.
665-692
Electronic Edition (link) BibTeX
- Xinan Yang, Stefan Bentink, Stefanie Scheid, Rainer Spang:
Similarities of Ordered Gene Lists.
693-708
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- H. X. Li, Shitong Wang, Yu Xiu:
Applying Robust Directional Similarity Based Clustering Approach Rdsc to Classification of Gene Expression Data.
745-768
Electronic Edition (link) BibTeX
- Xin Liu, Wei-Mou Zheng:
An Amino Acid Substitution Matrix for Protein Conformation Identification.
769-782
Electronic Edition (link) BibTeX
Volume 4,
Number 4,
August 2006
- 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
Electronic Edition (link) BibTeX
- Ho-Leung Chan, Jesper Jansson, Tak Wah Lam, Siu-Ming Yiu:
Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix.
807-832
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Haifeng Li, Xin Chen, Keshu Zhang, Tao Jiang:
A General Framework for Biclustering Gene Expression Data.
911-993
Electronic Edition (link) BibTeX
Volume 4,
Number 5,
October 2006
- Zhipeng Cai, Maysam Heydari, Guohui Lin:
Iterated Local Least Squares Microarray Missing Value Imputation.
935-958
Electronic Edition (link) BibTeX
- Chenhong Zhang, Mikelis G. Bickis, Fang-Xiang Wu, Anthony J. Kusalik:
Optimally-connected Hidden Markov Models for Predicting Mhc-binding Peptides.
959-980
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Victor Olman, Chindo Hicks, Peng Wang, Ying Xu:
Gene Expression Data Analysis in Subtypes of Ovarian Cancer Using Covariance Analysis.
999-1014
Electronic Edition (link) BibTeX
- Xiu-Feng Wan, Guohui Lin, Dong Xu:
Rnall: an Efficient Algorithm for Predicting Rna Local Secondary Structural Landscape in Genomes.
1015-1032
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Xing Qiu, Andrei Yakovlev:
Some Comments on Instability of False Discovery Rate Estimation.
1057-1068
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Hirokazu Anai, Shigeo Orii, Katsuhisa Horimoto:
Symbolic-numeric Estimation of Parameters in Biochemical Models by Quantifier Elimination.
1097-1118
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
Volume 4,
Number 6,
December 2006
- Liangjiang Wang, Susan J. Brown:
Prediction of Dna-binding Residues from Sequence Features.
1141-1158
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Jian Guo, Xian Pu, Yuanlie Lin, Howard Leung:
Protein Subcellular Localization Based on Psi-blast and Machine Learning.
1181-1196
Electronic Edition (link) BibTeX
- Zeyar Aung, Kian-Lee Tan:
Matalign: Precise Protein Structure Comparison by Matrix Alignment.
1197-1216
Electronic Edition (link) BibTeX
- Timur S. Shakuov:
The Comparison of Three Methods for Chromosomal Abnormality Detection.
1217-1226
Electronic Edition (link) BibTeX
- William J. Heuett, Hong Qian:
Combining Flux and Energy Balance Analysis to Model Large-scale Biochemical Networks.
1227-1244
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- 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
Electronic Edition (link) BibTeX
- Ching-Tai Chen, Hsin-Nan Lin, Ting-Yi Sung, Wen-Lian Hsu:
Hyplosp: a Knowledge-based Approach to Protein Local Structure Prediction.
1287-1308
Electronic Edition (link) BibTeX
- Arvind Gupta, Ján Manuch, Xiaohong Zhao, Ladislav Stacho:
Characterization of the Existence of Galled-tree Networks.
1309-1328
Electronic Edition (link) BibTeX
- Ket Fah Chong, Kang Ning, Hon Wai Leong, Pavel A. Pevzner:
Modeling and Characterization of Multi-charge Mass Spectra for Peptide Sequencing.
1329-1352
Electronic Edition (link) BibTeX
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