Publications

Selected Leeds Omics related publications...

Recurrent coding sequence variation explains only a small fraction of the genetic architecture of colorectal cancer.

Timofeeva MN, Kinnersley B, Farrington SM, Whiffin N, Palles C, Svinti V, Lloyd A, Gorman M, Ooi L-Y, Hosking FJ, Barclay E, Zgaga L, Dobbins S, Martin L, Theodoratou E, Broderick P, Tenesa A, Smillie C, Grimes G, Hayward C, Campbell A, Porteous D, Deary IJ, Harris SE, Northwood EL, Barrett JH, Smith G, Wolf CR, Forman D, Morreau H, Ruano D, Tops C, Wijnen J, Schrumpf M, Boot A, Vasen HFA, Hes FJ, van Wezel T, Franke A, Lieb W, Schafmayer C, Hampe J, Buch S, Propping P, Hemminki K, Försti A, Westers H, Hofstra R, Pinheiro M, Pinto C, Teixeira M, Ruiz-Ponte C, Fernández-Rozadilla C, Carracedo A, Castells A, Castellvi-Bel S, Campbell H, Bishop DT, Tomlinson IPM, Dunlop MG, Houlston RS. Recurrent coding sequence variation explains only a small fraction of the genetic architecture of colorectal cancer. Scientific Reports, 2015; 5:16286.

Genome-wide meta-analysis identifies five new susceptibility loci and confirms a further two loci for cutaneous malignant melanoma.

Law MH, Bishop DT, Lee JE, Brossard M, Martin NG, Moses EK, Song F, Barrett JH, Kumar R, Easton DF, Pharoah PDP, Swerdlow AJ, Kypreou KP, Taylor JC, Harland M, Randerson-Moor J, Akslen LA, Andresen PA, Avril M-F, Azizi E, Bianchi Scarrà G, Brown KM, Dębniak T, Duffy DL, Elder DE, Fang S, Friedman E, Galan P, Ghiorzo P, Gillanders EM, Goldstein AM, Gruis NA, Hansson J, Helsing P, Hočevar M, Höiom V, Ingvar C, Kanetsky PA, Chen WV, GenoMEL Consortium, Essen-Heidelberg Investigators, The SDH Study Group, Q-MEGA and QTWIN Investigators, AMFS Investigators, ATHENS Melanoma Study Group, Landi MT, Lang J, Lathrop GM, Lubiński J, Mackie RM, Mann GJ, Molven A, Montgomery GW, Novaković S, Olsson H, Puig S, Puig-Butille JA, Qureshi AA, Radford-Smith GL, van der Stoep N, van Doorn R, Whiteman DC, Craig JE, Schadendorf D, Simms LA, Burdon KP, Nyholt DR, Pooley KA, Orr N, Stratigos AJ, Cust AE, Ward SV, Hayward NK, Han J, Schulze H-J, Dunning AM, Newton Bishop JA, Demenais F, Amos CI, MacGregor S, Iles MM. Genome-wide meta-analysis identifies five new susceptibility loci and confirms a further two loci for cutaneous malignant melanoma. Nature Genetics 2015; 47:987-95.

Telomere length and common disease: study design and analytical challenges.

Barrett JH, Iles MM, Dunning AM, Pooley KA. Telomere length and common disease: study design and analytical challenges. Hum Genetics 2015; 134: 679-689.

A large-scale genetic analysis reveals a strong contribution of the HLA class II region to giant cell arteritis susceptibility.

Carmona FD, Mackie SL, Martín J-E, Taylor JC, Vaglio A, Eyre S, Bossini-Castillo L, Castañeda S, Cid MC, Hernández-Rodríguez J, Prieto-González S, Solans R, Ramentol-Sintas M, González-Escribano MF, Ortiz-Fernández L, Morado IC, Narváez J, Miranda-Filloy JA, Spanish GCA Group, Beretta L, Lunardi C, Cimmino MA, Gianfreda D, Santilli D, Ramirez GA, Soriano A, Muratore F, Pazzola G, Addimanda O, Wijmenga C, Witte T, Schirmer JH, Moosig F, Schönau V, Franke A, Palm Ø, Molberg Ø, Diamantopoulos AP, Carette S, Pagnoux C, Cuthbertson D, Hoffman GS, Langford CA, Khalidi NA, Koening CL, McAlear CA, Moreland L, Monach PA, Seo P, Sreih A, Warrington KJ, Ytterberg SR, Gregersen PK, Pease CT, Gough A, Green M, Hordon L, Jarrett S, Watts R, Levy S, Patel Y, Kamath S, Dasgupta B, Worthington J, Koeleman BPC, de Bakker PIW, Barrett JH, Salvarani C, Merkel PA, González-Gay MA, Morgan AW, Martín J. A large-scale genetic analysis reveals a strong contribution of the HLA class II region to giant cell arteritis susceptibility. American Journal of Human Genetics 2015; 96:565-80.

Fine mapping of genetic susceptibility loci for melanoma reveals a mixture of single variant and multiple variant regions.

Barrett JH, Taylor JC, Bright C, Harland M, Dunning AM, Akslen LA, Andresen P, Avril M-F, Azizi E, Bianchi Scarra G, Brossard M, Brown K, Debniak T, Elder D, Friedman E, Ghiorzo P, Gillanders E, Gruis N, Hansson J, Helsing P, Hocevar M, Hoiom V, Ingvar C, Landi MT, Lang J, Lathrop GM, Lubinski J, Mackie R, Molven A, Novakovic S, Olsson H, Puig S, Puig-Butille JA, van der Stoep N, van Doorn R, van Workum W, Goldstein Am, Kanetsky PA, Pharoah PDP, Demenais F, Hayward NK, Newton Bishop JA, Bishop DT, Iles MM. Fine mapping of genetic susceptibility loci for melanoma reveals a mixture of single variant and multiple variant regions, International Journal of Cancer 2015; 136: 1351-1360.

The effect on melanoma risk of genes previously associated with telomere length.

Iles MM, Bishop DT, Taylor JC, Hayward NK, Brossard M, Cust AE, Dunning AM, Lee JE, Moses EK, Akslen LA, AMFS investigators, Andresen PA, Avril M-F, Azizi E, Bianchi Scarrà G, Brown KM, Dębniak T, Elder DE, Friedman E, Ghiorzo P, Gillanders EM, Goldstein AM, Gruis NA, Hansson J, Harland M, Helsing P, Hočevar M, Höiom V, IBD investigators, Ingvar C, Kanetsky PA, Landi MT, Lang J, Lathrop GM, Lubiński J, Mackie RM, Martin NG, Molven A, Montgomery GW, Novaković S, Olsson H, Puig S, Puig-Butille JA, QMEGA and QTWIN investigators, Radford-Smith GL, Randerson-Moor J, SDH Study Group, van der Stoep N, van Doorn R, Whiteman DC, MacGregor S, Pooley KA, Ward SV, Mann GJ, Amos CI, Pharoah PDP, Demenais F, Law MH, Newton Bishop JA, Barrett JH on behalf of the GenoMEL Consortium. The effect on melanoma risk of genes previously associated with telomere length. Journal of the National Cancer Institute 2014; 106(10).

Evidence of NLRP3-inflammasome activation in rheumatoid arthritis (RA); genetic variants within the NLRP3-inflammasome complex in relation to susceptibility to RA and response to anti-TNF treatment.

Mathews RJ, Robinson JI, Battellino M, Wong C, Taylor JC, Eyre S, Churchman SM, Wilson AG, Isaacs JD, Hyrich K, Barton A, Plant D, Savic S, Cook GP, Sarzi-Puttini P, Emery P, Barrett JH, Morgan AW, McDermott MF. Evidence of NLRP3-inflammasome activation in rheumatoid arthritis (RA); genetic variants within the NLRP3-inflammasome complex in relation to susceptibility to RA and response to anti-TNF treatment. Annals of the Rheumatic Diseases 2014; 73: 1202-1210.

MTHFR functional genetic variation and methotrexate treatment response in rheumatoid arthritis: A meta-analysis.

Morgan MD, Al-Shaarawy N, Martin S, Robinson JI, Twigg S, YEAR Consortium, Magdy AA, Omar AS, Ghattas MH, Emery P, Barrett JH* and Morgan AW* (* joint last authors). MTHFR functional genetic variation and methotrexate treatment response in rheumatoid arthritis: A meta-analysis. Pharmacogenomics 2014; 15: 467-475.

A variant in FTO shows association with melanoma risk not due to BMI.

