Jonathan Marchini's Home Page



me
I am an Associate Professor in the Department of Statistics, University of Oxford, UK.

I am also a Tutorial Fellow in Statistics at 
Somerville 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




 News         Research          Publications         Software          Teaching        Cycling       VSO          Links













































News

16 June 2014 Our paper on calling genotypes and phasing has been published in Nature Communications

O. Delaneau, J. Marchini, The 1000 Genomes Project Consortium (2014) Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nature Communications

We have released a new version of SHAPEIT2 that implements this functionality.


We have also released a new version of IMPUTE2 that fixes a bug in the panel merging functionality, and provided a minor update our phased version of the 1000 Genomes Phase 1 dataset.

17 Apr 2014
Jared O'Connell's paper on a general method for phasing related samples has been published in PLoS Genetics

J. O'Connell, D. Gurdasani, O. Delaneau, et al. (2014) A general approach for haplotype phasing across the full spectrum of relatedness. PLoS Genetics

The method is implemented within SHAPEIT2 and also in a standalone package called duoHMM.

24 Mar 2014 We have just released a new version of SHAPEIT (v2 r767) that implements functionality for (a) using phase information in sequencing reads to help phasing, and (b) phasing in general pedigrees. This work is associated with the following two publications

O. Delaneau, B. Howie, A. Cox, J-F. Zagury, J. Marchini (2013) Haplotype estimation using sequence reads. American Journal of Human Genetics 93 (4) 787-696 [LINK]

J. O'Connell, D. Gurdasani, O. Delaneau, et al. (2014) A general approach for haplotype phasing across the full spectrum of relatedness. PLoS Genetics (in press)
 
18 Oct 2013 
We have done very well this year at the American Society of Human Genetics meeting in Boston, with 4 members of the group being selected to give a talk about their research. Here are the details

Jared O'Connell Haplotype phasing across the full spectrum of relatedness.
Platform presentation #192 Presentation Time: 03:15PM-03:30PM Session Location: Grand Ballroom West, Level 3, Convention Center

Marie Forest Simultaneous estimation of population size changes and splits times from population level resequencing studies
Platform presentation #268 Presentation Time: 08:00AM-08:15AM Session Location: Grand Ballroom West, Level 3, Convention Center

Jonathan Marchini A haplotype map derived from whole genome low-coverage sequencing of over 25,000 individuals.
Platform presentation #349 Presentation Time: 02:00PM-02:15PM Session Location: Grand Ballroom West, Level 3, Convention Center

Olivier Delaneau A new method for genotype calling and phasing for the 1000 Genomes Project leads to improved downstream imputation accuracy.
Platform presentation #352 Presentation Time: 02:45PM-03:00PM Session Location: Grand Ballroom West, Level 3, Convention Center

Valentina Iotchkova Bayesian sparse models of high-dimensional correlated traits in related and unrelated individuals.
Poster # 1777F Presentation Time: Fri, Oct 25, 2013, 10:30AM-11:30AM

Warren Kretzschmar  Phasing and imputation of 12,000 1x coverage whole genome sequenced Chinese women.
Poster # 1895W Presentation Time: Wed, Oct 23, 2013, 10:30AM-11:30AM

3 Oct 2013
Our paper on using phase information in sequencing reads for haplotype estimation has been published by the American Journal of Human Genetics

O. Delaneau, B. Howie, A. J. Cox, J-F. Zagury, J. Marchini (2013) Haplotype estimation using sequencing reads. AJHG 93 (4) 687-696.


18 Sep 2013
We have just released a new version of the Phase 1 haplotypes from the 1000 Genomes Project. Using a set of validation genotypes at SNP and biallelic indels we have been able to show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low frequency. The haplotypes are available from the 1000GP website or the IMPUTE2 website.


21 Mar 2013
Our paper describing the genetic variation of short insertions and deletions using sequencing data from the 1000 Genomes Project has been published by Genome Research

S. Montgomery, D. Goode, E. Kvikstad, C. Albers, Z. Zhang, X. Mu, G. Ananda, B. Howie, K. Karczewski, K. Smith, V. Anaya, R. Richardson, J. Davis, D. MacArthur, A. Sidow, L. Duret, M. Gerstein, K. Markova, J. Marchini, G. McVean and G. Lunter (2013) The origin, evolution and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Research doi: 10.1101/gr.148718.112

29 Dec 2012
Our paper describing the SHAPEIT (v2) method is now available from the Nature Methods website

O. Delaneau, J-F. Zagury and J. Marchini (2012) Improved whole chromosome phasing for disease and population genetic studies. Nature Methods 10, 5-6. + [Supplementary Material]

This paper presents a significantly new algorithm for haplotype estimation that combines together the best ideas from IMPUTE2 and SHAPEIT1. The new method clearly outperforms other existing methods in terms of phasing performance and is very competitive computationally.

6 Dec 2012 We have just released a new version of MULTIMIX (v1.1.0). This new version allows for missing data.

4 Dec 2012
We have just released a new versions of SHAPEIT (v2). The paper on this new version has now been accepted in Nature Methods and will appear soon.

10 Nov 2012
Olivier Delaneau has won a Charles Epstein Post-Doctoral Award (worth $2,000) at the ASHG conference in San Francisco for his work on SHAPEIT2. Well done Olivier! Androniki Menelaou made the final of the Pre-Doctoral competition (worth $1,000) but did not win a prize.


