Jonathan Marchini's Home Page

I am a University Lecturer in Statistical Genomics in the Mathematical Genetics group, Department of Statistics, University of Oxford, UK. I am also a Senior Research Fellow at Mansfield College and the Senior Member of OUCC.     Address:  Department of Statistics, 1 South Parks Road, Oxford OX1 3TG, UK      Telephone:   01865 271125           Fax:  01865 281333              E-mail:  marchini <at> stats.ox.ac.uk

• Analysis of next-generation sequencing data, specifically analysis of the 1000 Genomes project data.
  
• SNP genotype calling
• CNV detection and genotyping
• Methods for detecting gene-gene interactions
• Haplotype inference
• Genotype imputation
• Coalescent based approaches for detection and fine-mapping of disease genes in association studies
• Bayesian modelling of genotype-phenotype association
• Methods for detection of population structure from genetic datasets
  

Group Members and Collaborators

• Olivier Delaneau
  

• Niall Cardin (now at UCSF)
• Jason Liu

• Claire Churchhouse
• Androniki Menelaou
• Valentina Iotchkova
• Eleni Frangou
• Peter Kecskemethy (jointly supervised with Chris Holmes) [DTC student]
  
• Jared O'Connell
• Marie Forest (jointly supervised with Simon Myers)
  
• Melissa Maczka (jointly supervised with Chris Martin and Mark Woolrich) [DTC student]
  

• Teresa Ferreira (now a postdoc at WTCHG, Oxford)
  
• Joanne Gale
  
• Bryan Howie (now a postdoc at Chicago)
  
• Robert Johnson (based at the FMRIB Center)
  
• Zhan Su (now a postdoc at WTCHG, Oxford) [DTC student]
  

• HapMap Project
• Wellcome Trust Case-Control Consortium 
• 1000 Genomes Project
• UK10K Project
  

Publications

• O. Delaneau, J. Marchini, JF. Zagury (2011) A linear complexity phasing method for thousands of genomes. Nature Methods doi:10.1038/nmeth.1785 [Link]
  
• B. Howie, J. Marchini, M. Stephens (2011) Genotype Imputation with Thousands of Genomes. G3 : Genes, Genomes, Genetics. doi: 10.1534/g3.111.001198 [Link]
  
• N. Cardin, C. Holmes, WTCCC, P. Donnelly, J. Marchini (2011) Bayesian hierarchical mixture modeling to assign copy number from a targeted CNV array. Genetic Epidemiology DOI: 10.1002/gepi.20604 [Link]
  
• Z. Su, J. Marchini, P. Donnelly (2011) HAPGEN2: simulation of multiple disease SNPs. Bioinformatics. doi: 10.1093/bioinformatics/btr341 [Link]
  
• T. Ferreira and J. Marchini (2011) Modeling interactions with known risk loci—a Bayesian model averaging approach. Annals of Human Genetics 75 (1) 1-9 [Link]
• M.Soler Artigas et al. (2011) Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. Nature Genetics 43 1082-90 [Link]
• I. Tomlinson et al. (2011) Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer. PLoS Genet 7(6):e1002105
• L. Southam et al. (2011)  The effect of genome-wide association scan quality control on imputation outcome for common variants. Eur J Hum Genet 19(5):610-614
  

• J. Marchini and B. Howie (2010) Genotype imputation for genome-wide association studies. Nature Reviews Genetics [Link]
  
• J. Liu et al. (2010) Meta-analysis and imputation refines the association of 15q25 with smoking quantity. Nature Genetics 42, 436–440 [Link].
• Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Wellcome Trust Case-Control Consortium. Nature. 2010;464;713-20. [Link]
• The 1000 Genomes Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 [Link]
  
  

•  Z. Su, N. Cardin, WTCCC, P. Donnelly, J. Marchini (2009) A Bayesian method for detecting and characterizing allelic heterogeneity and boosting signals in genome-wide association studies. Statistical Science 24(4) 430-450. [Article pdf] [Supplementary Material]
  
• B. Howie, P. Donnelly, J. Marchini (2009) A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies. PLoS Genetics  5(6): e1000529 [Open Access Article]
  
• C. Spencer, Z. Su, P. Donnelly, J. Marchini (2009) Designing Genome-Wide Association Studies: Sample Size, Power, Imputation, and the Choice of Genotyping Chip. PLoS Genetics 5(5). [Link]
• M. Jallow et al. (2009) Genome-wide and fine-resolution association analysis of malaria in West Africa. Nature Genetics 41, 657 - 665 (2009) 
• M. O'Donovan et al. (2009) Analysis of 10 independent samples provides evidence for association between schizophrenia and a SNP flanking fibroblast growth factor receptor 2. Mol Psychiatry. 2009 Jan;14(1):30-6
  

• C. Barnes, V. Plagnol, T. Fitzgerald, R. Redon, J. Marchini, D. Clayton, M. Hurles (2009) A robust statistical method for case-control association testing with copy number variation. Nature Genetics Oct;40(10):1245-52.
• J. Barrett et al. (2008) Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet 40(8):955-962 Aug 2008 23.   
  