Iles MM, Law MH, Stacey SN, Han J, Fang S, Pfeiffer R, Harland M, MacGregor S, Taylor JC, Aben KK, Akslen LA, Avril M-F, Azizi E, Bakker B, Benediktsdottir KR, Bergman W, Bianchi Scarrà G, Brown KM, Calista D, Chaudru V, Concetta Fargnoli M, Cust AE, Demenais F, de Waal AC, Dębniak T, Elder DE, Friedman E, Galan P, Ghiorzo P, Gillanders EM, Goldstein AM, Gruis NA, Hansson J, Helsing P, Hočevar M, Höiom V, Hopper JL, Ingvar C, Janssen M, Jenkins MA, Kanetsky PA, Kiemeney LA, Lang J, Lathrop GM, Leachman S, Lee JE, Lubiński J, Mackie RM, Mann GJ, Mayordomo JI, Molven A, Mulder S, Nagore E, Novaković S, Okamoto I, Olafsson JH, Olsson H, Pehamberger H, Peris K, Pilar Grasa M, Planelles D, Puig S, Puig-Butille JA, Q-MEGA and AMFS investigators, Randerson-Moor J, Requena C, Rivoltini L, Rodolfo M, Santinami M, Sigurgeirsson B, Snowden H, Song F, Sulem P, Thorisdottir K, Tuominen R, Van Belle P, van der Stoep N, van Rossum MM, Wei Q, Wendt J, Zelenika D, Zhang m, Landi MT, Thorleifsson G, Bishop DT, Amos CI, Hayward NK, Stefansson K, Newton Bishop JA, Barrett JH. A variant in FTO shows association with melanoma risk not due to BMI. Nature Genetics 2013; 45: 428-32.

SNP prioritization using a Bayesian probability of association.

Thompson JR, Gögele M, Weichenberger CX, Modenese M, Attia J, Barrett JH, Boehnke M, De Grandi A, Domingues FS, Hicks AA, Marroni F, Pattaro C, Ruggeri F, Borsani G, Casari G, Parmigiani G, Pastore A, Pfeufer A, Schwienbacher C, Taliun D, CKDGen Consortium, Fox CS, Pramstaller PP, Minelli C. SNP prioritization using a Bayesian probability of association. Genetic Epidemiology 2013; 37: 214-221.

Importance of different types of prior knowledge in selecting genome-wide findings for follow-up.

Minelli C, De Grandi A, Weichenberger CX, Gögele M, Modenese M, Attia J, Barrett JH, Boehnke M, Borsani G, Casari G, Fox CS, Freina T, Hicks AA, Marroni F, Parmigiani G, Pastore A, Pattaro C, Pfeufer A, Ruggeri F, Schwienbacher C, Taliun D, Pramstaller PP, Domingues FS, Thompson JR. Importance of different types of prior knowledge in selecting genome-wide findings for follow-up. Genetic Epidemiology 2013; 37: 205-13.

Pathway analysis of a melanoma genome-wide association study: Analysis of genes related to tumour immunosuppression.

Schoof N, Iles MM, GenoMEL consortium, Bishop DT, Newton Bishop JA and Barrett JH. Pathway analysis of a melanoma genome-wide association study: Analysis of genes related to tumour immunosuppression. PLoS ONE, 2011; 6(12):e29451.

Two-stage analyses of sequence variants in association with quantitative traits.

Barrett JH and Nsengimana J. Two-stage analyses of sequence variants in association with quantitative traits. BMC Proceedings, 2011; 5(Suppl 9):S53.

Genome-wide association study identifies novel loci predisposing to cutaneous melanoma.

Amos CI, Wang L-E, Lee JE, Gershenwald JE, Chen WV, Fang S, Kosoy R, Zhang M, Qureshi AA, Vattathil S, Schacherer CW, Gardner JM, Wang Y, Bishop DT, Barrett JH, GenoMEL Investigators, MacGregor S, Hayward NK, Martin NG, Duffy DL, Q-Mega Investigators, Mann GJ, Cust A, Hopper J, AMFS Investigators, Brown KM, Grimm EA, Xu Y, Han Y, Jing K, McHugh C, Laurie CC, Doheny KF, Pugh EW, Seldin MF, Han J, Wei Q. Genome-wide association study identifies novel loci predisposing to cutaneous melanoma. Human Molecular Genetics, 2011; 20:5012-23.

Genome-wide association study identifies three new melanoma susceptibility loci.

Barrett JH, Iles MM, Harland M, Taylor JC, Aitken JF, Andresen PA, Akslen LA, Armstrong BK, Avril M-F, Azizi E, Bakker B, Bergman W, Bianchi-Scarrà G, Bressac-de Paillerets B, Calista D, Cannon-Albright LA, Corda E, Cust AE, Dębniak T, Duffy D, Dunning A, Easton DF, Friedman E, Galan P, Ghiorzo P, Giles GG, Hansson J, Hocevar M, Höiom V, Hopper JL, Ingvar C, Janssen B, Jenkins MA, Jönsson G, Kefford RF, Landi G, Landi MT, Lang J, Lubiński J, Mackie R, Malvehy J, Martin NG, Molven A, Montgomery GW, van Nieuwpoort FA, Novakovic S, Olsson H, Pastorino L, Puig S, Puig-Butille JA, Randerson-Moor J, Snowden H, Tuominen R, Van Belle P, van der Stoep N, Whiteman D.C., Zelenika D., Han J., Fang S., Lee JE, Wei Q, Lathrop GM, Gillanders EM, Brown KM, Goldstein AM, Kanetsky PA, Mann GJ, MacGregor S, Elder DE, Amos CI, Hayward NK, Gruis NA, Demenais F, Newton Bishop JA, Bishop DT on behalf of the GenoMEL Consortium. Genome-wide association study identifies three new melanoma susceptibility loci. Nature Genetics, 2011; 43:1108-13.

