List of works by Paul Flicek

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

scientific article

A CTCF-independent role for cohesin in tissue-specific transcription

scientific article

A CpG mutational hotspot in a ONECUT binding site accounts for the prevalent variant of hemophilia B Leyden

scientific article

A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection

scientific article published on 24 October 2019

A comparative encyclopedia of DNA elements in the mouse genome

scientific article

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

scientific article

A draft human pangenome reference

scientific article published on 10 May 2023

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

scholarly article

A high-resolution map of human evolutionary constraint using 29 mammals

scientific article

A joint NCBI and EMBL-EBI transcript set for clinical genomics and research

scientific article published in April 2022

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction.

scientific article published on 12 October 2017

A standard variation file format for human genome sequences

scientific article (publication date: 2010)

A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog

scientific article published on 15 February 2018

Accessing Livestock Resources in Ensembl

scientific article published on 28 April 2021

Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans

scientific article

Adaptation of Proteins to the Cold in Antarctic Fish: A Role for Methionine?

article

Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks

scientific article published on 20 February 2017

Alignment of 1000 Genomes Project Reads to Reference Assembly GRCh38.

scientific article

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

scientific article published on 09 September 2019

An improved pig reference genome sequence to enable pig genetics and genomics research

scientific article published on 01 June 2020

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

scientific article

An integrated map of structural variation in 2,504 human genomes

scientific article

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

scientific article

Applications of the 1000 Genomes Project resources

scientific article

Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis

scientific article published on 04 March 2015

Author Correction: Comparative and demographic analysis of orang-utan genomes

correction of a scholarly article

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

scholarly article

Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022

scientific article published on 01 November 2019

Author Correction: Perspectives on ENCODE

scholarly article

Avianbase: a community resource for bird genomics

scientific article

BLUEPRINT to decode the epigenetic signature written in blood.

scientific article

CAST-ChIP maps cell-type-specific chromatin states in the Drosophila central nervous system.

scientific article published on 3 October 2013

CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression

scientific article

CTCF maintains regulatory homeostasis of cancer pathways

scientific article published on 07 August 2018

Cell type specific novel lncRNAs and circRNAs in the BLUEPRINT haematopoietic transcriptomes atlas

scientific article published on 23 July 2020

Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal

scientific article

Characterizing genetic variants for clinical action

scientific article

Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes

scientific article published on 01 January 2019

Chromosome assembly of large and complex genomes using multiple references

scientific article published on 19 October 2018

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

scientific article

Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains

scientific article published on 07 January 2020

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes

scientific article

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

scientific journal article

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

scientific article published on 03 September 2013

Combined HAT/EZH2 modulation leads to cancer-selective cell death.

scientific article published on 22 May 2018

Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

scientific article published on 26 May 2013

Comparative analysis of neutrophil and monocyte epigenomes

Comparative and demographic analysis of orang-utan genomes

scientific article

Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression

article

Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression.

scientific article published on 27 November 2017

Computational approaches to identify functional genetic variants in cancer genomes

scientific article published on August 2013

Computational approaches to interpreting genomic sequence variation

scientific article

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses

scientific article published on 21 February 2011

Consistent annotation of gene expression arrays

scientific article

Convergent genomic signatures of domestication in sheep and goats.

scientific article published on 6 March 2018

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals

scientific article

Correction to: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome

scientific article published on 07 May 2019

Corrigendum: High-throughput discovery of novel developmental phenotypes.

scientific article published on 8 November 2017

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

scientific article

DbVar and DGVa: public archives for genomic structural variation

scientific article (publication date: 2013)

De novo assembly and genotyping of variants using colored de Bruijn graphs

scientific article published on 8 January 2012

Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage.

scientific article published on November 2016

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals

scientific article

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

scientific article (publication date: 15 August 2010)

Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium.

scientific article published on 26 June 2017

Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems

scientific article published in November 2016

Divergence in gene expression within and between two closely related flycatcher species

scientific article published on 29 February 2016

Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils

scientific article published on 01 September 2018

EGASP: the human ENCODE Genome Annotation Assessment Project

scientific article

Enhancer evolution across 20 mammalian species

scientific article

Ensembl 2006.

scientific article

Ensembl 2007

scientific article

Ensembl 2008

scientific article

Ensembl 2009

scientific article (publication date: 2009)

Ensembl 2011

scientific article

Ensembl 2012

scientific article

Ensembl 2013

scientific article

Ensembl 2014

scientific article

Ensembl 2015

scientific article (publication date: 2015)

Ensembl 2016

scientific article

Ensembl 2017

scientific article

Ensembl 2018.

