Literature DB >> 31249003

A periodic table of cell types.

Bo Xia1, Itai Yanai2,3.   

Abstract

Single cell biology is currently revolutionizing developmental and evolutionary biology, revealing new cell types and states in an impressive range of biological systems. With the accumulation of data, however, the field is grappling with a central unanswered question: what exactly is a cell type? This question is further complicated by the inherently dynamic nature of developmental processes. In this Hypothesis article, we propose that a 'periodic table of cell types' can be used as a framework for distinguishing cell types from cell states, in which the periods and groups correspond to developmental trajectories and stages along differentiation, respectively. The different states of the same cell type are further analogous to 'isotopes'. We also highlight how the concept of a periodic table of cell types could be useful for predicting new cell types and states, and for recognizing relationships between cell types throughout development and evolution.
© 2019. Published by The Company of Biologists Ltd.

Keywords:  Cell atlas; Cell states; Cell types; Periodic table; Single cell RNA-seq

Year:  2019        PMID: 31249003      PMCID: PMC6602355          DOI: 10.1242/dev.169854

Source DB:  PubMed          Journal:  Development        ISSN: 0950-1991            Impact factor:   6.868


  100 in total

Review 1.  Neuronal specification in the spinal cord: inductive signals and transcriptional codes.

Authors:  T M Jessell
Journal:  Nat Rev Genet       Date:  2000-10       Impact factor: 53.242

2.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

Review 3.  T-cell development and the CD4-CD8 lineage decision.

Authors:  Ronald N Germain
Journal:  Nat Rev Immunol       Date:  2002-05       Impact factor: 53.106

4.  A unifying concept: the history of cell theory.

Authors:  P Mazzarello
Journal:  Nat Cell Biol       Date:  1999-05       Impact factor: 28.824

Review 5.  Trophoblast differentiation during embryo implantation and formation of the maternal-fetal interface.

Authors:  Kristy Red-Horse; Yan Zhou; Olga Genbacev; Akraporn Prakobphol; Russell Foulk; Michael McMaster; Susan J Fisher
Journal:  J Clin Invest       Date:  2004-09       Impact factor: 14.808

6.  Genomic analysis of the hierarchical structure of regulatory networks.

Authors:  Haiyuan Yu; Mark Gerstein
Journal:  Proc Natl Acad Sci U S A       Date:  2006-09-26       Impact factor: 11.205

Review 7.  Place cells, grid cells, and the brain's spatial representation system.

Authors:  Edvard I Moser; Emilio Kropff; May-Britt Moser
Journal:  Annu Rev Neurosci       Date:  2008       Impact factor: 12.449

Review 8.  Pancreas and beta-cell development: from the actual to the possible.

Authors:  L Charles Murtaugh
Journal:  Development       Date:  2006-12-21       Impact factor: 6.868

9.  Adult ependymal cells are postmitotic and are derived from radial glial cells during embryogenesis.

Authors:  Nathalie Spassky; Florian T Merkle; Nuria Flames; Anthony D Tramontin; José Manuel García-Verdugo; Arturo Alvarez-Buylla
Journal:  J Neurosci       Date:  2005-01-05       Impact factor: 6.167

10.  Direct evidence for the pancreatic lineage: NGN3+ cells are islet progenitors and are distinct from duct progenitors.

Authors:  Guoqiang Gu; Jolanta Dubauskaite; Douglas A Melton
Journal:  Development       Date:  2002-05       Impact factor: 6.868

View more
  14 in total

1.  Gene expression pattern of trophoblast-specific transcription factors in trophectoderm by analysis of single-cell RNA-seq data of human blastocyst.

Authors:  Yajun Liu; Yi Zhang; Shiwen Li; Jinquan Cui
Journal:  Funct Integr Genomics       Date:  2021-02-05       Impact factor: 3.410

Review 2.  Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods.

Authors:  Zoe A Clarke; Tallulah S Andrews; Jawairia Atif; Delaram Pouyabahar; Brendan T Innes; Sonya A MacParland; Gary D Bader
Journal:  Nat Protoc       Date:  2021-05-24       Impact factor: 13.491

Review 3.  What is a cell type and how to define it?

Authors:  Hongkui Zeng
Journal:  Cell       Date:  2022-07-21       Impact factor: 66.850

Review 4.  Exploring tissue architecture using spatial transcriptomics.

Authors:  Anjali Rao; Dalia Barkley; Gustavo S França; Itai Yanai
Journal:  Nature       Date:  2021-08-11       Impact factor: 49.962

Review 5.  Understanding the Adult Mammalian Heart at Single-Cell RNA-Seq Resolution.

Authors:  Ernesto Marín-Sedeño; Xabier Martínez de Morentin; Jose M Pérez-Pomares; David Gómez-Cabrero; Adrián Ruiz-Villalba
Journal:  Front Cell Dev Biol       Date:  2021-05-12

6.  muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data.

Authors:  Helena L Crowell; Charlotte Soneson; Pierre-Luc Germain; Daniela Calini; Ludovic Collin; Catarina Raposo; Dheeraj Malhotra; Mark D Robinson
Journal:  Nat Commun       Date:  2020-11-30       Impact factor: 14.919

7.  A comprehensive survey of developmental programs reveals a dearth of tree-like lineage graphs and ubiquitous regeneration.

Authors:  Somya Mani; Tsvi Tlusty
Journal:  BMC Biol       Date:  2021-05-21       Impact factor: 7.431

Review 8.  How a cell decides its own fate: a single-cell view of molecular mechanisms and dynamics of cell-type specification.

Authors:  Maria Mircea; Stefan Semrau
Journal:  Biochem Soc Trans       Date:  2021-12-17       Impact factor: 5.407

9.  Vision, challenges and opportunities for a Plant Cell Atlas.

Authors:  Suryatapa Ghosh Jha; Alexander T Borowsky; Benjamin J Cole; Noah Fahlgren; Andrew Farmer; Shao-Shan Carol Huang; Purva Karia; Marc Libault; Nicholas J Provart; Selena L Rice; Maite Saura-Sanchez; Pinky Agarwal; Amir H Ahkami; Christopher R Anderton; Steven P Briggs; Jennifer An Brophy; Peter Denolf; Luigi F Di Costanzo; Moises Exposito-Alonso; Stefania Giacomello; Fabio Gomez-Cano; Kerstin Kaufmann; Dae Kwan Ko; Sagar Kumar; Andrey V Malkovskiy; Naomi Nakayama; Toshihiro Obata; Marisa S Otegui; Gergo Palfalvi; Elsa H Quezada-Rodríguez; Rajveer Singh; R Glen Uhrig; Jamie Waese; Klaas Van Wijk; R Clay Wright; David W Ehrhardt; Kenneth D Birnbaum; Seung Y Rhee
Journal:  Elife       Date:  2021-09-07       Impact factor: 8.140

Review 10.  Human Cell Atlas and cell-type authentication for regenerative medicine.

Authors:  Yulia Panina; Peter Karagiannis; Andreas Kurtz; Glyn N Stacey; Wataru Fujibuchi
Journal:  Exp Mol Med       Date:  2020-09-15       Impact factor: 8.718

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.