Guy St C Slater

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc Automated generation of heuristics for biological sequence comparison
    Guy St C Slater
    The Ensembl Group, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 6:31. 2005
  2. pmc Improvements to services at the European Nucleotide Archive
    Rasko Leinonen
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D39-45. 2010
  3. pmc VectorBase: a data resource for invertebrate vector genomics
    Daniel Lawson
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 37:D583-7. 2009
  4. pmc A database and API for variation, dense genotyping and resequencing data
    Daniel Rios
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 11:238. 2010
  5. 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
  6. pmc EMMA--mouse mutant resources for the international scientific community
    Phil Wilkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D570-6. 2010
  7. pmc Ensembl variation resources
    Yuan Chen
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Genomics 11:293. 2010
  8. pmc An effective model for natural selection in promoters
    Michael M Hoffman
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
    Genome Res 20:685-92. 2010
  9. pmc EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
    Albert J Vilella
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 19:327-35. 2009
  10. doi request reprint ENFIN--A European network for integrative systems biology
    Pascal Kahlem
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    C R Biol 332:1050-8. 2009

Detail Information

Publications92

  1. pmc Automated generation of heuristics for biological sequence comparison
    Guy St C Slater
    The Ensembl Group, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 6:31. 2005
    ....
  2. pmc Improvements to services at the European Nucleotide Archive
    Rasko Leinonen
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D39-45. 2010
    ..In this article, we briefly describe the content and scope of our archive and introduce major improvements to our services...
  3. pmc VectorBase: a data resource for invertebrate vector genomics
    Daniel Lawson
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 37:D583-7. 2009
    ..We have continued to develop both the software infrastructure and tools for interrogating the stored data...
  4. pmc A database and API for variation, dense genotyping and resequencing data
    Daniel Rios
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 11:238. 2010
    ..The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and manipulation of such data necessitating the redesign of existing genome-wide bioinformatics resources...
  5. 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
    ....
  6. pmc EMMA--mouse mutant resources for the international scientific community
    Phil Wilkinson
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D570-6. 2010
    ..g. Ensembl. Other resources are able to display EMMA data by accessing our Distributed Annotation System server. EMMA database access is publicly available at http://www.emmanet.org...
  7. pmc Ensembl variation resources
    Yuan Chen
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Genomics 11:293. 2010
    ..Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics...
  8. pmc An effective model for natural selection in promoters
    Michael M Hoffman
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, United Kingdom
    Genome Res 20:685-92. 2010
    ..The results show the first clear correlations between such a model and evolutionary processes...
  9. pmc EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
    Albert J Vilella
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 19:327-35. 2009
    ..All data are made available in a number of formats and will be kept up to date with the Ensembl project...
  10. doi request reprint ENFIN--A European network for integrative systems biology
    Pascal Kahlem
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    C R Biol 332:1050-8. 2009
    ..The computational work includes the development of a database infrastructure (EnCORE), bioinformatics analysis methods and a novel platform for protein function analysis FuncNet...
  11. 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...
  12. 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...
  13. pmc Petabyte-scale innovations at the European Nucleotide Archive
    Guy Cochrane
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 37:D19-25. 2009
    ....
  14. pmc Major submissions tool developments at the European Nucleotide Archive
    Clara Amid
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D43-7. 2012
    ....
  15. pmc Advanced genomic data mining
    Xose M Fernandez-Suarez
    European Bioinformatics Institute, Ensembl Group, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Comput Biol 4:e1000121. 2008
  16. pmc The HGNC Database in 2008: a resource for the human genome
    Elspeth A Bruford
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    Nucleic Acids Res 36:D445-8. 2008
    ..genenames.org, with direct links to the searchable HGNC database and other related database resources, such as the HCOP orthology search tool and manually curated gene family webpages...
  17. pmc Reactome: a database of reactions, pathways and biological processes
    David Croft
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 39:D691-7. 2011
    ..The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice...
  18. pmc The European Nucleotide Archive
    Rasko Leinonen
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 39:D28-31. 2011
    ....
  19. ncbi request reprint Genome information resources - developments at Ensembl
    Martin P Hammond
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Trends Genet 20:268-72. 2004
    ..Users can now display their own data in the context of other annotation. In addition, a fast and flexible data retrieval system, EnsMart, has been developed...