scientific article published on 16 November 2017

Ensembl 2019

scientific article published on 01 January 2019

Ensembl 2020

scientific article published on 01 January 2020

Ensembl 2021

scientific article published on 02 November 2020

Ensembl 2022

scientific article published on 19 October 2021

Ensembl 2023

scientific article published in November 2022

Ensembl BioMarts: a hub for data retrieval across taxonomic space

scientific article

Ensembl Genomes 2020-enabling non-vertebrate genomic research

scientific article published on 01 January 2020

Ensembl comparative genomics resources

scientific article published on 20 February 2016

Ensembl comparative genomics resources

scientific article published on 2 May 2016

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

scientific article (publication date: 2017)

Ensembl regulation resources

scientific article published on 17 February 2016

Ensembl variation resources

scientific article published in 2010

Ensembl variation resources

article

Ensembl's 10th year

scientific article

Epigenome data release: a participant-centered approach to privacy protection

scientific article

Epigenomic and functional dynamics of human bone marrow myeloid differentiation to mature blood neutrophils

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

scientific article published on 07 March 2019

Erratum: Corrigendum: The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

article

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

scientific article

Evolution of transcription factor binding in metazoans - mechanisms and functional implications

scientific article

Evolutionary biology: The handiwork of tinkering

scientific article published in August 2013

Extending reference assembly models

scientific article

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

scientific article

FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community

scientific article published on 12 October 2018

Federated discovery and sharing of genomic data using Beacons

scientific article published on 01 March 2019

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

scientific article

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding

scientific article

Functional Annotation of Rare Genetic Variants

Functional annotation of noncoding sequence variants.

scientific article published on 2 February 2014

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

scientific article published on 28 April 2009

Functional signatures of evolutionarily young CTCF binding sites

scientific article published on 23 September 2020

Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome

scientific article published on 10 March 2017

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

GENCODE 2021 ⬇️

scientific article published on 03 December 2020

GENCODE reference annotation for the human and mouse genomes

scientific article published on 01 January 2019

GENETICS. The Human Variome Project

scientific article

Gene finding in the chicken genome

scientific article

Gene prediction: compare and CONTRAST.

scientific article published on January 2007

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

scientific article

Genetic variation and gene expression across multiple tissues and developmental stages in a non-human primate

article

Genome analysis of the platypus reveals unique signatures of evolution

scientific article

Genome analysis of the platypus reveals unique signatures of evolution

scientific article published in Nature

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

scientific article

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

article

Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat

scientific article published on 25 July 2013

Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat.

scientific article published on 22 December 2017

Genome-wide nucleotide-level mammalian ancestor reconstruction

scientific article (publication date: November 2008)

Getting the Entire Message: Progress in Isoform Sequencing

scientific article published on 16 August 2019

Gibbon genome and the fast karyotype evolution of small apes

scientific article

Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression

scientific article

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

scientific article published on 10 November 2020

Guidelines for the Safe Use of Radioactive Materials During Localization and Resection of the Sentinel Lymph Node

scientific article published on 01 January 1999

Haplosaurus computes protein haplotypes for use in precision drug design

scientific article published in Nature Communications

High-throughput discovery of novel developmental phenotypes

scientific article published on 14 September 2016

IPD-IMGT/HLA Database

scientific article published on 01 January 2020

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

scientific article (publication date: 4 January 2017)

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

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

scientific article published on 21 December 2018

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

scientific article published on 18 January 2018

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

scientific article

Initial sequencing and comparative analysis of the mouse genome

scientific article

Insights into hominid evolution from the gorilla genome sequence

scientific article

Integrating genomic homology into gene structure prediction.

scientific article published in January 2001

Integrative annotation of variants from 1092 humans: application to cancer genomics

scientific article

International network of cancer genome projects

scientific article

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution

article

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.

scientific article

Journal club

LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions

scientific article published on 18 February 2021

LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order

scientific article published on 26 February 2016

Latent regulatory potential of human-specific repetitive elements

scientific article published on 13 December 2012

Leveraging European infrastructures to access 1 million human genomes by 2022

scientific article published on 27 August 2019

Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map.

scientific article

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

scientific article

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

scientific article published on 26 November 2013

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

scientific article

Maps for the world of genomic medicine: the 2011 CSHL Personal Genomes meeting

scientific article

Mining Unique-m Substrings from Genomes.

scientific article published in March 2010

Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data

scientific article

Modernizing reference genome assemblies

scientific article

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density

scientific article published on 28 December 2020

Multi-omics profiling reveals a distinctive epigenome signature for high-risk acute promyelocytic leukemia.

scientific article

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

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

scientific article published on 16 April 2019

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis

scientific article published in 2010

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

scientific article

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

Optimized design and assessment of whole genome tiling arrays.

