Co-expression networks for plant biology: why and how

X Rao, RA Dixon - Acta biochimica et biophysica Sinica, 2019 - academic.oup.com
Co-expression network analysis is one of the most powerful approaches for interpretation of
large transcriptomic datasets. It enables characterization of modules of co-expressed genes …

It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data

J Xie, A Ma, A Fennell, Q Ma, J Zhao - Briefings in bioinformatics, 2019 - academic.oup.com
Biclustering is a powerful data mining technique that allows clustering of rows and columns,
simultaneously, in a matrix-format data set. It was first applied to gene expression data in …

QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data

J Xie, A Ma, Y Zhang, B Liu, S Cao, C Wang, J Xu… - …, 2020 - academic.oup.com
Motivation The biclustering of large-scale gene expression data holds promising potential
for detecting condition-specific functional gene modules (ie biclusters). However, existing …

Biclustering data analysis: a comprehensive survey

EN Castanho, H Aidos, SC Madeira - Briefings in Bioinformatics, 2024 - academic.oup.com
Biclustering, the simultaneous clustering of rows and columns of a data matrix, has proved
its effectiveness in bioinformatics due to its capacity to produce local instead of global …

Nitrogen remobilization and conservation, and underlying senescence‐associated gene expression in the perennial switchgrass Panicum virgatum

J Yang, E Worley, Q Ma, J Li, I Torres‐Jerez… - New …, 2016 - Wiley Online Library
Improving nitrogen (N) remobilization from aboveground to underground organs during
yearly shoot senescence is an important goal for sustainable production of switchgrass …

Transcriptome-wide effects of expansin gene manipulation in etiolated Arabidopsis seedling

IA Ilias, K Negishi, K Yasue, N Jomura… - Journal of plant …, 2019 - Springer
Expansin is a non-enzymatic protein which plays a pivotal role in cell wall loosening by
inducing stress relaxation and extension in the plant cell wall. Previous studies on …

Dynamic changes in transcriptome and cell wall composition underlying brassinosteroid-mediated lignification of switchgrass suspension cells

X Rao, H Shen, S Pattathil, MG Hahn… - Biotechnology for …, 2017 - Springer
Background Plant cell walls contribute the majority of plant biomass that can be used to
produce transportation fuels. However, the complexity and variability in composition and …

[HTML][HTML] Transcriptome-Based Screening of Candidate Low-Temperature-Associated Genes and Analysis of the BocARR-B Transcription Factor Gene Family in …

S Bian, D Shao, Q Zhao, Q Li, Y Ren - International Journal of Molecular …, 2024 - mdpi.com
Low temperature is a significant abiotic stress factor that not only impacts plant growth,
development, yield, and quality but also constrains the geographical distribution of …

Downregulation of a UDP-Arabinomutase Gene in Switchgrass (Panicum virgatum L.) Results in Increased Cell Wall Lignin While Reducing Arabinose-Glycans

JD Willis, JA Smith, M Mazarei, JY Zhang… - Frontiers in plant …, 2016 - frontiersin.org
Background: Switchgrass (Panicum virgatum L.) is a C4 perennial prairie grass and a
dedicated feedstock for lignocellulosic biofuels. Saccharification and biofuel yields are …

[HTML][HTML] Irreversibility of the cell wall modification acts as a limiting factor in desiccation tolerance of Oryza sativa ssp. Indica cv MR303

IA Ilias, A Wagiran, KA Azizan, I Ismail, AFA Samad - Plant Stress, 2024 - Elsevier
Desiccation tolerance has emerged as a potential strategy for crop improvement. However,
the application of desiccation tolerance in crops, particularly rice, has been challenging and …