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Sökning: WFRF:(Pavie Benjamin)

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1.
  • Chen, Wei-Ting, et al. (författare)
  • Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease
  • 2020
  • Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 182:4, s. 976-
  • Tidskriftsartikel (refereegranskat)abstract
    • Although complex inflammatory-like alterations are observed around the amyloid plaques of Alzheimer's disease (AD), little is known about the molecular changes and cellular interactions that characterize this response, We investigate here, in an AD mouse model, the transcriptional changes occurring in tissue domains in a 100-mu m diameter around amyloid plaques using spatial transcriptomics. We demonstrate early alterations in a gene co-expression network enriched for myelin and oligodendrocyte genes (OLIGs), whereas a multicellular gene co-expression network of plaque-induced genes (PIGs) involving the complement system, oxidative stress, lysosomes, and inflammation is prominent in the later phase of the disease. We confirm the majority of the observed alterations at the cellular level using in situ sequencing on mouse and human brain sections. Genome-wide spatial transcriptomics analysis provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases.
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2.
  • Rubens, Ulysse, et al. (författare)
  • BIAFLOWS : A Collaborative Framework to Reproducibly Deploy and Benchmark Bioimage Analysis Workflows.
  • 2020
  • Ingår i: Patterns (New York, N.Y.). - : Elsevier BV. - 2666-3899. ; 1:3
  • Tidskriftsartikel (refereegranskat)abstract
    • Image analysis is key to extracting quantitative information from scientific microscopy images, but the methods involved are now often so refined that they can no longer be unambiguously described by written protocols. We introduce BIAFLOWS, an open-source web tool enabling to reproducibly deploy and benchmark bioimage analysis workflows coming from any software ecosystem. A curated instance of BIAFLOWS populated with 34 image analysis workflows and 15 microscopy image datasets recapitulating common bioimage analysis problems is available online. The workflows can be launched and assessed remotely by comparing their performance visually and according to standard benchmark metrics. We illustrated these features by comparing seven nuclei segmentation workflows, including deep-learning methods. BIAFLOWS enables to benchmark and share bioimage analysis workflows, hence safeguarding research results and promoting high-quality standards in image analysis. The platform is thoroughly documented and ready to gather annotated microscopy datasets and workflows contributed by the bioimaging community.
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