European Genome-Wide Association Study Identifies SLC14A1 as a New Urinary Bladder Cancer Susceptibility Gene.

Rafnar T, Vermeulen SH, Sulem P, Thorleifsson G, Aben KK, Witjes JA, Grotenhuis AJ, Verhaegh GW, Hulsbergen-van de Kaa C, Besenbacher S, Gudbjartsson D, Stacey S, Gudmundsson J, Johannsdottir H, Bjarnason H, Zanon C, Helgadottir H, Jonasson JG, Tryggvadottir L, Jonsson E, Geirsson G, Nikulasson S, Petursdottir V, Bishop DT, Chung-Sak S, Choudhury A, Elliott F, Barrett JH, Knowles MA, de Verdier PJ, Ryk C, Lindblom A, Rudnai P, Gurzau E, Koppova K, Vineis P, Polidoro S, Guarrera S, Sacerdote C, Panadero A, Sanz-Velez JI, Sanchez M, Valdivia G, Garcia-Prats MD, Hengstler JG, Selinski S, Gerullis H, Ovsiannikov D, Khezri A, Aminsharifi A, Malekzadeh M, van de Berg LH, Ophoff RA, Veldink JH, Ghaderi A, Golka K, Mayordomo JI, Matullo G, Kumar R, Steineck G, Kiltie AE, Thorsteinsdottir U, Kong A, Stefansson K, Kiemeney LA. European Genome-Wide Association Study Identifies SLC14A1 as a New Urinary Bladder Cancer Susceptibility Gene. Human Molecular Genetics 2011; 20: 4268-81.

Genetic variants within the MAP kinase signalling network and anti- TNF treatment response in rheumatoid arthritis patients.

Coulthard LR, Taylor JC, Eyre S, BRAGGSS Biologics in Rheumatoid Arthritis Genetics, Robinson JI, Wilson AG, Isaacs JD, Hyrich K, Emery P, Barton A, Barrett JH, Morgan AW, and McDermott MF. Genetic variants within the MAP kinase signalling network and anti- TNF treatment response in rheumatoid arthritis patients. Annals of the Rheumatic Diseases 2011; 70: 98-103.

Dissection of the FCGR3A association with RA: increased association in men and with autoantibody positive disease.

Jewell R, Conway C, Mitra A, Randerson-Moor J, Lobo S, Nsengimana J, Harland M, Marples M, Edward S, Cook M, Powell B, Boon A, de Kort F, Parker K, Cree I, Barrett JH, Knowles M, Bishop DT and Newton-Bishop JA. Patterns of expression of DNA repair genes and relapse from melanoma. Clinical Cancer Research 2010; 16: 5211-21.106. Robinson JI, Barrett JH, Taylor JC, YEAR consortium, Naven M, Corscadden D, BRAGGSS, Barton A, Wilson AG, Emery P, Isaacs JD, Morgan AW. Dissection of the FCGR3A association with RA: increased association in men and with autoantibody positive disease. Annals of Rheumatic Diseases 2010; 69:1054-7.

Polymorphisms in xenobiotic metabolizing enzymes and diet influence colorectal adenoma risk.

Northwood EL, Elliott F, Forman D, Barrett JH, Wilkie MJ, Carey FA, Steele RJ, Wolf R, Bishop T, Smith G. Polymorphisms in xenobiotic metabolizing enzymes and diet influence colorectal adenoma risk. Pharmacogenetics and Genomics 2010; 20: 315-26.

A sequence variant at 4p16.3 confers susceptibility to urinary bladder cancer.