7 Nov 2012 Claire Churchhouse's paper has been published in Genetic Epidemiology

C. Churchhouse and J. Marchini (2012) Multiway Admixture Deconvolution Using Phased or Unphased Ancestral Panels. Genetic Epidemiology.

In this paper we develop a method for carrying out admixture deconvolution with more than two source ancestral populations. The method can handle both phased or unphased data from the source and/or sample populations. The method was used to analyze data from Phase 1 of the 1000 Genomes Project which was recently published in Nature. The MULTIMIX software implementing this approach will appear here soon.

1 November 2012
Jonathan Marchini has been awarded a Philip Leverhulme Prize

1 November 2012
The latest 1000 Genomes Project paper has been published in Nature today.

The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65.

This is a big international collaboration that has sort to sequence a large number of individuals from around the world with the aim of mapping the majority of the genetic variation with frequency above 1%. Members of our group that contributed to the analysis were Olivier Delaneau, Claire Churchhouse, Jason Liu and myself. The project has been reported in the mainstream press.

1 November 2012 The company Affymetrix has launched a new genotyping chip that was designed using our software IMPUTE2. They have issued a press release here giving the details.  http://phx.corporate-ir.net/phoenix.zhtml?c=116408&p=irol-newsArticle&ID=1752709

23 October 2012 Androniki Menelaou's paper
has been published in Bioinformatics.

A. Menelaou and J. Marchini (2012) Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold. Bioinformatics.

In this paper we show that combining low-coverage sequence data with microarray genotyping on the same subjects can lead to high quality haplotype reference sets that produce a notable boost in downstream imputation accuracy. The MVNcall software implementing this approach will appear here soon.

2 October 2012
Jared O'Connell won the poster prize at the recent Genomics of Common Diseases conference in Potomac, MD, USA.

27 August 2012
We have done very well this year with accepted talks at the American Society of Human Genetics meeting. Olivier Delaneau and Androniki Menelaou have made the final of the post-doctoral and pre-doctoral Charles J. Epstein Trainee Awards

24 August 2012
Claire Churchouse has succesfully passed her viva. Her thesis entitled 'Bayesian Methods for Estimating Human Ancestry Using Whole Genome SNP Data' was examined be Dr Lachlan Coin and Dr Simon Myers. Claire is now off to start a postdoc with David Althuler at the Broad Institute of Harvard and MIT. Good luck Claire!

22 July 2012
Our new paper (with Bryan Howie as co-lead author) on pre-phasing based imputation has now appeared in Nature Genetics.

B. Howie, C. Fuchsberger, M. Stephens, J. Marchini, G. Abecasis (2012) Fast and accurate genotype imputation in genome-wide association studies through pre-phasing.  Nature Genetics. DOI: 10.1038/ng.2354


20 July 2012
  Jared O'Connell's paper on a new method for calling genotypes from array and sequence data has now appeared in Genetic Epidemiology

J. O'Connell, J. Marchini (2012) Joint Genotype Calling With Array and Sequence Data. Genetic Epidemiology. DOI: 10.1002/gepi.21657


29 June 2012
Androniki Menelaou has succesfully passed her viva. Her thesis entitled 'LD-based SNP and genotype calling from next-generation sequencing reads" was examined be Dr Vincent Plagnol and Prof Gil McVean. Androniki is now off to start a postdoc with Paul de Bakker at UMC Utrecht. Good luck Androniki!

30 April 2012
Victoria Hore has joined the group for her DTC project. Welcome Vicky!

12 April 2012
Warren Kretzschmar has joined the group for his rotation project. Welcome Winni!

15 March 2012
Olivier Delaneau's paper on the SHAPEIT method has now appeared in Nature Methods

O. Delaneau, J. Marchini, JF. Zagury (2012) A linear complexity phasing method for thousands of genomes. Nature Methods doi:10.1038/nmeth.1785



























  






















Research

The main focus of my research is the development of statistical methods for the localization, detection and characterization of the genes that underly human disease. Some of the areas we are currently working on include
I am also interested in statistical image analysis and pattern recognition and have collaborated with the The Oxford Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB).

I currently hold an MRC New Investigator award.


Group Members and Collaborators

  Post-Docs (past)
  DPhil Students (current)   
  DPhil Students (past + where they went next)   Projects  

  Collaborators  









































Publications

 2014

 2013
  2012
  2011
  2010
  2009
  2008

  2007
  2006   2005
  2004
  2003
  2002
  2001   2000
  1997

Software


Genome-wide Association Study Software

  
R Packages










































Teaching

At Somerville College
In the Statistics Department, University of Oxford
Outside Oxford
























































VSO

Between September 1995 and September 1998 I worked as a VSO volunteer in Tanzania, teaching A-level Mathematics in a rural government run school near Iringa (map).

VSO enables men and women to work alongside people in poorer countries in order to share skills, build capabilities and promote international understanding and action, in the pursuit of a more equitable world.


If you are at all interested in applying to VSO and want to know more check out the webpage
Volunteer with VSO

Here
are some pictures which I hope give you an idea of the time I spent in Tanzania.

I am more than happy to chat to anyone who want to know more about this. I can't recommend it as enough. So just drop me an email if you are interested.























Cycling

I am passionate about cycling. I compete in road races and ride for the Beeline Bikes RT.

My race bike is a Colnago C50, but i also have a Colnago Master, Cervelo P2, De Rosa Macro and Bianchi Via Nirone.

I am also the Senior Member of the Oxford University Cycling Club.

I try my best to follow The Rules.