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Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data.

Gusnanto A, Tcherveniakov P, Shuweihdi F, Samman M, Rabbitts P, Wood HM.

Bioinformatics. 2015 Aug 15;31(16):2713-20. doi: 10.1093/bioinformatics/btv191. Epub 2015 Apr 5.


Estimating optimal window size for analysis of low-coverage next-generation sequence data.

Gusnanto A, Taylor CC, Nafisah I, Wood HM, Rabbitts P, Berri S.

Bioinformatics. 2014 Jul 1;30(13):1823-9. doi: 10.1093/bioinformatics/btu123. Epub 2014 Mar 5.


Partial least squares and logistic regression random-effects estimates for gene selection in supervised classification of gene expression data.

Gusnanto A, Ploner A, Shuweihdi F, Pawitan Y.

J Biomed Inform. 2013 Aug;46(4):697-709. doi: 10.1016/j.jbi.2013.05.008. Epub 2013 Jun 7.


Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data.

Gusnanto A, Wood HM, Pawitan Y, Rabbitts P, Berri S.

Bioinformatics. 2012 Jan 1;28(1):40-7. doi: 10.1093/bioinformatics/btr593. Epub 2011 Oct 28.


Estimating the number of true discoveries in genome-wide association studies.

Lee W, Gusnanto A, Salim A, Magnusson P, Sim X, Tai ES, Pawitan Y.

Stat Med. 2012 May 20;31(11-12):1177-89. doi: 10.1002/sim.4391. Epub 2011 Oct 11.


Identification of candidate genes linking systemic inflammation to atherosclerosis; results of a human in vivo LPS infusion study.

Sivapalaratnam S, Farrugia R, Nieuwdorp M, Langford CF, van Beem RT, Maiwald S, Zwaginga JJ, Gusnanto A, Watkins NA, Trip MD, Ouwehand WH.

BMC Med Genomics. 2011 Aug 10;4:64. doi: 10.1186/1755-8794-4-64.


Transcription profiling in human platelets reveals LRRFIP1 as a novel protein regulating platelet function.

Goodall AH, Burns P, Salles I, Macaulay IC, Jones CI, Ardissino D, de Bono B, Bray SL, Deckmyn H, Dudbridge F, Fitzgerald DJ, Garner SF, Gusnanto A, Koch K, Langford C, O'Connor MN, Rice CM, Stemple D, Stephens J, Trip MD, Zwaginga JJ, Samani NJ, Watkins NA, Maguire PB, Ouwehand WH; Bloodomics Consortium.

Blood. 2010 Nov 25;116(22):4646-56. doi: 10.1182/blood-2010-04-280925. Epub 2010 Sep 10.


A HaemAtlas: characterizing gene expression in differentiated human blood cells.

Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D, Hardie DL, Angenent WG, Attwood AP, Ellis PD, Erber W, Foad NS, Garner SF, Isacke CM, Jolley J, Koch K, Macaulay IC, Morley SL, Rendon A, Rice KM, Taylor N, Thijssen-Timmer DC, Tijssen MR, van der Schoot CE, Wernisch L, Winzer T, Dudbridge F, Buckley CD, Langford CF, Teichmann S, Göttgens B, Ouwehand WH; Bloodomics Consortium.

Blood. 2009 May 7;113(19):e1-9. doi: 10.1182/blood-2008-06-162958. Epub 2009 Feb 19.


Identification of variation in the platelet transcriptome associated with glycoprotein 6 haplotype.

Burns P, Gusnanto A, Macaulay IC, Rankin A, Tom B, Langford CF, Dudbridge F, Ouwehand WH, Watkins NA; Bloodomics Consortium.

Platelets. 2008 Jun;19(4):258-67. doi: 10.1080/09537100801947434.


Estimation of significance thresholds for genomewide association scans.

Dudbridge F, Gusnanto A.

Genet Epidemiol. 2008 Apr;32(3):227-34. doi: 10.1002/gepi.20297.


Robust smooth segmentation approach for array CGH data analysis.

Huang J, Gusnanto A, O'Sullivan K, Staaf J, Borg A, Pawitan Y.

Bioinformatics. 2007 Sep 15;23(18):2463-9. Epub 2007 Jul 27.


A PCR-based expression signature of malignancy in follicular thyroid tumors.

Foukakis T, Gusnanto A, Au AY, Höög A, Lui WO, Larsson C, Wallin G, Zedenius J.

Endocr Relat Cancer. 2007 Jun;14(2):381-91.


Improving the power to detect differentially expressed genes in comparative microarray experiments by including information from self-self hybridizations.

Gusnanto A, Tom B, Burns P, Macaulay I, Thijssen-Timmer DC, Tijssen MR, Langford C, Watkins N, Ouwehand W, Berzuini C, Dudbridge F.

Comput Biol Chem. 2007 Jun;31(3):178-85. Epub 2007 Mar 24.


Identification of differentially expressed genes and false discovery rate in microarray studies.

Gusnanto A, Calza S, Pawitan Y.

Curr Opin Lipidol. 2007 Apr;18(2):187-93. Review.


Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins.

Macaulay IC, Tijssen MR, Thijssen-Timmer DC, Gusnanto A, Steward M, Burns P, Langford CF, Ellis PD, Dudbridge F, Zwaginga JJ, Watkins NA, van der Schoot CE, Ouwehand WH.

Blood. 2007 Apr 15;109(8):3260-9. Epub 2006 Dec 27.


Fold-change estimation of differentially expressed genes using mixture mixed-model.

Gusnanto A, Ploner A, Pawitan Y.

Stat Appl Genet Mol Biol. 2005;4:Article26. Epub 2005 Sep 21.


Detecting multiple associations in genome-wide studies.

Dudbridge F, Gusnanto A, Koeleman BP.

Hum Genomics. 2006 Mar;2(5):310-7. Review.


Multidimensional local false discovery rate for microarray studies.

Ploner A, Calza S, Gusnanto A, Pawitan Y.

Bioinformatics. 2006 Mar 1;22(5):556-65. Epub 2005 Dec 20.


Platelet genomics and proteomics in human health and disease.

Macaulay IC, Carr P, Gusnanto A, Ouwehand WH, Fitzgerald D, Watkins NA.

J Clin Invest. 2005 Dec;115(12):3370-7. Review.


False discovery rate, sensitivity and sample size for microarray studies.

Pawitan Y, Michiels S, Koscielny S, Gusnanto A, Ploner A.

Bioinformatics. 2005 Jul 1;21(13):3017-24. Epub 2005 Apr 19.

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