Kiemeney LA, Sulem P, Besenbacher S, Vermeulen SH, Sigurdsson A, Thorleifsson G, Stacey SN, Gudmundsson J, Zanon C, Kostic J, Bjarnason H, Palsson ST, Skarphedinsson OB, Gudjonsson SA, Witjes JA, Grotenhuis AJ, Verhaegh GW, Bishop DT, Sak SC, Choudhury A, Elliott F, Barrett JH, Hurst CD, de Verdier PJ, Rudnai P, Gurzau E, Koppova K, Vineis P, Polidoro S, Guarrera S, Sacerdote C, Campagna M, Placidi D, Arici C, Zeegers MP, Kellen E, Gutierrez BS, Sanz-Velez JI, Sanchez-Zalabardo M, Valdivia G, Garcia-Prats MD, Hengstler JG, Blaszkewicz M, Dietrich H, Ophoff RA, van den Berg LH, Alexiusdóttir K, Kristjansson K, Geirsson G, Nikulasson S, Petursdottir V, Kong A, Thorgeirsson T, Mungan NA, Lindblom A, van Es MA, Porru S, Buntinx F, Golka K, Mayordomo JI, Kumar R, Matullo G, Steineck G, Kiltie AE, Aben KKH, Jonsson E, Thorsteinsdottir U, Knowles MA, Rafnar T, Stefansson K. A sequence variant at 4p16.3 confers susceptibility to urinary bladder cancer. Nature Genetics 2010; 42: 415-419.

Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi.

Falchi M, Bataille V, Hayward NK, Duffy DL, Newton Bishop JA, Pastinen T, Cervino A, Zhao ZZ, Deloukas P, Soranzo N, Elder D, Barrett JH, Martin NG, Bishop DT, Montgomery GW, Spector TD. Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi. Nature Genetics, 2009, 41: 915-9.

Genome-wide association study identifies three loci associated with melanoma risk.

Bishop DT, Demenais F, Iles MM, Harland M, Taylor JC, Corda E, Randerson-Moor J, Aitken JF, Avril M-F, Azizi E, Bakker B, Bianchi-Scarrà G, Bressac-de Paillerets B, Calista D, Cannon-Albright LA, Chin-a-Woeng T, Dębniak T, Galore-Haskel G, Ghiorzo P, Gut I, Hansson J, Hocevar M, Höiom V, Hopper JL, Ingvar C, Kanetsky PA, Kefford RF, Landi MT, Lang J, Lubiński J, Mackie R, Malvehy J, Mann GJ, Martin NG, Montgomery GW, van Nieuwpoort FA, Novakovic S, Olsson H, Puig S, Weiss M, van Workum W, Zelenika D, Brown KM, Goldstein AM, Gillanders EM, Boland A, Galan P, Elder DE, Gruis NA, Hayward NK, Lathrop GM, Barrett JH, Newton Bishop JA. Genome-wide association study identifies three loci associated with melanoma risk. Nature Genetics, 2009, 41:920-5.

Sample size determination in clinical proteomic profiling experiments using mass spectrometry for class comparison.

Cairns DA, Barrett JH, Billingham LJ, Stanley AJ, Xinarianos G, Field JK, Johnson PJ, Selby PJ and Banks RE. Sample size determination in clinical proteomic profiling experiments using mass spectrometry for class comparison. Proteomics, 2009; 9:74-86.

Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.

Cairns DA, Perkins DN, Stanley AJ, Thompson D, Barrett JH, Selby PJ and Banks RE. Integrated multi-level quality control for proteomic profiling studies using mass spectrometry. BMC Bioinformatics, 2008; 9: 519.

Application of the Random Forest Classification Method to Peaks Detected from Mass Spectrometric Proteomic Profiles of Cancer Patients and Controls.

Barrett Jennifer H and Cairns David A. Application of the Random Forest Classification Method to Peaks Detected from Mass Spectrometric Proteomic Profiles of Cancer Patients and Controls. Statistical Applications in Genetics and Molecular Biology 2008, 7(2), Article 4.

Genome-wide association analysis of coronary artery disease.

Samani NJ, Erdmann J, Hall AS, Hengstenberg C, Mangino M, Mayer B, Dixon RJ, Meitinger T, Braund P, Wichmann H-E, Barrett JH, König IR, Stevens S, Szymczak S, Tregouet D-A, Iles MM, Pahlke F, Pollard H, Lieb W, Cambien F, Fischer M, Ouwehand W, Blankenberg S, Balmforth AJ, Baessler A, Ball SG, Strom TM, Braenne I, Gieger C, Deloukas P, Tobin MD, Ziegler A, Thompson JR and Schunkert H for the WTCCC and the Cardiogenics Consortium. Genome-wide association analysis of coronary artery disease. New England Journal of Medicine 2007, 357: 443-453.

The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.

The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007, 447: 661-678.

Piezo1 integration of vascular architecture with physiological force.

Li J, Hou B, Tumova S, Muraki K, Bruns A, Ludlow MJ, Sedo A, Hyman AJ, McKeown L, Young RS, Yuldasheva NY, Majeed Y, Wilson LA, Rode B, Bailey MA, Kim HR, Fu Z, Carter DA, Bilton J, Imrie H, Ajuh P, Dear TN, Cubbon RM, Kearney MT, Prasad KR, Evans PC, Ainscough JF, Beech DJ. Piezo1 integration of vascular architecture with physiological force. Nature. 2014; 515 (7526):279-282.
DOI disc logo 10.1038/nature13701

Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes.

