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MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans

Ting-Hua Huang, Bin Fan, Max F Rothschild, Zhi-Liang Hu, Kui Li, Shu-Hong Zhao
2007 BMC Bioinformatics  
Results from applying the tool for chicken/human and D. melanogaster/D. pseudoobscura pair-wise genome alignments showed that the tool can be used for genome wide pre-miRNA predictions.  ...  Utilizing these features and combining some improvements of the current pre-miRNA prediction methods, we implemented a computational learning method SVM (support vector machine) to build a high throughput  ...  Rothschild and Z-L Hu was provided in part by USDA Pig Genome Coordination funds, the Iowa Agriculture and Home Economics Experiment Station, and Hatch and the State of Iowa funds.  ... 
doi:10.1186/1471-2105-8-341 pmid:17868480 pmcid:PMC2206061 fatcat:7o7qooincfbuzplhh6nldf7jdm

Computational tools for plant small RNA detection and categorization

Lionel Morgado, Frank Johannes
2017 Briefings in Bioinformatics  
Frank Johannes is an assistant professor for population epigenetics and epigenomics at the Technical University of Munich.  ...  nontrivial bioinformatic approaches.  ...  Other studies implemented comparable but slightly altered approaches for rice [93, 94] and Arabidopsis [95] .  ... 
doi:10.1093/bib/bbx136 pmid:29059285 fatcat:2cgfz3s4tfdx5oo2vwahhq2l3e

Ensemble-based classification approach for micro-RNA mining applied on diverse metagenomic sequences

Sherin M ElGokhy, Mahmoud ElHefnawi, Amin Shoukry
2014 BMC Research Notes  
Our new approach could thus be used for mining metagenomic sequences and finding new and homologous miRNAs.  ...  Different approaches for identification of miRNAs have been proposed based on homology, thermodynamic parameters, and cross-species comparisons.  ...  Acknowledgements This research has been supported by the Ministry of Higher Education (MoHE) of Egypt through an PH.D. fellowship.  ... 
doi:10.1186/1756-0500-7-286 pmid:24884968 pmcid:PMC4051165 fatcat:choeoz7kcnhixewnmn6ezde64u

A practical guide to the art of RNA gene prediction

I. M. Meyer
2007 Briefings in Bioinformatics  
It discusses our current view of RNA genes as well as recent computational analyses of RNA genes and concludes with an outlook to future directions in algorithm development and data analyses.  ...  The most successful approaches today employ a comparative approach in which sets of homologous sequences are analyzed simultaneously.  ...  Acknowledgements I would like to thank the organizers and participants of the RNA workshop 2006 in Benasque, Spain, for many inspiring discussions.  ... 
doi:10.1093/bib/bbm011 pmid:17483123 fatcat:3lp5mvn6abasfjpal73vzhg3qa

Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential

Claudia Cava, Gloria Bertoli, Isabella Castiglioni
2015 BMC Systems Biology  
and challenges offered by the application of such integrative approaches.  ...  Development of human cancer can proceed through the accumulation of different genetic changes affecting the structure and function of the genome.  ...  [278] evaluated genome-wide correlations between GE and CN by following an approach based on the Wilcoxon test.  ... 
doi:10.1186/s12918-015-0211-x pmid:26391647 pmcid:PMC4578257 fatcat:bzzqlyknfrg73otnrwvciic7dy

A Functional Genomics Approach for Characterizing the Role of Six Transcription Factors in Muscle Development

Alphonse Chu, Université D'Ottawa / University Of Ottawa, Université D'Ottawa / University Of Ottawa
Using the C2C12 cell line, a model for skeletal muscle differentiation, I used a functional genomics approach, employing siRNA specific to both these TFs, to characterize their role in skeletal myogenesis  ...  Six1 and Six4 are homeodomain TFs known to be essential for skeletal muscle development in mice.  ...  MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans. BMC Bioinformatics 8, 341.Hubner, K., Sahle, S., and Kummer, U. (2011) .  ... 
doi:10.20381/ruor-3765 fatcat:lrnpvbpxljdjthl7xfwndg2xue