Paul Flicek

发表

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

Helen E. Parkinson, Jacqueline A. L. MacArthur, Emily Bowler, 2016, Nucleic Acids Res..

ncRNA orthologies in the vertebrate lineage

Paul Flicek, Miguel Pignatelli, Albert J. Vilella, 2016, Database J. Biol. Databases Curation.

Sense from sequence reads: methods for alignment and assembly

Paul Flicek, Ewan Birney, E. Birney, 2009, Nature Methods.

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

Wan Choi, Oliver Hofmann, Roland Eils, 2017, bioRxiv.

The Ensembl REST API: Ensembl Data for Any Language

Alessandro Vullo, Paul Flicek, Miguel Pignatelli, 2014, Bioinform..

Integrating genomic homology into gene structure prediction

Ian Korf, Paul Flicek, Daniel Duan, 2001, ISMB.

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

Daniel Rios, Yuan Chen, Paul Flicek, 2010, BMC Bioinformatics.

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

Peggy Hall, Heather Junkins, Joannella Morales, 2013, Nucleic Acids Res..

Gene finding in the chicken genome

Eduardo Eyras, Paul Flicek, Stylianos E. Antonarakis, 2005, BMC Bioinformatics.

dbVar and DGVa: public archives for genomic structural variation

Chao Chen, Deanna M. Church, Paul Flicek, 2012, Nucleic Acids Res..

Federated discovery and sharing of genomic data using Beacons

David Haussler, Angela Page, Mikael Linden, 2019, Nature Biotechnology.

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation

Alessandro Vullo, Matthew R. Laird, Daniel R. Zerbino, 2016, bioRxiv.

Making sense of big data in health research: Towards an EU action plan

Magnus Rattray, Thomas Lengauer, Haralampos Karanikas, 2016, Genome Medicine.

eHive: An Artificial Intelligence workflow system for genomic analysis

Paul Flicek, Albert J. Vilella, Leo Gordon, 2010, BMC Bioinformatics.

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

Helen E. Parkinson, Jacqueline A. L. MacArthur, Maria Cerezo, 2018, Nucleic Acids Res..

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data

Paul Flicek, Ernesto Lowy, Anne-Marie Tassé, 2016, Nucleic Acids Res..

Optimized design and assessment of whole genome tiling arrays

Paul Flicek, Ewan Birney, Martijn A. Huynen, 2007, ISMB/ECCB.

The human-induced pluripotent stem cell initiative—data resources for cellular genetics

Helen E. Parkinson, Paul Flicek, Laura Clarke, 2016, Nucleic Acids Res..

GENCODE reference annotation for the human and mouse genomes

Mark Gerstein, Tomás Di Domenico, Jane Loveland, 2018, Nucleic Acids Res..

Ensembl variation resources

Laurent Gil, Paul Flicek, Fiona Cunningham, 2018, Database J. Biol. Databases Curation.

Optimising oligonucleotide array design for ChIP-on-chip

Paul Flicek, Ewan Birney, Martijn A. Huynen, 2007, BMC Bioinformatics.

Ensembl 2011

Daniel Rios, Yuan Chen, Paul Flicek, 2010, Nucleic Acids Res..

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis

Daniel R. Zerbino, Paul Flicek, Nathan Johnson, 2013, Bioinform..

Author Correction: Identification of genes required for eye development by high-throughput screening of mouse knockouts

Damian Smedley, Paul Flicek, Helen Parkinson, 2019, Communications Biology.

Ensembl 2013

Laurent Gil, Paul Flicek, Fiona Cunningham, 2012, Nucleic Acids Res..

IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex

James Robinson, Paul Flicek, Steven G. E. Marsh, 2016, Nucleic Acids Res..

Ensembl 2015

Alessandro Vullo, Daniel R. Zerbino, Laurent Gil, 2014, Nucleic Acids Res..

nGASP – the nematode genome annotation assessment project

Lincoln Stein, Paul Flicek, Todd W. Harris, 2008, BMC Bioinformatics.

Ensembl 2019

Astrid Gall, Alessandro Vullo, Jane Loveland, 2018, Nucleic Acids Res..

Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants

Jacqueline A. L. MacArthur, Laurent Gil, Joannella Morales, 2013, Nucleic Acids Res..

Ensembl 2017

Alessandro Vullo, Matthew R. Laird, Daniel R. Zerbino, 2016, Nucleic Acids Res..

Methodology article Consistent annotation of gene expression arrays

Paul Flicek, Glenn Proctor, Benoit Ballester, 2010 .

Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor

Daniel Rios, Yuan Chen, Paul Flicek, 2022 .

The IPD and IMGT/HLA database: allele variant databases

James Robinson, Paul Flicek, Steven G. E. Marsh, 2014, Nucleic Acids Res..

Alignment of 1000 Genomes Project reads to reference assembly GRCh38

Paul Flicek, David Richardson, Laura Clarke, 2017, GigaScience.

Soft windowing application to improve analysis of high-throughput phenotyping data

Damian Smedley, Jong Kyoung Kim, Paul Flicek, 2019, Bioinformatics.

The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

Gautier Koscielny, Henrik Westerberg, Damian Smedley, 2013, Nucleic Acids Res..

Ensembl variation resources

Laurent Gil, Paul Flicek, Fiona Cunningham, 2010, BMC Genomics.

Ensembl 2006

Andreas Prlic, Damian Smedley, Daniel Rios, 2005, Nucleic Acids Res..

Efficient masking of plant genomes by combining kmer counting and curated repeats

James E. Allen, Paul Flicek, Guy Naamati, 2021, bioRxiv.

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Irene Papatheodorou, Lincoln D Stein, Weijia Xu, 2020, Nucleic Acids Res..