Bruce, A.W., I.J. Donaldson, I.C. Wood, S.A. Yerbury, M.I. Sadowski, M. Chapman, B. Gottgens, and N.J. Buckley, *Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes.* Proc Natl Acad Sci U S A, 2004. *101*(28): p. 10458-63.

Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

Johnson, R., R.J. Gamblin, L. Ooi, A.W. Bruce, I.J. Donaldson, D.R. Westhead, I.C. Wood, R.M. Jackson, and N.J. Buckley, *Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.* Nucleic Acids Res, 2006. *34*(14): p. 3862-77.

Evolution of the vertebrate gene regulatory network controlled by the transcriptional repressor REST.

Johnson, R., R.J. Gamblin, L. Ooi, A.W. Bruce, I.J. Donaldson, D.R. Westhead, I.C. Wood, R.M. Jackson, and N.J. Buckley, *Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.* Nucleic Acids Res, 2006. *34*(14): p. 3862-77.3. Johnson, R., J. Samuel, C.K. Ng, R. Jauch, L.W. Stanton, and I.C. Wood, *Evolution of the vertebrate gene regulatory network controlled by the transcriptional repressor REST.* Mol Biol Evol, 2009. *26*(7): p. 1491-507.

KvDB; mining and mapping sequence variants in voltage-gated potassium channels.

Stead, L.F., I.C. Wood, and D.R. Westhead, *KvDB; mining and mapping sequence variants in voltage-gated potassium channels.* Hum Mutat, 2010. *31*(8): p. 908-17.

KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels.

Stead, L.F., I.C. Wood, and D.R. Westhead, *KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels.* Bioinformatics, 2011. *27*(16): p. 2181-6.

Comparative analysis of metazoan chromatin organisation.

The modENCODE consortium. (2014) Comparative analysis of metazoan chromatin organisation. Nature 512(7515):449-452.

Extreme HOT regions are CpG dense promoters in C. elegans and humans.

Chen R.A.-J., Stempor P., Down T.A., Zeiser E., Feuer S. and Ahringer J. (2014) Extreme HOT regions are CpG dense promoters in C. elegans and humans. Genome Research 24(7):1138-1146.

PRDE-1 is a nuclear factor essential for the biogenesis of Ruby motif dependent piRNAs in C.

Weick, E.-M.*, Sarkies, P.*, Silva, N., Chen, R.A.-J., Moss, S.M.M., Cording, A.C., Ahringer, J., Enrique Martinez-Perez, E and Miska, E. (2014) PRDE-1 is a nuclear factor essential for the biogenesis of Ruby motif dependent piRNAs in C. elegans. Genes Dev 28(7):783-796.

The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures.

Chen R.A.-J*., Down T.A*., Stempor P., Chen, Q.B., Egelhofer T.A., Hillier L.W., Jeffers T.E. , Ahringer J.A. (2013) The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Genome Research 23(8):1339-1347.

Hsp70 isoforms are essential for the formation of KSHV replication and transcription compartments.

Baquero-Perez, B. & Whitehouse, A. (2015). Hsp70 isoforms are essential for the formation of KSHV replication and transcription compartments. PLoS Pathogens, 11(11):e1005274.

NEDDylation is essential for Kaposi's sarcoma-associated herpesvirus latency and lytic reactivation and represents a novel anti-KSHV target.

Hughes, D.J., Wood, J.J., Jackson, B.R., Baquero-Perez, B. & Whitehouse, A. (2015). NEDDylation is essential for Kaposi’s sarcoma-associated herpesvirus latency and lytic reactivation and represents a novel anti-KSHV target. PLoS Pathogens, 11(3):e1004771.

A novel mechanism inducing genomic instability in Kaposi’s sarcoma-associated herpesvirus infected cells.

Jackson, B.R., Norenberg, M. & Whitehouse, A. (2014). A novel mechanism inducing genomic instability in Kaposi’s sarcoma-associated herpesvirus infected cells. PLoS Pathogens, 10(5): e1004098.

Merkel cell polyomavirus small T antigen mediates microtubule destabilisation to promote cell motility and migration.

Knight, L.M., Stakaityte, G., Wood, J.J., Griffiths, D.A., Howell, G.J., Abdul-Sada, H., Wheat, R., Blair, G.E., Macdonald, A., Blackbourn, D.J. & Whitehouse, A. (2015). Merkel cell polyomavirus small T antigen mediates microtubule destabilisation to promote cell motility and migration. Journal of Virology, 89, 35-47.

