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A Machine Learning Approach for MicroRNA Precursor Prediction in Retro-transcribing Virus Genomes

Müşerref Duygu Saçar Demirci, Mustafa Toprak, Jens Allmer
2016 Journal of Integrative Bioinformatics  
The difficulty in experimental detection of pre-miRNAs increased the usage of computational approaches. Most of these approaches rely on machine learning especially classification.  ...  SummaryIdentification of microRNA (miRNA) precursors has seen increased efforts in recent years.  ...  In this study we created a workflow to predict miRNAs in 5 retro-transcribing virus genomes with human host (Human endogenous retrovirus K113, Hepatitis B virus (strain ayw), Human T lymphotropic virus  ... 
doi:10.1515/jib-2016-303 fatcat:nvvn7fo7urb4rajggujfipduim


Müşerref Duygu Saçar Demirci
2018 Anadolu University Journal of Science and Technology. A : Applied Sciences and Engineering  
In this work, a machine learning based approach was applied to identify and analyze potential miRNAs that might be originated from 60 single strand DNA (ssDNA) viruses' genomes.  ...  The results suggest that 53 of these viruses may possibly produce proper miRNA precursors.  ...  Jens Allmer for critical feedback on the manuscript.  ... 
doi:10.18038/aubtda.345972 fatcat:dh5ia223hfbh5eucl27prme2wa

Host-virus interaction: a new role for microRNAs

Vinod Scaria, Manoj Hariharan, Souvik Maiti, Beena Pillai, Samir K Brahmachari
2006 Retrovirology  
MicroRNAs (miRNAs) are a new class of 18-23 nucleotide long non-coding RNAs that play critical roles in a wide spectrum of biological processes.  ...  Recent reports also throw light into the role of microRNAs as critical effectors in the intricate host-pathogen interaction networks. Evidence suggests that both virus and hosts encode microRNAs.  ...  Elayanambi Sundaramoorthy for reviewing the manuscript and providing valuable suggestions.  ... 
doi:10.1186/1742-4690-3-68 pmid:17032463 pmcid:PMC1626483 fatcat:wqtrioybwnhw5ctfygjukhnpte

Next generation sequencing for profiling expression of miRNAs: technical progress and applications in drug development

Jie Liu, Steven F. Jennings, Weida Tong, Huixiao Hong
2011 Journal of Biomedical Science and Engineering  
Profiling of miRNAs by NGS has progressed rapidly and is a promising field for applications in drug development.  ...  miRNAs are non-coding RNAs that play a regulatory role in expression of genes and are associated with diseases.  ...  A machine-learning approach based on the random forest method [58] is used to detect new miRNAs in miRanalyzer.  ... 
doi:10.4236/jbise.2011.410083 pmid:22457835 pmcid:PMC3312786 fatcat:66ea7pamyzdsrcip43qwl5k4vu

Cellular versus viral microRNAs in host-virus interaction

Z. Ghosh, B. Mallick, J. Chakrabarti
2008 Nucleic Acids Research  
MicroRNAs (miRNAs) mark a new paradigm of RNAdirected gene expression regulation in a wide spectrum of biological systems.  ...  This interplay has important consequences, both for the virus and the host.  ...  ACKNOWLEDGEMENTS We thank the reviewers for their useful comments and suggestions to improve the manuscript.  ... 
doi:10.1093/nar/gkn1004 pmid:19095692 pmcid:PMC2651794 fatcat:uahvueppavbk7ietrphhjihq7i

Sequencing and Characterisation of an Extensive Atlantic Salmon (Salmo salar L.) MicroRNA Repertoire

Michaël Bekaert, Natalie R. Lowe, Stephen C. Bishop, James E. Bron, John B. Taggart, Ross D. Houston, Sofia Consuegra
2013 PLoS ONE  
The Atlantic salmon miRNAs experimentally identified in this study provide a robust large-scale resource for functional genome research in salmonids.  ...  While miRNA have been characterised in detail for many other species, this is not yet the case for Atlantic salmon.  ...  and sampling, and Mr Richard Talbot and Mrs Karen Troup for assistance with the miRNA library preparation and sequencing at ARK-Genomics.  ... 
doi:10.1371/journal.pone.0070136 pmid:23922936 pmcid:PMC3726450 fatcat:siry5jbgvnfg3ejcezu7niyxfu

Evolutionary patterns of non-coding RNAs

2005 Theory in biosciences  
The analysis of the transcription of non-coding RNAs (ncRNAs) suggests that small RNAs in general are genetically mobile in the sense that their association with a hostgene (e.g. when transcribed from  ...  We furthermore discuss the statistical distribution of microRNAs in metazoans, which suggests an explosive increase in the microRNA repertoire in vertebrates.  ...  This work was supported in part by the Austrian Fonds zur Förderung der Wissenschaftlichen Forschung, Project No.  ... 
doi:10.1016/j.thbio.2005.01.002 pmid:18202870 fatcat:3alkigssu5boppb5egbw2x6njy

Importance of Micrornas in Human Cancer Development: A Molecular Analytical Approach

