A5042637168- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Advanced Proteomics Techniques and Applications
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- Animal Virus Infections Studies
- RNA and protein synthesis mechanisms
- Plant Virus Research Studies
- T-cell and Retrovirus Studies
- Gene expression and cancer classification
- Lymphoma Diagnosis and Treatment
- Respiratory viral infections research
- Metabolomics and Mass Spectrometry Studies
- Protein Degradation and Inhibitors
- DNA Repair Mechanisms
- Viral gastroenteritis research and epidemiology
- Viral Infections and Immunology Research
- Cancer Immunotherapy and Biomarkers
- Advanced Biosensing Techniques and Applications
- Plant and Fungal Interactions Research
- Viral Infections and Outbreaks Research
- Mass Spectrometry Techniques and Applications
- Machine Learning in Bioinformatics
- Thyroid Disorders and Treatments
Centre National de la Recherche Scientifique
2011-2024
Inserm
2012-2024
CEA Grenoble
2021-2024
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2021-2024
Université Grenoble Alpes
2021-2024
Institut de Recherche Interdisciplinaire de Grenoble
2021-2024
Institut Néel
2022
Biologie Labor
2022
KU Leuven
2016-2019
European Institute of Oncology
2019
For many years, defects in the ribosome have been associated to cancer. Recently, somatic mutations and deletions affecting ribosomal protein genes were identified a few leukemias solid tumor types. However, systematic analysis of all 81 known across cancer types is lacking. We screened mutation copy number data respectively 4926 7322 samples from 16 six altered (RPL5, RPL11, RPL23A, RPS5, RPS20 RPSA). RPL5 was located at significant peak heterozygous deletion or mutated 11% glioblastoma,...
Abstract Here, we present the first metagenomic study of viral communities from four perennial ponds (gueltas) located in central Sahara (Mauritania). Three gueltas (Ilij, Molomhar and Hamdoun) are at source three different wadis belonging to same hydrologic basin, whereas fourth (El Berbera) belongs a basin. Overall, sequences tailed bacteriophages were most abundant all metagenomes although electron microscopy sequencing confirmed presence other groups, such as large DNA viruses. We...
The study of the human virome is still in its infancy, especially with regard to viral content blood people who are apparently disease free. In this study, genome a new giant virus that related amoeba-infecting pathogen Marseillevirus was recovered from donated blood, using high-throughput sequencing. Viral antigens were identified by an immunoconversion assay. visualized transmission electron microscopy and fluorescence situ hybridization grown T lymphocytes. Specific antibody reactions...
ObjectivesThe cystic fibrosis (CF) airway is now considered the site of a complex microbiota, where cross-talking between microbes and lateral gene transfer are believed to contribute adaptation bacteria this specific environment emergence multidrug-resistant bacteria. The objective study was retrieve analyse sequences associated with antimicrobial resistance from CF viromes database.
Abstract Somatic ribosomal protein mutations have recently been described in cancer, yet their impact on cellular transcription and translation remains poorly understood. Here, we integrate mRNA sequencing, ribosome footprinting, polysomal RNA sequencing mass spectrometry datasets from a mouse lymphoid cell model to characterize the T-cell acute lymphoblastic leukemia (T-ALL) associated RPL10 R98S mutation. Surprisingly, induces changes levels primarily through transcriptional rather than...
ABSTRACT Coprolites are fossilized fecal material that can reveal information about ancient intestinal and environmental microbiota. Viral metagenomics has allowed systematic characterization of viral diversity in human-associated specimens, but little is known the fossil remains. Here, we analyzed community a 14th-century coprolite from closed barrel Middle Ages site Belgium using electron microscopy metagenomics. Viruses infect eukaryotes, bacteria, archaea were detected, confirmed...
Abstract Background Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- genome-derived custom protein databases. However, empirical observations reveal that these large proteogenomic databases produce lower-sensitivity peptide identifications. Various strategies have been proposed avoid this, including the generation of reduced transcriptome-informed databases, which only contain whose transcripts are detected sample-matched...
Abstract Ribosomopathies are congenital disorders caused by mutations in ribosomal proteins (RP) or assembly factors and characterized cellular hypoproliferation at an early stage. Paradoxically, many of these have elevated risk to progress hyperproliferative cancer a later In addition, somatic RP recently been identified various types, for example, the recurrent RPL10-R98S mutation T-cell acute lymphoblastic leukemia (T-ALL) RPS15 chronic lymphocytic (CLL). We previously showed that...
Pericarditis is a common human disease defined by inflammation of the pericardium. Currently, 40% to 85% pericarditis cases have no identified etiology. Most these are thought be caused an infection undetected, unsuspected or unknown viruses. In this work, we used culture- and sequence-independent approach investigate viral DNA communities present in pericardial fluids. Seven metagenomes were generated from fluid patients affected etiology one metagenome was sudden infant death case. As...
Viruses infecting bacteria (bacteriophages) represent the most abundant viral particles in human body. They participate control of human-associated bacterial communities and play an important role dissemination virulence genes. Here, we present identification a new filamentous single-stranded DNA phage family Inoviridae, named Ralstonia Inoviridae Phage 1 (RIP1), blood. Metagenomics PCR analyses detected RIP1 genome blood serum, absence concomitant infection or contamination, suggesting...
Abstract Label-free bottom-up proteomics using mass spectrometry and liquid chromatography has long established as one of the most popular high-throughput analysis workflow for proteome characterization. However, it produces data hindered by complex heterogeneous missing values, which imputation remained problematic. To cope with this, we introduce Pirat, an algorithm that harnesses this challenge following unprecedented approach. Notably, models instrument limit estimating a global...
Tumor mutational burden (TMB) has been proposed as a predictive biomarker for immunotherapy response in cancer patients, it is thought to enrich tumors with high neoantigen load. TMB assessed by whole-exome sequencing considered the gold standard but remains confined research settings. In clinical setting, targeted gene panels sampling various genomic sizes along diverse strategies estimate were and no real emerged yet.We provide community TMBleR, tool measure impact of panel-based...
<div>Abstract<p>Ribosomopathies are congenital disorders caused by mutations in ribosomal proteins (RP) or assembly factors and characterized cellular hypoproliferation at an early stage. Paradoxically, many of these have elevated risk to progress hyperproliferative cancer a later In addition, somatic RP recently been identified various types, for example, the recurrent RPL10-R98S mutation T-cell acute lymphoblastic leukemia (T-ALL) RPS15 chronic lymphocytic (CLL). We previously...
SUMMARY Label-free bottom-up proteomics using mass spectrometry and liquid chromatography has long been established as one of the most popular high-throughput analysis workflows for proteome characterization. However, it produces data hindered by complex heterogeneous missing values, which imputation remained problematic. To cope with this, we introduce Pirat, an algorithm that harnesses this challenge original likelihood maximization strategy. Notably, models instrument limit learning a...
Abstract Viruses infecting bacteria, known as bacteriophages, represent the most abundant viral particles in human body. They participate control of associated bacterial communities and play an important role dissemination virulence genes. Here we present identification a new genetic element, named RIP1, virome. RIP1 shares conserved structural genes with single-stranded DNA viruses Inoviridae family. Furthermore structure-function studies identified nuclear subcellular localization...