Paul Flicek
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View article: Structural and transduction patterns of human-specific polymorphic SVA insertions
Structural and transduction patterns of human-specific polymorphic SVA insertions Open
View article: Mapping the genomes of Earth’s interconnected biodiversity
Mapping the genomes of Earth’s interconnected biodiversity Open
View article: Germline and somatic variation influence nuclear-mitochondrial crosstalk in tumourigenesis
Germline and somatic variation influence nuclear-mitochondrial crosstalk in tumourigenesis Open
Hepatocellular carcinoma is the most prevalent primary liver cancer and arises from hepatocytes, which are very metabolically active and contain abundant mitochondria. Despite extensive characterisation of nuclear driver genes and pathways…
View article: Genetic background sets the trajectory of cancer evolution
Genetic background sets the trajectory of cancer evolution Open
Human cancers are heterogeneous. Their genomes evolve from genetically diverse germlines in complex and dynamic environments, including exposure to potential carcinogens. This heterogeneity of humans, our environmental exposures, and subse…
View article: GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing
GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing Open
Accurate and complete gene annotations are indispensable for understanding how genome sequences encode biological functions. For twenty years, the GENCODE consortium has developed reference annotations for the human and mouse genomes, beco…
View article: Strand-resolved mutagenicity of DNA damage and repair
Strand-resolved mutagenicity of DNA damage and repair Open
DNA base damage is a major source of oncogenic mutations 1 . Such damage can produce strand-phased mutation patterns and multiallelic variation through the process of lesion segregation 2 . Here we exploited these properties to reveal how …
View article: DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts
DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts Open
Background DNA methylation is an important epigenetic modification which has numerous roles in modulating genome function. Its levels are spatially correlated across the genome, typically high in repressed regions but low in transcription …
View article: Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints
Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints Open
The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical…
View article: Transcriptomics and chromatin accessibility in multiple African population samples
Transcriptomics and chromatin accessibility in multiple African population samples Open
Mapping the functional human genome and impact of genetic variants is often limited to European-descendent population samples. To aid in overcoming this limitation, we measured gene expression using RNA sequencing in lymphoblastoid cell li…
View article: GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation
GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation Open
Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a s…
View article: The complete sequence of a human Y chromosome
The complete sequence of a human Y chromosome Open
View article: Comparative analysis of repeat content in plant genomes, large and small
Comparative analysis of repeat content in plant genomes, large and small Open
The DNA Features pipeline is the analysis pipeline at EMBL-EBI that annotates repeat elements, including transposable elements. With Ensembl’s goal to stay at the cutting edge of genome annotation, we proved that this pipeline needed an up…
View article: Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision
Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision Open
View article: Pangenome graph construction from genome alignments with Minigraph-Cactus
Pangenome graph construction from genome alignments with Minigraph-Cactus Open
View article: Increased mutation and gene conversion within human segmental duplications
Increased mutation and gene conversion within human segmental duplications Open
View article: Recombination between heterologous human acrocentric chromosomes
Recombination between heterologous human acrocentric chromosomes Open
The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications 1,2 . Although the resolution of these regions in the fir…
View article: The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits
The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits Open
View article: Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes
Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes Open
View article: Calling pangenes from plant genome alignments confirms presence-absence variation
Calling pangenes from plant genome alignments confirms presence-absence variation Open
Consistent gene annotation in crops is becoming harder as genomes for new cultivars are frequently published. Gene sets from recently sequenced accessions have different gene identifiers to those on the reference accession, and might be of…
View article: Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision
Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision Open
The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed by computational detection tools. During the last decade, a plethora of such tools have been developed, but a systematic comp…
View article: Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes
Analysis of genome-wide knockout mouse database identifies candidate ciliopathy genes Open
View article: The complete sequence of a human Y chromosome
The complete sequence of a human Y chromosome Open
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure including long palindromes, tandem repeats, and segmental duplications 1–3 . As a result, more than half of the Y chromo…
View article: GENCODE: reference annotation for the human and mouse genomes in 2023
GENCODE: reference annotation for the human and mouse genomes in 2023 Open
GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consorti…
View article: The IPD-IMGT/HLA Database
The IPD-IMGT/HLA Database Open
It is 24 years since the IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The database now contains over 35 000 alleles…
View article: Ensembl 2023
Ensembl 2023 Open
Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both th…
View article: High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios
High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios Open
View article: Author Correction: Comparative and demographic analysis of orang-utan genomes
Author Correction: Comparative and demographic analysis of orang-utan genomes Open
In this Article, we reported genome sequencing data from five Sumatran and five Bornean orang-utans. In re-analysing these data, Banes et al.1 found that eight of the ten samples were mislabelled, and we wish to correct the original public…
View article: DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts
DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts Open
Background DNA methylation is an important epigenetic modification which has numerous roles in modulating genome function. Its levels are spatially correlated across the genome, typically high in repressed regions but low in transcription …
View article: A Draft Human Pangenome Reference
A Draft Human Pangenome Reference Open
The Human Pangenome Reference Consortium (HPRC) presents a first draft human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% o…
View article: Standardized annotation of translated open reading frames
Standardized annotation of translated open reading frames Open
Ribosome profiling (Ribo-seq) has extended our understanding of the translational ‘vocabulary’ of the human genome, uncovering thousands of open reading frames (ORFs) within long noncoding RNAs (lncRNAs) and presumed untranslated regions (…