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

Gusnanto, A., Tcherveniakov, P., Shuweihdi, F., Rabbitts, P., Wood, H.M. (2015) Stratifying tumour subtypes based oncopy number alteration profiles using next-generation sequence data, Bioinformatics, 31, 2713-2720

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

Gusnanto, A., Taylor, C., Nafisah, I., Wood, H., Rabbitts, P., Berri, S. (2014) Estimating optimal window size for analysis of low-coverage next-generation sequence data, Bioinformatics, 30 (13): 1823-1829

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

Gusnanto, A., Ploner, A., Shuweihdi, F., Pawitan, Y. (2013). Partial least squares and logistic regression estimates for gene selection in supervised classification of gene expression data. Journal of Biomedical Informatics, 46(4):697-709

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

Gusnanto, A., Wood, H., Pawitan, Y., Rabbitts, P., Berri, S. (2012). Correcting for cancer genome size and tumor cell content enables better estimation of copy number alterations from next generation sequence data, Bioinformatics, 28(1): 40-47

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

Lee, W., Gusnanto, A., Salim, A., Magnusson, P., Sim, X., Tai, E.S., Pawitan, Y. (2012). Estimating the number of true discoveries in genome-wide association studies, Statistics in Medicine, 31: 1177-1189

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

Sivapalaratnam, S., Farrugia, R., Nieuwdorp, M., Langford, C., van Beem, R., Maiwald, S., Zwaginga, J., Gusnanto, A., Watkins, N., Trip, M., and Ouwehand, W. (2011). Identification of candidate genes linking systemic inflammation links to atherosclerosis; results of a human in vivo LPS infusion study, BMC Medical Genomics, 4: 64

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

Goodall, A., Burns, P., Bray, S., Salles, I., Macaulay, I., Jones, C., Angenent, W., Attwood, A., Bently, D., de Bono, B., Deckmyn, H., Dixon, R., Dunn, R., Farrugia, R., Fitzgerald, D., Foad, N., Garner, S., Gusnanto, A., Gwilliam, et al. (2010). Transcription profiling in human platelets reveals LRRFIP1 as a novel protein regulating platelet function, Blood, 116(22): 4646-4656

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

Watkins, N., Gusnanto, A., de Bono, B., et al. (2009). A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood, 113(19), 4479-4480

Toll like receptor 4 activation elicits pro-atherogenic gene activation in monocytes in humans.

Sivapalaratnam, S., Farrugia, R., Nieuwdorp, M., Gusnanto, A., et al. (2008). Toll like receptor 4 activation elicits pro-atherogenic gene activation in monocytes in humans. Circulation, 118(18)

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

Burns, P., Gusnanto, A., Macaulay, I., et al. (2008). Identification of variation in the platelet transcriptome associated with glycoprotein 6 haplotype. Platelets, 19(4), 258-267

Estimation of significance thresholds for genomewide association scans. Genetic Epidemiology.

Dudbridge, F., and Gusnanto, A. (2008). Estimation of significance thresholds for genomewide association scans. Genetic Epidemiology, 32: 227-234

Robust smooth segmentation approach for array CGH data analysis.

Huang, J., Gusnanto, A., O’Sullivan, K., Staaf, J., Borg, Å., Pawitan, Y. (2007). Robust smooth segmentation approach for array CGH data analysis. Bioinformatics, 23(18): 2463-2469

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 D., Tijssen M., Langford C., Watkins N., Ouwehand W., Berzuini C., Dudbridge F. (2007). 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

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

Gusnanto, A., Calza, S., Pawitan, Y. (2007). Identification of differentially expressed genes and false discovery rate in microarray studies. Current Opinion in Lipidology,18(2),187-193.

Comparative gene expression profiling of megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet receptors.

Macaulay, I., Tijssen, M., Thijssen-Timmer, D., Gusnanto, A., Steward, M., Carr, P., Langford C., Ellis, P., Dudbridge, F., Zwaginga, J., Watkins, N., van der Schoot, E., Ouwehand, W. (2006). Comparative gene expression profiling of megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet receptors. Blood, 109, 3260-3269.

Novel Activatory and Inhibitory Platelet Receptors Identified Through Comparative Gene Expression Profiling of Megakaryocytes and Erythroblasts.

Macaulay, I. C., Tijssen, M. R., Thijssen-Timmer, D., Gusnanto, A., Carr, P., Steward, M., Langford, C., Ellis, P., Dudbridge, F., Zwaginga, J., Watkins, N. A., van der Schoot, E., Ouwehand, W. H. (2006). Novel Activatory and Inhibitory Platelet Receptors Identified Through Comparative Gene Expression Profiling of Megakaryocytes and Erythroblasts. Transfusion Medicine, 16, Supplement 1, 46-46(1)

Detecting multiple associations in genomewide studies.

