On the performance of pre-microRNA detection algorithms.
TLDR
An extensible framework is presented, izMiR, which allows for the unbiased comparison of existing algorithms, adding new ones, and combining multiple approaches into ensemble methods and demonstrates that combining all of the methods into one ensemble approach, for the first time, allows reliable purely computational pre-miRNA detection in large eukaryotic genomes.Abstract:
MicroRNAs are crucial for post-transcriptional gene regulation, and their dysregulation has been associated with diseases like cancer and, therefore, their analysis has become popular. The experimental discovery of miRNAs is cumbersome and, thus, many computational tools have been proposed. Here we assess 13 ab initio pre-miRNA detection approaches using all relevant, published, and novel data sets while judging algorithm performance based on ten intrinsic performance measures. We present an extensible framework, izMiR, which allows for the unbiased comparison of existing algorithms, adding new ones, and combining multiple approaches into ensemble methods. In an exhaustive attempt, we condense the results of millions of computations and show that no method is clearly superior; however, we provide a guideline for biomedical researchers to select a tool. Finally, we demonstrate that combining all of the methods into one ensemble approach, for the first time, allows reliable purely computational pre-miRNA detection in large eukaryotic genomes.As the experimental discovery of microRNAs (miRNAs) is cumbersome, computational tools have been developed for the prediction of pre-miRNAs. Here the authors develop a framework to assess the performance of existing and novel pre-miRNA prediction tools and provide guidelines for selecting an appropriate approach for a given data set.read more
Citations
More filters
Journal ArticleDOI
Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection
TL;DR: C comprehending mode of actions of miRNAs and their possible roles during SARS-CoV-2 infections could create new opportunities for the development and improvement of new therapeutics.
Journal ArticleDOI
Tracking a mass mortality outbreak of pen shell Pinna nobilis populations: A collaborative effort of scientists and citizens.
Miguel Cabanellas-Reboredo,Maite Vázquez-Luis,Baptiste Mourre,Elvira Álvarez,Salud Deudero,Angel Amores,Piero Addis,Enric Ballesteros,Agustín Barrajón,Stefania Coppa,José Rafael García-March,Salvatore Giacobbe,Francisca Giménez Casalduero,Louis Hadjioannou,Santiago V Jiménez-Gutiérrez,Stelios Katsanevakis,Diego K. Kersting,Vesna Mačić,Borut Mavrič,Francesco Paolo Patti,Serge Planes,Patricia Prado,Jordi Sánchez,Jose Tena-Medialdea,Jean de Vaugelas,Nardo Vicente,Fatima Zohra Belkhamssa,Ivan Zupan,Iris E. Hendriks +28 more
TL;DR: The results strongly suggest that the parasite has probably dispersed regionally by surface currents, and that the disease expression seems to be closely related to temperatures above 13.5 °C and to a salinity range between 36.5–39.7 psu.
Posted ContentDOI
Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection
TL;DR: A machine learning based miRNA prediction analysis for the SARS-CoV-2 genome was performed to identify miRNA-like hairpins and searched for potential miRNA – based interactions between the viral miRNAs and human genes and human miRNAAs and viral genes.
Journal ArticleDOI
Adiabatic frequency shifting in epsilon near zero materials: The role of group velocity
Jacob B. Khurgin,Matteo Clerici,Vincenzo Bruno,Lucia Caspani,Clayton DeVault,Jongbum Kim,Amr Shaltout,Alexandra Boltasseva,Vladimir M. Shalaev,Marcello Ferrera,Daniele Faccio,Nathaniel Kinsey +11 more
TL;DR: In this paper, the authors investigated the adiabatic frequency shift (AFS) process in epsilon-near zero (ENZ) materials and showed that the frequency shift can be achieved in a shorter length if operating in the vicinity of the ENZ point.
Journal ArticleDOI
An innovative paradigm of methods in microRNAs detection: highlighting DNAzymes, the illuminators.
TL;DR: In this review, different methods of miRNA detection, along with related advantages and disadvantages are discussed, with a special focus on DNAzymes and DNAzyme-derived methods.
References
More filters
Journal ArticleDOI
Circulating microRNAs as stable blood-based markers for cancer detection
Patrick S. Mitchell,Rachael K. Parkin,Evan M. Kroh,Brian R. Fritz,Brian R. Fritz,Stacia K. Wyman,Era L. Pogosova-Agadjanyan,Amelia Peterson,Jennifer Noteboom,Kathy O'Briant,April Allen,Daniel W. Lin,Daniel W. Lin,Daniel W. Lin,Nicole Urban,Charles W. Drescher,Beatrice S. Knudsen,Derek L. Stirewalt,Robert Gentleman,Robert L. Vessella,Robert L. Vessella,Peter S. Nelson,Daniel Martin,Daniel Martin,Muneesh Tewari +24 more
TL;DR: It is shown here that miRNAs are present in human plasma in a remarkably stable form that is protected from endogenous RNase activity and established the measurement of tumor-derived mi RNAs in serum or plasma as an important approach for the blood-based detection of human cancer.
Journal ArticleDOI
The impact of microRNAs on protein output
TL;DR: The impact of micro RNAs on the proteome indicated that for most interactions microRNAs act as rheostats to make fine-scale adjustments to protein output.
Journal ArticleDOI
Biogenesis of small RNAs in animals.
TL;DR: This Review summarizes the current knowledge of how these intriguing molecules are generated in animal cells.
Journal ArticleDOI
MicroRNAs AND THEIR REGULATORY ROLES IN PLANTS
TL;DR: The importance of miRNA-directed gene regulation during plant development is now particularly clear and typically at the cores of gene regulatory networks, targeting genes that are themselves regulators, such as those encoding transcription factors and F-box proteins.
Journal ArticleDOI
Vienna RNA secondary structure server
TL;DR: The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures.