Publications

Sumner JG, Charleston MA, Jermiin LS, Jarvis PD, Markov invariants, plethysms, and phylogenetics, J Theor Biol, in press, 2008
Gandhi KS, McKay FC, Schibeci SD, Arthur JW, Heard RN, Stewart GJ, Booth DR, BAFF is a biological response marker to IFNbeta treatment in multiple sclerosis, Journal of Interferon & Cytokine Research, in press, 2008
Ho JW, Stefani M, dos Remedios CG, Charleston MA, Differential variability analysis of gene expression and its application to human diseases, Bioinformatics, 24(13):390-8, 2008
Jermiin LS, Jayaswal V, Ababneh F, Robinson J, Phylogenetic model evaluation, Methods Mol Biol., 452:331-64, 2008
McHugh L and Arthur JW, Computational methods for protein identification from mass spectrometry data, PLoS Computational Biology, 4(2):0001-0012, 2008 [Open Access]
Arthur JW, Identification and characterization of microbial proteins using peptide mass fingerprinting strategies, in Clinical Bioinformatics, ed. Trent R, 2008
Yang JYH, Microarrays - Planning your experiment, in Clinical Bioinformatics, ed. Trent R, 2008

Jayaswal V, Poladian L, Jermiin LS, Single- and multi-objective analysis of primate evolution using a genetic algorithm, Proceedings of the IEEE Congress on Evolutionary Computation, 4146-4153, 2007
Hyman IT, Ho SY, Jermiin LS, Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA, Mol. Phyologenet. Evol. 45(3):792-812, 2007
Cattley S and Arthur JW, BioManager: the use of a bioinformatics web application as a teaching tool in undergraduate bioinformatics training, Briefings in Bioinformatics, 8:457-465, 2007
McHugh L and Arthur JW, Machine learning in protein identification, Proceedings of Bioinformatics Australia 2007, 59, 2007
Golubchik T, Wise MJ, Easteal S, Jermiin LS, Mind the gaps: Evidence of bias in estimates of multiple sequence alignments, Molecular Biological Evolution, 24:2433-2442, 2007
Lam L, Arthur JW, Semsarian C, Proteome map of the normal murine ventricular myocardium, Proteomics, 7:3629-3633, 2007
Chiu C, Tebo M, Ingles J, Yeates L, Arthur JW, Lind JM, Semsarian C, Genetic screening of calcium regulation genes in familial hypertrophic cardiomyopathy, Journal of Molecular and Cellular Cardiology 43:337-343, 2007
Ball HJ, Sanchez-Perez A, Weiser S, Austin CJD, Astelbauer F, Miu J, McQuillan JA, Stocker R, Jermiin L, Hunt NH, Characterization of an indoleamine 2,3-dioxygenase-like protein found in humans and mice, Gene 396:203-213, 2007
Jayaswal V, Robinson J, and Jermiin L, Estimation of phylogeny and invariant sites under the general Markov model of nucleotide sequence evolution, Systematic Biology 56(2):155-162, 2007
Woodruff PG, Boushey HA, Dolganov, GM, Barker CS, Yang YH, Donnelly S, Ellwanger A, Sidhu SS, Dao-Pick TP, Pantoja, C, Erle, DJ, Yamamoto KR, Fahy JV, Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids, Proc Natl Acad Sci USA 104(40): 1585863, 2007.
Winn VD, Haimov-Kochman R, Paquet AC, Yang YJ, Madhusudhan MS, Gormley M, Feng KT, Bernlohr DA, McDonagh S, Pereira L, Sali A, and Fisher SJ, Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term, Endocrinology 148(3):105979, 2007
Xiao YY, Segal M, Yang YH, and Yeh RF, A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarray. Bioinformatics 23(12): 145967, 2007
Williams E, Xiao YY, Sickles H, Shafer P, Yona G, Yang YH, and Lin DM, Spatial and temporal molecular heterogeneity in the mouse olfactory bulb. BMC Developmental Biology 7:48, 2007
Zhang Y, Chen M, Zhou BB, Jermiin LS, Larkum AW, Evolution of the inner light-harvesting antenna protein family of cyanobacteria, algae, and plants, J. Mol. Evol. 64(3):321-31, 2007
Al Mazari A, Zomaya AY, Charleston M, Salem H, Maher A, Garsia RJ, Lability of antiretroviral drug resistance mutations correlates with immunological and virological responses, Curr. HIV Res. 5(4):403-409, 2007

