SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation-Reference-Cited by-同舟云学术

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

Published:2017-04-04 Issue:15 Volume:33 Page:2314-2321
ISSN:1367-4803
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Matsumoto Hirotaka¹,Kiryu Hisanori²,Furusawa Chikara³⁴,Ko Minoru S H⁵,Ko Shigeru B H⁵,Gouda Norio⁵,Hayashi Tetsutaro¹,Nikaido Itoshi¹

Affiliation:

1. Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, Wako, Saitama, Japan

2. Department of Computational Biology and Medical Sciences, Faculty of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan

3. Quantitative Biology Center (QBiC), RIKEN, Suita, Osaka, Japan

4. Universal Biology Institute, The University of Tokyo, Bunkyo-ku, Tokyo, Japan

5. Department of Systems Medicine, Keio University School of Medicine, Tokyo, Japan

Funder

Core Research for Evolutional Science and Technology

CREST

Japan Science and Technology Agency

JST

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

http://academic.oup.com/bioinformatics/article-pdf/33/15/2314/25158052/btx194.pdf

Reference44 articles.

1. Real-time quantification of protein expression at the single-cell level via dynamic protein synthesis translocation reporters;Aymoz;Nat. Commun,2016

2. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles;Bansal;Bioinformatics,2006

3. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells;Buettner;Nat. Biotechnol,2015

4. Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear;Burns;Nat Commun,2015

5. Dnmt3a is essential for hematopoietic stem cell differentiation;Challen;Nat. Genet,2012

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