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sRNAtoolbox: an integrated collection of small RNA research tools
2015
Nucleic Acids Research
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Small RNA research is a rapidly growing field. ...
To facilitate integrated sRNA research, we developed sRNAtoolbox, a set of independent but interconnected tools for expression profiling from high-throughput sequencing data, consensus differential expression ...
This makes sRNAtoolbox a very flexible and easy to use set of small RNA research tools. ...
doi:10.1093/nar/gkv555
pmid:26019179
pmcid:PMC4489306
fatcat:ff5jj7krwvb5xpm23xolo2f4nm
sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression
2019
Nucleic Acids Research
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Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. ...
Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing ...
ACKNOWLEDGEMENTS The authors acknowledge the usage of the computational infrastructure of the Computational Epigenomics Lab of the University of Granada. ...
doi:10.1093/nar/gkz415
pmid:31114926
pmcid:PMC6602500
fatcat:pzqld3qrmjfkxbe3tgfnmzcixy
Identification of Stress Associated microRNAs in Solanum lycopersicum by High-Throughput Sequencing
2019
Genes
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An inverse correlation between the expression profiles of 4 selected miRNAs (sly-miR171a, sly-miR172c, sly-newmiR22-3p and sly-miR167c-3p) and their target genes (Kinesin, PPR, GRAS40, ABC transporter, ...
Reverse transcription quantitative PCR (RT-qPCR) was used to validate high-throughput expression analysis data, confirming the expression profiles of 10 out of 11 randomly selected miRNAs. ...
The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. ...
doi:10.3390/genes10060475
fatcat:fodek5owsnguzis3jstizlxxla
sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms
2022
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The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. ...
With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. ...
ACKNOWLEDGEMENTS The authors thank all collaborators and users who provided insightful feedback and suggestions to improve sRNAtoolbox and also acknowledge the usage of the computational infrastructure ...
doi:10.1093/nar/gkac363
pmid:35556129
fatcat:gehgrmgxkbgdxnfvunaanrz5ra
Next Generation Sequencing of urine exfoliated cells: an approach of prostate cancer microRNAs research
2018
Scientific Reports
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Total RNA was extracted from urine and sequenced using an HiSeq2500 System (Illumina). QPCR assay was used to validate the highest NGS results in PCA patients and in age-matched, caucasian men. ...
The present research confirmed the potential use of miRNAs as non-invasive biomarkers in the diagnosis of PCa, potentially reducing the invasiveness of actual clinical strategy. ...
Acknowledgements The authors would like to thank Gabriel Falcinelli and Anna Beatrice Casano for their skillful technical assistance and Diana Cella for improving the use of English in the manuscript. ...
doi:10.1038/s41598-018-24236-y
pmid:29740090
pmcid:PMC5940782
fatcat:uy2xagrxdjhjldb2gezlusdop4
Editorial: The 17th Annual Nucleic Acids Research Web Server Issue 2019
2019
Nucleic Acids Research
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of small RNAs; RNA workbench 2.0, an extensive collection of RNA analysis tools; RNAmod for the annotation of mRNA modifications, and HNADOCK for modeling RNA/DNA 3D complex structures. ...
In the DNA and RNA category, papers include Web 3DNA 2.0 for analysis and visualization of DNA structure (cover image); tRNAviz for analysis of tRNA sequences; sRNAbench and sRNAtoolbox 2019 for analysis ...
Among the papers for protein analysis is the 20th anniversary publication of PSIPRED, a collection of tools for structure annotation; IntFOLD for protein structure prediction; LOMETS2 for threading based ...
doi:10.1093/nar/gkz521
pmid:31251385
pmcid:PMC6602506
fatcat:rgrvinsmkvbkpik7htwywlm7nq
Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements
2021
Biology
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Cells regulate TE expression against uncontrolled activity that can lead to developmental defects and disease, using multiple strategies, such as DNA chemical modification, small RNA (sRNA) silencing, ...
A plethora of tools and machine learning approaches have been developed for prediction, annotation, and expression profiling of sRNAs, for methylation analysis of TEs, as well as for genome-wide methylation ...
-C.G. and P.A. would like to thank Eva Klimentová for her help with the initial literature research for the bioinformatics tools.
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/biology10090896
pmid:34571773
pmcid:PMC8465862
fatcat:5a5osyvzfjhc3jogue42lgrtyy
Assessing the Potential Interactions between Cellular miRNA and Arboviral Genomic RNA in the Yellow Fever Mosquito, Aedes aegypti
2019
Viruses
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Although the role of exogenous small interfering RNA (siRNA) and P-element induced wimpy testis (PIWI)-interacting RNA (piRNA) pathways in mosquito antiviral immunity is increasingly better understood, ...
