Nicolas Fernandez Nuñez

Nicolas Fernandez Nuñez
Institute of Research for Development | IRD · 233 - Translational Research Applied to HIV and Infectious Diseases (TransVIHMI)

Master of Science
Scientific computing expert at U233 TransVIHMI, IRD, University of Montpellier, focusing on viruses genomics.

About

39
Publications
5,327
Reads
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681
Citations
Introduction
Je cultive et jardine dans mon âme, des questions à défricher à creuser, des pensées à essaimer ou à laisser germer, de galère, j’amasse et je rame. Qui parle sème, des idées à laisser mûrir, qui écoute récolte, des pensées à cueillir, à accueillir, des savoirs à prendre, racine. Avec tout ce que je sais on pourrait écrire un livre, avec tout ce que je ne sais pas en remplir des milliers, bâtir des palais si vaste que même leurs ruines nous suffiraient. Curiosité mon amie, dynamique, ma magie, … sans les mensonges, tes histoires sont pour moi des contes de fées, des contes de faits. Théo Drieu Balade Mentale
Additional affiliations
March 2021 - June 2021
Institute of Research for Development
Position
  • Engineer
May 2019 - October 2020
French National Centre for Scientific Research
Position
  • Engineer
Description
  • IGMM’s ambition is to conduct fundamental research of excellence that is relevant to molecular and cellular medicine, with a particular emphasis on cancer and specific infectious and genetic diseases.
November 2017 - January 2019
Institut Agronomique néo-Calédonien
Position
  • Engineer
Description
  • L’Institut agronomique néo-Calédonien est un organisme de recherche original et unique en Nouvelle-Calédonie. Il mène des recherches finalisées en appui au développement rural du pays, centrées autour des enjeux d'agriculture durable, d'environnement exceptionnel à préserver, et de transformation du monde rural.
Education
September 2010 - October 2012
Université de Montpellier
Field of study
  • Biotechnology
September 2007 - August 2010
Université de Montpellier
Field of study
  • Microbiology & Immunology

