Research Topics
Species | Jonathan MarchiniSummaryAffiliation: University of Oxford Country: UK Publications
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Detail Information
Publications
Genotype imputation for genome-wide association studiesJonathan Marchini
Department of Statistics, University of Oxford, Oxford, UK
Nat Rev Genet 11:499-511. 2010....- Joint genotype calling with array and sequence dataJared O'Connell
Wellcome Trust Center of Human Genetics, Oxford, United Kingdom
Genet Epidemiol 36:527-37. 2012..This method provides a foundation for future efforts to fuse genetic data from different sources, for example, when combining data from exome sequencing and exome microarrays... 
Comparing methods of analyzing fMRI statistical parametric mapsJonathan Marchini
Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
Neuroimage 22:1203-13. 2004..Within this framework, we highlight the role of the loss function, which explicitly penalizes the types of errors that may occur in a given analysis...
A comparison of phasing algorithms for trios and unrelated individualsJonathan Marchini
Department of Statistics, University of Oxford, Oxford OX1 3TG, United Kingdom
Am J Hum Genet 78:437-50. 2006..Finally, we evaluated methods of estimating the value of r(2) between a pair of SNPs and concluded that all methods estimated r(2) well when the estimated value was >or=0.8...- A new multipoint method for genome-wide association studies by imputation of genotypesJonathan Marchini
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Nat Genet 39:906-13. 2007..A notable future use of our method will be to boost power by combining data from genome-wide scans that use different SNP sets... - Bayesian hierarchical mixture modeling to assign copy number from a targeted CNV arrayNiall Cardin
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, United Kingdom
Genet Epidemiol 35:536-48. 2011..We illustrate the methods performance using real data from the Wellcome Trust Case Control Consortium's CNV association study and using simulated data... - A flexible and accurate genotype imputation method for the next generation of genome-wide association studiesBryan N Howie
Department of Statistics, University of Oxford, Oxford, UK
PLoS Genet 5:e1000529. 2009.... - Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chipChris C A Spencer
Department of Statistics, University of Oxford, Oxford, United Kingdom
PLoS Genet 5:e1000477. 2009..Our results have been encapsulated into an R software package that allows users to design future association studies and our methods provide a framework with which new chip sets can be evaluated... - HAPGEN2: simulation of multiple disease SNPsZhan Su
Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
Bioinformatics 27:2304-5. 2011..However, the inability of current methods to simulate multiple nearby disease SNPs on the same chromosome can limit their application... - Two-stage two-locus models in genome-wide associationDavid M Evans
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
PLoS Genet 2:e157. 2006.... - Meta-analysis and imputation refines the association of 15q25 with smoking quantityJason Z Liu
Department of Statistics, University of Oxford, Oxford, UK
Nat Genet 42:436-40. 2010..Our fine-mapping approach identified a SNP showing the highest significance, rs55853698, located within the promoter region of CHRNA5. Conditional analysis also identified a secondary locus (rs6495308) in CHRNA3... - Genome-wide strategies for detecting multiple loci that influence complex diseasesJonathan Marchini
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Nat Genet 37:413-7. 2005..These results suggest that searching for interactions among genetic loci can be fruitfully incorporated into analysis strategies for genome-wide association studies... - The effects of human population structure on large genetic association studiesJonathan Marchini
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Nat Genet 36:512-7. 2004..The results of our analysis can guide the design of large-scale association studies... - A model-based approach to capture genetic variation for future association studiesSusana Eyheramendy
Department of Statistics, University of Oxford, Oxford, OX1 3TG, United Kingdom
Genome Res 17:88-95. 2007..We also propose new methods to select the tagging SNPs. We empirically show by using HapMap data that our approach is able to capture significantly more genetic variation than methods based solely on a pairwise LD measure... - Modeling interactions with known risk loci-a Bayesian model averaging approachTeresa Ferreira
Department of Statistics, University of Oxford, UK
Ann Hum Genet 75:1-9. 2011..We show that the method has good power both when the association is the result of marginal effects only, and when interaction with a known locus occurs. The method is implemented as an option in the program SNPTEST... - Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's diseaseJeffrey C Barrett
Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
Nat Genet 40:955-62. 2008..The expanded molecular understanding of the basis of this disease offers promise for informed therapeutic development... - Comparing algorithms for genotype imputationJonathan Marchini
Am J Hum Genet 83:535-9; author reply 539-40. 2008 - A robust statistical method for case-control association testing with copy number variationChris Barnes
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nat Genet 40:1245-52. 2008..We illustrate the power of these methods for testing for association with binary and quantitative traits, and have made this software available as the R package CNVtools... - Common variants near MC4R are associated with fat mass, weight and risk of obesityRuth J F Loos
MRC Epidemiology Unit, Addenbrooke s Hospital, Cambridge CB2 0QQ, UK
Nat Genet 40:768-75. 2008.... - Genome-wide detection and characterization of positive selection in human populationsPardis C Sabeti
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
Nature 449:913-8. 2007.... - A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHCPaul I W de Bakker
Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts 02142, USA
Nat Genet 38:1166-72. 2006.... - A second generation human haplotype map of over 3.1 million SNPsKelly A Frazer
The Scripps Research Institute, 10550 North Torrey Pines Road MEM275, La Jolla, California 92037, USA
Nature 449:851-61. 2007..Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations... - Intra-individual variation in resting metabolic rate during the menstrual cycleC Jeya K Henry
Nutrition and Food Science Group, School of Biological and Molecular Sciences, Oxford Brookes University, Gipsy Lane Campus, Headington, OX3 0BP
Br J Nutr 89:811-7. 2003..In conclusion, the findings from our present study show that RMR cannot be assumed to be 'stable' in all women. The implications of intra-individual variation in RMR and its impact on energy balance needs further research...