Ian Dunham

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc The evolution of imprinting: chromosomal mapping of orthologues of mammalian imprinted domains in monotreme and marsupial mammals
    Carol A Edwards
    Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
    BMC Evol Biol 7:157. 2007
  2. ncbi request reprint The DNA sequence of human chromosome 22
    I Dunham
    Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nature 402:489-95. 1999
  3. ncbi request reprint Human genome sequences: enigmatic variations
    Ian Dunham
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Mutagenesis 17:457-61. 2002
  4. pmc Ensembl 2013
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK
    Nucleic Acids Res 41:D48-55. 2013
  5. pmc Ensembl 2012
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D84-90. 2012
  6. ncbi request reprint Replication timing of human chromosome 6
    Kathryn Woodfine
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Cell Cycle 4:172-6. 2005
  7. pmc Ensembl 2011
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 39:D800-6. 2011
  8. pmc Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines
    Matthew P A Davis
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    PLoS ONE 7:e41762. 2012
  9. pmc Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level
    Alexander W Bruce
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
    Genome Res 19:994-1005. 2009
  10. pmc Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution
    Pawandeep Dhami
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    PLoS ONE 5:e12339. 2010

Research Grants

Detail Information

Publications46

  1. pmc The evolution of imprinting: chromosomal mapping of orthologues of mammalian imprinted domains in monotreme and marsupial mammals
    Carol A Edwards
    Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
    BMC Evol Biol 7:157. 2007
    ..There are several theories to account for how the mechanism evolved including the hypothesis that it was driven by the evolution of X-inactivation, or that it arose from an ancestrally imprinted chromosome...
  2. ncbi request reprint The DNA sequence of human chromosome 22
    I Dunham
    Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nature 402:489-95. 1999
    ..4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome...
  3. ncbi request reprint Human genome sequences: enigmatic variations
    Ian Dunham
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Mutagenesis 17:457-61. 2002
    ..The sequence of the human genome should be completed in 2003. The next steps are to obtain accurate annotation of the genes within the sequence and to begin to define the sequences of multiple human genomes...
  4. pmc Ensembl 2013
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK
    Nucleic Acids Res 41:D48-55. 2013
    ..Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces...
  5. pmc Ensembl 2012
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D84-90. 2012
    ..Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project...
  6. ncbi request reprint Replication timing of human chromosome 6
    Kathryn Woodfine
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Cell Cycle 4:172-6. 2005
    ..Positive correlations are observed between replication timing and a number of genomic features including GC content, repeat content and transcriptional activity...
  7. pmc Ensembl 2011
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 39:D800-6. 2011
    ..Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types...
  8. pmc Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines
    Matthew P A Davis
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    PLoS ONE 7:e41762. 2012
    ..Additionally, our experiments have revealed a novel candidate for Dgcr8-independent microRNA genesis and highlighted the challenges currently facing miRNA annotation...
  9. pmc Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level
    Alexander W Bruce
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
    Genome Res 19:994-1005. 2009
    ..These relationships have never been reported in mammalian systems for any transcription factor...
  10. pmc Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution
    Pawandeep Dhami
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
    PLoS ONE 5:e12339. 2010
    ..We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing...
  11. pmc A genome annotation-driven approach to cloning the human ORFeome
    John E Collins
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Biol 5:R84. 2004
    ..We obtained clones representing 70% of genes on human chromosome 22, whereas searching available cDNA clone collections found at best 48% from a single collection and 60% for all collections combined...
  12. pmc Complete MHC haplotype sequencing for common disease gene mapping
    C Andrew Stewart
    Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 14:1176-87. 2004
    ....
  13. pmc Ensembl's 10th year
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D557-62. 2010
    ....
  14. pmc Finishing the finished human chromosome 22 sequence
    Charlotte G Cole
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Genome Biol 9:R78. 2008
    ..While these gaps constitute only approximately 1% of the sequence, knowledge of the full complement of human genes and regulatory elements is incomplete without their sequences...
  15. pmc MiR-25 regulates Wwp2 and Fbxw7 and promotes reprogramming of mouse fibroblast cells to iPSCs
    Dong Lu
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS ONE 7:e40938. 2012
