International Journal of Bioinformatics Research and Applications (IJBRA), Volume 2

Volume 2, Number 1, 2006

• B. M. Broom, T. J. McDonnell, D. Subramanian:
  Predicting altered pathways using extendable scaffolds. 3-18
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• Jesse Mecham, Mark J. Clement, Quinn Snell, Todd Freestone, Kevin D. Seppi, Keith A. Crandall:
  Jumpstarting phylogenetic analysis. 19-35
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• Raja Loganantharaj:
  Discriminating TATA box from putative TATA boxes in plant genome. 36-51
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• Janet Siebert, Krzysztof J. Cios, M. Karen Newell:
  A rich analytical environment for flow cytometry experimental results. 52-62
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• Jugal K. Kalita, Kaushal Chandrashekar, Reena Hans, P. Selvam, M. K. Newell:
  Computational modelling and simulation of the immune system. 63-88
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• Matthew J. Zukoski, Terrance Boult, Tunc Iyriboz:
  A novel approach to medical image compression. 89-103
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Volume 2, Number 2, 2006

• Jian Guo, Yuanlie Lin, Zhirong Sun:
  Protein sub-cellular localisation prediction by analysis of short-range residue correlations. 105-118
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• Scott F. Smith:
  Homology search with binary and trinary scoring matrices. 119-131
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• Shibin Qiu, Terran Lane:
  RNA string kernels for RNAi off-target evaluation. 132-146
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• Guohui Lin, Xiang Wan, Theodore Tegos, Yingshu Li:
  Statistical evaluation of NMR backbone resonance assignment. 147-160
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• Ruhong Zhou, Ajay K. Royyuru, Prasanna Athma, Frank Suits, B. David Silverman:
  Magnitude and spatial orientation of the hydrophobic moments of multi-domain proteins. 161-176
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• Tuan D. Pham:
  Handling missing DNA microarray data by kriging estimators. 177-192
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• Seoung Bum Kim, Kwok-Leung Tsui, Mark Borodovsky:
  Multiple testing in large-scale contingency tables: inferring patterns of pair-wise amino acid association in beta-sheets. 193-217
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Volume 2, Number 3, 2006

• Xiaomeng Wu, Xiu-Feng Wan, Gang Wu, Dong Xu, Guohui Lin:
  Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method. 219-248
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• Sunil K. Mathur, Atul M. Doke, Ajit Sadana:
  Identification of hair cycle-associated genes from time-course gene expression profile using fractal analysis. 249-258
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• Yuan-Shun Dai, Mathew J. Palakal, Shielly Hartanto, Xiaolong Wang, Yanming Guo:
  A Grid-Based Pseudo-Cache solution for MISD biomedical problems with high confidentiality and efficiency. 259-281
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• Rajesh Chowdhary, Limsoon Wong, Vladimir B. Bajic:
  Finding functional promoter motifs by computational methods: a word of caution. 282-288
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• Yinglei Song, Chunmei Liu, Russell L. Malmberg, Congzhou He, Liming Cai:
  Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots. 289-304
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• Svetlana Ekisheva, Mark Borodovsky:
  Probabilistic models for biological sequences: selection and Maximum Likelihood estimation. 305-324
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• Xiaohua Hu:
  GE-Miner: integration of cluster ensemble and text mining for comprehensive gene expression analysis. 325-338
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Volume 2, Number 4, 2006

• Fumihiko Ino, Yasuhiro Kawasaki, Takahito Tashiro, Yoshikazu Nakajima, Yoshinobu Sato, Shinichi Tamura, Kenichi Hagihara:
  A parallel implementation of 2-D/3-D image registration for computer-assisted surgery. 341-358
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• Yongchang Ji, Dan C. Marinescu:
  Rotational and translational alignment errors in 3D reconstruction of virus structures at high resolution. 359-370
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• Jorg Bernsdorf, Sarah E. Harrison, Stephen M. Smith, Patricia V. Lawford, D. Rodney Hose:
  Concurrent numerical simulation of flow and blood clotting using the lattice Boltzmann technique. 371-380
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• Nan Jiang, Wendy Xinyu Wu, Ian Mitchell:
  MESSM: a framework for protein fold recognition using Neural Networks and Support Vector Machines. 381-393
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• Timothy F. Oliver, Bertil Schmidt, Douglas L. Maskell, Darran Nathan, Ralf Clemens:
  High-speed Multiple Sequence Alignment on a reconfigurable platform. 394-406
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• Yuri Dotsenko, Cristian Coarfa, Luay Nakhleh, John M. Mellor-Crummey, Usman Roshan:
  PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction. 407-419
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• Yiming Li:
  Numerical solutions of a master equation for protein folding kinetics. 420-429
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• Xiandong Meng, Vipin Chaudhary:
  Optimised fine and coarse parallelism for sequence homology search. 430-441
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