11 Result(s)

Article

ENVirT: 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...

Duleepa Jayasundara, Damayanthi Herath, Damith Senanayake… in BMC Bioinformatics (2019)

Article

Accurate 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...

Duleepa Jayasundara, I Saeed, BC Chang, Sen-Lin Tang… in BMC Bioinformatics (2015)

Article

A 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...

Chalini D Wijetunge, Isaam Saeed, Berin A Boughton, Ute Roessner… in BMC Genomics (2015)

Article

Inferring 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...

Kaushalya C Amarasinghe, Jason Li, Sally M Hunter, Georgina L Ryland… in BMC Genomics (2014)

Article

Erratum to: CoNVEX: copy number variation estimation in exome sequencing data using HMM

Kaushalya C Amarasinghe, Jason Li, Saman K Halgamuge in BMC Bioinformatics (2013)

Article

CoNVEX: 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...

Kaushalya C Amarasinghe, Jason Li, Saman K Halgamuge in BMC Bioinformatics (2013)

Article

The 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...

Isaam Saeed, Saman K Halgamuge in BMC Genomics (2009)

Article

Binning 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...

Chon-Kit Kenneth Chan, Arthur L Hsu, Saman K Halgamuge, Sen-Lin Tang in BMC Bioinformatics (2008)

Article

Genome 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...

Jason Li, Saman K Halgamuge, Sen-Lin Tang in BMC Evolutionary Biology (2008)

Article

Gene 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...

Jason Li, Saman K Halgamuge, Christopher I Kells, Sen-Lin Tang in BMC Bioinformatics (2007)