International Journal of Bioinformatics Research and Applications (IJBRA), Volume 4

Volume 4, Number 1, 2008

• ZhenQiu Liu, Dechang Chen, Jianjun Paul Tian:
  Classification of proteomic data with multiclass Logistic Partial Least Squares algorithm. 1-10
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• Suely Oliveira, Sang-Cheol Seok:
  A matrix-based multilevel approach to identify functional protein modules. 11-27
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• Imad Rahal, Riad Rahhal, Baoying Wang, William Perrizo:
  CARIBIAM: Constrained Association Rules using Interactive Biological IncrementAl Mining. 28-48
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• Yong Li, Xiujuan Chen, Saeid Belkasim, Yi Pan:
  High performance bio-image database retrieval using MPI. 49-63
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• Deyu Zhou, Yulan He, Chee Keong Kwoh:
  Extracting Protein-Protein Interactions from MEDLINE using the Hidden Vector State model. 64-80
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• Marcel H. Schulz, Sebastian Bauer, Peter N. Robinson:
  The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences. 81-95
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• Jianxin Wang, De Yang:
  UPNT: Uniform Projection and Neighbourhood Thresholding method for motif discovery. 96-106
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• Patricia Buendia, Timothy M. Collins, Giri Narasimhan:
  The role of internal node sequences and the molecular clock in the analysis of serially-sampled data. 107-121
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Volume 4, Number 2, 2008

• Peng Chen, De-Shuang Huang, Xing-Ming Zhao, Xueling Li:
  Predicting contact map using Radial Basis Function Neural Network with Conformational Energy Function. 123-136
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• Yong Chen, Guojun Li:
  An effective algorithm of motif finding problem. 137-149
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• Jing Li:
  A novel strategy for detecting multiple loci in Genome-Wide Association Studies of complex diseases. 150-163
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• Xingqin Qi, Jichang Wu, Shuguang Li, Guojun Li:
  Sorting by transpositions: dealing with length-weighted models. 164-171
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• J. Cui, C. Chen, H. Lu, P. Shen:
  Modelling of the mitochondrial apoptosis network. 172-187
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• Aili Han, Daming Zhu, Jingchang Pan:
  DNA solution based on sequence alignment to the Minimum Spanning Tree problem. 188-200
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• Jian Tian, Xuexia Guo, Xiaoyu Chu, Ningfeng Wu, Jun Guo, Bin Yao:
  Predicting the protein family of Methyl Parathion Hydrolase. 201-210
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• Zhihua Liu, Xiao Sun:
  Coronavirus phylogeny based on Base-Base Correlation. 211-220
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Volume 4, Number 3, 2008

• Ivan Merelli, Alessandro Orro, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi:
  A parallel protein surface reconstruction system. 221-239
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• Jamil Ahmad, Olivier Roux, Gilles Bernot, Jean-Paul Comet, Adrien Richard:
  Analysing formal models of genetic regulatory networks with delays. 240-262
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• Xutao Deng, Huimin Geng, Hesham H. Ali:
  A Hidden Markov Model approach to predicting yeast gene function from sequential gene expression data. 263-273
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• Jonas Gamalielsson, Björn Olsson:
  GOSAP: Gene Ontology-Based Semantic Alignment of Biological Pathways. 274-294
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• Kunpeng Zhang, Yun Xu, Guoliang Chen:
  PECB: prediction of enzyme catalytic residues based on Naive Bayes classification. 295-305
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• Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders:
  Creating gene set activity profiles with time-series expression data. 306-323
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• Liza S. Z. Larsen, Christopher D. Wassman, G. Wesley Hatfield, Richard H. Lathrop:
  Computationally Optimised DNA Assembly of synthetic genes. 324-336
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• Liping Du, Shuanhu Wu, Alan Wee-Chung Liew, David Keith Smith, Hong Yan:
  Spectral analysis of microarray gene expression time series data of Plasmodium falciparum. 337-349
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Volume 4, Number 4, 2008

• Z. Wu, Y. Zhang:
  Solving large double digestion problems for DNA restriction mapping by using branch-and-bound integer linear programming. 351-362
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• Bo Geng, Xiaobo Zhou, Y. S. Hung, Stephen Wong:
  Comparison of Bayesian and regression models in missing enzyme identification. 363-374
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• Xing-Ming Zhao, Luonan Chen, Kazuyuki Aihara:
  Protein function prediction with the shortest path in functional linkage graph and boosting. 375-384
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• Morihiro Hayashida, Fuyan Sun, Sachiyo Aburatani, Katsuhisa Horimoto, Tatsuya Akutsu:
  Integer programming-based approach to allocation of reporter genes for cell array analysis. 385-399
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• Martin Brown, Fei He, Lam Fat Yeung:
  Robust measurement selection for biochemical pathway experimental design. 400-416
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• Haiyong Liao, Michael Ng, Eric Fung, Pak C. Sham:
  Unidimensional nonnegative scaling for genome-wide Linkage Disequilibrium maps. 417-434
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• Hirokazu Tozaki, Taiichiro Kobe, Kazuyuki Aihara, Hideo Iwasaki:
  An attempt to reveal a role of a transcription/translation feedback loop in the cyanobacterial KaiC protein-based circadian system by using a semi-synthetic method. 435-444
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• Zhi-Ping Liu, Ling-Yun Wu, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
  Protein cavity clustering based on community structure of pocket similarity network. 445-460
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