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sRNAtoolbox: an integrated collection of small RNA research tools

Antonio Rueda, Guillermo Barturen, Ricardo Lebrón, Cristina Gómez-Martín, Ángel Alganza, José L. Oliver, Michael Hackenberg
2015 Nucleic Acids Research  
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  
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

López-Galiano, Sentandreu, Martínez-Ramírez, Rausell, Real, Camañes, Ruiz-Rivero, Crespo-Salvador, García-Robles
2019 Genes  
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

Ernesto Aparicio-Puerta, Cristina Gómez-Martín, Stavros Giannoukakos, José María Medina, Chantal Scheepbouwer, Adrián García-Moreno, Pedro Carmona-Saez, Bastian Fromm, Michiel Pegtel, Andreas Keller, Juan Antonio Marchal, Michael Hackenberg
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

Gabriella Guelfi, Giovanni Cochetti, Valentina Stefanetti, Danilo Zampini, Silvana Diverio, Andrea Boni, Ettore Mearini
2018 Scientific Reports  
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  
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

Ilektra-Chara Giassa, Panagiotis Alexiou
2021 Biology  
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

Yen, Chen, Sreenu, Kohl, Failloux
2019 Viruses  
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

Antonella Baldassarre, Cristina Felli, Giorgio Prantera, Andrea Masotti
2017 Genes  
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

Tobias Fehlmann, Fabian Kern, Omar Laham, Christina Backes, Jeffrey Solomon, Pascal Hirsch, Carsten Volz, Rolf Müller, Andreas Keller
2021 Nucleic Acids Research  
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]

Dana Zeid, Thomas J. Gould
2022 bioRxiv   pre-print
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

Martin Bilbao-Arribas, Naiara Abendaño, Endika Varela-Martínez, Ramsés Reina, Damián de Andrés, Begoña M. Jugo
2019 BMC Genomics  
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

Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang, Wen He, Li Xi, Sachin Mathur, Michael Agostino, Theresa Paradis, David von Schack, Michael Vincent, Baohong Zhang
2017 BMC Bioinformatics  
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

Sivarajan Karunanithi, Martin Simon, Marcel H. Schulz
2019 PeerJ  
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]

Duy N. Do, Pier-Luc Dudemaine, Bridget Fomenky, Eveline M. Ibeagha-Awemu
2017 Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health  
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 ( 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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