  20. pmc GeneWise and Genomewise
    Ewan Birney
    The European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 14:988-95. 2004
    ..The GeneWise algorithm was developed from a principled combination of hidden Markov models (HMMs). Both algorithms are highly accurate and can provide both accurate and complete gene structures when used with the correct evidence...
  21. pmc Integrating biological data--the Distributed Annotation System
    Andrew M Jenkinson
    European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 9:S3. 2008
    ..DAS continues to expand its applicability and evolve in response to new challenges facing integrative bioinformatics...
  22. ncbi request reprint The International Protein Index: an integrated database for proteomics experiments
    Paul J Kersey
    EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Proteomics 4:1985-8. 2004
    ..IPI (the International Protein Index) has been developed to address these issues and offers complete nonredundant data sets representing the human, mouse and rat proteomes, built from the Swiss-Prot, TrEMBL, Ensembl and RefSeq databases...
  23. pmc Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    Daniel R Zerbino
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
    Genome Res 18:821-9. 2008
    ..Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies...
  24. pmc Mouse genomic variation and its effect on phenotypes and gene regulation
    Thomas M Keane
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK
    Nature 477:289-94. 2011
    ..These sequences provide a starting point for a new era in the functional analysis of a key model organism...
  25. ncbi request reprint Biological database design and implementation
    Ewan Birney
    EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Brief Bioinform 5:31-8. 2004
    ..Our experience has led us to emphasise simplicity and conservative technology choices when building these databases. This is a short paper of advice that we hope is useful to people designing their own biological database...
  26. pmc The European Bioinformatics Institute's data resources
    Catherine Brooksbank
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 31:43-50. 2003
    ..The EBI's databases and tools are all available on our website at www.ebi.ac.uk...
  27. ncbi request reprint Genome browsing with Ensembl: a practical overview
    Giulietta Spudich
    EMBL Outstation EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB101SD, UK
    Brief Funct Genomic Proteomic 6:202-19. 2007
    ..Genes and annotation are accessible through the Ensembl browser (http://www.ensembl.org), and through direct queries of its databases using the Perl API (Application Programme Interface), MySQL or BioMart...
  28. ncbi request reprint Comparative genomics: genome-wide analysis in metazoan eukaryotes
    Abel Ureta-Vidal
    EnsEMBL Project, Room A2 06, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nat Rev Genet 4:251-62. 2003
    ..Each of these areas improves the methods of deciphering long genomic sequences and uncovering what lies hidden in them...
  29. pmc The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates
    Laurence Ettwiller
    EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
    Genome Biol 6:R104. 2005
    ..We then used deeper comparative analysis across vertebrates to identify the active instances of these motifs. We have shown experimentally in Medaka fish that a subset of these predictions is involved in transcription...
  30. pmc The Ensembl core software libraries
    Arne Stabenau
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    Genome Res 14:929-33. 2004
    ..The architecture of the core software libraries, the schema, and the factors influencing their design are described. All code and data are freely available...
  31. pmc Efficient storage of high throughput DNA sequencing data using reference-based compression
    Markus Hsi-Yang Fritz
    European Molecular Biology Laboratory s European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
    Genome Res 21:734-40. 2011
    ....
  32. pmc Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler
    Daniel R Zerbino
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    PLoS ONE 4:e8407. 2009
    ..Despite the short length of their reads, micro-read sequencing technologies have shown their usefulness for de novo sequencing. However, especially in eukaryotic genomes, complex repeat patterns are an obstacle to large assemblies...
  33. pmc The systematic annotation of the three main GPCR families in Reactome
    Bijay Jassal
    European Bioinformatics Institute, Hinxton, Cambridge CB101SD, UK
    Database (Oxford) 2010:baq018. 2010
    ..Database URL: http://www.reactome.org...
  34. pmc VectorBase: a home for invertebrate vectors of human pathogens
    Daniel Lawson
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
    Nucleic Acids Res 35:D503-5. 2007
    ....
  35. ncbi request reprint Estimating the neutral rate of nucleotide substitution using introns
    Michael M Hoffman
    European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, England
    Mol Biol Evol 24:522-31. 2007
    ..Although the intron method may be more useful for shorter evolutionary distances, it is less useful at longer distances due to the poor alignment of less-conserved positions...
