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Evolution of viral codon usage preferences:manipulation of translation accuracy and evasion of immune response

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Publications

The multi-level phenotypic impact of synonymous substitutions: heterologous gene expression in human cells

Author(s): Marion A.L. Picard, Fiona Leblay, Cécile Cassan, Anouk Willemsen, Josquin Daron, Frédérique Bauffe, Mathilde Decourcelle, Antonin Demange, Ignacio G. Bravo
Published in: biorxiv, 2021
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.01.07.475042

Human cellular homeostasis buffers trans-acting translational effects of heterologous gene expression with very different codon usage bias

Author(s): Arthur J Jallet, Antonin Demange, Fiona Leblay, Mathilde Decourcelle, Khadija El Koulali, Marion AL Picard, Ignacio G Bravo
Published in: biorxiv, 2021
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.12.09.471957

Genome plasticity in Papillomaviruses and de novo emergence of E5 oncogenes

Author(s): Marta Félez-Sánchez, Anouk Willemsen, Ignacio Bravo
Published in: biorxiv, 2018
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/337477

Macroecology suggests cancer-causing papillomaviruses form non-neutral communities

Author(s): Marta Felez-Sanchez, Carmen Lia Murall, Ignacio G. Bravo
Published in: biorxiv, 2017
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/187047

Ecological opportunity, radiation events and genomic innovations shaped the episodic evolutionary history of papillomaviruses

Author(s): Anouk Willemsen, Ignacio G. Bravo
Published in: biorxiv, 2021
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.03.08.982421

Subfunctionalisation of paralogous genes and evolution of differential codon usage preferences: the showcase of polypyrimidine tract binding proteins

Author(s): Jérôme Bourret, Fanni Borvető, Ignacio G. Bravo
Published in: biorxiv, 2021
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.08.30.274191

Origin and evolution of papillomavirus (onco)genes and genomes

Author(s): Anouk Willemsen, Ignacio G. Bravo
Published in: Philos Trans R Soc Lond B Biol Sci ., 2019, ISSN 1471-2970
Publisher: The Royal Society Publishing
DOI: 10.1098/rstb.2018.0303

COUSIN (COdon Usage Similarity INdex): A Normalized Measure of Codon Usage Preferences

Author(s): Jérôme Bourret, Samuel Alizon, Ignacio G Bravo
Published in: Genome Biology and Evolution, 2019, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1101/600361

Why Human Papillomavirus Acute Infections Matter

Author(s): Samuel Alizon, Carmen Murall, Ignacio Bravo
Published in: Viruses, 9/10, 2017, Page(s) 293, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v9100293

Genome Sequences of Two Novel Papillomaviruses Isolated from Healthy Skin of Pudu puda and Cervus elaphus Deer

Author(s): Beatriz Mengual-Chuliá, Ulrich Wittstatt, Philipp Olias, Ignacio G. Bravo
Published in: Genome Announcements, 6/18, 2018, ISSN 2169-8287
Publisher: American Society for Microbiology
DOI: 10.1128/genomeA.00298-18

Two Novel, Distantly Related Papillomaviruses Isolated from Healthy Skin of the Timor Deer ( Rusa timorensis )

Author(s): Beatriz Mengual-Chuliá, Gudrun Wibbelt, Marc Gottschling, Ignacio G. Bravo
Published in: Genome Announcements, 6/24, 2018, ISSN 2169-8287
Publisher: American Society for Microbiology
DOI: 10.1128/genomeA.00505-18

Evolutionary Changes after Translational Challenges imposed by Horizontal Gene Transfer

Author(s): Stéphanie Bedhomme, Dolors Amorós-Moya, Luz M Valero, Nùria Bonifaci, Miquel-Àngel Pujana, Ignacio G Bravo
Published in: Genome Biology and Evolution, 2019, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evz031

Transmission between Archaic and Modern Human Ancestors during the Evolution of the Oncogenic Human Papillomavirus 16

Author(s): Ville N. Pimenoff, Cristina Mendes de Oliveira, Ignacio G. Bravo
Published in: Molecular Biology and Evolution, 34/1, 2017, Page(s) 4-19, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msw214

Plasmid and clonal interference during post horizontal gene transfer evolution

Author(s): S. Bedhomme, D. Perez Pantoja, I. G. Bravo
Published in: Molecular Ecology, 26/7, 2017, Page(s) 1832-1847, ISSN 0962-1083
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mec.14056

Genome Plasticity in Papillomaviruses and De Novo Emergence of E5 Oncogenes

Author(s): Anouk Willemsen, Marta Félez-Sánchez, Ignacio G Bravo
Published in: Genome Biology and Evolution, 2019, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evz095

Papillomaviruses infecting cetaceans exhibit signs of genome adaptation following a recombination event

Author(s): Fanni Borvető, Ignacio G Bravo, Anouk Willemsen
Published in: Virus Evolution, 2020, ISSN 2057-1577
Publisher: Oxford Academic
DOI: 10.1093/ve/veaa038

Variability in Codon Usage in Coronaviruses Is Mainly Driven by Mutational Bias and Selective Constraints on CpG Dinucleotide

Author(s): Josquin Daron, Ignacio G. Bravo
Published in: Viruses, 2021, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13091800