MicroRNA discovery in the human parasite Echinococcus multilocularis from genome-wide data.

[1]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[2]  M. Zuker,et al.  Structural analysis by energy dot plot of a large mRNA. , 1993, Journal of molecular biology.

[3]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[4]  Teuvo Kohonen,et al.  Self-Organizing Maps , 2010 .

[5]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[6]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[7]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[8]  A. Yoo,et al.  LIN-12/Notch Activation Leads to MicroRNA-Mediated Down-Regulation of Vav in C. elegans , 2005, Science.

[9]  Fei Li,et al.  Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine , 2005, BMC Bioinformatics.

[10]  Peter F. Stadler,et al.  Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data , 2006, ISMB.

[11]  Bin Fan,et al.  MiRFinder: an improved approach and software implementation for genome-wide fast microRNA precursor scans , 2007, BMC Bioinformatics.

[12]  Peng Jiang,et al.  MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features , 2007, Nucleic Acids Res..

[13]  I. K. Jordan,et al.  Origin and Evolution of Human microRNAs From Transposable Elements , 2007, Genetics.

[14]  Louise C. Showe,et al.  Learning from positive examples when the negative class is undetermined- microRNA gene identification , 2008, Algorithms for Molecular Biology.

[15]  P. Saetrom,et al.  Robust machine learning algorithms predict microRNA genes and targets. , 2007, Methods in enzymology.

[16]  Weixiong Zhang,et al.  MicroRNA prediction with a novel ranking algorithm based on random walks , 2008, ISMB.

[17]  Charles C. Kim,et al.  The microRNA bantam Functions in Epithelial Cells to Regulate Scaling Growth of Dendrite Arbors in Drosophila Sensory Neurons , 2009, Neuron.

[18]  Li Li,et al.  Computational approaches for microRNA studies: a review , 2010, Mammalian Genome.

[19]  A. Lal,et al.  MicroRNAs and their target gene networks in breast cancer , 2010, Breast Cancer Research.

[20]  P. Poirazi,et al.  MatureBayes: A Probabilistic Algorithm for Identifying the Mature miRNA within Novel Precursors , 2010, PloS one.

[21]  Shuigeng Zhou,et al.  MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features , 2010, BMC Bioinformatics.

[22]  Georgina Stegmayer,et al.  *omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants , 2010, BMC Bioinformatics.

[23]  A. T. Freitas,et al.  Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi , 2010, BMC Genomics.

[24]  P. Torgerson,et al.  The Global Burden of Alveolar Echinococcosis , 2010, PLoS neglected tropical diseases.

[25]  A. Kolokythas,et al.  MicroRNA-7 targets IGF1R (insulin-like growth factor 1 receptor) in tongue squamous cell carcinoma cells. , 2010, The Biochemical journal.

[26]  C. Spillane,et al.  Genome-wide identification of novel microRNAs and their target genes in the human parasite Schistosoma mansoni. , 2011, Genomics.

[27]  Ana M. Aransay,et al.  miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments , 2011, Nucleic Acids Res..

[28]  M. Berriman,et al.  Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel , 2012, BMC Genomics.

[29]  S. Asurmendi,et al.  Identification of Echinococcus granulosus microRNAs and their expression in different life cycle stages and parasite genotypes. , 2011, International journal for parasitology.

[30]  M. Tewari,et al.  MicroRNA profiling: approaches and considerations , 2012, Nature Reviews Genetics.

[31]  Sebastian D. Mackowiak,et al.  miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades , 2011, Nucleic acids research.

[32]  R. Islam,et al.  MiRANN: a reliable approach for improved classification of precursor microRNA using Artificial Neural Network model. , 2012, Genomics.

[33]  Marek Sikora,et al.  HuntMi: an efficient and taxon-specific approach in pre-miRNA identification , 2013, BMC Bioinformatics.

[34]  Chun-Nan Hsu,et al.  MetaMirClust: discovery of miRNA cluster patterns using a data-mining approach. , 2012, Genomics.

[35]  Rolf Backofen,et al.  Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches , 2012, Bioinform..

[36]  Alexander Schliep,et al.  The discriminant power of RNA features for pre-miRNA recognition , 2013, BMC Bioinformatics.

[37]  Jacqueline A. Keane,et al.  The genomes of four tapeworm species reveal adaptations to parasitism , 2013, Nature.

[38]  E. Hovig,et al.  Substantial Loss of Conserved and Gain of Novel MicroRNA Families in Flatworms , 2013, Molecular biology and evolution.

[39]  Stefan L Ameres,et al.  Diversifying microRNA sequence and function , 2013, Nature Reviews Molecular Cell Biology.

[40]  L. Hood,et al.  A Review of Computational Tools in microRNA Discovery , 2013, Front. Genet..

[41]  F. Wang,et al.  Comparative analysis of known miRNAs across platyhelminths , 2013, The FEBS journal.

[42]  R. Ji,et al.  Improved and Promising Identification of Human MicroRNAs by Incorporating a High-Quality Negative Set , 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[43]  Caner Bagci,et al.  Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene Expression , 2014, Genom. Proteom. Bioinform..

[44]  Jiuyong Li,et al.  Identifying miRNAs, targets and functions , 2012, Briefings Bioinform..

[45]  Li Zhao,et al.  Genome-wide sequencing of small RNAs reveals a tissue-specific loss of conserved microRNA families in Echinococcus granulosus , 2014, BMC Genomics.

[46]  miR-281, an abundant midgut-specific miRNA of the vector mosquito Aedes albopictus enhances dengue virus replication , 2014, Parasites & Vectors.

[47]  L. Kamenetzky,et al.  microRNA profiling in the zoonotic parasite Echinococcus canadensis using a high-throughput approach , 2015, Parasites & Vectors.

[48]  Georgina Stegmayer,et al.  miRNAfe: A comprehensive tool for feature extraction in microRNA prediction , 2015, Biosyst..

[49]  K. Brehm,et al.  High-throughput characterization of Echinococcus spp. metacestode miRNomes. , 2015, International journal for parasitology.