Johann Pellet
A5087276026- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Biomedical Text Mining and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Asthma and respiratory diseases
- Artificial Intelligence in Healthcare
- Viral Infections and Outbreaks Research
- Epigenetics and DNA Methylation
- Neonatal Respiratory Health Research
- Mosquito-borne diseases and control
- Metabolomics and Mass Spectrometry Studies
- Gene expression and cancer classification
- Air Quality and Health Impacts
- Cancer-related gene regulation
- interferon and immune responses
- Nutrition, Genetics, and Disease
- Advanced Proteomics Techniques and Applications
- Health, Environment, Cognitive Aging
- Transplantation: Methods and Outcomes
- Biochemical and Molecular Research
- Fungal and yeast genetics research
- BRCA gene mutations in cancer
- Influenza Virus Research Studies
- COVID-19 epidemiological studies
European Institute for Systems Biology and Medicine
2015-2024
Université Claude Bernard Lyon 1
2008-2020
Inserm
2008-2018
Centre National de la Recherche Scientifique
2013-2018
Institute for Systems Biology
2015-2018
Centre International de Recherche en Infectiologie
2016-2018
École Normale Supérieure de Lyon
2018
University Hospital of Lausanne
2017
University of Illinois Chicago
2017
Shanghai Jiao Tong University
2017
A proteome-wide mapping of interactions between hepatitis C virus (HCV) and human proteins was performed to provide a comprehensive view the cellular infection. total 314 protein-protein HCV identified by yeast two-hybrid 170 literature mining. Integration this data set into reconstructed interactome showed that interacting with are enriched in highly central interconnected proteins. global analysis on basis functional annotation highlighted enrichment pathways targeted HCV. network...
The evidence supporting an association between traffic-related air pollution exposure and incident childhood asthma is inconsistent may depend on genetic factors.To identify gene-environment interaction effects using genome-wide single-nucleotide polymorphism (SNP) data exposure. Identified loci were further analyzed at epigenetic transcriptomic levels.We used land use regression models to estimate individual (represented by outdoor NO2 levels) the birth address performed a study for...
The development of computational approaches in systems biology has reached a state maturity that allows their transition to medicine. Despite this progress, intuitive visualisation and context-dependent knowledge representation still present major bottleneck. In paper, we describe the Disease Maps Project, an effort towards community-driven computationally readable comprehensive disease mechanisms. We outline key principles framework required for success initiative, including use best...
ABSTRACT The influenza virus transcribes and replicates its genome inside the nucleus of infected cells. Both activities are performed by viral RNA-dependent RNA polymerase that is composed three subunits PA, PB1, PB2, recent studies have shown it requires host cell factors to transcribe replicate genome. To identify these cellular partners, we generated a comprehensive physical interaction map between each subunit proteome. A total 109 human interactors were identified yeast two-hybrid...
Most insights into the cascade of immune events after acute respiratory syncytial virus (RSV) infection have been obtained from animal experiments or in vitro models. In this study, we investigated host gene expression profiles nasopharyngeal (NP) swabs and whole blood samples during natural RSV rhinovirus (hRV) (acute versus early recovery phase) 83 hospitalized patients <2 years old with lower tract infections. Respiratory induced strong persistent innate responses including interferon...
Large collections of protein-encoding open reading frames (ORFs) established in a versatile recombination-based cloning system have been instrumental to study protein functions high-throughput assays. Such 'ORFeome' resources developed for several organisms but virology, plasmid covering significant fraction the virosphere are still needed. In this perspective, we present ViralORFeome 1.0 (http://www.viralorfeome.com), an open-access database and management that provides integrated set...
Multilevel data integration is becoming a major area of research in systems biology. Within this area, multi-'omics datasets on complex diseases are more readily available and there need to set standards good practices for integrated analysis biological, clinical environmental data. We present framework plan generate single signatures disease states. The divided into four steps: dataset subsetting, feature filtering, 'omics-based clustering biomarker identification. illustrate the usefulness...
Breast cancer is the most frequently diagnosed in females globally. However, we know relatively little about trends males. This study describes United Kingdom (UK) secular breast from 2000 to 2021 for both sexes. We describe a population-based cohort using UK primary care Clinical Practice Research Datalink (CPRD) GOLD and Aurum databases. There were 5,848,436 eligible 5,539,681 males aged 18+ years, with ≥ one year of prior data availability period. estimated crude incidence rates (IR),...
Abstract Background When modeling in Systems Biology and Medicine, the data is often extensive, complex heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient storage processing encoded relationships. They furthermore support queries on structure Results We present Java-based framework STON (SBGN TO Neo4j). imports translates metabolic, signalling gene regulatory pathways represented Graphical Notation into graph-oriented format...
ABSTRACT HTLV-1, HIV-1 and HIV-2 western blot analysis of sera from patients with multiple sclerosis (MS), other neurological diseases blood donors, revealed a rather frequent cross-reactivity retroviral proteins in the MS group, though no patient was positive corresponding specific ELISA serology. Statistical significant difference between group two control groups for reverse transcriptase fragments HTLV-1 p24. The general significance these observations is discussed light hypothesis...
High-throughput screening of protein-protein interactions opens new systems biology perspectives for the comprehensive understanding cell physiology in normal and pathological conditions. In this context, yeast two-hybrid system appears as a promising approach to efficiently reconstruct protein interaction networks at proteome-wide scale. This method generates large amount raw sequence data, i.e. ISTs (Interaction Sequence Tags), which urgently need appropriate tools their systematic...
Charles Auffray, PhDMichael Sagner, MDOur colleague Herman Goossens pointed out that "millions of Europeans are questioning what the European Union does for them" and invited community to "shout about Union's successes" (Nature 542:273). A short answer was given by Nobel Committee in 2012 when it awarded Peace Prize "for over 6 decades contributed advancement peace reconciliation, democracy human rights Europe." As a matter fact, great contributions science society have been made Europe,...
Chronic lung allograft dysfunction (CLAD) is the major long-term complication of transplantation (LT), occurring in up to 50% cases within 5 years post-LT and rising 75% after 10 years. The two most common phenotypes are a bronchiolitis obliterans syndrome (BOS) less frequently restrictive (RAS). Through an integrative systems biology research strategy, our aim was perform omics data integration using exploratory analysis methods order predict future CLAD before any decline function. Whole...
<b>Background:</b> Recent advances in systems medicine allow detailed reconstruction of molecular interactions particular diseases e.g. Parkinson9s disease map (Fujita <i>et al.</i>, Molecular Neurobiology, 2013) and Atlas Cancer Signalling Networks (Kuperstein Oncogenesis, 2015). <b>Objectives:</b> 1. Integration current knowledge on asthma into a network interactions. 2. Explore applications for functional analysis interpretation multi-omics data. <b>Methods:</b> The standard Systems...
Abstract The response of pathophysiological research to emerging epidemics often occurs after the epidemic and, as a consequence, has little no impact on improving patient outcomes or developing high-quality evidence inform clinical management strategies during epidemic. Rapid and informed guidance (research) responses severe infectious disease outbreaks requires quick compilation integration existing knowledge. As case study we chose Zika virus (ZIKV) outbreak that started in 2015 develop...
The response of pathophysiological research to emerging epidemics often occurs after the epidemic and, as a consequence, has little no impact on improving patient outcomes or developing high-quality evidence inform clinical management strategies during epidemic. Rapid and informed guidance (research) responses severe infectious disease outbreaks requires quick compilation integration existing knowledge. As case study we chose Zika virus (ZIKV) outbreak that started in 2015 develop...