Closure of the NCBI SRA and implications for the long-term future of genomics data storage

Mark Gerstein, Paul Flicek, Rob Knight, 2011, Genome Biology.

DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control

Roland Eils, Paul Flicek, Helene Kretzmer, 2015, Nature Genetics.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation

Paul Flicek, Damian Keefe, Michael J Gilchrist, 2009, Proceedings of the National Academy of Sciences.

A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans

Gail Clement, Jie Huang, Antonio Ciampi, 2014, Nature Communications.

A standard variation file format for human genome sequences

Karen Eilbeck, Paul Flicek, Fiona Cunningham, 2010, Genome Biology.

Random monoallelic gene expression increases upon embryonic stem cell differentiation.

Jan H Bergmann, Paul Flicek, John C Marioni, 2014, Developmental cell.

Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers

Paul Flicek, Simon Heath, Angelika Merkel, 2015, Genome research.

Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project

Paul Flicek, Magali Ruffier, Laura Clarke, 2019, Wellcome open research.

Computational approaches to interpreting genomic sequence variation

Paul Flicek, G. Ritchie, P. Flicek, 2014, Genome Medicine.

The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation

Damian Smedley, Paul Flicek, Steve D. M. Brown, 2018, Conservation Genetics.

Avianbase: a community resource for bird genomics

Paul Flicek, Bo Li, Bronwen L. Aken, 2015, Genome Biology.

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Mary Goldman, Brian Craft, Jingchun Zhu, 2016, Nature Communications.

The functional spectrum of low-frequency coding variation

Paul Flicek, Kristian Cibulskis, Gabor T Marth, 2011, Genome Biology.

Transcriptional diversity during lineage commitment of human blood progenitors

Randy J. Read, William J. Astle, Paul Flicek, 2014, Science.

Chromosome assembly of large and complex genomes using multiple references.

Joel Armstrong, Benedict Paten, Paul Flicek, 2018, Genome research.

Identification of genetic elements in metabolism by high-throughput mouse phenotyping

Paul Flicek, Steve D. M. Brown, Hiroshi Masuya, 2018, Nature Communications.

Multi-platform discovery of haplotype-resolved structural variation in human genomes

Li Ding, Amina Noor, Ali Bashir, 2018, Nature Communications.

Corrigendum: TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport

Gail Clement, Jie Huang, Inês Barroso, 2016, Nature Communications.

Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis

Paul Flicek, Laurence Ettwiller, Gregory E. Crawford, 2015, Cell reports.

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity

Paul Flicek, Stefan Engelen, Adriana Alberti, 2019, Molecular ecology resources.

Erratum to: Making sense of big data in health research: towards an EU action plan

Magnus Rattray, Thomas Lengauer, Haralampos Karanikas, 2016, Genome Medicine.

Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level.

Paul Flicek, Ian Dunham, Shane C. Dillon, 2009, Genome research.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Mark Gerstein, Benedict Paten, Paul Flicek, 2017, bioRxiv.

Functional Annotation of Rare Genetic Variants

Paul Flicek, G. Ritchie, P. Flicek, 2015 .

Mining Unique-m Substrings from Genomes

Rolf Apweiler, Zhenyu Jia, Paul Flicek, 2010, Journal of proteomics & bioinformatics.

An integrated functional genomics approach identifies the regulatory network directed by brachyury (T) in chordoma

Paul Flicek, Dina Halai, Nadège Presneau, 2012, The Journal of pathology.

The International Genome Sample Resource (IGSR) collection of open human genomic variation resources

Paul Flicek, Emily Perry, Susan Fairley, 2019, Nucleic Acids Res..

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

Maria Cerezo, Paul Flicek, Yaniv Erlich, 2016, Nature Genetics.

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

Boris Lenhard, Paul Flicek, Rachel Patton McCord, 2013, Genome research.

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.

Inanç Birol, Edwin Cuppen, Paul Flicek, 2010, Genome research.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Mark Gerstein, Kevin Struhl, Zhiping Weng, 2008, Genome research.

Leveraging European infrastructures to access 1 million human genomes by 2022

Arcadi Navarro, Søren Brunak, Jaap Heringa, 2019, Nature Reviews Genetics.

CHD7 Targets Active Gene Enhancer Elements to Modulate ES Cell-Specific Gene Expression

Lusy Handoko, Paul Flicek, Thomas LaFramboise, 2010, PLoS genetics.

Gene prediction: compare and CONTRAST

Paul Flicek, P. Flicek, 2007, Genome Biology.

Increased DNA methylation variability in type 1 diabetes across three immune effector cell types

Paul Flicek, Nicole Soranzo, Simon Heath, 2016, Nature Communications.

Variant calling on the GRCh38 assembly with the data from phase three of the 1000 Genomes Project

Paul Flicek, Magali Ruffier, Laura Clarke, 2019, Wellcome open research.

Sixteen diverse laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Mark Gerstein, Jane Loveland, Dent Earl, 2018, Nature Genetics.

Haplosaurus computes protein haplotypes for use in precision drug design

Paul Flicek, Fiona Cunningham, William Spooner, 2018, Nature Communications.

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Mark Gerstein, Jane Loveland, Dent Earl, 2018, bioRxiv.

regulatory modules cis occupied Cohesin regulates tissue-specific expression by stabilising highly

Paul Flicek, Michael D. Wilson, Stephen Watt, 2012 .

Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin

Boris Lenhard, Paul Flicek, Thomas Carroll, 2015 .

Latent Regulatory Potential of Human-Specific Repetitive Elements

Paul Flicek, Rory Stark, Michael D. Wilson, 2013, Molecular cell.

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

Paul Flicek, Alvis Brazma, Klara Stefflova, 2012, Genome research.