Classification of proteomic data with multiclass Logistic Partial Least Squares algorithm
DOI: 10.1504/IJBRA.2008.017160 | Zhenqiu Liu, Dechang Chen, Jianjun Paul Tian | Early detection of cancer is crucial for successful treatments. In this paper, we propose a multiclass Logistic Partial Least Squares (LPLS) algorithm for classification of normal vs. cancer using Mass Spectrometry (MS). LPLS combines the m... | 1 - 10 |
A matrix-based multilevel approach to identify functional protein modules
DOI: 10.1504/IJBRA.2008.017160 | Suely Oliveira, Sang-Cheol Seok | Identifying functional modules is believed to reveal most cellular processes. There have been many computational approaches to investigate the underlying biological structures (Bader and Hogue, 2003; Dhillon et al., 2005; Krogan et al., 200... | 11 - 27 |
CARIBIAM: Constrained Association Rules using Interactive Biological IncrementAl Mining
DOI: 10.1504/IJBRA.2008.017160 | Imad Rahal, Riad Rahhal, Baoying Wang, William Perrizo | This paper analyses annotated genome data by applying a very central data-mining technique known as Association Rule Mining (ARM) with the aim of discovering rules and hypotheses capable of yielding deeper insights into this type of data. I... | 28 - 48 |
High performance bio-image database retrieval using MPI
DOI: 10.1504/IJBRA.2008.017160 | Yong Li, Xiujuan Chen, Saeid Belkasim, Yi Pan | Fast and accurate 3D object reconstruction and partial 3D component retrieval from 2D image slices represent a difficult and challenging problem. To group related objects on different layers in an image stack, image segmentation and sequent... | 49 - 63 |
Extracting Protein-Protein Interactions from MEDLINE using the Hidden Vector State model
DOI: 10.1504/IJBRA.2008.017160 | Deyu Zhou, Yulan He, Chee Keong Kwoh | A major challenge in text mining for biomedicine is automatically extracting protein-protein interactions from the vast amount of biomedical literature. We have constructed an information extraction system based on the Hidden Vector State (... | 64 - 80 |
The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences
DOI: 10.1504/IJBRA.2008.017160 | Marcel H. Schulz, Sebastian Bauer, Peter N. Robinson | Efficient searching for specific subsequences in a set of longer sequences is an important component of many bioinformatics algorithms. Generalised suffix trees and suffix arrays allow searches for a pattern of length n in time proportional... | 81 - 95 |
UPNT: Uniform Projection and Neighbourhood Thresholding method for motif discovery
DOI: 10.1504/IJBRA.2008.017160 | Jianxin Wang, De Yang | Motif discovery is a significant problem in Bioinformatics. According to the complexity of most signals in biologic sequences, there are no extremely good models or dependable algorithms to solve this problem. This paper introduces the Unif... | 96 - 106 |
The role of internal node sequences and the molecular clock in the analysis of serially-sampled data
DOI: 10.1504/IJBRA.2008.017160 | Patricia Buendia, Timothy M. Collins, Giri Narasimhan | Algorithms that infer phylogenetic relationships between serially-sampled sequences have been developed in recent years to assist in the analysis of rapidly-evolving human pathogens. Our study consisted of evaluating seven relevant methods ... | 107 - 121 |