• R. Loos et al. (2008) Common variants near MC4R are associated with fat mass, weight and risk of obesity. Nat Genet 40(6):768-775. 24.   
  

• J. Marchini, B. Howie, S. Myers, G. McVean and P. Donnelly (2007) A new multipoint method for genome-wide association studies via imputation of genotypes. Nature Genetics 39 : 906-913 [Free Access PDF][Supplementary Material][News and Views Article]
  
• The Wellcome Trust Case Control Consortium (2007) Genomewide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447;661-78. PMID: 17554300 DOI: 10.1038/nature05911.
• The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. NATURE 449(7164):851-U3 18
  
• Zeggini et al. (2007) Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science. Jun 1;316(5829):1336-41. Epub 2007 Apr 26. (link)
• M. Newport et al. (2007) Association scan of 14,500 nonsynonymous SNPs in four diseases identifies autoimmunity variants. NAT GENET 39(11):1329-1337.
  
  

• J. Marchini, D. Cutler, N. Patterson, M. Stephens, E. Eskin, E. Halperin, S. Lin, Z.S. Qin, H.M. Munro, G.R. Abecasis, P. Donnelly, and International HapMap Consortium (2006) A Comparison of Phasing Algorithms for Trios and Unrelated Individuals. Amercan Journal of Human Genetics, 78 437-450 [PDF] [Datasets].
• P. De Bakker et al. (2006) A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet 38(10):1166-1172.
• D. Evans, J. Marchini, A. Morris, J. Cardon (2006) Two-stage two-locus models in genome-wide association. PLoS Genet 2(9):e157
  

• J. Marchini, P. Donnelly and L. R Cardon (2005) Genome-wide strategies for detecting multiple loci influencing complex diseases. Nature Genetics, 37 413-417 [PDF] [Supplementary Material] [News and Views article]
• The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320. 2005. [Abstract] [PDF]
  

• J. Marchini, L. Cardon, M. Phillips, and P. Donnelly (2004) The effects of human population structure on large genetic association studies. Nature Genetics 36 512 - 517. [PDF]
• The International HapMap Consortium (2004).  Integrating ethics and science in the International HapMap Project.  Nature Reviews Genetics, 5  467-475. [PDF]
• J. Marchini and A. Presanis (2004) Comparing methods of analysing fMRI statistical parametric maps. NeuroImage, 22 (3) 1203-1213
  

• Marchini, J. L. and Cardon, L. R., (2003) Discussion of Nicholson et al. (2003) Assessing population differentiation and isolation from single-nucleotide polymorphism data. JRSS(B) 740-1.
• The International HapMap Consortium (2003). The international HapMap project. Nature 426 789-796. [PDF]
• Marchini, J. L. and Smith, S. M., (2003) On bias in the estimation of autocorrelations for fMRI voxel time series analysis. NeuroImage 18: 83-90
• Henry, C. J. K., Lightowler, H. J. and Marchini, J. (2003) Intra-individual variation inresting metabolic rate during the menstrual cycle. British Journal of Nutrition 89, 811-817
  

• Marchini, J. L. (2002) AnalyzeFMRI: An R package for the exploration and analysis of MRI and fMRI datasets. R News 2 (1): 17-23

• Banks, A. N., Marchini, J. L. and Guilford, T.C. (2001) Resolving navigational conflict: clock-shift experiments with homing pigeons. Proc. Royal Institute Navigation Conference, Oxford.

• Marchini, J. L., and Ripley, B. D., (2000) A New Statistical Approach to Detecting Significant Activation in Functional MRI. NeuroImage 12: 366-380

• Crichton, N. J., Hinde, J. P., and Marchini, J. L., (1997) Models for Diagnosing Chest Pain: Is CART helpful? Statistics in Medicine 16: 717-727

• popgen - R package for statistical and population genetics
  
• fastICA - R package that implement the FastICA alsgorithm
  
• AnalyzeFMRI - R package for visualisation and analysis of FMRI data
• GWApower - R package for estimating the power of genome-wide association studies
  
• JMisc - R package for miscellaneous code

• Mods Probability II (Hilary Term 2011)
• Part A Statistical Programming (Hilary Term 2011)
• Introduction to Probability and Statistics for Psychologists and Human Scientists (Old course material from 2002-2008)
  

• Wellcome Trust Advanced Course : Design and Analysis of Genetic-Based Association Studies
  

VSO