6 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

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

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

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)