Publications from SUBIT

Poladian L, Jermiin LS. Multi-objective evolutionary algorithms and phylogenetic inference with multiple data sets. Soft Computing 10, 359-368 [2006]
Wickham S, Large MCJ, Poladian L, Jermiin LS. Exaggeration and suppression of iridescence: the evolution of 2-dimentional butterfly structural colours. Journal of the Royal Society Interface 3, 99-108 [2006]
Arthur JW, Sanchez-Perez A, Cook DI, Scoring of predicted GRH2 phosphorylation sites in Nedd4-2, Bioinformatics 22(18):2192-2195, 2006 (PDF)
Chiu C, Lind JM, Ingles J, Arthur JW, and Semsarian C, Leu39ter mutation identified in the phospholamban gene in a family with hypertrophic cardiomyopathy, Heart, Lung, and Circulation 15S:S57-S58, 2006
Sutton R, Salem H, Maher A, Arthur JW, and Garcia R, Modelling the impact of T-20 (enfuviritide) resistance mutations on HIV envelope gp41 structures, Proceedings of the Australian Health and Medical Research Congress 465, 2006
Charleston MA, Galvani AP. A cophylogenetic perspective of host-pathogen evolution. DIMACS Series in Applied Mathematics ??, ???-??? [2006]
Ababneh F, Jermiin LS, Robinson J. Generation of the exact distribution and simulation of matched nucleotide sequences on a phylogenetic tree. Journal of Mathematical Modelling & Algorithms ??, ???-??? [2006]
Holland BR, Jermiin LS, Moulton V. Improved consensus network techniques for genome-scale phylogeny. Molecular Biology & Evolution ??, ???-??? [2006]
Charleston MA, Perkins SL. Traversing the tangle: algorithms and applications for cophylogenetic studies. Journal of Biomedical Informatics ??, ???-??? [2006]
Zhou BB, Till M, Zomaya AY, Jermiin LS. A parallel implementation of the maximum-likelihood method for phylogenetic analysis. International Journal of Computing and Engineering ??, ???-??? [2006]
Ababneh F, Jermiin LS, Ma C, Robinson J. Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics ??, ???-??? [2006]
Chen M, Hiller RG, Howe CJ, Larkum AWD. Unique origin and lateral transfer of prokaryotic chlorophyll-b and chlorophyll-d light-harvesting systems. Molecular Biology & Evolution 22, 21-28 [2005]
Slade PF, Wakeley J. The structured ancestral selection graph and the many-demes limit. Genetics 169, 1117-1131 [2005]
Murray S, Flø Jørgensen M, Ho SYW, Patterson DJ, Jermiin LS. Improving the analysis of dinoflagellate phylogeny based on rDNA. Protist 156, 269-286 [2005]
Mu J, Joy DA, Duan J, Huang Y, Carlton J, Walker J, Barnwell J, Beerli P Charleston MA, Pybus OG, Su X-Z. Host switch leads to emergence of Plasmodium virax malaria in humans. Molecular Biology & Evolution 22, 1686-1693 [2005]
Jayaswal V, Jermiin LS, Robinson J. Estimation of phylogeny using a general Markov model. Evolutionary Bioinformatics Online 1, 62-80 [2005]
Jermiin LS, Poladian L, Charleston MA. Is the “Big Bang” in animal evolution real? Science 310 1910-1911 [2005]
Jermiin LS, Ho SYW, Ababneh F, Robinson J, Larkum AWD. The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Systematic Biology 53, 638-643 [2004]
Ho SYW, Jermiin LS. Tracing the decay of the historical signal in biological sequence data. Systematic Biology 53, 623-637 [2004]
Hardy MP, Owczarek CM, Jermiin LS, Ejdebäck M, Hertzog PJ. Characterization of the type I interferon locus and identification of novel genes. Genomics 84, 331-345 [2004] (Data link)
Premzl M, Gready JE, Jermiin LS, Simonic T, Marshall Graves JA. Evolution of vertebrate genes related to Prion and Shadoo proteins - clues from comparative genomic analysis. Molecular Biology & Evolution 22, 2210-2231 [2004]
Poladian L, Jermiin LS. What might evolutionary algorithms (EA) and multi-objective optimisation (MOO) contribute to phylogenetics and the Total Evidence debate? Biological Applications of Genetic and Evolutionary Computing: In the Proceedings of the Genetic and Evolutionary Computing Conference (GECCO-2004, Seattle, USA, June 27-30, 2004).
Poladian L, Jermiin LS. Phylogenetic inference using evolutionary multi-objective optimisation. Post-deadline paper: In the Proceedings of the Genetic and Evolutionary Computing Conference (GECCO-2004, Seattle, USA, June 27-30, 2004).
Jermiin LS, Ho SYW, Ababneh F, Robinson J, Larkum AWD. Hetero: A program to simulate the evolution of DNA on a four-taxon tree. Applied Bioinformatics 2, 159-163 [2003] (Code link)
Kummerfeld SK, Weiss AS, Fekete A, Jermiin LS. AMID: Autonomous modeler of intragenic duplication. Applied Bioinformatics 2, 169-176 [2003] (Code link)