Ryan Joseph Spurney

College of Engineering

Works (3)

Updated: August 5th, 2023 21:16

2022 journal article

Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation

PLANT CELL, 34(1), 535–556.

By: H. Thomas*, L. Broeck  n, R. Spurney n, R. Sozzani  n & M. Frank *

MeSH headings : Capsicum / genetics; Capsicum / physiology; Gene Expression Regulation, Plant / physiology; Gene Regulatory Networks; Homeodomain Proteins / genetics; Homeodomain Proteins / metabolism; Solanum lycopersicum / genetics; Solanum lycopersicum / physiology; Plant Proteins / genetics; Plant Proteins / metabolism
TL;DR: A model system with Solanum lycopersicum ‘tomato’ and Capsicum annuum ‘pepper’ heterografting is developed, which expresses signs of anatomical junction failure within the first week of grafting, and SlWOX4 is the first gene to be functionally implicated in vegetable crop grafting. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: February 7, 2022

2021 article

Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap for Analysis, Visualization, and Key Gene Identification

MODELING TRANSCRIPTIONAL REGULATION, Vol. 2328, pp. 47–65.

By: R. Spurney n, M. Schwartz n, M. Gobble n, R. Sozzani  n & L. Broeck  n

author keywords: Gene regulatory network inference; RNA sequencing; Bioinformatics; Network visualization
MeSH headings : Algorithms; Amino Acid Motifs / genetics; Cluster Analysis; Computational Biology / methods; Gene Expression Profiling / methods; Gene Expression Regulation / genetics; Gene Regulatory Networks / genetics; Multigene Family; RNA-Seq / methods; Software; Spatio-Temporal Analysis; Workflow
TL;DR: This chapter aims to present a workflow feasible and accessible for plant biologists without a bioinformatics or computer science background and chooses TuxNet, a user-friendly graphical user interface that integrates RNA sequencing data analysis with GRN inference, for the purpose of providing a detailed tutorial. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: October 4, 2021

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, NC State University Libraries, ORCID
Added: December 9, 2019

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