Dudbridge, F., Gusnanto, A., and Koeleman, B. P. C. (2006). Detecting multiple associations in genomewide studies. Human Genomics, 2(5), 310-317.

Multidimensional local false discovery rate for microarray studies.

Ploner, A., Calza, S., Gusnanto, A., Pawitan, Y. (2006). Multidimensional local false discovery rate for microarray studies. Bioinformatics, 22(5), 556-565

Platelet genomics and proteomics in human health and disease.

Macaulay, I. C., Carr, P. Y., Gusnanto, A., Ouwehand, W. H., Fitzgerald, D., and Watkins, N. (2005). Platelet genomics and proteomics in human health and disease. Journal of Clinical Investigation, 115(12), 3370-3377

Fold-Change Estimation and Identification of Differentially Expressed Genes using Mixture Mixed-Model.

Gusnanto, A., Ploner, A., Pawitan, Y. (2005). Fold-Change Estimation and Identification of Differentially Expressed Genes using Mixture Mixed-Model, Statistical Applications in Genetics and Molecular Biology, 4(1), Article 26.

False discovery</p> <p>rate, sensitivity, and sample size for microarray studies.

Pawitan, Y., Michiels, S., Koscielny, S., Gusnanto, A., Ploner, A. (2005). False discovery rate, sensitivity, and sample size for microarray studies, Bioinformatics, 21, 3017-3024.

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 check points and gene expression.

Dreij, K., Bajak, E., Sundberg, K., Cotgreave, I. A., Jernström, B., Seidel, A., and Gusnanto, A. (2004). 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 check points and gene expression, Polycyclic Aromatic Compounds, 24, 549-566

A DNA microarray for fission yeast: minimal changes after temperature shift.

Xue, Y., Haas, S.A., Brino, L., Gusnanto, A., Reimers, M., Talibi, D., Vingron, M., Ekwall, K. and Wright, A.P.H. (2004) . A DNA microarray for fission yeast: minimal changes after temperature shift. Yeast, 21(1), 25-39

Understanding Protozoan Parasite Metabolism and Identifying Drug Targets through Constraint-based Modelling in Analysis of parasite biology – from metabolism to drug discovery in the series Drug Discovery in Infectious Diseases.

TOTANES, F.I., MCCONKEY, G.A., WESTHEAD, D., SHAMEER, S., &amp; FABIEN JOURDAN, F. (2016) Understanding Protozoan Parasite Metabolism and Identifying Drug Targets through Constraint-based Modelling in Analysis of parasite biology – from metabolism to drug discovery in the series Drug Discovery in Infectious Diseases (eds. S. Müller, R. Cerdan, O. Radulescu E. Guca)

MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format.

FORTH, T., MCCONKEY, G.A., &amp; WESTHEAD, D.R. (2010) MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format. Bioinformatics. 26(18):2352-3.

Gene function prediction using semantic similarity clustering and enrichment analysis in the malaria parasite Plasmodium falciparum.

TEDDER, P.M., BRADFORD, J.R., NEEDHAM, C.J., MCCONKEY, G.A., BULPITT, A.J., &amp; WESTHEAD, D.R. (2010) Gene function prediction using semantic similarity clustering and enrichment analysis in the malaria parasite Plasmodium falciparum. Bioinformatics 26:2431-7

PlasmoPredict: A gene function prediction website for Plasmodium falciparum. Trends in Parasitology.

TEDDER, P.M.R., BRADFORD, J.R., NEEDHAM, C.J., MCCONKEY, G.A., BULPITT, A.J., &amp; WESTHEAD, D.R. (2010) PlasmoPredict: A gene function prediction website for Plasmodium falciparum. Trends in Parasitology, 26, 107-10.

Bayesian data integration and enrichment analysis for predicting gene function in malaria.

TEDDER, P.M.R., BRADFORD, J.R., NEEDHAM, C.J., MCCONKEY, G.A., BULPITT, A.J., &amp; WESTHEAD, D.R. (2009) Bayesian data integration and enrichment analysis for predicting gene function in malaria. Computability in Europe, CiE 2009.

The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes.

WHITAKER, J. W., MCCONKEY, G. A. &amp; WESTHEAD, D. R. (2009) The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes. Genome Biology, 10, 36-42.

metaTIGER: a metabolic evolution resource.

WHITAKER, J. W., LETUNIC, I., MCCONKEY, G. A. & WESTHEAD, D. R. (2009) metaTIGER: a metabolic evolution resource. Nucleic Acids Research, 37, D531-8.

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