Benjamin Dartigues
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View article: P01.04.B TRANSCRIPTOMICS OF PERIPHERAL AND CORE AREAS OF GLIOBLASTOMA REVEALS CNTN2 AS A POTENTIAL THERAPEUTIC TARGET
P01.04.B TRANSCRIPTOMICS OF PERIPHERAL AND CORE AREAS OF GLIOBLASTOMA REVEALS CNTN2 AS A POTENTIAL THERAPEUTIC TARGET Open
BACKGROUND Glioblastoma (GB) is an aggressive brain tumor with inevitable recurrence due to the persistence of infiltrative cells in the peritumoral brain. These cells, located in the non-enhancing but FLAIR-hyperintense periphery, are not…
View article: Metabolism-based scoring of cutaneous squamous cell carcinoma to predict tumour features and responses to treatment with dihydroorotate dehydrogenase inhibitors
Metabolism-based scoring of cutaneous squamous cell carcinoma to predict tumour features and responses to treatment with dihydroorotate dehydrogenase inhibitors Open
Background Alteration in metabolic activities is a critical step in cancer progression. Myriad metabolic-based therapy options are increasingly being proposed for human tumours. However, emerging evidence highlights interpatient metabolic …
View article: BioHackEU24 report: Integrating Bioconductor packages with the ELIXIR Research Software Ecosystem using EDAM
BioHackEU24 report: Integrating Bioconductor packages with the ELIXIR Research Software Ecosystem using EDAM Open
This project seeks to enhance the ELIXIR Research Software Ecosystem (RSEc) by increasing the findability, accessibility, interoperability, and reusability (FAIR principles) of Bioconductor’s extensive collection of over 2,000 bioinformati…
View article: Exploiting metabolic vulnerability in glioblastoma using a brain-penetrant drug with a safe profile
Exploiting metabolic vulnerability in glioblastoma using a brain-penetrant drug with a safe profile Open
Glioblastoma is one of the most treatment-resistant and lethal cancers, with a subset of self-renewing brain tumour stem cells (BTSCs), driving therapy resistance and relapse. Here, we report that mubritinib effectively impairs BTSC stemne…
View article: Paired transcriptomics of glioblastoma peripheral and core areas reveals CNTN2 as a potential therapeutic target
Paired transcriptomics of glioblastoma peripheral and core areas reveals CNTN2 as a potential therapeutic target Open
View article: Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins
Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins Open
Palaeoproteomics is a rapidly evolving discipline, and practitioners are constantly developing novel strategies for the analyses and interpretations of complex, degraded protein mixtures. The community has also established standards of goo…
View article: DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data
DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data Open
Motivation Many diseases, such as cancer, are characterized by an alteration of cellular metabolism allowing cells to adapt to changes in the microenvironment. Stable isotope-resolved metabolomics (SIRM) and downstream data analyses are wi…
View article: Datasets of the DIMet manuscript
Datasets of the DIMet manuscript Open
Datasets for reproducing the results of the manuscript "DIMet : An open-source tool for Differential analysis of targeted Isotope-labeled Metabolomics data". DIMet tool is available here, and the tool documentation is accessible in the DIM…
View article: Minimal datasets for testing DIMet
Minimal datasets for testing DIMet Open
Two datasets to test the DIMet tool, which is available here, the tool documentation is accessible in the DIMet wiki page, and also in Galaxy. Depending on the user case, download one .zip file: Users of the Galaxy version of DIMet: downlo…
View article: Exploiting a metabolic vulnerability in brain tumour stem cells using a brain-penetrant drug with safe profile
Exploiting a metabolic vulnerability in brain tumour stem cells using a brain-penetrant drug with safe profile Open
Glioblastoma (GB) remains one of the most treatment refractory and fatal tumour in humans. GB contains a population of self-renewing stem cells, the brain tumour stem cells (BTSC) that are highly resistant to therapy and are at the origin …
View article: Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins
Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins Open
Palaeoproteomics is a rapidly evolving discipline, and practitioners are constantly developing novel strategies for the analyses and interpretations of complex, degraded protein mixtures. The community has also established standards of goo…
View article: Datasets of the DIMet manuscript
Datasets of the DIMet manuscript Open
<p>Datasets for reproducing the results of the manuscript "<em>DIMet : An open-source tool for Differential analysis of targeted Isotope-labeled Metabolomics data". </em>DIMet tool is available <a href="https://github.…
View article: Datasets of the DIMet manuscript
Datasets of the DIMet manuscript Open
Datasets for reproducing the results of the manuscript "DIMet : An open-source tool for Differential analysis of targeted Isotope-labeled Metabolomics data". DIMet tool is available here, and the tool documentation is accessible i…
View article: Minimal datasets for testing DIMet
Minimal datasets for testing DIMet Open
Two datasets to test the DIMet tool, which is available here, the tool documentation is accessible in the DIMet wiki page, and also in Galaxy. Depending on the user case, download one .zip file: Users of the Galaxy version…
View article: Lactate dehydrogenases promote glioblastoma growth and invasion via a metabolic symbiosis
Lactate dehydrogenases promote glioblastoma growth and invasion via a metabolic symbiosis Open
View article: DeepSpot: A deep neural network for RNA spot enhancement in single-molecule fluorescence in-situ hybridization microscopy images
DeepSpot: A deep neural network for RNA spot enhancement in single-molecule fluorescence in-situ hybridization microscopy images Open
Detection of RNA spots in single-molecule fluorescence in-situ hybridization microscopy images remains a difficult task, especially when applied to large volumes of data. The variable intensity of RNA spots combined with the high noise lev…
View article: DeepSpot: a deep neural network for RNA spot enhancement in smFISH microscopy images
DeepSpot: a deep neural network for RNA spot enhancement in smFISH microscopy images Open
Detection of RNA spots in single molecule FISH microscopy images remains a difficult task especially when applied to large volumes of data. The small size of RNA spots combined with high noise level of images often requires a manual adapta…
View article: Interrogating RNA and protein spatial subcellular distribution in smFISH data with DypFISH
Interrogating RNA and protein spatial subcellular distribution in smFISH data with DypFISH Open
Advances in single-cell RNA sequencing have allowed for the identification of cellular subtypes on the basis of quantification of the number of transcripts in each cell. However, cells might also differ in the spatial distribution of molec…
View article: DypFISH Datasets
DypFISH Datasets Open
Datasets corresponding to the results presented in the manuscript "DypFISH: Dynamic Patterned FISH to Interrogate RNA and Protein Spatial and Temporal Subcellular Distribution" by A. Savulescu et al. are available on the accompanying websi…
View article: Specific expression of lactate dehydrogenases in glioblastoma controls intercellular lactate transfer to promote tumor growth and invasion
Specific expression of lactate dehydrogenases in glioblastoma controls intercellular lactate transfer to promote tumor growth and invasion Open
Lactate is a central metabolite in brain physiology, involved in the astrocyte-neuron lactate shuttle, but also contributes to tumor development. Glioblastoma (GBM) is the most common and malignant primary brain tumor in adults, recognized…
View article: Engineering selective competitors for the discrimination of highly conserved protein-protein interaction modules
Engineering selective competitors for the discrimination of highly conserved protein-protein interaction modules Open
Designing highly specific modulators of protein-protein interactions (PPIs) is especially challenging in the context of multiple paralogs and conserved interaction surfaces. In this case, direct generation of selective and competitive inhi…
View article: The invasive proteome of glioblastoma revealed by laser-capture microdissection
The invasive proteome of glioblastoma revealed by laser-capture microdissection Open
Background Glioblastomas are heterogeneous tumors composed of a necrotic and tumor core and an invasive periphery. Methods Here, we performed a proteomics analysis of laser-capture micro-dissected glioblastoma core and invasive areas of pa…
View article: DypFISH: Dynamic Patterned FISH to Interrogate RNA and Protein Spatial and Temporal Subcellular Distribution
DypFISH: Dynamic Patterned FISH to Interrogate RNA and Protein Spatial and Temporal Subcellular Distribution Open
SUMMARY Advances in single cell RNA sequencing have allowed for the identification and characterization of cellular subtypes based on quantification of the number of transcripts in each cell. However, cells may differ not only in the numbe…
View article: DypFISH: Dynamic Patterned FISH to Interrogate RNA and Protein Spatial and Temporal Subcellular Distribution
DypFISH: Dynamic Patterned FISH to Interrogate RNA and Protein Spatial and Temporal Subcellular Distribution Open
View article: GCN2 phosphorylates HIV-1 integrase and decreases HIV-1 replication by limiting viral integration
GCN2 phosphorylates HIV-1 integrase and decreases HIV-1 replication by limiting viral integration Open
View article: Erratum to: COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access
Erratum to: COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access Open
View article: COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access
COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access Open
Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between r…