Research Topics
Genomes and Genes | Paul FlicekSummaryAffiliation: Wellcome Trust Genome Campus Country: UK Publications
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Publications
Ensembl's 10th yearPaul Flicek
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Nucleic Acids Res 38:D557-62. 2010....- Ensembl 2013Paul 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... - The functional spectrum of low-frequency coding variationGabor T Marth
Department of Biology, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA
Genome Biol 12:R84. 2011.... - Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and developmentMarilyn B Renfree
The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
Genome Biol 12:R81. 2011..Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development... - Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineagesDominic Schmidt
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
Cell 148:335-48. 2012..Repeat-driven dispersal of CTCF binding is a fundamental, ancient, and still highly active mechanism of genome evolution in mammalian lineages... - Ensembl 2012Paul 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... - Locus Reference Genomic sequences: an improved basis for describing human DNA variantsRaymond Dalgleish
Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
Genome Med 2:24. 2010..Further information can be found on the LRG web site: http://www.lrg-sequence.org... - A standard variation file format for human genome sequencesMartin G Reese
Omicia, 2200 Powell Street, Suite 525, Emeryville, CA 94608, USA
Genome Biol 11:R88. 2010.... - Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasetsSebastian Oeder
Institute of Medical Microbiology, Immunology and Hygiene Technical University Munich, Munich, Germany
BMC Genomics 8:200. 2007..The ability to quantitatively assess changes in NAT expression for many different transcripts in multiple samples would facilitate our understanding of this relatively new class of RNA molecules... - Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcriptsPaul Flicek
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Genome Biol 7:S8.1-9. 2006..MARS is able to use an arbitrary number of informant sequences and predicts a number of alternative transcripts at each gene locus... - The need for speedPaul Flicek
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Genome Biol 10:212. 2009..DNA sequence data are being produced at an ever-increasing rate. The Bowtie sequence-alignment algorithm uses advanced data structures to help data analysis keep pace with data generation... - Ensembl 2011Paul 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... - Gene prediction: compare and CONTRASTPaul Flicek
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SD, UK
Genome Biol 8:233. 2007.... - Ensembl 2008P Flicek
European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Nucleic Acids Res 36:D707-14. 2008..We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure... 
Sense from sequence reads: methods for alignment and assemblyPaul 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...- Ensembl variation resourcesYuan 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... - A database and API for variation, dense genotyping and resequencing dataDaniel 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... - Insights into hominid evolution from the gorilla genome sequenceAylwyn Scally
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
Nature 483:169-75. 2012..The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution... - A map of human genome variation from population-scale sequencingRichard M Durbin
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
Nature 467:1061-73. 2010..These methods and public data will support the next phase of human genetic research... - Consistent annotation of gene expression arraysBenoit Ballester
European Bioinformatics Institute EMBL, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
BMC Genomics 11:294. 2010.... - eHive: an artificial intelligence workflow system for genomic analysisJessica Severin
European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
BMC Bioinformatics 11:240. 2010..The number of calculations required for this task grows approximately quadratically with the number of species. We currently support 50 species in Ensembl and we expect the number to continue to grow in the future... - Deriving the consequences of genomic variants with the Ensembl API and SNP Effect PredictorWilliam McLaren
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Bioinformatics 26:2069-70. 2010..ensembl.org/. The Ensembl API (http://www.ensembl.org/info/docs/api/api_installation.html for installation instructions) is open source software... - The variant call format and VCFtoolsPetr 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. AVAILABILITY: http://vcftools.sourceforge.net.. - Extensive compensatory cis-trans regulation in the evolution of mouse gene expressionAngela Goncalves
European Bioinformatics Institute EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
Genome Res 22:2376-84. 2012..We propose that expression levels of genes regulated by this mechanism are fine-tuned by cis variants that arise following regulatory changes in trans, suggesting that many cis variants are not the primary targets of natural selection... - nGASP--the nematode genome annotation assessment projectAvril Coghlan
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
BMC Bioinformatics 9:549. 2008..elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase... - Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modulesAndre J Faure
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
Genome Res 22:2163-75. 2012..Finally, we observe that the presence of mirrored CTCF binding events at promoters and their nearby cohesin-bound enhancers is associated with elevated expression levels... - The 1000 Genomes Project: data management and community accessLaura Clarke
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Nat Methods 9:459-62. 2012..Members of the project data coordination center have developed and deployed several tools to enable widespread data access... - De novo assembly and genotyping of variants using colored de Bruijn graphsZamin Iqbal
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
Nat Genet 44:226-32. 2012..Last, we estimate classical human leukocyte antigen (HLA) genotypes at HLA-B, the most variable gene in the human genome... - Ensembl BioMarts: a hub for data retrieval across taxonomic spaceRhoda J Kinsella
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Database (Oxford) 2011:bar030. 2011..ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/... - Considerations for the inclusion of 2x mammalian genomes in phylogenetic analysesAlbert 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... - DbVar and DGVa: public archives for genomic structural variationIlkka Lappalainen
European Bioinformatics Institute, Hinxton, CB10 1SD Cambridgeshire, UK
Nucleic Acids Res 41:D936-41. 2013..Additionally, we have made significant improvements in providing access to these data via web and FTP interfaces... - Maps for the world of genomic medicine: the 2011 CSHL Personal Genomes meetingXiangqun Zheng-Bradley
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Hum Mutat 33:1016-9. 2012.... 
Optimized design and assessment of whole genome tiling arraysStefan 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...- Population genomics of human gene expressionBarbara E Stranger
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nat Genet 39:1217-24. 2007..We also explore several methodologies that improve the current state of analysis of gene expression variation... - Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence levelAlexander 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... - Finding and sharing: new approaches to registries of databases and services for the biomedical sciencesDamian 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... - Variation in genome-wide mutation rates within and between human familiesDonald F Conrad
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
Nat Genet 43:712-4. 2011..These observations suggest considerable variation in mutation rates within and between families... - The landscape of histone modifications across 1% of the human genome in five human cell linesChristoph 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... - Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolutionLadeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 432:695-716. 2004..The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture... - Gene finding in the chicken genomeEduardo 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... - EGASP: the human ENCODE Genome Annotation Assessment ProjectRoderic 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... - Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny mapPaul Flicek
Department of Computer Science and Engineering, Washington University, St. Louis, Missouri 63130, USA
Genome Res 13:46-54. 2003..Our human annotation using the mouse assembly is conservative, predicting only 25,622 genes, and appears to be one of the best de novo annotations of the human genome to date... - Initial sequencing and comparative analysis of the mouse genomeRobert 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.... - 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.... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targetsDavid 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... - Recommendations of the 2006 Human Variome Project meetingRichard G H Cotton
Genomic Disorders Research Centre, St Vincent s Hospital Melbourne, 35 Victoria Parade, Melbourne, Victoria 3065, Australia
Nat Genet 39:433-6. 2007..Here we summarize the background of the project, the meeting and its recommendations... - SNP and haplotype mapping for genetic analysis in the ratKathrin 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... - TranscriptSNPView: a genome-wide catalog of mouse coding variationFiona Cunningham
Nat Genet 38:853. 2006 - Genome analysis of the platypus reveals unique signatures of evolutionWesley 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... - A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysisThomas 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....