Literature DB >> 32584459

A cell type annotation Jamboree-Revival of а communal science forum.

Leonid Peshkin1, Marc W Kirschner1.   

Abstract

Cell Atlases are currently being constructed for human tissues as well as several model organisms. New technologies make creation of vast datasets in many species possible, but the value of such data crucially depends on the quality of annotation. The tools of annotating single cell data and creating knowledge representations comparable across organisms have been lagging. We argue that successfully creating Cell Atlases will require a revival of a boot-camp style forum for communal annotation combined with an intensive learning workshop, dubbed a "Jamboree". We report on our experience of successfully developing a structure and curriculum and running such a Jamboree for Xenopus Embryonic Cell Types at the Janelia Farms campus of the Howard Hughes Medical Institute.
© 2020 Wiley Periodicals LLC.

Entities:  

Keywords:  Xenopus embryology; annotation Jamboree; cell atlas; single cell transcriptomics

Year:  2020        PMID: 32584459      PMCID: PMC8049540          DOI: 10.1002/dvg.23383

Source DB:  PubMed          Journal:  Genesis        ISSN: 1526-954X            Impact factor:   2.487


  6 in total

1.  The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.

Authors:  James A Briggs; Caleb Weinreb; Daniel E Wagner; Sean Megason; Leonid Peshkin; Marc W Kirschner; Allon M Klein
Journal:  Science       Date:  2018-04-26       Impact factor: 47.728

2.  A new view of embryo development and regeneration.

Authors:  Richard M Harland
Journal:  Science       Date:  2018-06-01       Impact factor: 47.728

3.  Development cell by cell.

Authors:  Elizabeth Pennisi
Journal:  Science       Date:  2018-12-21       Impact factor: 47.728

4.  Microsampling Capillary Electrophoresis Mass Spectrometry Enables Single-Cell Proteomics in Complex Tissues: Developing Cell Clones in Live Xenopus laevis and Zebrafish Embryos.

Authors:  Camille Lombard-Banek; Sally A Moody; M Chiara Manzini; Peter Nemes
Journal:  Anal Chem       Date:  2019-03-18       Impact factor: 6.986

5.  Identification of a regeneration-organizing cell in the Xenopus tail.

Authors:  C Aztekin; T W Hiscock; J C Marioni; J B Gurdon; B D Simons; J Jullien
Journal:  Science       Date:  2019-05-17       Impact factor: 47.728

6.  SPRING: a kinetic interface for visualizing high dimensional single-cell expression data.

Authors:  Caleb Weinreb; Samuel Wolock; Allon M Klein
Journal:  Bioinformatics       Date:  2018-04-01       Impact factor: 6.937

  6 in total
  1 in total

1.  Sobp modulates the transcriptional activation of Six1 target genes and is required during craniofacial development.

Authors:  Andre L P Tavares; Karyn Jourdeuil; Karen M Neilson; Himani D Majumdar; Sally A Moody
Journal:  Development       Date:  2021-09-06       Impact factor: 6.862

  1 in total

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