Paul Flicek

Explainable machine learning relates histological to genomic pathology

This paper uses machine learning to predict genomic alterations from H&E images of liver tumors, revealing genotype-phenotype links and highlighting genetic background limitations.

Germline and somatic variation influence nuclear-mitochondrial crosstalk in tumourigenesis

This study investigates how germline and somatic genetic variations affect mitochondrial DNA content, mutation patterns, and gene expression in liver tumors across four mouse strains.

The GENCODE CLS project: massively expanding the lncRNA catalog through capture long-read RNA sequencing

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

Strand-resolved mutagenicity of DNA damage and repair

The paper investigates how strand-asymmetric processes like replication and transcription influence DNA damage, repair, and mutagenesis, revealing mechanisms that shape cancer genome evolution.

Transcriptomics and chromatin accessibility in multiple African population samples

The paper identifies novel transcripts, eQTLs, and caQTLs in African populations and fine-maps GWAS signals for complex diseases.

Calling pangenes from plant genome alignments confirms presence-absence variation

The paper introduces get_pangenes to identify pangenes from genome alignments, showing it outperforms existing methods and confirms presence-absence variation in barley.

The complete sequence of a human Y chromosome

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision

The paper benchmarks 16 circRNA detection tools across three human cell types, finding large differences in sensitivity but consistent precision, and recommends tool combinations for improved detection.

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

Recombination between heterologous human acrocentric chromosomes

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

The paper presents a high coverage whole genome sequencing resource of 3,202 samples, including 602 trios, generated from the expanded 1000 Genomes Project.

DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts

The paper identifies DNA methylation patterns at TF binding sites across species, linking them to functional roles and evolutionary changes.

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

This paper outlines a community-driven initiative to create a consolidated catalog of human Ribo-seq ORFs, addressing the lack of standardized annotation for these features.

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

The paper introduces a hybrid repeat masking method for plant genomes using k-mer counting and curated repeat libraries, achieving efficient and accurate results.

The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data

The paper describes the Ensembl COVID-19 resource, which integrates SARS-CoV-2 genomic data and variant annotations to support research on virus variants and their impact on therapeutics and vaccines.

Mako: a graph-based pattern growth approach to detect complex structural variants

Mako detects complex structural variants using a graph-based pattern growth approach, achieving 70% validation rate on real data and identifying 15 CSV types including two novel ones.

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

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

The paper presents 64 haplotype-resolved human genomes using long-read sequencing and identifies structural variants, SV-eQTLs, and adaptive selection candidates.

Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development

The paper identifies brain-region specific splicing patterns at single-cell and spatial resolution in postnatal mice, revealing cell-type specific and region-specific isoform expression.

Functional signatures of evolutionarily young CTCF binding sites

The paper investigates evolutionarily young CTCF binding sites in two Mus subspecies, finding some functional signatures and a novel immune locus formed by tandem duplication.

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

The paper presents improved pig reference genomes using long-read sequencing, enhancing continuity and accuracy for pig genetics and genomics research.

LINE elements are a reservoir of regulatory potential in mammalian genomes

The paper investigates how LINE elements contribute to the evolution of tissue-specific and shared regulatory regions across mammalian genomes.

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

The paper investigates how CTCF binding patterns across species contribute to the stability and evolution of TAD boundaries through clustered binding sites.

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

The paper presents the tuatara genome, highlighting its evolutionary significance and unique features compared to other vertebrates.

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

The paper presents a chromosome-level genome assembly of Atlantic herring, enabling the detection of a supergene and improved analysis of selection signals.

Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data

The paper introduces a method called soft windowing to improve analysis of high-throughput phenotyping data by reducing false positives and increasing significant results.

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

The paper identifies novel long non-coding RNAs and circular RNAs in hematopoietic cells using BLUEPRINT consortium data, highlighting their cell type specificity.

Systematic re-annotation of 191 genes associated with early-onset epilepsy unmasks de novo variants linked to Dravet syndrome in novel SCN1A exons

The paper updates gene annotations for 191 epilepsy genes, reclassifying variants and identifying new de novo SCN1A variants in Dravet syndrome patients.

Variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility

The paper identifies how variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility and cell count differences.

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

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.