Paul Flicek
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Explore the profile of Paul Flicek including associated specialties, affiliations and a list of published articles.
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263
Citations
56539
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Recent Articles
1.
Vromman M, Anckaert J, Bortoluzzi S, Buratin A, Chen C, Chu Q, et al.
Nat Methods
. 2025 Jan;
22(2):448.
PMID: 39825083
No abstract available.
2.
Kaur G, Perteghella T, Carbonell-Sala S, Gonzalez-Martinez J, Hunt T, Madry T, et al.
bioRxiv
. 2024 Nov;
PMID: 39554180
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...
3.
Rimoldi M, Wang N, Zhang J, Villar D, Odom D, Taipale J, et al.
Genome Biol
. 2024 Jun;
25(1):146.
PMID: 38844976
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...
4.
Benjelloun B, Leempoel K, Boyer F, Stucki S, Streeter I, Orozco-terWengel P, et al.
Mol Ecol
. 2023 Dec;
33(20):e17257.
PMID: 38149334
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...
5.
DeGorter M, Goddard P, Karakoc E, Kundu S, Yan S, Nachun D, et al.
bioRxiv
. 2023 Nov;
PMID: 37986808
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...
6.
Contreras-Moreira B, Saraf S, Naamati G, Casas A, Amberkar S, Flicek P, et al.
Genome Biol
. 2023 Oct;
24(1):223.
PMID: 37798615
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...
7.
Rhie A, Nurk S, Cechova M, Hoyt S, Taylor D, Altemose N, et al.
Nature
. 2023 Aug;
621(7978):344-354.
PMID: 37612512
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications. As a result,...
8.
Argentin J, Bolser D, Kersey P, Flicek P
Front Plant Sci
. 2023 Jul;
14:1103035.
PMID: 37521909
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...
9.
Vromman M, Anckaert J, Bortoluzzi S, Buratin A, Chen C, Chu Q, et al.
Nat Methods
. 2023 Jul;
20(8):1159-1169.
PMID: 37443337
The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed using computational tools. Numerous such tools have been developed, but a systematic comparison with...
10.
Liao W, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, et al.
Nature
. 2023 May;
617(7960):312-324.
PMID: 37165242
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These...