Yuan Chen | Senior Computer Biologist

Chen, Yuan

I am working in the Sanger Institute Human Evolution Group, mainly focus on bioinformatics support for data analysis for various projects, such as 1000 Genomes, Isolated population, Y-chromosome, Gorilla, 500 Exomes, the Gene Selection Detection Projects.

May 2010 - present, at Sanger Institute Human Evolution Group. I have developed some pipelines using PERL, MYSQL database and Rscript to provide data for analysis for various projects. Those projects are mainly related to using variation data in different populations as tools to study their evolutionary history.

Sept 2001 - April 2010, at European Bioinformatics Institute (EBI). I have been involved in creating and maintaining the variation database in Ensembl Project, prediction of SNPs consequences on genes, proteins analysis for the human chromosomes sequenced by Sanger Centre, also involved in SNPs calling and data analysis for various species, such as Human, Mouse, Rat, Platypus and Tetraodons, using software developed in Sanger Institute, PERL scripts and MYSQL database.

Sept. 1998 - August 2001, at Sanger Center. I investigated SNP detection using overlap clones from chromosome 22 using PERL scripts.

Sept. 1986 - April 1996, research assistant at Manchester University. I did research on molecular modelling projects, also on looking for evidences for horizontal gene transfer by scan DNA/protein sequences stored in EMBL, SwissProt to find the similarities in sequence level, using C programing and PARADOX database, also gained Master of Science degree in Bio-computing.

Sept. 1985 - Sept.1986, I worked as Physician in a hospital in Wuhan, China.

Sept.1980 - July1985, studied for Bachelor of Medicine (equivalent to M.B., Ch.B) at Dept. of Medicine, Tong-Ji Medical University, Wuhan, P.R. China.

Publications

  • Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding.

    Xue Y, Prado-Martinez J, Sudmant PH, Narasimhan V, Ayub Q et al.

    Science (New York, N.Y.) 2015;348;6231;242-245

  • Revisiting the thrifty gene hypothesis via 65 loci associated with susceptibility to type 2 diabetes.

    Ayub Q, Moutsianas L, Chen Y, Panoutsopoulou K, Colonna V et al.

    American journal of human genetics 2014;94;2;176-85

  • A calibrated human Y-chromosomal phylogeny based on resequencing.

    Wei W, Ayub Q, Chen Y, McCarthy S, Hou Y et al.

    Genome research 2013;23;2;388-95

  • Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing.

    Xue Y, Chen Y, Ayub Q, Huang N, Ball EV et al.

    American journal of human genetics 2012;91;6;1022-32

  • An integrated map of genetic variation from 1,092 human genomes.

    1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA et al.

    Nature 2012;491;7422;56-65

  • High altitude adaptation in Daghestani populations from the Caucasus.

    Pagani L, Ayub Q, MacArthur DG, Xue Y, Baillie JK et al.

    Human genetics 2012;131;3;423-33

  • A map of human genome variation from population-scale sequencing.

    1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD et al.

    Nature 2010;467;7319;1061-73

  • A database and API for variation, dense genotyping and resequencing data.

    Rios D, McLaren WM, Chen Y, Birney E, Stabenau A et al.

    BMC bioinformatics 2010;11;238

  • Ensembl variation resources.

    Chen Y, Cunningham F, Rios D, McLaren WM, Smith J et al.

    BMC genomics 2010;11;293

  • Locus Reference Genomic sequences: an improved basis for describing human DNA variants.

    Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE et al.

    Genome medicine 2010;2;4;24

  • A first-generation linkage disequilibrium map of human chromosome 22.

    Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S et al.

    Nature 2002;418;6897;544-8

  • A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence.

    Dawson E, Chen Y, Hunt S, Smink LJ, Hunt A et al.

    Genome research 2001;11;1;170-8

Chen, Yuan