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Use of adaptive network burst detection methods for multielectrode array data and the generation of artificial spike patterns for method evaluation.

Mendis GD, Morrisroe E, Petrou S, Halgamuge SK.

J Neural Eng. 2016 Apr;13(2):026009. doi: 10.1088/1741-2560/13/2/026009.


A new peak detection algorithm for MALDI mass spectrometry data based on a modified Asymmetric Pseudo-Voigt model.

Wijetunge CD, Saeed I, Boughton BA, Roessner U, Halgamuge SK.

BMC Genomics. 2015;16 Suppl 12:S12. doi: 10.1186/1471-2164-16-S12-S12.


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

Jayasundara D, Saeed I, Chang BC, Tang SL, Halgamuge SK.

BMC Bioinformatics. 2015;16 Suppl 18:S3. doi: 10.1186/1471-2105-16-S18-S3.


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

Wijetunge CD, Saeed I, Boughton BA, Spraggins JM, Caprioli RM, Bacic A, Roessner U, Halgamuge SK.

Bioinformatics. 2015 Oct 1;31(19):3198-206. doi: 10.1093/bioinformatics/btv356.


ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing.

Jayasundara D, Saeed I, Maheswararajah S, Chang BC, Tang SL, Halgamuge SK.

Bioinformatics. 2015 Mar 15;31(6):886-96. doi: 10.1093/bioinformatics/btu754.


Inferring copy number and genotype in tumour exome data.

Amarasinghe KC, Li J, Hunter SM, Ryland GL, Cowin PA, Campbell IG, Halgamuge SK.

BMC Genomics. 2014 Aug 28;15:732. doi: 10.1186/1471-2164-15-732.


Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment.

Li J, Doyle MA, Saeed I, Wong SQ, Mar V, Goode DL, Caramia F, Doig K, Ryland GL, Thompson ER, Hunter SM, Halgamuge SK, Ellul J, Dobrovic A, Campbell IG, Papenfuss AT, McArthur GA, Tothill RW.

PLoS One. 2014 Apr 21;9(4):e95217. doi: 10.1371/journal.pone.0095217.


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

Amarasinghe KC, Li J, Halgamuge SK.

BMC Bioinformatics. 2013;14 Suppl 2:S2. doi: 10.1186/1471-2105-14-S2-S2.


CONTRA: copy number analysis for targeted resequencing.

Li J, Lupat R, Amarasinghe KC, Thompson ER, Doyle MA, Ryland GL, Tothill RW, Halgamuge SK, Campbell IG, Gorringe KL.

Bioinformatics. 2012 May 15;28(10):1307-13. doi: 10.1093/bioinformatics/bts146.


Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition.

Saeed I, Tang SL, Halgamuge SK.

Nucleic Acids Res. 2012 Mar;40(5):e34. doi: 10.1093/nar/gkr1204.


Gene functionality's influence on the second codon: A large-scale survey of second codon composition in three domains.

Tang SL, Chang BC, Halgamuge SK.

Genomics. 2010 Aug;96(2):92-101. doi: 10.1016/j.ygeno.2010.04.001.


The oligonucleotide frequency derived error gradient and its application to the binning of metagenome fragments.

Saeed I, Halgamuge SK.

BMC Genomics. 2009 Dec 3;10 Suppl 3:S10. doi: 10.1186/1471-2164-10-S3-S10.


Fast splice site detection using information content and feature reduction.

Baten AK, Halgamuge SK, Chang BC.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S8. doi: 10.1186/1471-2105-9-S12-S8.


Binning sequences using very sparse labels within a metagenome.

Chan CK, Hsu AL, Halgamuge SK, Tang SL.

BMC Bioinformatics. 2008 Apr 28;9:215. doi: 10.1186/1471-2105-9-215.


Genome classification by gene distribution: an overlapping subspace clustering approach.

Li J, Halgamuge SK, Tang SL.

BMC Evol Biol. 2008 Apr 23;8:116. doi: 10.1186/1471-2148-8-116.


Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing.

Chan CK, Hsu AL, Tang SL, Halgamuge SK.

J Biomed Biotechnol. 2008;2008:513701. doi: 10.1155/2008/513701.


Dynamic self-organizing maps with controlled growth for knowledge discovery.

Alahakoon D, Halgamuge SK, Srinivasan B.

IEEE Trans Neural Netw. 2000;11(3):601-14. doi: 10.1109/72.846732.


Splice site identification using probabilistic parameters and SVM classification.

Baten AK, Chang BC, Halgamuge SK, Li J.

BMC Bioinformatics. 2006 Dec 18;7 Suppl 5:S15. Erratum in: BMC Bioinformatics. 2007 Jul 5;8:241.

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