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Dr Arief Gusnanto

Lecturer
Statistics

Contact details

Room: Satellite 10.14
Tel: +44 (0)113 3435135
Email: A.Gusnanto @ leeds.ac.uk

Research interests

My research interest are in the development of statistical methods and inference in the field of statistical bioinformatics, biology, medicine, statistical genetics, genetic epidemiology, chemometrics, and high-dimensional data.

Current postgraduate students

Samira Abushilah (2014)
Khaled Alqahtani (2013)
Mohammed Alshahrani (2014)
Huda Alshanbari (2013)
Kyriaki Myrissa (2011)

Publications

Gusnanto A, Gosling JP, Pope C Identification of transcript regulatory patterns in cell differentiation. Bioinformatics, 2017
DOI:10.1093/bioinformatics/btx406
View abstract

Shuweihdi F, Taylor CC, Gusnanto A Classification of form under heterogeneity and non-isotropic errors Journal of Applied Statistics, 44, 1495-1508, 2017
DOI:10.1080/02664763.2016.1214246
View abstract

De Cat C, Gusnanto A, Serratrice L IDENTIFYING A THRESHOLD FOR THE EXECUTIVE FUNCTION ADVANTAGE IN BILINGUAL CHILDREN Studies in Second Language Acquisition, 1-33, 2017
DOI:10.1017/S0272263116000486
View abstract

Nooney C, Gusnanto A, Gilks WR, Barber S Do protein structures evolve around 'anchor' residues? In Geometry Driven Statistics, 311-336, 2015
DOI:10.1002/9781118866641.ch16
View abstract

Gusnanto A, Tcherveniakov P, Shuweihdi F, Samman M, Rabbitts P, Wood HM Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data Bioinformatics, 31, 2713-2720, 2015
DOI:10.1093/bioinformatics/btv191
View abstract

Dye L; Schnell R; Croden F; Camidge D; Myrissa K; Garner F; Gusnanto A; Lawton C Relationships between menstrual cycle phase, dietary fibre intake, bowel function and digestive symptomsANNALS OF NUTRITION AND METABOLISM, 385-385 2015

Gusnanto A, Pawitan Y Sparse alternatives to ridge regression: a random effects approach Journal of Applied Statistics, 42, 12-26, 2015
DOI:10.1080/02664763.2014.929640
View abstract

Nooney C, Gusnanto A, Gilks WR, Barber S Do protein structures evolve around 'anchor' residues? GEOMETRY DRIVEN STATISTICS, 313-336, 2015

Gusnanto A, Taylor CC, Nafisah I, Wood HM, Rabbitts P, Berri S Estimating optimal window size for analysis of low-coverage next-generation sequence data. Bioinformatics, 30, 1823-1829, 2014
DOI:10.1093/bioinformatics/btu123
View abstract

Gusnanto A, Pawitan Y Sparse alternatives to ridge regression: a random effects approach Journal of Applied Statistics, 2014
DOI:10.1080/02664763.2014.929640
View abstract

Gusnanto A, Ploner A, Shuweihdi F, Pawitan Y Partial least squares and logistic regression random-effects estimates for gene selection in supervised classification of gene expression data Journal of Biomedical Informatics, 46, 697-709, 2013
DOI:10.1016/j.jbi.2013.05.008
View abstract

Myrissa K, Dye L, Gusnanto A, Danks R, Lawton C PREDICTORS OF WEIGHT LOSS AND/OR WEIGHT LOSS MAINTENANCE: AN INTERNET BASED SURVEY ANNALS OF NUTRITION AND METABOLISM, 63, 1362-1362, 2013

Lee W, Gusnanto A, Salim A, Magnusson P, Sim X, Tai ES, Pawitan Y Estimating the number of true discoveries in genome-wide association studies. Stat Med, 31, 1177-1189, 2012
DOI:10.1002/sim.4391
View abstract

Lee W, Gusnanto A, Salim A, Magnusson P, Sim X, Tai ES, Pawitan Y Estimating the number of true discoveries in genome-wide association studies Statistics in Medicine, 31, 1177-1189, 2012
DOI:10.1002/sim.4391
View abstract

Gusnanto A, Wood HM, Pawitan Y, Rabbitts P, Berri S Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. Bioinformatics, 28, 40-47, 2012
DOI:10.1093/bioinformatics/btr593
View abstract

Sivapalaratnam S, Farrugia R, Nieuwdorp M, Langford CF, van Beem RT, Maiwald S, Zwaginga JJ, Gusnanto A, Watkins NA, Trip MD, Ouwehand WH Identification of candidate genes linking systemic inflammation to atherosclerosis; results of a human in vivo LPS infusion study. BMC Med Genomics, 4, 64, 2011
DOI:10.1186/1755-8794-4-64
View abstract

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 J-J, Samani NJ, Watkins NA, Maguire PB, Ouwehand WH, Bloodomics Consortium Transcription profiling in human platelets reveals LRRFIP1 as a novel protein regulating platelet function. Blood, 116, 4646-4656, 2010
DOI:10.1182/blood-2010-04-280925
View abstract

Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D, Hardie DL, Angenent WGJ, 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, Gottgens B, Ouwehand WH, Bloodomics Consortium A HaemAtlas: characterizing gene expression in differentiated human blood cells BLOOD, 113, E1-E9, 2009
DOI:10.1182/blood-2008-06-162958

Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D, Hardie DL, Angenent WGJ, 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 A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood, 113, e1-e9, 2009
DOI:10.1182/blood-2008-06-162958
View abstract

Sivapalaratnam S, Farrugia R, Nieuwdorp M, Gusnanto A, Watkins NA, Zwaginga JJ, Ouwehand WH, Trip MD, Stroes ES, Kastelein JJ Toll Like Receptor 4 Activation Elicits Pro-atherogenic Gene Activation In Monocytes In Humans CIRCULATION, 118, S563-S563, 2008

Burns P, Gusnanto A, Macaulay IC, Rankin A, Tom B, Langford CF, Dudbridge F, Ouwehand WH, Watkins NA, Bloodomics Consortium Identification of variation in the platelet transcriptome associated with glycoprotein 6 haplotype. Platelets, 19, 258-267, 2008
DOI:10.1080/09537100801947434
View abstract

Dudbridge F, Gusnanto A Estimation of significance thresholds for genomewide association scans. Genet Epidemiol, 32, 227-234, 2008
DOI:10.1002/gepi.20297
View abstract

Huang J, Gusnanto A, O'Sullivan K, Staaf J, Borg A, Pawitan Y Robust smooth segmentation approach for array CGH data analysis BIOINFORMATICS, 23, 2463-2469, 2007
DOI:10.1093/bioinformatics/btm359

Gusnanto A; Dudbridge E Estimating significance threshold for genomewide association scansGENETIC EPIDEMIOLOGY, 629-629 2007

Gusnanto A; Dudbridge F Estimating genome-wide significance levels for associationANN HUM GENET, 556-557 2007

Gusnanto A, Tom BDM, Burns P, Macaulay I, Thijssen-Timmer DC, Tijssen M, Langford C, Watkins N, Ouwehand W, Berzuini C, Dudbridge F Improving the power to detect differentially expressed genes in comparative microarray experiments by including information from self-self hybridizations Computational Biology and Chemistry, 31, 178-185, 2007
DOI:10.1016/j.compbiolchem.2007.03.005

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 Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins BLOOD, 109, 3260-3269, 2007
DOI:10.1182/blood-2006-07-036269

Gusnanto A A PCR-based expression signature of malignancy in follicular thyroid tumors Endocrine-related cancer, 14, 381-391, 2007

Gusnanto A Identification of differentially expressed genes and false discovery rate in microarray studies None, 18, 187-193, 2007

Macaulay IC; Tijssen MR; Thijssen-Timmer DC; Gusnanto A; Steward M; Tom B; Carr P; Voermans C; De Jong IW; Dudbridge F Novel transmembrane megakaryocyte proteins identified by comparative gene expression profiling of in vitro differentiated human megakaryocytes and erythroblastsBRIT J HAEMATOL, 26-26 2006

Ploner A, Calza S, Gusnanto A, Pawitan Y Multidimensional local false discovery rate for microarray studies Bioinformatics, 22, 556-565, 2006
DOI:10.1093/bioinformatics/btk013

Dudbridge F, Gusnanto A, Koeleman BPC Detecting multiple associations in genome-wide studies. Hum Genomics, 2, 310-317, 2006
View abstract

Macaulay IC, Carr P, Gusnanto A, Ouwehand WH, Fitzgerald D, Watkins NA Platelet genomics and proteomics in human health and disease. J Clin Invest, 115, 3370-3377, 2005
DOI:10.1172/JCI26885
View abstract

Gusnanto A; Ploner A; Pawitan Y Fold-Change Estimation and Identification of Differentially Expressed Genes using Mixture Mixed-Model. 2005

Gusnanto A, Ploner A, Pawitan Y Fold-change estimation of differentially expressed genes using mixture mixed-model Statistical Applications in Genetics and Molecular Biology, 4, 2005
View abstract

Gusnanto A, Ploner A, Pawitan Y Fold-change estimation of differentially expressed genes using mixture mixed-model STAT APPL GENET MO B, 4, 2005

Gusnanto A False discovery rate, sensitivity, and sample size for microarray studies Bioinformatics, 21, 3017-3024, 2005

Dreij K, Bajak E, Sundberg K, Cotgreave I, Jernstrom B, Seidel A, Gusnanto A DNA adducts of benzo[a]pyrene- and dibenzo[a,l]pyrene-diol epoxides in human lung epithelial cells: Kinetics of adduct removal, effects on cell cycle checkpoints, and gene expression POLYCYCLIC AROMATIC COMPOUNDS, 24, 549-566, 2004
DOI:10.1080/10406630490471645

Xue Y, Haas SA, Brino L, Gusnanto A, Reimers M, Talibi D, Vingron M, Ekwall K, Wright APH A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast, 21, 25-39, 2004
DOI:10.1002/yea.1053
View abstract

Gusnanto A A DNA microarray for fission yeast: minimal changes after temperature shift Yeast, 21, 25-39, 2004

Xue YT; Haas S; Brino L; Gusnanto A; Riemers M; Talibi D; Vingron M; Ekwall K; Wright APH A DNA microarray for genome-wide gene expression analysis in fission yeast.YEAST, S333-S333 2003

Gusnanto A, Pawitan Y, Huang J, Lane W Variable selection in random calibration of near infrared instruments: ridge regression and partial least squares regression settings Journal of Chemometrics, 17, 174-185, 2003
DOI:10.1002/cem.787