    ..Recent studies also demonstrate that some miRNAs have important roles in reprogramming somatic cells to induced pluripotent stem cells (iPSCs)...
  16. pmc High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta
    Caroline Daelemans
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1 SA, UK
    BMC Genet 11:25. 2010
    ..Using two allele-specific high-throughput technologies alongside bioinformatics predictions, normal term human placenta was screened to find new imprinted genes and to ascertain the extent of ASE in this tissue...
  17. ncbi request reprint The DNA sequence and biological annotation of human chromosome 1
    S G Gregory
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
    Nature 441:315-21. 2006
    ....
  18. pmc DNA sequence and analysis of human chromosome 9
    S J Humphray
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 429:369-74. 2004
    ..We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection...
  19. ncbi request reprint The organization of the gamma-glutamyl transferase genes and other low copy repeats in human chromosome 22q11
    J E Collins
    Sanger Centre, Hinxton, Cambs, UK
    Genome Res 7:522-31. 1997
    ..This approach has allowed us to resolve the previous cDNA and mapping information relating to GGT and link it to the physical map of 22q11...
  20. ncbi request reprint The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X
    D R Bentley
    The Sanger Centre, Hinxton, Cambridge, UK
    Nature 409:942-3. 2001
    ..By measuring the remaining gaps, we can assess chromosome length and coverage in sequenced clones...
  21. ncbi request reprint SAM: a system for iteratively building marker maps
    C Soderlund
    Sanger Centre, Cambridge, UK
    Comput Appl Biosci 11:645-55. 1995
    ..SAM is also being used at various other laboratories...
  22. ncbi request reprint The DNA sequence and analysis of human chromosome 6
    A J Mungall
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 425:805-11. 2003
    ..Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome...
  23. pmc The DNA sequence and analysis of human chromosome 13
    A Dunham
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
    Nature 428:522-8. 2004
    ..Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb...
  24. ncbi request reprint Replication timing of the human genome
    Kathryn Woodfine
    The Welcome Trust Sanger Institute, Welcome Genome Campus, Cambridge, UK
    Hum Mol Genet 13:191-202. 2004
    ..We show a positive correlation, both genome-wide and at a high resolution, between replication timing and a range of genome parameters including GC content, gene density and transcriptional activity...
  25. doi request reprint Hes6 is required for actin cytoskeletal organization in differentiating C2C12 myoblasts
    Caroline M P Malone
    MRC Cancer Cell Unit, Hutchison MRC Research Centre, Addenbrooke s Hospital, Cambridge, UK
    Exp Cell Res 317:1590-602. 2011
    ..The knockdown phenotype is rescued by expression of Hes6 cDNA resistant to siRNA. These results define a novel role for Hes6 in actin cytoskeletal dynamics in post mitotic myoblasts...
  26. ncbi request reprint Novel microsatellite markers and single nucleotide polymorphisms refine the tylosis with oesophageal cancer (TOC) minimal region on 17q25 to 42.5 kb: sequencing does not identify the causative gene
    Joanne E Langan
    Molecular Genetics and Oncology Group, Department of Clinical Dental Sciences, University of Liverpool, Edward s Building, Daulby Street, L69 3GN, Liverpool, UK
    Hum Genet 114:534-40. 2004
    ..One known and two putative genes are located within this region but none of these genes shows tylosis-specific mutations within their protein-coding regions. Alternative mechanisms of disease gene action must therefore be considered...
  27. ncbi request reprint A first-generation linkage disequilibrium map of human chromosome 22
    Elisabeth Dawson
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 418:544-8. 2002
    ..This study demonstrates the feasibility of developing genome-wide maps of LD...
  28. pmc Sequencing and association analysis of the type 1 diabetes-linked region on chromosome 10p12-q11
    Sergey Nejentsev
    Juvenile Diabetes Research Foundation Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
    BMC Genet 8:24. 2007
    ..Here, we studied sequence polymorphisms in 23 Mb on chromosome 10p12-q11, including the putative IDDM10 region, to identify genes associated with T1D...
  29. pmc The landscape of histone modifications across 1% of the human genome in five human cell lines
    Christoph M Koch
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SA, United Kingdom
    Genome Res 17:691-707. 2007
    ..These results provide an overview of the functional relationship among histone modifications and gene expression in human cells...
  30. pmc A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence
    E Dawson
    The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 11:170-8. 2001
    ..These experiments confirmed 92% of the potential variants in a panel of 92 individuals. [Details of the SNPs and RFLP assays can be found at http://www.sanger.ac.uk and in dbSNP.]..
  31. pmc The portability of tagSNPs across populations: a worldwide survey
    Anna Gonzalez-Neira
    Unitat de Biologia Evolutiva, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
    Genome Res 16:323-30. 2006
    ..This high degree of portability lends promise to the search for disease association in different populations, once tagSNPs are defined in a few reference populations like those analyzed in the HapMap initiative...
