MicroRNAs in the oriental fruit fly, Bactrocera dorsalis: extending Drosophilid miRNA conservation to the Tephritidae

[1]  Robert D. Finn,et al.  Rfam 12.0: updates to the RNA families database , 2014, Nucleic Acids Res..

[2]  S. Hou,et al.  Characterizing the developmental transcriptome of the oriental fruit fly, Bactrocera dorsalis (Diptera: Tephritidae) through comparative genomic analysis with Drosophila melanogaster utilizing modENCODE datasets , 2014, BMC Genomics.

[3]  Krzysztof Fujarewicz,et al.  Analysis options for high-throughput sequencing in miRNA expression profiling , 2014, BMC Research Notes.

[4]  S. Griffiths-Jones,et al.  Fast-evolving microRNAs are highly expressed in the early embryo of Drosophila virilis , 2014, RNA.

[5]  F. Stokvis,et al.  Half of the European fruit fly species barcoded (Diptera, Tephritidae); a feasibility test for molecular identification , 2013, ZooKeys.

[6]  Ana Kozomara,et al.  miRBase: annotating high confidence microRNAs using deep sequencing data , 2013, Nucleic Acids Res..

[7]  F. Jankovics,et al.  Viability, Longevity, and Egg Production of Drosophila melanogaster Are Regulated by the miR-282 microRNA , 2013, Genetics.

[8]  Sean R. Eddy,et al.  Infernal 1.1: 100-fold faster RNA homology searches , 2013, Bioinform..

[9]  R. Bhatnagar,et al.  Development associated profiling of chitinase and microRNA of Helicoverpa armigera identified chitinase repressive microRNA , 2013, Scientific Reports.

[10]  S. Asgari,et al.  An insect trypsin-like serine protease as a target of microRNA: utilization of microRNA mimics and inhibitors by oral feeding. , 2013, Insect biochemistry and molecular biology.

[11]  J. Dubnau,et al.  MicroRNA-276a Functions in Ellipsoid Body and Mushroom Body Neurons for Naive and Conditioned Olfactory Avoidance in Drosophila , 2013, The Journal of Neuroscience.

[12]  K. Peterson,et al.  Do miRNAs have a deep evolutionary history? , 2012, BioEssays : news and reviews in molecular, cellular and developmental biology.

[13]  Davis J. McCarthy,et al.  Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.

[14]  Sebastian D. Mackowiak,et al.  Identification of Novel and Known miRNAs in Deep‐Sequencing Data with miRDeep2 , 2011, Current protocols in bioinformatics.

[15]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

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

[17]  E. Lai,et al.  Vive la différence: biogenesis and evolution of microRNAs in plants and animals , 2011, Genome Biology.

[18]  Ammar S Naqvi,et al.  Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. , 2011, Genome research.

[19]  Selene L. Fernandez-Valverde,et al.  Dynamic isomiR regulation in Drosophila development. , 2010, RNA.

[20]  Wolfgang Huber,et al.  Genome-wide analysis of mRNA decay patterns during early Drosophila development , 2010, Genome Biology.

[21]  Anjali J. Koppal,et al.  Supplementary data: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites , 2010 .

[22]  S. Griffiths-Jones,et al.  miRBase: microRNA Sequences and Annotation , 2010, Current protocols in bioinformatics.

[23]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[24]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[25]  V. Kim,et al.  Biogenesis of small RNAs in animals , 2009, Nature Reviews Molecular Cell Biology.

[26]  P. Zamore,et al.  Small silencing RNAs: an expanding universe , 2009, Nature Reviews Genetics.

[27]  V. Ambros,et al.  Drosophila let-7 microRNA is required for remodeling of the neuromusculature during metamorphosis. , 2008, Genes & development.

[28]  S. Cohen,et al.  Temporal Reciprocity of miRNAs and Their Targets during the Maternal-to-Zygotic Transition in Drosophila , 2008, Current Biology.

[29]  Manolis Kellis,et al.  Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. , 2007, Genome research.

[30]  Manolis Kellis,et al.  Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. , 2007, Genome research.

[31]  M. Robinson,et al.  Small-sample estimation of negative binomial dispersion, with applications to SAGE data. , 2007, Biostatistics.

[32]  R. Vargas,et al.  Wheat Germ Oil and Its Effects on a Liquid Larval Rearing Diet for Oriental Fruit Flies (Diptera: Tephritidae) , 2007, Journal of economic entomology.

[33]  Peter F. Stadler,et al.  Memory Efficient Folding Algorithms for Circular RNA Secondary Structures , 2006, German Conference on Bioinformatics.

[34]  M. Levine,et al.  Spatial regulation of microRNA gene expression in the Drosophila embryo. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

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

[36]  D. Marks,et al.  The small RNA profile during Drosophila melanogaster development. , 2003, Developmental cell.

[37]  V. Ambros,et al.  Temporal regulation of microRNA expression in Drosophila melanogaster mediated by hormonal signals and broad-Complex gene activity. , 2003, Developmental biology.

[38]  G. Rubin,et al.  Computational identification of Drosophila microRNA genes , 2003, Genome Biology.

[39]  G. Ruvkun,et al.  A uniform system for microRNA annotation. , 2003, RNA.

[40]  W. Pearson,et al.  Current Protocols in Bioinformatics , 2002 .

[41]  V. Ambros,et al.  The expression of the let-7 small regulatory RNA is controlled by ecdysone during metamorphosis in Drosophila melanogaster. , 2002, Developmental biology.

[42]  B. Reinhart,et al.  Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA , 2000, Nature.

[43]  Simon Conway Morris,et al.  The shape of life, genes, development, and the evolution of animal form , 1996 .

[44]  S. Gould.  The Shape of Life , 1996 .

[45]  S. Saul,et al.  Translocation-based genetic sexing system for the oriental fruit fly (Diptera: Tephritidae) based on pupal color dimorphism , 1995 .

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

[47]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[48]  Timothy R Hughes,et al.  SMAUG is a major regulator of maternal mRNA destabilization in Drosophila and its translation is activated by the PAN GU kinase. , 2007, Developmental cell.

[49]  S. Cohen,et al.  microRNA functions. , 2007, Annual review of cell and developmental biology.

[50]  A. Clarke,et al.  Invasive phytophagous pests arising through a recent tropical evolutionary radiation: the Bactrocera dorsalis complex of fruit flies. , 2005, Annual review of entomology.

[51]  Sam Griffiths-Jones,et al.  The microRNA Registry , 2004, Nucleic Acids Res..