By using prediction tools with distinct algorithms, several miRNA binding sites were commonly found within different genotypes/and or lineages of each arbovirus. ...
Conflict of Interests: the authors declare no competing interests. Viruses 2019, 11, 540 ...
doi:10.3390/v11060540
pmid:31185697
pmcid:PMC6631873
fatcat:c5hknxydkraexnivgrwt5no264
Circulating microRNAs and Bioinformatics Tools to Discover Novel Diagnostic Biomarkers of Pediatric Diseases
2017
Genes
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MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the post-transcriptional level. ...
We will also discuss specific bioinformatics tools and databases for circulating miRNAs focused on the identification and discovery of novel diagnostic biomarkers of pediatric diseases. ...
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/genes8090234
pmid:28925938
pmcid:PMC5615367
fatcat:p5bxz54qwbd2vee4nlagpcyaji
miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale
2021
Nucleic Acids Research
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After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new features. ...
Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. ...
RNA research projects. ...
doi:10.1093/nar/gkab268
pmid:33872372
pmcid:PMC8262700
fatcat:h7fs5vikpvfqpaafcy4eijhlsu
Chronic nicotine exposure alters sperm small RNA content in a C57BL/6J mouse model: Implications for multigenerational inheritance
[article]
2022
bioRxiv
pre-print
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In an effort to identify germline mechanisms underlying these multigenerational phenotypes, the current study sequenced small RNA extracted from sperm of males chronically administered nicotine using our ...
A literature review of previous research on these transcripts suggested an enrichment for regulation of psychological stress and learning. mRNAs predicted to be regulated by differentially expressed sperm ...
The sRNAde tool was used to perform DEseq2 differential expression analysis. Full analysis settings in sRNAtoolbox are detailed in Supplementary file 1. ...
doi:10.1101/2022.04.27.489636
fatcat:2f564ess2rfgtc2hl7qfdy2e3i
Expression analysis of lung miRNAs responding to ovine VM virus infection by RNA-seq
2019
BMC Genomics
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MicroRNAs (miRNAs) are short endogenous, single-stranded, noncoding small RNA molecules of approximately 22 nucleotides in length. ...
This miRNA could be an indicator for the severity of the lung lesions, or a putative target for therapeutic intervention. ...
Availability of data and materials The datasets generated and analyzed during the current study are available in the NCBI's Gene Expression Omnibus repository and are accessible through GEO Series accession ...
doi:10.1186/s12864-018-5416-0
fatcat:osxszn7kbnbezhltejmfh4lf6q
QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing
2017
BMC Bioinformatics
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Although many open-source tools for microRNA (miRNA)-seq data analyses are available, challenges remain in accurate miRNA quantification from large-scale miRNA-seq dataset. ...
First, it takes advantage of high redundancy of miRNA reads and introduces joint mapping of multiple samples to reduce computational time. ...
Acknowledgements The authors would like to thank Marc Halushka at Johns Hopkins University School of Medicine for help and assistance with running miRge.
Funding Not applicable. ...
doi:10.1186/s12859-017-1601-4
pmid:28320324
pmcid:PMC5359966
fatcat:s2czg5nswjdvdk5bguf6rzvdtm
Automated analysis of small RNA datasets with RAPID
2019
PeerJ
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Understanding the role of short-interfering RNA (siRNA) in diverse biological processes is of current interest and often approached through small RNA sequencing. ...
RAPID also facilitates an automated comparison of multiple datasets, with one of the normalization techniques dedicated for siRNA knockdown analysis, and integrates differential expression analysis using ...
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ...
doi:10.7717/peerj.6710
pmid:30993044
pmcid:PMC6462184
fatcat:62bhqpotavew3cpuxfpywududa
Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity
[chapter]
2017
Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health
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In this chapter, we present an overview of common frameworks for generating and processing RNA sequence data to obtain ncRNA transcripts. ...
on tools for livestock species. ...
Among the most popular integrated tools, DIANA-tools (www.microrna.gr) covers a wide scope and research scenarios integrating several tools such as DIANA-microT-CDS, DIANA-TarBase v7.0, DIANA-miRGen v3.0 ...
doi:10.5772/intechopen.69872
fatcat:qcwzw6aot5ew3bhosfqieumrge
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