☰Phil Ewels

Publications

The cornerstone of the scientific method, peer reviewed journals are an important track record for any scientist.

I've been lucky to work with some amazing people on some amazing projects. Here are some of the results.

ORCiDGoogle ScholarResearch Gate

2026

Convergent and lineage-specific genomic changes shape adaptations in sugar-consuming birds

Science (2026)

Osipova E, Ko M, Petricek K, Sin S, Brown T, Winkler S, Pippel M, Jarrells J, Weiche S, ... , Sackton T

pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics

Molecular & Cellular Proteomics (2026)

Yue Q, Dai C, Kamatchinathan S, Bandla C, Webel H, Larrea A, Bittremieux W, Uszkoreit J, Müller T, ... , Perez-Riverol Y

2025

Empowering bioinformatics communities with Nextflow and nf-core

Genome Biology (2025)

Langer B, Amaral A, Baudement M, Bonath F, Charles M, Chitneedi P, Clark E, Di Tommaso P, Djebali S, ... , community t

A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines

Nature Methods (2025)

Chen Y, Davidson N, Wan Y, Yao F, Su Y, Gamaarachchi H, Sim A, Patel H, Low H, ... , Göke J

2024

Convergent and lineage-specific genomic changes contribute to adaptations in sugar-consuming birds
Preprint

bioRxiv (2024)

Osipova E, Ko M, Petricek K, Yung Wa Sin S, Brown T, Winkler S, PIppel M, Jarrells J, Weiche S, ... , Sackton T

Empowering bioinformatics communities with Nextflow and nf-core
Preprint

bioRxiv (2024)

Langer B, Amaral A, Baudement M, Bonath F, Charles M, Chitneedi P, Clark E, Di Tommaso P, Djebali S, ... , the nf-core community.

2023

A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements

G3: Genes, Genomes, Genetics (2023)

Arnqvist G, Westerberg I, Galbraith J, Sayadi A, Scofield D, Olsen R, Immonen E, Bonath F, Ewels P, Suh A

2022

Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma

Blood Advances (2022)

Peña-Pérez L, Frengen N, Hauenstein J, Gran C, Gustafsson C, Eisfeldt J, Kierczak M, Taborsak-Lines F, Olsen R, ... , Månsson R

Ten simple rules for making a software tool workflow-ready

PLOS Computational Biology (2022)

Brack P, Crowther P, Soiland-Reyes S, Owen S, Lowe D, Williams A, Groom Q, Dillen M, Coppens F, ... , Goble C

Local selection signals in the genome of blue tits emphasize regulatory and neuronal evolution

Molecular Ecology (2022)

Mueller J, Botero‐Delgadillo E, Espíndola‐Hernández P, Gilsenan C, Ewels P, Gruselius J, Kempenaers B

2021

DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics

Journal of Proteome Research (2021)

Bichmann L, Gupta S, Rosenberger G, Kuchenbecker L, Sachsenberg T, Ewels P, Alka O, Pfeuffer J, Kohlbacher O, Röst H

Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes

Clinical Epigenetics (2021)

Wojewodzic M, Leithaug M, Lauritzen M, Lyle R, Haglund S, Rubin C, Ewels P, Grotmol T, Rounge T

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines
Preprint

bioRxiv (2021)

Chen Y, Davidson N, Wan Y, Patel H, Yao F, Low H, Hendra C, Watten L, Sim A, ... , SG-NEx consortium

2020

Linked-read sequencing enables haplotype-resolved resequencing at population scale

Molecular Ecology Resources (2020)

Lutgen D, Ritter R, Olsen R, Schielzeth H, Gruselius J, Ewels P, García J, Shirihai H, Schweizer M, ... , Burri R

Building an international consortium for tracking coronavirus health status

Nature Medicine (2020)

Segal E, Zhang F, Lin X, King G, Shalem O, Shilo S, Allen W, Alquaddoomi F, Altae-Tran H, ... , Wilmes P

The nf-core framework for community-curated bioinformatics pipelines

Nature Biotechnology (2020)

