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Article
Particle Swarm Optimisation for Protein Motif Discovery
In this paper, a modified particle swarm optimisation algorithm is proposed for protein sequence motif discovery. Protein sequences are represented as a chain of symbols and a protein sequence motif is a short...
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Open AccessGene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages
Existing methods for whole-genome comparisons require prior knowledge of related species and provide little automation in the function prediction process. Bacteriophage genomes are an example that cannot be ea...
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Article
Polynomial kernel adaptation and extensions to the SVM classifier learning
Three extensions to the Kernel-AdaTron training algorithm for Support Vector Machine classifier learning are presented. These extensions allow the trained classifier to adhere more closely to the constraints i...
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Article
Open AccessGenome classification by gene distribution: An overlap** subspace clustering approach
Genomes of lower organisms have been observed with a large amount of horizontal gene transfers, which cause difficulties in their evolutionary study. Bacteriophage genomes are a typical example. One recent app...
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Article
Open AccessBinning sequences using very sparse labels within a metagenome
In metagenomic studies, a process called binning is necessary to assign contigs that belong to multiple species to their respective phylogenetic groups. Most of the current methods of binning, such as BLAST, k-me...
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Article
Structure adaptation of hierarchical knowledge-based classifiers
This paper introduces a new method to identify the qualified rule-relevant nodes to construct hierarchical neuro-fuzzy systems (HNFSs). After learning, the proposed method analyzes the entire history of activi...
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Article
Open AccessThe oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments
The characterisation, or binning, of metagenome fragments is an important first step to further downstream analysis of microbial consortia. Here, we propose a one-dimensional signature, OFDEG, derived from the...
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Article
Open AccessCoNVEX: copy number variation estimation in exome sequencing data using HMM
One of the main types of genetic variations in cancer is Copy Number Variations (CNV). Whole exome sequenicng (WES) is a popular alternative to whole genome sequencing (WGS) to study disease specific genomic v...
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Open AccessErratum to: CoNVEX: copy number variation estimation in exome sequencing data using HMM
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Article
Exploratory analysis of high-throughput metabolomic data
In order to make sense of the sheer volume of metabolomic data that can be generated using current technology, robust data analysis tools are essential. We propose the use of the growing self-organizing map (G...
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Article
Open AccessInferring copy number and genotype in tumour exome data
Using whole exome sequencing to predict aberrations in tumours is a cost effective alternative to whole genome sequencing, however is predominantly used for variant detection and infrequently utilised for dete...
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Article
Open AccessAccurate reconstruction of viral quasispecies spectra through improved estimation of strain richness
Estimating the number of different species (richness) in a mixed microbial population has been a main focus in metagenomic research. Existing methods of species richness estimation ride on the assumption that the...
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Article
Open AccessA new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model
Mass Spectrometry (MS) is a ubiquitous analytical tool in biological research and is used to measure the mass-to-charge ratio of bio-molecules. Peak detection is the essential first step in MS data analysis. P...
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Open AccessENVirT: inference of ecological characteristics of viruses from metagenomic data
Estimating the parameters that describe the ecology of viruses,particularly those that are novel, can be made possible using metagenomic approaches. However, the best-performing existing methods require databa...