Publications

Publications (39)
Article
Full-text available
In Guinea, genomic surveillance has been established to generate sequences of and to identify locally circulating SARS-CoV-2 variants. This study aims to describe the distributions, genetic diversity, and origins of SARS-CoV-2 lineages circulating in Guinea during the COVID-19 pandemic. A migration analysis was performed by selecting all sequences...
Article
Full-text available
Background Several variants of SARS-CoV-2 have a demonstrated impact on public health, including high and increased transmissibility, severity of infection, and immune escape. Therefore, this study aimed to determine the SARS-CoV-2 lineages and better characterize the dynamics of the pandemic during the different waves in Guinea. Methods Whole gen...
Preprint
In Guinea, genomic surveillance has been established to generate sequences and identify locally circulating SARS-CoV-2 variants. This study aims to describe the distribution, genetic diversity, evolution, and origin of SARS-CoV-2 lineages circulating in Guinea during the COVID-19 pandemic. We performed a migration analysis by selecting all sequence...
Article
Full-text available
Recent reports raise concerns on the changing epidemiology of mpox in the Democratic Republic of the Congo (DRC). High-quality genomes were generated for 337 patients from 14/26 provinces to document whether the increase in number of cases is due to zoonotic spillover events or viral evolution, with enrichment of APOBEC3 mutations linked to human a...
Preprint
Full-text available
Background: Recent reports raise concerns on the changing epidemiology of mpox in the Democratic Republic of the Congo (DRC), with increasing case counts, sexual contact-mediated clusters, and sustained human-to-human transmission driven by a novel monkeypox virus (MPXV) subclade, Clade Ib. Only a limited number of Clade I MPXV genomes have been ch...
Article
Full-text available
In September 2022, deaths of pigs manifesting pox-like lesions caused by swinepox virus were reported in Tshuapa Province, Democratic Republic of the Congo. Two human mpox cases were found concurrently in the surrounding community. Specific diagnostics and robust sequencing are needed to characterize multiple poxviruses and prevent potential poxvir...
Article
Full-text available
While the SARS-CoV-2 dynamic has been described globally, there is a lack of data from Sub-Saharan Africa. We herein report the dynamics of SARS-CoV-2 lineages from March 2020 to March 2022 in Cameroon. Of the 760 whole-genome sequences successfully generated by the national genomic surveillance network, 74% were viral sub-lineages of origin and no...
Article
Full-text available
Human Mpox cases are increasingly reported in Africa, with the highest burden in the Democratic Republic of Congo (DRC). While case reporting on a clinical basis can overestimate infection rates, laboratory confirmation by PCR can underestimate them, especially on suboptimal samples like blood, commonly used in DRC. Here we used a Luminex-based ass...
Preprint
Full-text available
Background Several variants of SARS-CoV-2 have a demonstrated impact on public health, including high and increased transmissibility, severity of infection and immune escape. Therefore, this study aimed to describe the genetic modifications and distribution of SARS-CoV-2 lineages and better characterize the dynamics of the pandemic during the diffe...
Article
Full-text available
Mortality due to sepsis remains unacceptably high, especially for septic shock patients. Murine models have been used to better understand pathophysiology mechanisms. However, the mouse model is still under debate. Herein we investigated the transcriptional response of mice injected with lipopolysaccharide (LPS) and compared it to either human cell...
Preprint
Full-text available
Mortality due to sepsis remains unacceptably high, especially for septic shock patients. Murine models have been used to better understand pathophysiology mechanisms. However, the mouse model is still under de-bate. Here we investigated the transcriptional response of mice injected with lipopolysaccharide (LPS) and compared it to either human cells...
Article
Full-text available
Due to their central role in ecosystems functioning and their ability to rapidly respond to environmental changes, soil microorganisms could potentially be used for monitoring ecosystems recovery in the context of degraded land restoration. However, these belowground organisms have been, to date, largely neglected. Here, we investigated fungal and...
Article
Shewanella algae C6G3 can reduce dissimilatively nitrate into ammonium and manganese-oxide (MnIV) into MnII. It has the unusual ability to produce anaerobically nitrite from ammonium in the presence of MnIV. To gain insight into their metabolic capabilities, global mRNA expression patterns were investigated by RNA-seq and qRT-PCR in cells growing w...
Article
Objectives: Fluoroquinolone (FQ)-resistant mutants were previously selected from the live vaccine strain (LVS) of Francisella tularensis (F. tularensis) subsp. holarctica. This study further characterised all genetic changes that occurred in these mutants during the evolutionary trajectory toward high-level FQ resistance, and their potential impact...
Article
Full-text available
Aims Understanding how soil aggregate stability (MWD) is influenced by microbial diversity and abundance can be crucial for ecological restoration in severely disturbed areas. We investigated the relationships between plant and soil microbial diversity and MWD of an ultramafic Ferralsol along a vegetational succession gradient in New Caledonia, whe...
Article
Full-text available
Background: Plasmodium falciparum malaria remains a major health problem in Africa. The mechanisms of pathogenesis are not fully understood. Transcriptomic studies may provide new insights into molecular pathways involved in the severe form of the disease. Methods: Blood transcriptional levels were assessed in patients with cerebral malaria, non...
Conference Paper
Full-text available
New Caledonia, an archipelago located in the South West Pacific, is renowned for its exceptional flora and considered one of the world's most important biodiversity hotspot. The flora of New Caledonia is characterized by the occurrence of ultramafic outcrops that disproportionally contributes to the high levels of plant diversity and endemism. Howe...
Article
Full-text available
Autologous hematopoietic stem cell transplantation (auto-HSCT) is a standard treatment in multiple myeloma and relapsed or refractory lymphomas. After auto-HSCT, hematologic reconstitution and infectious complications are the main two critical issues. Though many patients develop infectious complications after therapeutic intensification, it remain...
Article
Full-text available
Shewanella algae C6G3 can reduce dissimilatively nitrate into ammonium and manganese-oxide (MnIV) into MnII. It has the unusual ability to produce anaerobically nitrite from ammonium in the presence of MnIV. To gain insight into their metabolic capabilities, global mRNA expression patterns were investigated by RNA-seq and qRT-PCR in cells growing w...
Article
Full-text available
In mammals, both sterile wounding and infection induce inflammation and activate the innate immune system, and the combination of both challenges may lead to severe health defects, revealing the importance of the balance between the intensity and resolution of the inflammatory response for the organism's fitness. Underlying mechanisms remain howeve...
Article
Full-text available
Major depressive disorder (MDD) is a highly prevalent mental illness whose therapy management remains uncertain, with more than 20% of patients who do not achieve response to antidepressants. Therefore, identification of reliable biomarkers to predict response to treatment will greatly improve MDD patient medical care. Due to the inaccessibility an...
Article
Full-text available
Our previous transcriptomic analysis of Glossina palpalis gambiensis experimentally infected or not with Trypanosoma brucei gambiense aimed to detect differentially expressed genes (DEGs) associated with infection. Specifically, we selected candidate genes governing tsetse fly vector competence that could be used in the context of an anti-vector st...
Article
Gene expression in mammals is precisely regulated by the combination of promoters and gene-distal regulatory regions, known as enhancers. Several studies have suggested that some promoters might have enhancer functions. However, the extent of this type of promoters and whether they actually function to regulate the expression of distal genes have r...
Article
Histone replacement by transition proteins (TPs) and protamines (Prms) constitutes an essential step for the successful production of functional male gametes, yet nothing is known on the underlying functional interplay between histones, TPs, and Prms. Here, by studying spermatogenesis in the absence of a spermatid-specific histone variant, H2A.L.2,...
Article
Full-text available
Chemotherapies allow complete remission in more than 50 % of patients with acute myeloid leukemia (AML), however, with frequent relapse. This suggests that residual leukemic cells may escape to chemotherapy and immune system. Natural killer (NK) cells from AML patients (AML-NK) have a weaker natural cytotoxicity-activating receptors (NCRs) expressi...
Article
Full-text available
frontal lobe, microarray, functional network, lateral fluid percussion trauma, rotational trauma Traumatic brain injury (TBI) can have many different origins, such as motor vehicle accidents, falls, sport activities, assaults or, blast waves from explosions. Brain damage following TBI may result in an increased risk of developing secondary patholog...
Article
Full-text available
Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. The identification and the characterization of enhancers are challenging in mammals due to their genome complexity. Here we develop CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer ac...

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