  32. ncbi request reprint Functional annotation of noncoding sequence variants
    Graham R S Ritchie
    1 European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK 2 Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Nat Methods 11:294-6. 2014
    ..Here we present genome-wide annotation of variants (GWAVA), a tool that supports prioritization of noncoding variants by integrating various genomic and epigenomic annotations. ..
  33. pmc Genome-wide meta-analysis identifies new susceptibility loci for migraine
    Verneri Anttila
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Nat Genet 45:912-7. 2013
    ..Three of these loci were identified in disease subgroup analyses. Brain tissue expression quantitative trait locus analysis suggests potential functional candidate genes at four loci: APOA1BP, TBC1D7, FUT9, STAT6 and ATP5B...
  34. pmc Reevaluating human gene annotation: a second-generation analysis of chromosome 22
    John E Collins
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 13:27-36. 2003
    ..We suggest that our revised annotation criteria provide a paradigm for future annotation of the human genome...
  35. pmc Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis
    Ian Sudbery
    Work performed at Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Genomics 11:175. 2010
    ..We have conducted a careful examination of off-target effects during an siRNA screen for novel regulators of the TRAIL apoptosis induction pathway(s)...
  36. ncbi request reprint An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22
    Adam Jarmuz
    RNA Editing Group, MRC Clinical Sciences Centre, Imperial College, Hammersmith Hospital Campus, Du Cane Road, London, W12 ONN, UK
    Genomics 79:285-96. 2002
    ..Tissue-specific expression of these genes in a variety of cell lines, along with other evidence, suggests a role for these enzymes in growth or cell cycle control...
  37. ncbi request reprint hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes
    Philippe Lamesch
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genomics 89:307-15. 2007
    ..dfci.harvard.edu). This expansion of the original ORFeome resource greatly increases the potential experimental search space for large-scale proteomics studies, which will lead to the generation of more comprehensive datasets...
  38. pmc Evidence for widespread reticulate evolution within human duplicons
    Michael S Jackson
    Institute of Human Genetics, University of Newcastle upon Tyne, International Centre for Life, Newcastle upon Tyne, United Kingdom
    Am J Hum Genet 77:824-40. 2005
    ..This finding has important implications for efforts to finish the human genome sequence, complicates comparative sequence analysis of duplicon families, and could profoundly influence the tempo of gene-family evolution...
  39. ncbi request reprint Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays
    Alvaro Rada-Iglesias
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
    Hum Mol Genet 14:3435-47. 2005
    ..Our data suggests that a similar approach could be used for the in vivo characterization of all predicted/uncharacterized TF and that the analysis could be scaled to the whole genome...
  40. pmc Small regions of overlapping deletions on 6q26 in human astrocytic tumours identified using chromosome 6 tile path array-CGH
    K Ichimura
    Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Addenbrooke s Hospital, Cambridge, UK
    Oncogene 25:1261-71. 2006
    ..We confirmed the high frequency of chromosome 6 deletions in AA and GB, and identified two novel commonly deleted regions that may harbour TSGs...
  41. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  42. ncbi request reprint A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications
    Patrick G Buckley
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
    Hum Mol Genet 11:3221-9. 2002
    ..Furthermore, comprehensive epigenetic profiling of 22q-located genes and high-resolution analysis of replication timing across the entire chromosome can be studied using our array...
  43. pmc The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer
    Ying Liu
    Cancer Research UK Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
    BMC Genet 3:20. 2002
    ..To accelerate the identification of genes, we sequenced the entire contig of approximately 1.1 Mb. Seven genes were identified within the region of allele loss between D6S264 and D6S149...
  44. pmc Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    David S Johnson
    Department of Genetics, Stanford University Medical Center, Stanford, California 94305, USA
    Genome Res 18:393-403. 2008
    ..The spike-in DNA samples and the data presented here provide a stable benchmark against which future ChIP platforms, protocol improvements, and analysis methods can be evaluated...
  45. doi request reprint Epigenetic marking prepares the human HOXA cluster for activation during differentiation of pluripotent cells
    Stuart P Atkinson
    North East Institute for Stem Cell Research, University of Newcastle upon Tyne, International Centre for Life, Newcastle upon Tyne, United Kingdom
    Stem Cells 26:1174-85. 2008
    ..The precise locations of such modified histones may be involved in controlling the colinear expression of genes from the cluster...

Research Grants1

  1. Detecting Human Functional Sequences with Microarrays
    Ian Dunham; Fiscal Year: 2006
    ..All data will be deposited with the ENCODE consortium as soon as it is shown to be reliable by replication and preliminary analysis. ..