Works (6)

Updated: August 5th, 2023 21:16

2020 journal article

tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks

PLANT JOURNAL, 101(3), 716–730.

By: R. Spurney n, L. Broeck n, N. Clark n, A. Fisher n, M. Balaguer n & R. Sozzani n

author keywords: Arabidopsis thaliana; gene regulatory network inference; graphical user interface; RNA sequencing processing; stem cell maintenance; technical advance
MeSH headings : Algorithms; Arabidopsis / genetics; Bayes Theorem; Computational Biology; Gene Expression Regulation, Plant; Gene Regulatory Networks / genetics; Genome, Plant / genetics; Sequence Analysis, RNA; Transcriptome
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: December 9, 2019

2019 journal article

Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks

NATURE COMMUNICATIONS, 10.

By: N. Clark n, E. Buckner n, A. Fisher n, E. Nelson n, T. Nguyen n, A. Simmons*, M. Balaguer n, T. Butler-Smith n ...

MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Asymmetric Cell Division / genetics; Asymmetric Cell Division / physiology; Cell Differentiation; Cell Division; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / growth & development; Stem Cells / cytology; Stem Cells / metabolism; Transcription Factors / metabolism; Transcriptome; Ubiquitination / genetics; Ubiquitins / genetics
TL;DR: In the Arabidopsis root, a stem-cell-ubiquitous gene, TESMIN-LIKE CXC2 (TCX2), controls stem cell division by regulating stem cell-type specific networks and orchestrates the coordinated division of different stem cell types. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: December 30, 2019

2017 journal article

Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(36), E7632–E7640.

By: M. Balaguer n, A. Fisher n, N. Clark n, M. Fernandez-Espinosa*, B. Moller*, D. Weijers*, J. Lohmann*, C. Williams n ...

author keywords: root stem cell; root development; cell-type expression profile; gene regulatory network; modeling
MeSH headings : Algorithms; Arabidopsis / genetics; Bayes Theorem; Cluster Analysis; Computational Biology / methods; Gene Expression Profiling / methods; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Plant Roots / genetics; Stem Cells / metabolism; Transcription Factors / genetics; Transcriptome / genetics
TL;DR: A computational pipeline that uses gene expression datasets for inferring relationships among genes and predicting their importance and a gene regulatory network inference algorithm that combines clustering with dynamic Bayesian network inference that identified PERIANTHIA as an important molecular regulator of quiescent center function. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Gene and networks regulating the root stem cell niche of Arabidopsis

Curr Opin Plant Biol, 29, 38–43.

By: A. Fisher n & R. Sozzani n

MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / growth & development; Asymmetric Cell Division; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / growth & development; Stem Cells / cytology
TL;DR: This review will discuss several studies that characterized many of the genetic programs and molecular mechanisms regulating stem cell ACD and their identity in the Arabidopsis root and highlight how the growing use of mathematical modeling provides a comprehensive and quantitative perspective on the design rules governing stemcell ACDs. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy

Elife, 5.

By: N. Clark, E. Hinde, C. Winter, A. Fisher, G. Crosti, I. Blilou, E. Gratton, P. Benfey, R. Sozzani

Source: NC State University Libraries
Added: August 6, 2018

2014 review

Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants

[Review of ]. ANNALS OF BOTANY, 113(7), 1083–1105.

author keywords: Asymmetric cell division; embryo; root; stomata; lateral root; cortex endodermis initial; omics; Arabidopsis thaliana; Zea mays; maize
MeSH headings : Arabidopsis / embryology; Arabidopsis / genetics; Arabidopsis / growth & development; Asymmetric Cell Division; Genomics; Magnoliopsida / embryology; Magnoliopsida / genetics; Magnoliopsida / growth & development; Models, Genetic; Plant Roots / embryology; Plant Roots / genetics; Plant Roots / growth & development; Plant Shoots / embryology; Plant Shoots / genetics; Plant Shoots / growth & development
TL;DR: This review describes how asymmetric cell divisions are regulated during development and in different cell types in both the root and the shoot of plants, and highlights ways in which omics and modelling approaches have been used to elucidate these regulatory mechanisms. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

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