Publications

Publications

2021

Nicolás‐Párraga et al, Virology Journal. Human DNA decays faster with time than viral dsDNA: an analysis on HPV16 using pathology archive samples spanning 85 years.

Brives and Froissart, Revue d’anthropologie des connaissances. Évolutions et involutions dans la biomédecine.

Froissart and Brives, Journal of Evolutionary Biology. Evolutionary Biology and Development Model of Medicines: A Necessary “Pas de Deux” for Future Successful Bacteriophage Therapy.

2020

Borveto et al, Virus Evolution. Papillomaviruses infecting cetaceans exhibit signs of genome adaptation following a recombination event.

Willemsen et al, Virology Journal. Genomic and phylogenetic characterization of ChPV2, a novel goat PV closely related to the Xi‐PV1 species infecting bovines.

Vasudevan et al, Zurich Open Repository and Archive. Loop 1 of APOBEC3C Regulates its Antiviral Activity against HIV-1.

Carmen Lía-Murall et al, Vaccine. HPV cervical infections and serological status in vaccinated and unvaccinated women.

Flores-Miramontes et al, Frontiers in Cellular and Infection Microbiology. Detection of Alpha, Beta, Gamma and Unclassified Human Papillomaviruses in Cervical Cancer Samples From Mexican women.

2019

Bourret et al, Genome Biology and Evolution. COUSIN (COdon Usage Similarity INdex): a normalized measure of codon usage preferences.

Bourret et al, BioRXiv. COUSIN (COdon Usage Similarity INdex): a normalized measure of codon usage preferences.

Alizon et al, Philosophical Transactions of the Royal Society of London B. Towards a multi-level and a multi-disciplinary approach to DNA oncovirus virulence.

Willemsen et al, Genome Biology and Evolution Genome plasticity in Papillomaviruses and de novo emergence of E5 oncogenes.

Murall et al, BMJ Open. Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study.

Pedergnana et al, Journal of Interferon and Cytokine Research. Impact of IFNL4 Genetic Variants on Sustained Virologic Response and Viremia in Hepatitis C Virus Genotype 3 Patients.

Xu et al, Nature Genetics. Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma.

Bedhomme et al, Genome Biology and Evolution. Evolutionary changes after translational challenges imposed by horizontal gene transfer.

Houlihan et al, Sexually Transmitted Infections. Human papillomavirus DNA detected in fingertip, oral and bathroom samples from unvaccinated adolescent girls in Tanzania.

François et al, Viruses. A New Prevalent Densovirus Discovered in Acari. Insight from Metagenomics in Viral Communities Associated with Two-Spotted Mite (Tetranychus urticae) Populations.

François et al, Viruses. “French Phage Network” Annual Conference 2018-Fourth Meeting Report.

Chetwin et al, Scientific reports. Antimicrobial and inflammatory properties of South African clinical Lactobacillus isolates and vaginal probiotics.

Willemsen and Bravo, Philosophical transactions of the Royal Society of London. Origin and evolution of papillomavirus (onco)genes and genomes.

Picard et al, Genome Biology and Evolution. Dosage compensation throughout the Schistosoma mansoni lifecycle: specific chromatinlandscape of the Z chromosome.

Salines et al, International Journal of Food Microbiology. Persistent viremia and presence of hepatitis E virus RNA in pig muscle meat after experimental co-infection with porcine reproductive and respiratory syndrome virus.

2018

Taberna et al, Frontiers in Oncology. The use of HPV16-E5, EGFR, and pEGFR as prognostic biomarkers for oropharyngeal cancer patients.

Pimenoff et al, International Journal of Cancer. Disctinct geographic clustering of oncogenic human papillomaviruses multiple infections in cervical cancers: results from a worldwide cross-sectional study.

Mena et al, Oral Oncology. Double positivity for HPV-DNA/p16ink4a is the biomarker with strongest diagnostic accuracy and prognostic value for human papillomavirus related oropharyngeal cancer patients.

Mengual-Chulia et al, Genome Anouncements. Two Novel, Distantly Related Papillomaviruses Isolated from Healthy Skin of the Timor Deer (Rusa timorensis).

Mengual-Chulia et al, Genome Anouncements. Genome Sequences of Two Novel Papillomaviruses Isolated from Healthy Skin of Pudu puda and Cervus elaphus Deer.

Lucas et al, Scientific reports. Evidence of CD4+ T cell-mediated immune pressure on the Hepatitis C virus genome.

Ramamurthy et al, Hepatology. Impact of IFNL4 genotype on Interferon-stimulated Gene Expression during DAA therapy for Hepatitis C.

