Discovering microRNAs and their targets in the red flour beetle Tribolium castaneum from expressed sequence tags

Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389 Berezikov, 2006, Approaches to microRNA discovery, Nat. Genet., 38, 10.1038/ng1794 Conesa, 2005, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 21, 3674, 10.1093/bioinformatics/bti610 Enright, 2003, MicroRNA targets in Drosophila, Genome Biol., 5, 10.1186/gb-2003-5-1-r1 Freitak, 2012, Gender- and stressor-specific microRNA expression in Tribolium castaneum, Biol. Lett., 8, 860, 10.1098/rsbl.2012.0273 Griffiths-Jones, 2003, Rfam: an RNA family database, Nucleic Acids Res., 31, 439, 10.1093/nar/gkg006 Kim, 2005, MicroRNA biogenesis: coordinated cropping and dicing, Nat. Rev. Mol. Cell Biol., 6, 376, 10.1038/nrm1644 Kozomara, 2013, miRBase: annotating high confidence microRNAs using deep sequencing data, Nucleic Acids Res., 42, 10.1093/nar/gkt1181 Krzywinski, 2009, Circos: an information aesthetic for comparative genomics, Genome Res., 19, 1639, 10.1101/gr.092759.109 Lee, 1993, The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14, Cell, 75, 843, 10.1016/0092-8674(93)90529-Y Lewis, 2005, Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets, Cell, 120, 15, 10.1016/j.cell.2004.12.035 Li, 2006, Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences, Bioinformatics, 22, 1658, 10.1093/bioinformatics/btl158 Lynch, 2011, The evolution of dorsal-ventral patterning mechanisms in insects, Genes Dev., 25, 107, 10.1101/gad.2010711 Marco, 2010, Functional shifts in insect microRNA evolution, Genome biology and evolution, 2, 686, 10.1093/gbe/evq053 Moriya, 2007, KAAS: an automatic genome annotation and pathway reconstruction server, Nucleic Acids Res., 35 Ninova, 2016, MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum, Genome Res., 26, 85, 10.1101/gr.193367.115 Patanun, 2013, Computational identification of microRNAs and their targets in cassava (Manihot esculenta Crantz), Mol. Biotechnol., 53, 257, 10.1007/s12033-012-9521-z Richards, 2008, The genome of the model beetle and pest Tribolium castaneum, Nature, 452, 949, 10.1038/nature06784 Singh, 2008, In silico prediction and characterization of microRNAs from red flour beetle (Tribolium castaneum), Insect Mol. Biol., 17, 427, 10.1111/j.1365-2583.2008.00816.x Usha, 2017, Computational identification of MicroRNAs and their targets from finger millet (Eleusine coracana), Interdisciplinary Sciences: Computational Life Sciences, 9, 72 Zhang, 2006, Conservation and divergence of plant microRNA genes, Plant J., 46, 243, 10.1111/j.1365-313X.2006.02697.x Zuker, 2003, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic acid research, 31, 3406, 10.1093/nar/gkg595