  36. ncbi request reprint Optimized design and assessment of whole genome tiling arrays
    Stefan Graf
    EMBL European Bioinformatics Institute, Hinxton, Cambridge, UK
    Bioinformatics 23:i195-204. 2007
    ..We have identified a number of design parameters to be optimized including uniqueness of the probe sequences within the whole genome, melting temperature and self-hybridization potential...
  37. doi request reprint Sense from sequence reads: methods for alignment and assembly
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Methods 6:S6-S12. 2009
    ..We discuss the current algorithmic approaches and future directions of these fundamental tools and provide specific examples for some commonly used tools...
  38. pmc EnsMart: a generic system for fast and flexible access to biological data
    Arek Kasprzyk
    European Bioinformatics Institute EBI, Hinxton, Cambridge CB10 1SH, UK
    Genome Res 14:160-9. 2004
    ..Both implementations and the database are freely available for local installation, and can be extended or adapted to 'non-Ensembl' data sets...
  39. pmc Allele-specific and heritable chromatin signatures in humans
    Ewan Birney
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Hum Mol Genet 19:R204-9. 2010
    ..A detailed understanding of the relationship between normal genetic variation and chromatin variation can shed light on how polymorphisms in non-coding regions in the human genome might underlie phenotypic variation and disease...
  40. pmc Finding and sharing: new approaches to registries of databases and services for the biomedical sciences
    Damian Smedley
    European Bioinformatics Institute, Genome Campus, Hinxton, Cambridgeshire, CB10 1SA
    Database (Oxford) 2010:baq014. 2010
    ..We expect such approaches will result in improved discovery, uptake and utilization of data resources. Database URL: http://www.casimir.org.uk/casimir_ddf...
  41. ncbi request reprint Databases and tools for browsing genomes
    Ewan Birney
    European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, United Kingdom
    Annu Rev Genomics Hum Genet 3:293-310. 2002
    ..This article reviews the database systems and tools for analysis that have so far been developed to address this...
  42. pmc Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database
    Guy Cochrane
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nucleic Acids Res 36:D5-12. 2008
    ..Priorities are discussed in terms of how reliably information can be captured, the long-term benefits of its capture and the ease with which it can be captured...
  43. pmc The variant call format and VCFtools
    Petr Danecek
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
    Bioinformatics 27:2156-8. 2011
    ..VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API...
  44. pmc Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species
    Paul J Kersey
    Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 40:D91-7. 2012
    ....
  45. pmc Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses
    Albert J Vilella
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    Genome Biol 12:401. 2011
    ..A response to 2x genomes - depth does matter by MC Milinkovitch, R Helaers, E Depiereux, AC Tzika and T Gabaldón. Genome Biol 2010, 11:R16...
  46. ncbi request reprint ENFIN a network to enhance integrative systems biology
    Pascal Kahlem
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Ann N Y Acad Sci 1115:23-31. 2007
    ..We will give an overview of the projects tackled within ENFIN and discuss the challenges associated with integration for systems biology...
  47. pmc The Pfam protein families database
    Alex Bateman
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nucleic Acids Res 30:276-80. 2002
    ..New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource...
  48. ncbi request reprint Picking pyknons out of the human genome
    Alison Meynert
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
    Cell 125:836-8. 2006
    ..Although it is unclear how pyknons might have arisen, it is possible that they may be involved in a new form of gene regulation...
  49. pmc Reactome: a knowledge base of biologic pathways and processes
    Imre Vastrik
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Genome Biol 8:R39. 2007
    ..Finally, we describe the use of Reactome both as a learning resource and as a computational tool to aid in the interpretation of microarrays and similar large-scale datasets...
  50. pmc Discovering novel cis-regulatory motifs using functional networks
    Laurence M Ettwiller
    European Bioinformatics Institute EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    Genome Res 13:883-95. 2003
    ....
  51. pmc Patterns of somatic mutation in human cancer genomes
    Christopher Greenman
    Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 446:153-8. 2007
    ..Systematic sequencing of cancer genomes therefore reveals the evolutionary diversity of cancers and implicates a larger repertoire of cancer genes than previously anticipated...