Ewels P, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia M, Di Tommaso P, Nahnsen S

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

F1000Research (2020)

Garcia M, Juhos S, Larsson M, Olason P, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, Díaz De Ståhl T, ... , Nystedt B

2019

Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats

Molecular Phylogenetics and Evolution (2019)

Schweizer M, Warmuth V, Alaei Kakhki N, Aliabadian M, Förschler M, Shirihai H, Ewels P, Gruselius J, Olsen R, ... , Burri R

nf-core: Community curated bioinformatics pipelines
Preprint

bioRxiv (2019)

Ewels P, Peltzer A, Fillinger S, Alneberg J, Patel H, Wilm A, Garcia M, Di Tommaso P, Nahnsen S

2017

Cluster Flow: A user-friendly bioinformatics workflow tool

F1000Research (2017)

Ewels P, Krueger F, Käller M, Andrews S

2016

Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women

Archives of Toxicology (2016)

Engström K, Wojdacz T, Marabita F, Ewels P, Käller M, Vezzi F, Prezza N, Gruselius J, Vahter M, Broberg K

MultiQC: summarize analysis results for multiple tools and samples in a single report

Bioinformatics (2016)

Ewels P, Magnusson M, Lundin S, Käller M

Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression

Nucleic Acids Research (2016)

Ivanov M, Kals M, Lauschke V, Barragan I, Ewels P, Käller M, Axelsson T, Lehtiö J, Milani L, Ingelman-Sundberg M

A Complete Overhaul of the Electron Energy-Loss Spectroscopy and X-Ray Absorption Spectroscopy Database: eelsdb.eu

Microscopy and Microanalysis (2016)

Ewels P, Sikora T, Serin V, Ewels C, Lajaunie L

2015

HiCUP: pipeline for mapping and processing Hi-C data

F1000Research (2015)

Wingett S, Ewels P, Furlan-Magaril M, Nagano T, Schoenfelder S, Fraser P, Andrews S

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

Proceedings of the National Academy of Sciences (2015)

Patalano S, Vlasova A, Wyatt C, Ewels P, Camara F, Ferreira P, Asher C, Jurkowski T, Segonds-Pichon A, ... , Sumner S

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

Nature Genetics (2015)

Mifsud B, Tavares-Cadete F, Young A, Sugar R, Schoenfelder S, Ferreira L, Wingett S, Andrews S, Grey W, ... , Osborne C

Global Reorganization of the Nuclear Landscape in Senescent Cells

Cell Reports (2015)

Chandra T, Ewels P, Schoenfelder S, Furlan-Magaril M, Wingett S, Kirschner K, Thuret J, Andrews S, Fraser P, Reik W

2014

Understanding functional miRNA–target interactions in vivo by site-specific genome engineering

Nature Communications (2014)

Bassett A, Azzam G, Wheatley L, Tibbit C, Rajakumar T, McGowan S, Stanger N, Ewels P, Taylor S, ... , Fulga T

2011

Meet the neighbours: tools to dissect nuclear structure and function

Briefings in Functional Genomics (2011)

Osborne C, Ewels P, Young A

2009

Large Scale Association Analysis of Novel Genetic Loci for Coronary Artery Disease

Arteriosclerosis, Thrombosis, and Vascular Biology (2009)

Coronary Artery Disease Consortium

2008

Sorting nexin-1 defines an early phase of Salmonella-containing vacuole-remodeling during Salmonella infection

Journal of Cell Science (2008)

Bujny M, Ewels P, Humphrey S, Attar N, Jepson M, Cullen P

High-Throughput Genotyping of Salmonella enterica Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia

Journal of Clinical Microbiology (2008)

Baker S, Holt K, van de Vosse E, Roumagnac P, Whitehead S, King E, Ewels P, Keniry A, Weill F, ... , Dougan G

Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease

Nature Genetics (2008)

the Wellcome Trust Case Control Consortium, Fisher S, Tremelling M, Anderson C, Gwilliam R, Bumpstead S, Prescott N, Nimmo E, Massey D, ... , Satsangi J

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