Noncoding RNA: current deep sequencing data analysis approaches and challenges

D Veneziano, S Di Bella, G Nigita, A Lagana… - Human …, 2016 - Wiley Online Library
One of the most significant biological discoveries of the last decade is represented by the
reality that the vast majority of the transcribed genomic output comprises diverse classes of …

Emerging techniques to decipher microRNAs (miRNAs) and their regulatory role in conferring abiotic stress tolerance of plants

A Banerjee, A Roychoudhury… - Plant Biotechnology …, 2016 - Springer
MicroRNAs (miRNAs) are a distinct class of non-coding, small regulatory RNAs which have
evolved significantly in generating abiotic stress tolerance across a variety of model plants …

Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight host candidate genes associated with quantitative disease resistance

M Derbyshire, M Mbengue, M Barascud… - Molecular Plant …, 2019 - Wiley Online Library
Fungal plant pathogens secrete effector proteins and metabolites to cause disease.
Additionally, some species transfer small RNAs (sRNAs) into plant cells to silence host …

Evolution of flower color pattern through selection on regulatory small RNAs

D Bradley, P Xu, II Mohorianu, A Whibley, D Field… - Science, 2017 - science.org
Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-
wide differences in color patterns in snapdragon flowers are caused by an inverted …

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 …

miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets

C Paicu, I Mohorianu, M Stocks, P Xu, A Coince… - …, 2017 - academic.oup.com
Motivation MicroRNAs are a class of∼ 21–22 nt small RNAs which are excised from a stable
hairpin-like secondary structure. They have important gene regulatory functions and are …

sRNA profiling in Aspergillus flavus reveals differentially expressed miRNA-like RNAs response to water activity and temperature

Y Bai, F Lan, W Yang, F Zhang, K Yang, Z Li… - Fungal Genetics and …, 2015 - Elsevier
Small non-coding RNA (sRNA) in various organisms remains a mysterious subject. Although
microRNAs (miRNAs) have been intensively investigated in plants and animals, the study of …

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 …

MicroRNAs associated with caste determination and differentiation in a primitively eusocial insect

DH Collins, I Mohorianu, M Beckers, V Moulton… - Scientific Reports, 2017 - nature.com
In eusocial Hymenoptera (ants, bees and wasps), queen and worker adult castes typically
arise via environmental influences. A fundamental challenge is to understand how a single …

Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution

A Tripathi, K Goswami, N Sanan-Mishra - Frontiers in Physiology, 2015 - frontiersin.org
microRNAs (miRs) are a class of 21–24 nucleotide long non-coding RNAs responsible for
regulating the expression of associated genes mainly by cleavage or translational inhibition …