Arnaud Meng

• PhD
• Bioinformatician at Institut Pasteur

High-throughput sequencing (HTS) generates unprecedented amounts of genomic data. These methodological breakthroughs are particularly interesting to study the biology of non- cultivable organisms for which there is no reference genome. To do so de novo assembly allows the reconstruction of a genome or a transcriptome based on sequenced DNA/RNA with...

Iron is an essential micronutrient involved in many biological processes and is often limiting for primary production in large regions of the World Ocean. Metagenomic and physiological studies have identified clades or ecotypes of marine phytoplankton that are specialized in iron depleted ecological niches. Although less studied, eukaryotic picophy...

Although cancer-associated fibroblast (CAF) heterogeneity is well-established, the impact of chemotherapy on CAF populations remains poorly understood. Here we address this question in high-grade serous ovarian cancer (HGSOC), in which we previously identified 4 CAF populations. While the global content in stroma increases in HGSOC after chemothera...

Background: Invasive lobular carcinoma (ILC) shows distinct clinicopathological features compared to invasive breast carcinoma of no special type (IBC-NST), including specific stromal characteristics. One of them concerns the singular infiltration pattern of lobular tumor cells, which induces minimal stromal reaction. In addition, a key function of...

Polar oceanographic regions are exposed to rapid changes in temperature, salinity and light fields that determine microbial species distributions, but resilience to an increasingly unstable climate is unknown. To unravel microbial genomic potential of the Northern Baffin Bay’s polynya, we constructed 8 metagenomes from the same latitude but targeti...

Although heterogeneity of FAP+ Cancer-Associated Fibroblasts (CAF) has been described in breast cancer, their plasticity and spatial distribution remain poorly understood. Here, we analyze trajectory inference, deconvolute spatial transcriptomics at single-cell level and perform functional assays to generate a high-resolution integrated map of brea...

Background : Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptome...

Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high‐throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and...

Les relations symbiotiques entre organismes sont essentielles pour l’évolution de la bio- diversité et le fonctionnement des écosystèmes. En milieu terrestre ou en milieu marin benthique les symbioses sont assez bien décrites. Si dans le plancton marin, les relations entre hôtes hétérotrophes et symbiontes photosynthétiques sont des phénomènes obse...

Background Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. The study of holobiont transcriptomes shares s...

Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and...

High-throughput sequencing technologies generate unprecedented amounts of genomic data. These recent methodological breakthrough are particularly interesting to study the biology of non-culturable organisms for which there is no reference genome. This is the case for many of the marine planktonic organisms, in which symbiotic interactions between m...