Walker et al, Journal of Viral Hepatitis. Host genetic factors associated with hepatocellular carcinoma in patients with hepatitis C virus infection: A systematic review.

Picard et al, Elife. Evolution of gene dosage on the Z-chromosome of schistosome parasites.

Kincaid-Smith et al, Genome Biology and Evolution. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites.

Willemsen et al, Heredity. Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses.

Bagdassarian et al, Viruses. The Amino-Terminal Region of Hepatitis E Virus ORF1 Containing a Methyltransferase (Met) and a Papain-Like Cysteine Protease (PCP) Domain Counteracts Type I Interferon Response.

2017

Alizon et al, Viruses. Why Human Papillomavirus Acute Infections Matter.

Parraga et al, International Journal of Cancer. Differential HPV16 variant distribution in squamous cell carcinoma, adenocarcinoma and adenosquamous cell carcinoma.

Pimenoff et al, Molecular Biology and Evolution. Transmission between Archaic and Modern Human Ancestors during the Evlolution of the Oncogenic Human Papillomavirus 16.

Pontremoli et al, Molecular Ecology. Evolutionary analysis of Old World arenaviruses reveals a major adaptative contribution of the viral polymerase.

Willemsen et al, BMC Evolutionary Biology. High virulence does not necessarily impede viral adaptation to a new host: a case study using a plant RNA virus.

Willemsen et al, Genome Biology and Evolution. 2b or Not 2b: Experimental Evolution of Functional Exogenous Sequences in a Plant RNA Virus.

2016

Felez-Sanchez et al, Infection, Genetics and Evolution. Searching beyond the usual papillomavirus suspects in squamous carcinomas of the vulva, penis and head and neck.

Mengual-Chulia et al, BMC Evolutionary Biology. Assessing parallel gene histories in viral genomes.

2015

Alemany et al, International Journal of Cancer. Human papillomavirus DNA prevalence and type distribution in anal carcinomas worldwide.

Felez Sanchez et al, Genome Biology and Evolution. Cancer, Warts, or Asymptomatic Infections: Clinical Presentation Matches Codon Usage Preferences in Human Papillomaviruses.

Mendes de Oliveira et al, Infection, Genetics and Evolution. High-level of viral genomic diversity in cervical cancers: A Brazilian study on human papillomavirus type 16.

2014

Alemany et al, European journal of Cancer. Large contribution of human papillomavirus in vaginal neoplastic lesions: A worlwide study in 597 samples.

Alemany et al, International Journal of Cancer. Time trends of human papillomavirus types in invasive cervical cancer, from 1940 to 2007.

Garcia Perez et al, Genome Biology and Evolution. Noval Papillomavriuses in Free-Ranging Iberian Bats: No Virus-Host Co-evolution, No Strict Host Specificity, and Hints for Recombination.

Godinez et al, Clinical Microbiology and Infection. Phylogenetically related, clinically different: human papillomavirus 6 and 11 variants distribution in genital warts and in laryngeal papillomatosis.

Ibáñez et al, Journal of Clinical Microbiology. Interlaboratory Reproducibility and Proficiency Testing within the Human Papillomavrius Cervical Cancer Screening Program in Catalonia, Spain.

Mengual-Chulia et al, Veterinary Microbiology. A novel papillomavirus isolated from anasal neoplasia in an Italian free-ranging chamois (Rupicapra r. rupicapra).

Pelchovich et al, FEBS Journal. Ribosomal mutations affecting the translation of genes that use non-optimal codons.

2013

de san José et al, European journal of Cancer. Worlwide human papillomavirus genotype attribution in over 2000 cases of intraepithelial and invasive lesions of the vulva.

Garcia-Perez et al, Veterinary Microbiology. Multiple evolutionary origins of bat papillomaviruses.

Godinez et al, Infection, Genetics and Evolution. Differential presence of Papillomavirus variants in cervical cancer: An analysis for HPV33, HPV45 and HPV58.

Guimera et al, American Journal of Surgical Pathology. The Occasional Role of Low-risk Human Papillomaviruses 6, 11, 42, 44 and 70 in Anogenital Carcinoma Defined by Laser Capture Microdissection/PCR Methodology.

Jacquin et al, Journal of Clinical Microbiology. Methylation of Human Papillomavirus Type 16 CpG Sites at E2-Binding Site 1 (E2BS1), E2BS2, and the Sp1-Binding Site in Cervical Cancer Samples as Dtermined by High-Resolution Melting Analysis-PCR.