  52. pmc An overview of Ensembl
    Ewan Birney
    EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 14:925-8. 2004
    ....
  53. ncbi request reprint A physical map of the mouse genome
    Simon G Gregory
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    Nature 418:743-50. 2002
    ..The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy...
  54. 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...
  55. doi request reprint Chromatin and heritability: how epigenetic studies can complement genetic approaches
    Ewan Birney
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Trends Genet 27:172-6. 2011
    ..In particular, I see more benefit to epigenetic studies being performed in the context of genetic studies, rather than as separate investigations...
  56. pmc A survey of homozygous deletions in human cancer genomes
    Charles Cox
    Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
    Proc Natl Acad Sci U S A 102:4542-7. 2005
    ..They may also reflect a tendency to reduce the adverse effects of homozygous deletions by minimizing the number of genes removed...
  57. pmc Gene finding in the chicken genome
    Eduardo Eyras
    Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain
    BMC Bioinformatics 6:131. 2005
    ..We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method...
  58. pmc Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags
    Simon J Hubbard
    Faculty of Life Sciences, The University of Manchester, Manchester, M60 1QD, United Kingdom
    Genome Res 15:174-83. 2005
    ....
  59. ncbi request reprint The genome sequence of the malaria mosquito Anopheles gambiae
    Robert A Holt
    Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
    Science 298:129-49. 2002
    ..An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect...
  60. ncbi request reprint Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster
    Evgeny M Zdobnov
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 298:149-59. 2002
    ....
  61. pmc Sockeye: a 3D environment for comparative genomics
    Stephen B Montgomery
    Canada s Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
    Genome Res 14:956-62. 2004
    ..By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization...
  62. pmc The Bioperl toolkit: Perl modules for the life sciences
    Jason E Stajich
    University Program in Genetics, Duke University, Durham, North Carolina 27710, USA
    Genome Res 12:1611-8. 2002
    ..We conclude with a discussion of how the open-source nature of the project has contributed to the development effort...
  63. pmc Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment
    Emmanouil T Dermitzakis
    Division of Medical Genetics, University of Geneva Medical School, CH 1211 Geneva, Switzerland
    Genome Res 14:852-9. 2004
    ..We propose models for a global role of CNGs in genome function and regulation, through long-distance cis or trans chromosomal interactions...
  64. ncbi request reprint Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation
    Laurence Ettwiller
    Developmental Biology Unit, EMBL Heidelberg, Heidelberg, Germany
    Nat Methods 4:563-5. 2007
    ..Newly discovered motifs and their features (identity, conservation, position in sequence) are displayed on a web interface...
  65. ncbi request reprint Immunity-related genes and gene families in Anopheles gambiae
    George K Christophides
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Science 298:159-65. 2002
    ..Representative expression profiles confirm that sequence diversification is accompanied by specific responses to different immune challenges. Alternative RNA splicing may also contribute to expansion of the immune repertoire...
  66. ncbi request reprint A SNP map of the rat genome generated from cDNA sequences
    Heike Zimdahl
    Max Delbrück Center for Molecular Medicine MDC, Robert Rossle Str 10, 13092 Berlin Buch, Germany
    Science 303:807. 2004
  67. ncbi request reprint Unrestricted free access works and must continue
    Steven Salzberg
    Nature 422:801. 2003
  68. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  69. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  70. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  71. pmc Dry work in a wet world: computation in systems biology
    Pascal Kahlem
    Mol Syst Biol 2:40. 2006
  72. 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...
  73. pmc Genome sequence of Aedes aegypti, a major arbovirus vector
    Vishvanath Nene
    Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
    Science 316:1718-23. 2007
    ..An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species...
  74. pmc The implications of alternative splicing in the ENCODE protein complement
    Michael L Tress
    Structural Computational Biology Programme, Spanish National Cancer Research Centre, E 28029 Madrid, Spain
    Proc Natl Acad Sci U S A 104:5495-500. 2007
    ....
  75. doi request reprint Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes
    Elliott H Margulies
    Genome Technology Branch, Genome Informatics Section, National Human Genome Research Institute, National Institutes of Health, 5625 Fishers Lane, Room 5N 01N, MSC9400, Bethesda, Maryland 20892, USA
    Nat Rev Genet 9:303-13. 2008
    ..Approaches to determining the biological significance of constrained sequence are also explored...
