Trends in the development of miRNA bioinformatics tools

L Chen, L Heikkinen, C Wang, Y Yang… - Briefings in …, 2019 - academic.oup.com
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via
recognition of cognate sequences and interference of transcriptional, translational or …

[HTML][HTML] Biogenesis, functions, interactions, and resources of non-coding RNAs in plants

H Chao, Y Hu, L Zhao, S Xin, Q Ni, P Zhang… - International Journal of …, 2022 - mdpi.com
Plant transcriptomes encompass a large number of functional non-coding RNAs (ncRNAs),
only some of which have protein-coding capacity. Since their initial discovery, ncRNAs have …

PmiREN: a comprehensive encyclopedia of plant miRNAs

Z Guo, Z Kuang, Y Wang, Y Zhao, Y Tao… - Nucleic acids …, 2020 - academic.oup.com
MicroRNAs (miRNAs) are small non-coding RNA molecules that function as diverse
endogenous gene regulators at the post-transcriptional level. In the past two decades, as …

System biology of metal tolerance in plants: an integrated view of genomics, transcriptomics, metabolomics, and phenomics

N Khalid, M Aqeel, A Noman - Plant Metallomics and Functional Omics: A …, 2019 - Springer
Heavy metal toxicity is heavily damaging constraint to quality and productivity of crops these
days. Plants exposed to heavy metals (HMs) contaminated sites respond at cellular …

The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs

MB Stocks, I Mohorianu, M Beckers, C Paicu… - …, 2018 - academic.oup.com
Motivation RNA interference, a highly conserved regulatory mechanism, is mediated via
small RNAs (sRNA). Recent technical advances enabled the analysis of larger, complex …

AUXIN RESPONSIVE FACTOR8 regulates development of the feeding site induced by root-knot nematodes in tomato

Y Noureddine, M da Rocha, J An… - Journal of …, 2023 - academic.oup.com
Root-knot nematodes (RKN) from the genus Meloidogyne induce the dedifferentiation of root
vascular cells into giant multinucleate feeding cells. These feeding cells result from an …

[HTML][HTML] Identification and expression profiling of microRNAs involved in the stigma exsertion under high-temperature stress in tomato

C Pan, L Ye, Y Zheng, Y Wang, D Yang, X Liu, L Chen… - BMC genomics, 2017 - Springer
Background Autogamy in cultivated tomato varieties is a derived trait from wild type tomato
plants, which are mostly allogamous. However, environmental stresses can cause …

PAREsnip2: a tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules

J Thody, L Folkes, Z Medina-Calzada, P Xu… - Nucleic acids …, 2018 - academic.oup.com
Small RNAs (sRNAs) are short, non-coding RNAs that play critical roles in many important
biological pathways. They suppress the translation of messenger RNAs (mRNAs) by …

[HTML][HTML] Machine learning approaches for plant miRNA prediction: challenges, advancements, and future directions

Z Kuang, Y Zhao, X Yang - Agriculture Communications, 2023 - Elsevier
MicroRNA (miRNA) is an important regulator of gene expression in plants that functions to
regulate plant development and growth. Signature sequences and secondary structures that …

noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise

I Moutsopoulos, L Maischak, E Lauzikaite… - Nucleic Acids …, 2021 - academic.oup.com
High-throughput sequencing enables an unprecedented resolution in transcript
quantification, at the cost of magnifying the impact of technical noise. The consistent …