SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data.pdf (623.02 kB)
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SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data

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journal contribution
posted on 14.06.2018, 16:02 by Steven Woodhouse, Nir Piterman, Christoph M. Wintersteiger, Berthold Göttgens, Jasmin Fisher
BACKGROUND: Reconstruction of executable mechanistic models from single-cell gene expression data represents a powerful approach to understanding developmental and disease processes. New ambitious efforts like the Human Cell Atlas will soon lead to an explosion of data with potential for uncovering and understanding the regulatory networks which underlie the behaviour of all human cells. In order to take advantage of this data, however, there is a need for general-purpose, user-friendly and efficient computational tools that can be readily used by biologists who do not have specialist computer science knowledge. RESULTS: The Single Cell Network Synthesis toolkit (SCNS) is a general-purpose computational tool for the reconstruction and analysis of executable models from single-cell gene expression data. Through a graphical user interface, SCNS takes single-cell qPCR or RNA-sequencing data taken across a time course, and searches for logical rules that drive transitions from early cell states towards late cell states. Because the resulting reconstructed models are executable, they can be used to make predictions about the effect of specific gene perturbations on the generation of specific lineages. CONCLUSIONS: SCNS should be of broad interest to the growing number of researchers working in single-cell genomics and will help further facilitate the generation of valuable mechanistic insights into developmental, homeostatic and disease processes.

History

Citation

BMC Systems Biology, 2018, 12:59

Author affiliation

/Organisation/COLLEGE OF SCIENCE AND ENGINEERING/Department of Informatics

Version

VoR (Version of Record)

Published in

BMC Systems Biology

Publisher

BioMed Central

eissn

1752-0509

Acceptance date

10/04/2018

Copyright date

2018

Available date

14/06/2018

Publisher version

https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-018-0581-y

Language

en