  76. pmc What everybody should know about the rat genome and its online resources
    Simon N Twigger
    Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
    Nat Genet 40:523-7. 2008
    ....
  77. doi request reprint Levers and fulcrums: progress in cis-regulatory motif models
    Ewan Birney
    Nat Methods 5:297-8. 2008
  78. pmc An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
    Vardhman K Rakyan
    Institute of Cell and Molecular Science, Barts and The London, London E1 2AT, United Kingdom
    Genome Res 18:1518-29. 2008
    ....
  79. pmc A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
    Thomas A Down
    Wellcome Trust Cancer Research UK Gurdon Institute, and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
    Nat Biotechnol 26:779-85. 2008
    ....
  80. pmc TranscriptSNPView: a genome-wide catalog of mouse coding variation
    Fiona Cunningham
    Nat Genet 38:853. 2006
  81. pmc Identification of novel peptide hormones in the human proteome by hidden Markov model screening
    Olivier Mirabeau
    Mouse Biology Unit, EMBL, 00016 Monterotondo, Italy
    Genome Res 17:320-7. 2007
    ..Peptide hormones and their receptors are important diagnostic and therapeutic targets, and our results suggest that spexin and augurin are novel peptide hormones likely to be involved in physiological homeostasis...
  82. pmc EGASP: the human ENCODE Genome Annotation Assessment Project
    Roderic Guigo
    Centre de Regulacio Genomica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
    Genome Biol 7:S2.1-31. 2006
    ..These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment...
  83. pmc In vivo validation of a computationally predicted conserved Ath5 target gene set
    Filippo Del Bene
    Developmental Biology Programme, European Molecular Biology Laboratory, Heidelberg, Heidelberg, Germany
    PLoS Genet 3:1661-71. 2007
    ..Thus, our procedure, applied to whole genomes, is a fast and predictive tool to in silico filter the target genes of a given transcription factor with defined binding site...
  84. ncbi request reprint Evolutionary genomics: come fly with us
    Ewan Birney
    Nature 450:184-5. 2007
  85. ncbi request reprint Report of an EU projects workshop on systems biology held in Brussels, Belgium on 8 December 2004
    Ewan Birney
    Syst Biol (Stevenage) 152:55-60. 2005
  86. pmc Update of the Anopheles gambiae PEST genome assembly
    Maria V Sharakhova
    Center for Global Health and Infectious Diseases, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN 46556 0369, USA
    Genome Biol 8:R5. 2007
    ....
  87. pmc Challenges and standards in integrating surveys of structural variation
    Stephen W Scherer
    The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, 101 College Street, Room 14 701, Ontario M5G 1L7, Canada
    Nat Genet 39:S7-15. 2007
    ..From this, we derive recommendations for standards to be adopted, with the aim of ensuring the accurate presentation of this form of genetic variation to facilitate ongoing research...
  88. ncbi request reprint The Anopheles gambiae genome: an update
    Emmanuel Mongin
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Trends Parasitol 20:49-52. 2004
    ..This article reviews progress and considers limitations in the current sequence assembly and gene annotation, as well as approaches to address these problems and outstanding issues that users of the data must bear in mind...
  89. pmc Confounding between recombination and selection, and the Ped/Pop method for detecting selection
    Paul F O'Reilly
    Department of Epidemiology and Public Health, Imperial College London, UK
    Genome Res 18:1304-13. 2008
    ..We apply the method to human HapMap and Perlegen data sets, finding confirmation of reported candidates as well as identifying new loci that may have undergone recent intense selection...
  90. pmc Genome analysis of the platypus reveals unique signatures of evolution
    Wesley C Warren
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 453:175-83. 2008
    ..Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation...
  91. doi request reprint SNP and haplotype mapping for genetic analysis in the rat
    Kathrin Saar
    Max Delbruck Center for Molecular Medicine, Robert Rossle Strae 10, 13125 Berlin, Germany
    Nat Genet 40:560-6. 2008
    ..We provide a detailed SNP map and demonstrate its utility for mapping of quantitative trait loci. This community resource is openly available and augments the genetic tools for this workhorse of physiological studies...