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Memorias de investigación
Artículos en revistas:
Digital framework to build, visualize and analyze gene expression atlases with cellular resolution in zebrafish early embryogenesis
Año:2013
Áreas de investigación
  • Tecnología electrónica y de las comunicaciones
Datos
Descripción
Gene expression atlases at the cellular level are a fundamental resource to quantify and understand embryogenesis multiscale processes in time and space.The automated reconstruction of prototypic atlases from multiple fluorescent in situ hybridization and nuclear counterstaining observed in 3D requires the development of dedicated computational strategies. Match-IT is an original tool requiring minimal human supervision to gather in a reference specimen, with resolution at the cellular level, gene expression patterns observed at various developmental stages from multiple fluorescent staining in different individuals with phenotypic variability. This framework was used to build a gene expression atlas for the zebrafish early embryogenesis from 51 different specimens, about 200,000 cell nuclei, 96 gene expression patterns for 9 different genes and 6 time cohorts spanning from 4 to 6.3 hpf (hours post fertilization). An interactive visualization application, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Automatic methods and tools are also proposed here to allow the assessment of gene expression at the single cell level and the automated identification, visualization and analysis of co-expression patterns and synexpression groups with their dynamics through developmental stages in a vertebrate early embryo.
Internacional
Si
JCR del ISI
Si
Título de la revista
Nature Methods
ISSN
1548-7091
Factor de impacto JCR
19,276
Información de impacto
Datos JCR del año 2011
Volumen
DOI
Número de revista
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Participantes
  • Autor: Carlos Castro Gonzalez (UPM)
  • Autor: Miguel Angel Luengo Oroz (UPM)
  • Autor: Louise Duloquin ((Institut de Neurobiologie Alfred Fessard, CNRS)
  • Autor: Thierry Savy (Institut des Systèmes Complexes, École Polytechnique)
  • Autor: Barbara Rizzi (Institut de Neurobiologie Alfred Fessard, CNRS)
  • Autor: Sophie Desnoulez (Institut de Neurobiologie Alfred Fessard, CNRS)
  • Autor: Yannick Kergosien (Institut des Systèmes Complexes, École Polytechnique)
  • Autor: Maria Jesus Ledesma Carbayo (UPM)
  • Autor: Paul Bourgine (Institut des Systèmes Complexes, École Polytechnique)
  • Autor: Nadine Peyriéras (Institut de Neurobiologie Alfred Fessard, CNRS)
  • Autor: Andres de Santos Lleo (UPM)
Grupos de investigación, Departamentos, Centros e Institutos de I+D+i relacionados
  • Creador: Departamento: Ingeniería Electrónica
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