NEAR UNSUPERVISED LEARNING FOR EARLY DISCOVERY OF NOVEL PATTERNS: METHODS, SCALABILITY AND LABEL DEPENDABILITY

A physarum-inspired prize-collecting steiner tree approach to identify subnetworks for drug repositioning

Yahui Sun, Pathima Nusrath Hameed, Karin Verspoor, Saman Halgamuge

2016-12-05

BACKGROUND: Drug repositioning can reduce the time, costs and risks of drug development by identifying new therapeutic effects for..

Accurate reconstruction of viral quasispecies spectra through improved estimation of strain richness

Duleepa Jayasundara, I Saeed, BC Chang, Sen-Lin Tang, Saman K Halgamuge

2015-12-09

BACKGROUND: Estimating the number of different species (richness) in a mixed microbial population has been a main focus in metagen..

Algorithm selection for black-box continuous optimization problems: A survey on methods and challenges

Mario A Munoz, Yuan Sun, Michael Kirley, Saman K Halgamuge

2015-10-01

Selecting the most appropriate algorithm to use when attempting to solve a black-box continuous optimization problem is a challeng..

EXIMS: an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data

Chalini D Wijetunge, Isaam Saeed, Berin A Boughton, Jeffrey M Spraggins, Richard M Caprioli, Antony Bacic, Ute Roessner, Saman K Halgamuge

2015-10-01

MOTIVATION: Matrix Assisted Laser Desorption Ionization-Imaging Mass Spectrometry (MALDI-IMS) in 'omics' data acquisition generate..

Extended Differential Grouping for Large Scale Global Optimization with Direct and Indirect Variable Interactions

Yuan Sun, Michael Kirley, Saman K Halgamuge

2015-01-01

Cooperative co-evolution is a framework that can be used to effectively solve large scale optimization problems. This approach emp..

Inferring copy number and genotype in tumour exome data

Kaushalya C Amarasinghe, Jason Li, Sally M Hunter, Georgina L Ryland, Prue A Cowin, Ian G Campbell, Saman K Halgamuge

2014-08-28

BACKGROUND: Using whole exome sequencing to predict aberrations in tumours is a cost effective alternative to whole genome sequenc..

Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment

Jason Li, Maria A Doyle, Isaam Saeed, Stephen Q Wong, Victoria Mar, David L Goode, Franco Caramia, Ken Doig, Georgina L Ryland, Ella R Thompson, Sally M Hunter, Saman K Halgamuge, Jason Ellul, Alexander Dobrovic, Ian G Campbell, Anthony T Papenfuss, Grant A McArthur, Richard W Tothill

2014-04-21

Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portion..

Changes in propagation delays for quantifying pharmacological effects on cortical cultures

DC Mendis, SK Halgamuge, E Morrisroe, S Petrou

2014-01-01

Multielectrode arrays (MEAs) can be used to capture electrophysiological activity of neuronal cultures with high spatio-temporal r..

On the Selection of Fitness Landscape Analysis Metrics for Continuous Optimization Problems

Yuan Sun, Saman K Halgamuge, Michael Kirley, Mario A Munoz

2014-01-01

Selecting the best algorithm for a given optimization problem is non-trivial due to large number of existing algorithms and high c..

Unsupervised learning for exploring MALDI imaging mass spectrometry 'omics' data

CD Wijetunge, I Saeed, SK Halgamuge, B Boughton, U Roessner

2014-01-01

Matrix Assisted Laser Desorption Ionization-Imaging Mass Spectrometry (MALDI-IMS) is an emerging data acquisition technology in bi..

Exploratory analysis of high-throughput metabolomic data

Chalini D Wijetunge, Zhaoping Li, Isaam Saeed, Jairus Bowne, Arthur L Hsu, Ute Roessner, Antony Bacic, Saman K Halgamuge

2013-12-01

In order to make sense of the sheer volume of metabolomic data that can be generated using current technology, robust data analysi..

Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances

Ching-Hung Tseng, Pei-Wen Chiang, Fuh-Kwo Shiah, Yi-Lung Chen, Jia-Rong Liou, Ting-Chang Hsu, Suhinthan Maheswararajah, Isaam Saeed, Saman Halgamuge, Sen-Lin Tang

2013-12-01

Extreme climatic activities, such as typhoons, are widely known to disrupt our natural environment. In particular, studies have re..

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

KC Amarasinghe, J Li, SK Halgamuge

2013-01-01

BACKGROUND: One of the main types of genetic variations in cancer is Copy Number Variations (CNV). Whole exome sequencing (WES) is..