Publications by authors named "Cedric Notredame"

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An nf-core framework for the systematic comparison of alternative modeling tools: the multiple sequence alignment case study.
Luisa Santus, Jose Espinosa-Carrasco, Leon Rauschning, Júlia Mir-Pedrol, Igor Trujnara, Cedric Notredame

NAR Genom Bioinform· September 2025

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A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function.
Alexander Sasse, Debashish Ray, Kaitlin U Laverty, Cyrus L Tam, Mihai Albu, Cedric Notredame

Nat Biotechnol· July 2025

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Empowering bioinformatics communities with Nextflow and nf-core.
Björn E Langer, Andreia Amaral, Marie-Odile Baudement, Franziska Bonath, Mathieu Charles, Cedric Notredame

Genome Biol· July 2025

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multistrap: boosting phylogenetic analyses with structural information.
Athanasios Baltzis, Luisa Santus, Björn E Langer, Cedrik Magis, Damien M de Vienne, Cedric Notredame

Nat Commun· January 2025

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Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes.
Alexander Sasse, Debashish Ray, Kaitlin U Laverty, Cyrus L Tam, Mihai Albu, Cedric Notredame

bioRxiv· October 2024

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Evolutionary analysis reveals the role of a non-catalytic domain of peptidyl arginine deiminase 2 in transcriptional regulation.
José Luis Villanueva-Cañas, Narcis Fernandez-Fuentes, Dominik Saul, Robyn Laura Kosinsky, Catherine Teyssier, Cedric Notredame

iScience· April 2024

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Towards the accurate alignment of over a million protein sequences: Current state of the art.
Luisa Santus, Edgar Garriga, Sebastian Deorowicz, Adam Gudyś, Cedric Notredame

Curr Opin Struct Biol· June 2023

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Phylogenetic and functional characterization of water bears (Tardigrada) tubulins.
Kamila Novotná Floriančičová, Athanasios Baltzis, Jiří Smejkal, Michaela Czerneková, Łukasz Kaczmarek, Cedric Notredame

Sci Rep· March 2023

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Highly significant improvement of protein sequence alignments with AlphaFold2.
Athanasios Baltzis, Leila Mansouri, Suzanne Jin, Björn E Langer, Ionas Erb, Cedric Notredame

Bioinformatics· November 2022

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Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania.
Bart Cuypers, Pieter Meysman, Ionas Erb, Wout Bittremieux, Dirk Valkenborg, Cedric Notredame

PLoS Pathog· September 2022

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A long noncoding RNA promotes parasite differentiation in African trypanosomes.
Fabien Guegan, K Shanmugha Rajan, Fábio Bento, Daniel Pinto-Neves, Mariana Sequeira, Cedric Notredame

Sci Adv· June 2022

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Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability.
Jia-Ming Chang, Evan W Floden, Javier Herrero, Olivier Gascuel, Paolo Di Tommaso, Cedric Notredame

Bioinformatics· July 2021

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Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation.
Edgar Garriga, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Cedric Notredame

Methods Mol Biol· April 2021

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An intrinsically disordered proteins community for ELIXIR.
Norman E Davey, M Madan Babu, Martin Blackledge, Alan Bridge, Salvador Capella-Gutierrez, Cedric Notredame

F1000Res· January 2020

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Large multiple sequence alignments with a root-to-leaf regressive method.
Edgar Garriga, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Cedric Notredame

Nat Biotechnol· December 2019

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A field guide for the compositional analysis of any-omics data.
Thomas P Quinn, Ionas Erb, Greg Gloor, Cedric Notredame, Mark F Richardson

Gigascience· September 2019

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Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards.
Jose Espinosa-Carrasco, Toni Hermoso Pulido, Ionas Erb, Mara Dierssen, Julia Ponomarenko, Cedric Notredame

Nucleic Acids Res· July 2019

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Protocol for Measuring Compulsive-like Feeding Behavior in Mice.
Marta Fructuoso, Jose Espinosa-Carrasco, Ionas Erb, Cedric Notredame, Mara Dierssen

Bio Protoc· July 2019

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Editorial: : a new journal for reproducible genomics in the Big Data era.
Cedric Notredame

NAR Genom Bioinform· April 2019

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Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty.
Maria Chatzou, Evan W Floden, Paolo Di Tommaso, Olivier Gascuel, Cedric Notredame

Syst Biol· November 2018

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Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools.
Jose Espinosa-Carrasco, Ionas Erb, Toni Hermoso Pulido, Julia Ponomarenko, Mara Dierssen, Cedric Notredame

iScience· November 2018

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[Nextflow, an efficient tool to improve computation numerical stability in genomic analysis].
Paolo Di Tommaso, Evan W Floden, Cedrik Magis, Emilio Palumbo, Cedric Notredame

Biol Aujourdhui· August 2018

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Extinction and reinstatement of an operant responding maintained by food in different models of obesity.
Aurelijus Burokas, Elena Martín-García, Jose Espinosa-Carrasco, Ionas Erb, Jerome McDonald, Cedric Notredame

Addict Biol· March 2018

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Time-course and dynamics of obesity-related behavioral changes induced by energy-dense foods in mice.
Jose Espinosa-Carrasco, Aurelijus Burokas, Marta Fructuoso, Ionas Erb, Elena Martín-García, Cedric Notredame

Addict Biol· March 2018

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Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani.
Pablo Prieto Barja, Pascale Pescher, Giovanni Bussotti, Franck Dumetz, Hideo Imamura, Cedric Notredame

Nat Ecol Evol· December 2017

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