Ahmed FE, Gouda MM, Ahmed NC
2021 Clinics of Surgery  
Current approaches for detecting microRNAs in blood and other body fluids is inadequate.  ...  For qRT-PCR applications, the tools include: a) Effective method of microRNA isolation from samples; b) RT-qPCR reagents optimized for microRNA detection; c) Assays specific to the microRNAs of interest  ...  By integrating these common features in a machine learning framework, we a vali-date and improved computational model for genome-wide microRNA target prediction.  ... 
doi:10.47829/cos.2021.6401 fatcat:ia5taaywgzdk7o3n7cuak46ezy

RNAs everywhere: genome-wide annotation of structured RNAs

Rolf Backofen, Stephan H. Bernhart, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic Rose (+4 others)
2007 Journal of Experimental Zoology Part B: Molecular and Developmental Evolution  
Starting with the discovery of microRNAs and the advent of genome-wide transcriptomics, non-protein-coding transcripts have moved from a fringe topic to a central field research in molecular biology.  ...  A series of exploratory studies are used to provide non-trivial examples for the discussion of some of the difficulties.  ...  Acknowledgments This work has been funded, in part, by the Austrian GEN-AU projects "bioinformatics integration network II" and "non coding RNA", and the German DFG Bioinformatics Initiative BIZ-6/1-2.  ... 
doi:10.1002/jez.b.21130 pmid:17171697 fatcat:3iozgrm3ozfs7p2ieffxjwllpm

Radiation vs Nuclear Size [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
To satisfy these needs, a publicly available and transparent machine learning tool is available that ranks all possible siRNAs for each targeted gene.  ...  Technologies: Machine operations for the performance of routine tasks in order to carry out analytical methods on a large scale and in a precise manner.  ...  It transcribes several nuclear genes ( TRNA polymerases replicate the genome of the RNA viruses.  ... 
doi:10.1007/978-1-4020-6754-9_14032 fatcat:sjsarml6jbh37bxjg25tyvucga

Abstracts from the 14th International Symposium on NeuroVirology October 25–28, 2016, Toronto, Ontario, Canada

2016 Journal of Neurovirology  
/or activated macrophages as well as a low level of HIV replication in central nervous system (CNS) reservoirs.  ...  However, synaptic injury, neuronal dysfunction, and damage in these patients are partially driven by immune activation and chronic inflammation in response to soluble factors released by HIV-infected and  ...  The amino acid sequence of the third variable (V3) loop of the HIV-1 envelope is highly predictive of co-receptor utilization preference during entry, and machine learning predictive algorithms have been  ... 
doi:10.1007/s13365-016-0478-8 pmid:27678092 fatcat:dxph35wjxzbmrnyhdcwnjlbmzq

Sycamore (Platanus spp) [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
A practical approach.  ...  Support: A statistical concept it is synonymous with log likelihood. ▶likelihood Support Vector Machine (SVM): A computer program based on the principle of supervised learning techniques.  ...  ▶meristem, ▶microRNA, ▶regeneration in animals, ▶activin, ▶nuclear transplantation, ▶cryopreservation, ▶niche, ▶embryo research, ▶oocyte, ▶transplantation, ▶grafting in medicine, ▶graft rejection, ▶transplantation  ... 
doi:10.1007/978-1-4020-6754-9_16470 fatcat:vd3dng4xina5piwpaioaz25tf4

Single Strand Assimilation [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
A practical approach.  ...  Support: A statistical concept it is synonymous with log likelihood. ▶likelihood Support Vector Machine (SVM): A computer program based on the principle of supervised learning techniques.  ...  ▶meristem, ▶microRNA, ▶regeneration in animals, ▶activin, ▶nuclear transplantation, ▶cryopreservation, ▶niche, ▶embryo research, ▶oocyte, ▶transplantation, ▶grafting in medicine, ▶graft rejection, ▶transplantation  ... 
doi:10.1007/978-1-4020-6754-9_15672 fatcat:2x2wsjganfaznnshm5kvluxr7a

Micro RNA-Biogenesis, Mechanism of Action and Applications-A Review

Subhabrata Ghosh
2011 International Journal of Research in Biotechnology and Biochemistry   unpublished
Recently, Micro RNA is used as a tool for reduction of expression of several genes or to control de expression of specific genes in eukaryotic genome.  ...  After the discovery of the first miRNA in the roundworm Caenorhabditis elegans, these short regulatory RNAs have been found to be an abundant class of RNAs in plants, animals, and DNA viruses.  ...  PFV is a retro-transcribing virus similar to the Human Immunodeficiency Virus (HIV), but codes for two additional proteins, Tas and Bet.  ... 

AASLD Abstracts 895-1142

2008 Hepatology  
BACKGROUND: Hepatitis B virus (HBV) is considered as a major risk factor for the progression to hepatocellular carcinoma (HCC).  ...  Optimal liver stiffness value was 6.9 kPa for diagnosis of significant fibrosis, which yielded a sensitivity of 70%, specificity of 79%, positive predictive value (PPV) of 82%, and negative predictive  ...  Principal component analysis (PCA) was done using Simca P and classifiers developed using the WEKA 3.5.7 machine learning algorithm package.  ... 
doi:10.1002/hep.22644 fatcat:npjzzrmvg5hvxlupppcl2qrnou
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