Genomics, Proteomics & Bioinformatics, Volume 4

Volume 4, Number 1, 2006

Taiho Kambe, Tomoyuki Suzuki, Masaya Nagao, Yuko Yamaguchi-Iwai:
Sequence Similarity and Functional Relationship Among Eukaryotic ZIP and CDF Transporters. 1-9
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Chun-Hong Zhao, Qi-Fu Li, Yan Zhao, Jing-Wen Niu, Zhi-Xing Li, Jin-An Chen:
Changes of Nuclear Matrix Proteins Following the Differentiation of Human Osteosarcoma MG-63 Cells. 10-17
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Neng-Sheng Ye, Rong-Li Zhang, Yan-Feng Zhao, Xue Feng, Yi-Ming Wang, Guo-An Luo:
Effect of 5-azacytidine on the Protein Expression of Porcine Bone Marrow Mesenchymal Stem Cells in vitro. 18-25
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Md. Salimullah, Masaki Mori, Koichi Nishigaki:
High-throughput Three-dimensional Gel Electrophoresis for Versatile Utilities: A Stacked Slice-gel System for Separation and Reactions (4SR). 26-33
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Jun Yang, Yi-Li Wang, Lü-Sheng Si:
Predicting the Nuclear Localization Signals of 107 Types of HPV L1 Proteins by Bioinformatic Analysis. 34-41
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Sudipto Saha, G. P. S. Raghava:
VICMpred: An SVM-based Method for the Prediction of Functional Proteins of Gram-negative Bacteria Using Amino Acid Patterns and Composition. 42-47
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Evangelia Petsalaki, Pantelis G. Bagos, Zoi I. Litou, Stavros J. Hamodrakas:
PredSL: A Tool for the N-terminal Sequence-based Prediction of Protein Subcellular Localization. 48-55
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Axel Mosig, Katrin Sameith, Peter F. Stadler:
Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences. 56-60
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Jing-Fa Liu, Wen-Qi Huang:
A Quasi-physical Algorithm for the Structure Optimization in an Off-lattice Protein Model. 61-66
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Volume 4, Number 2, May 2006

Jiang Qian, Jimmy Lin, Donald J. Zack:
Characterization of Binding Sites of Eukaryotic Transcription Factors. 67-79
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Thanigaimani Rajarathinam, Yen-Han Lin:
Topological Properties of Protein-Protein and Metabolic Interaction Networks of Drosophila melanogaster. 80-89
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Sebastian Noth, Guillaume Brysbaert, Arndt Benecke:
Normalization Using Weighted Negative Second Order Exponential Error Functions (NeONORM) Provides Robustness Against Asymmetries in Comparative Transcriptome Profiles and Avoids False Calls. 90-109
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Yi-Jing Shen, Shu-Guang Huang:
Improve Survival Prediction Using Principal Components of Gene Expression Data. 110-119
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George K. Acquaah-Mensah, Sonia M. Leach, Chittibabu Guda:
Predicting the Subcellular Localization of Human Proteins Using Machine Learning and Exploratory Data Analysis. 120-133
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Pascal Pernet, Arnaud Bruneel, Bruno Baudin, Michel Vaubourdolle:
PHProteomicDB: A Module for Two-dimensional Gel Electrophoresis Database Creation on Personal Web Sites. 134-136
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Volume 4, Number 3, August 2006

Asad Jan, Setsuko Komatsu:
Functional Characterization of Gibberellin-Regulated Genes in Rice Using Microarray System. 137-144
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Ying Shi, Ling Chen, Lance A. Liotta, Hong-Hui Wan, Griffin P. Rodgers:
Glia Maturation Factor Gamma (GMFG): A Cytokine-Responsive Protein During Hematopoietic Lineage Development and Its Functional Genomics Analysis. 145-155
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Reiko Hayashi, Takako Arauchi, Moe Tategu, Yuya Goto, Kenichi Yoshida:
A Combined Computational and Experimental Study on the Structure-Regulation Relationships of Putative Mammalian DNA Replication Initiator GINS. 156-164
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Shi-Shan Deng, Tian-Yong Xing, Hong-Ying Zhou, Ruo-Hong Xiong, You-Guang Lu, Bin Wen, Shang-Qing Liu, Hui-Jun Yang:
Comparative Proteome Analysis of Breast Cancer and Adjacent Normal Breast Tissues in Human. 165-172
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Zhang Zhang, Jun Yu:
Evaluation of Six Methods for Estimating Synonymous and Nonsynonymous Substitution Rates. 173-181
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Marcelo M. Brandão, Karina L. Silva-Brandão, Fernando F. Costa, Sara T. O. Saad:
Phylogenetic Analysis of RhoGAP Domain-Containing Proteins. 182-188
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D. Ashok Reddy, Chanchal K. Mitra:
Comparative Analysis of Transcription Start Sites Using Mutual Information. 189-195
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Stanislav O. Zakharkin, Kyoungmi Kim, Alfred A. Bartolucci, Grier P. Page, David B. Allison:
Optimal Allocation of Replicates for Measurement Evaluation Studies. 196-202
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Volume 4, Number 4, 2006

Xiao-Qian Zhao, Jian-Fei Hu, Jun Yu:
Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits. 203-211
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Sebastian Noth, Guillaume Brysbaert, François-Xavier Pellay, Arndt Benecke:
High-Sensitivity Transcriptome Data Structure and Implications for Analysis and Biologic Interpretation. 212-229
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T. Shashi Rekha, Chanchal K. Mitra:
Comparative Analysis of Splice Site Regions by Information Content. 230-237
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Toshihide Ono, Haretsugu Hishigaki:
Prediction of GPCR-G Protein Coupling Specificity Using Features of Sequences and Biological Functions. 238-244
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Xiao-Gang Ruan, Jin-Lian Wang, Jian-Geng Li:
A Network Partition Algorithm for Mining Gene Functional Modules of Colon Cancer from DNA Microarray Data. 245-252
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Sudipto Saha, Jyoti Zack, Balvinder Singh, G. P. S. Raghava:
VGIchan: Prediction and Classification of Voltage-Gated Ion Channels. 253-258
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Zhang Zhang, Jun Li, Xiao-Qian Zhao, Jun Wang, Gane Ka-Shu Wong, Jun Yu:
KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging. 259-263
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