Literature DB >> 35350228

Toward a unified information framework for cell atlas assembly.

Sijie Chen1, Yanting Luo1, Haoxiang Gao1, Fanhong Li1, Jiaqi Li1, Yixin Chen1, Renke You2, Hairong Lv1, Kui Hua1, Rui Jiang1, Xuegong Zhang1.   

Abstract

This perspective discusses the need and directions for the development of a unified information framework to enable the assembly of cell atlases and a revolution in medical research on the virtual body of assembled cell systems.
© The Author(s) 2021. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd.

Entities:  

Year:  2021        PMID： 35350228      PMCID： PMC8951195          DOI： 10.1093/nsr/nwab179

Source DB:  PubMed          Journal:  Natl Sci Rev        ISSN： 2053-714X            Impact factor:   23.178


  8 in total

1.  A roadmap for the Human Developmental Cell Atlas.

Authors:  Muzlifah Haniffa; Deanne Taylor; Sten Linnarsson; Bruce J Aronow; Gary D Bader; Roger A Barker; Pablo G Camara; J Gray Camp; Alain Chédotal; Andrew Copp; Heather C Etchevers; Paolo Giacobini; Berthold Göttgens; Guoji Guo; Ania Hupalowska; Kylie R James; Emily Kirby; Arnold Kriegstein; Joakim Lundeberg; John C Marioni; Kerstin B Meyer; Kathy K Niakan; Mats Nilsson; Bayanne Olabi; Dana Pe'er; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Rahul Satija; Sarah A Teichmann; Barbara Treutlein; Roser Vento-Tormo; Simone Webb
Journal:  Nature       Date:  2021-09-08       Impact factor: 69.504

2.  Profiling Tumor Infiltrating Immune Cells with CIBERSORT.

Authors:  Binbin Chen; Michael S Khodadoust; Chih Long Liu; Aaron M Newman; Ash A Alizadeh
Journal:  Methods Mol Biol       Date:  2018

3.  CellAtlasSearch: a scalable search engine for single cells.

Authors:  Divyanshu Srivastava; Arvind Iyer; Vibhor Kumar; Debarka Sengupta
Journal:  Nucleic Acids Res       Date:  2018-07-02       Impact factor: 16.971

4.  The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

Authors: 
Journal:  Nature       Date:  2019-10-09       Impact factor: 69.504

Review 5.  Toward a Common Coordinate Framework for the Human Body.

Authors:  Jennifer E Rood; Tim Stuart; Shila Ghazanfar; Tommaso Biancalani; Eyal Fisher; Andrew Butler; Anna Hupalowska; Leslie Gaffney; William Mauck; Gökçen Eraslan; John C Marioni; Aviv Regev; Rahul Satija
Journal:  Cell       Date:  2019-12-12       Impact factor: 41.582

6.  The Human Cell Atlas.

Authors:  Aviv Regev; Sarah A Teichmann; Eric S Lander; Ido Amit; Christophe Benoist; Ewan Birney; Bernd Bodenmiller; Peter Campbell; Piero Carninci; Menna Clatworthy; Hans Clevers; Bart Deplancke; Ian Dunham; James Eberwine; Roland Eils; Wolfgang Enard; Andrew Farmer; Lars Fugger; Berthold Göttgens; Nir Hacohen; Muzlifah Haniffa; Martin Hemberg; Seung Kim; Paul Klenerman; Arnold Kriegstein; Ed Lein; Sten Linnarsson; Emma Lundberg; Joakim Lundeberg; Partha Majumder; John C Marioni; Miriam Merad; Musa Mhlanga; Martijn Nawijn; Mihai Netea; Garry Nolan; Dana Pe'er; Anthony Phillipakis; Chris P Ponting; Stephen Quake; Wolf Reik; Orit Rozenblatt-Rosen; Joshua Sanes; Rahul Satija; Ton N Schumacher; Alex Shalek; Ehud Shapiro; Padmanee Sharma; Jay W Shin; Oliver Stegle; Michael Stratton; Michael J T Stubbington; Fabian J Theis; Matthias Uhlen; Alexander van Oudenaarden; Allon Wagner; Fiona Watt; Jonathan Weissman; Barbara Wold; Ramnik Xavier; Nir Yosef
Journal:  Elife       Date:  2017-12-05       Impact factor: 8.140

7.  Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST.

Authors:  Zhi-Jie Cao; Lin Wei; Shen Lu; De-Chang Yang; Ge Gao
Journal:  Nat Commun       Date:  2020-07-10       Impact factor: 14.919

8.  A curated database reveals trends in single-cell transcriptomics.

Authors:  Valentine Svensson; Eduardo da Veiga Beltrame; Lior Pachter
Journal:  Database (Oxford)       Date:  2020-11-28       Impact factor: 3.451
  8 in total
  2 in total

1.  hECA: The cell-centric assembly of a cell atlas.

Authors:  Sijie Chen; Yanting Luo; Haoxiang Gao; Fanhong Li; Yixin Chen; Jiaqi Li; Renke You; Minsheng Hao; Haiyang Bian; Xi Xi; Wenrui Li; Weiyu Li; Mingli Ye; Qiuchen Meng; Ziheng Zou; Chen Li; Haochen Li; Yangyuan Zhang; Yanfei Cui; Lei Wei; Fufeng Chen; Xiaowo Wang; Hairong Lv; Kui Hua; Rui Jiang; Xuegong Zhang
Journal:  iScience       Date:  2022-04-28

2.  Unfolding the genotype-to-phenotype black box of cardiovascular diseases through cross-scale modeling.

Authors:  Xi Xi; Haochen Li; Shengquan Chen; Tingting Lv; Tianxing Ma; Rui Jiang; Ping Zhang; Wing Hung Wong; Xuegong Zhang
Journal:  iScience       Date:  2022-07-20
  2 in total

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