scientific article published on July 2007

Perspectives on ENCODE

scientific article published on 29 July 2020

Pervasive lesion segregation shapes cancer genome evolution

scientific article published on 24 June 2020

Planning the human variome project: the Spain report.

scientific article published in April 2009

Platelet function is modified by common sequence variation in megakaryocyte super enhancers

scientific article

Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history

Public data archives for genomic structural variation

scientific article

Publisher Correction: Federated discovery and sharing of genomic data using Beacons

scientific article published on 01 April 2019

Publisher Correction: The tuatara genome reveals ancient features of amniote evolution

scientific article published on 18 August 2020

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

scientific article

Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

scientific article published on 21 November 2015

Random monoallelic gene expression increases upon embryonic stem cell differentiation

scientific article

Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A

scientific article published on 02 December 2019

Recommendations of the 2006 Human Variome Project meeting

scientific article published in April 2007

Registered access: authorizing data access

scientific article published on 2 August 2018

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System

scientific article published on 4 September 2015

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

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

scientific article published on 21 March 2018

SNP and haplotype mapping for genetic analysis in the rat.

scientific article

Sense from sequence reads: methods for alignment and assembly

scientific article

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

scientific article

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

scientific article published on 01 October 2018

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

scientific article published on 01 March 2020

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

scientific article published on 12 February 2015

Standards recommendations for the Earth BioGenome Project

scientific article published on 18 January 2022

Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues

scientific article

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

scientific article published on 7 February 2008

The 1000 Genomes Project: data management and community access

scientific article (publication date: 27 April 2012)

The BLUEPRINT Data Analysis Portal.

scientific article

The DNA sequence of human chromosome 7

scientific article

The Deep Genome Project

scientific article published on 03 February 2020

The Earth BioGenome Project 2020: Starting the clock

scientific article published on 25 January 2022

The Ensembl REST API: Ensembl Data for Any Language

scientific article

The Ensembl Variant Effect Predictor

scientific article published on 06 June 2016

The Ensembl gene annotation system

scientific article published on 23 June 2016

The European Bioinformatics Institute (EMBL-EBI) in 2021

scientific article published on 25 November 2021

The European Genome-phenome Archive in 2021

scientific article published on 01 January 2022

The European Genome-phenome Archive of human data consented for biomedical research.

scientific article

The Evolutionary Fates of a Large Segmental Duplication in Mouse

scientific article published on 2 July 2016

The Human Pangenome Project: a global resource to map genomic diversity

scientific article published in April 2022

The IPD and IMGT/HLA database: allele variant databases

scientific article

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

scientific article published on 01 January 2020

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

scientific article published on 19 May 2018

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

scientific article

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

scientific article

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

scientific article published on 01 January 2019

The ensembl regulatory build

scientific article published on 24 March 2015

The functional spectrum of low-frequency coding variation

scientific article published on 14 September 2011

The genome of a songbird

scientific article

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

scientific article

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

scientific article

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

scientific article

The landscape of histone modifications across 1% of the human genome in five human cell lines

scientific article

The need for speed

scientific article (publication date: 2009)

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

scientific article

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia

scientific article published on 21 May 2018

The sheep genome illuminates biology of the rumen and lipid metabolism

scientific article

The tuatara genome reveals ancient features of amniote evolution

scientific article published on 5 August 2020

The tuatara genome: insights into vertebrate evolution from the sole survivor of an ancient reptilian order

scientific article published on 8 December 2019

Third Report on Chicken Genes and Chromosomes 2015.

scientific article published on 14 July 2015

Towards complete and error-free genome assemblies of all vertebrate species

scientific article

TranscriptSNPView: a genome-wide catalog of mouse coding variation

scientific article published on August 2006

Transcriptional activity and strain-specific history of mouse pseudogenes

scientific article published on 29 July 2020

Transcriptional diversity during lineage commitment of human blood progenitors

scientific article

Transcriptome and genome sequencing uncovers functional variation in humans

scientific article

Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets

scientific article

Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly

scientific article published on 27 November 2019

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts

scientific article published on 7 August 2006

VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

scientific article published on 28 October 2021

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

Visualising the Epigenome

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages.

scientific article published in February 2012

Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages

scientific article (publication date: 20 January 2012)

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

scientific article

Whole-genome fingerprint of the DNA methylome during human B cell differentiation

scientific article

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

scientific article

eHive: an artificial intelligence workflow system for genomic analysis

scientific article

nGASP--the nematode genome annotation assessment project

scientific article

ncRNA orthologies in the vertebrate lineage

scientific article published on 15 March 2016

β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance

scientific article

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