RNA editing in plants: A comprehensive survey of bioinformatics tools and databases
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Benjamini, 2001, Controlling the false discovery rate in behavior genetics research, Behav. Brain Res., 125, 279, 10.1016/S0166-4328(01)00297-2
Blanchette, 2004, Aligning multiple genomic sequences with the threaded blockset aligner, Genome Res., 14, 708, 10.1101/gr.1933104
Breiman, 2001, Random forests, Mach. Learn., 45, 5, 10.1023/A:1010933404324
Castandet, 2016, ChloroSeq, an optimized chloroplast RNA-seq bioinformatic pipeline, reveals remodeling of the organellar transcriptome under heat stress, G3 (Bethesda), 6, 2817, 10.1534/g3.116.030783
Chateigner-Boutin, 2008, CLB19, a pentatricopeptide repeat protein required for editing of rpoA and clpP chloroplast transcripts, Plant J., 56, 590, 10.1111/j.1365-313X.2008.03634.x
Cheng, 2016, Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants, Plant J., 85, 532, 10.1111/tpj.13121
Cui, 2006, ChloroplastDB: the chloroplast genome database, Nucleic Acids Res., 34, D692, 10.1093/nar/gkj055
Cummings, 2004, Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA, BMC Bioinf., 5, 132, 10.1186/1471-2105-5-132
Du, 2008, Prediction of C-to-U RNA editing sites in plant mitochondria using both biochemical and evolutionary information, J. Theor. Biol., 253, 579, 10.1016/j.jtbi.2008.04.006
Du, 2007, Prediction of C-to-U RNA editing sites in higher plant mitochondria using only nucleotide sequence features, Biochem. Biophys. Res. Commun., 358, 336, 10.1016/j.bbrc.2007.04.130
Du, 2009, CURE-Chloroplast: a chloroplast C-to-U RNA editing predictor for seed plants, BMC Bioinf., 10, 135, 10.1186/1471-2105-10-135
Edera, 2018, Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria, Plant Mol. Biol., 97, 215, 10.1007/s11103-018-0734-9
He, 2007, dbRES: a web-oriented database for annotated RNA editing sites, Nucleic Acids Res., 35, D141, 10.1093/nar/gkl815
Ichinose, 2016, RNA editing and its molecular mechanism in plant organelles, Genes, 8, 10.3390/genes8010005
Kim, 2013, TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions, Genome Biol., 14, R36, 10.1186/gb-2013-14-4-r36
Kim, 2015, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, 12, 357, 10.1038/nmeth.3317
Kingsford, 2008, What are decision trees?, Nat. Biotechnol., 26, 1011, 10.1038/nbt0908-1011
Kiran, 2010, DARNED: a DAtabase of RNa EDiting in humans, Bioinformatics, 26, 1772, 10.1093/bioinformatics/btq285
Knie, 2016, Reverse U-to-C editing exceeds C-to-U RNA editing in some ferns - a monilophyte-wide comparison of chloroplast and mitochondrial RNA editing suggests independent evolution of the two processes in both organelles, BMC Evol. Biol., 16, 134, 10.1186/s12862-016-0707-z
Langmead, B. and S.L. Salzberg, Fast gapped-read alignment with Bowtie 2. Nat. Methods. 9(4): p. 357-359.
Larkin, 2007, Clustal W and clustal X version 2.0, Bioinformatics, 23, 2947, 10.1093/bioinformatics/btm404
Lenz, 2018, Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0, BMC Bioinf., 19, 255, 10.1186/s12859-018-2244-9
Li, 2019, Plant editosome database: a curated database of RNA editosome in plants, Nucleic Acids Res., 47, D170, 10.1093/nar/gky1026
Licht, 2016, Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications, J. Cell Biol., 213, 15, 10.1083/jcb.201511041
Lo Giudice, 2018, REDIdb 3.0: a comprehensive collection of RNA editing events in plant organellar genomes, Front. Plant Sci., 9, 482, 10.3389/fpls.2018.00482
McKenna, 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297, 10.1101/gr.107524.110
Mitchell, 1998, 209
Mower, 2009, The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments, Nucleic Acids Res., 37, W253, 10.1093/nar/gkp337
O'Brien, 2003, GOBASE--a database of mitochondrial and chloroplast information, Nucleic Acids Res., 31, 176, 10.1093/nar/gkg090
Okuda, 2007, Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing, Proc. Natl. Acad. Sci. U. S. A., 104, 8178, 10.1073/pnas.0700865104
Phreaner, 1996, Incomplete editing of rps12 transcripts results in the synthesis of polymorphic polypeptides in plant mitochondria, Plant Cell, 8, 107
Picardi, 2013, REDItools: high-throughput RNA editing detection made easy, Bioinformatics, 29, 1813, 10.1093/bioinformatics/btt287
Picardi, 2010, Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing, Nucleic Acids Res., 38, 4755, 10.1093/nar/gkq202
Picardi, 2012, A Novel Computational Strategy to Identify A-to-I RNA Editing Sites by RNA-Seq Data: de Novo Detection in Human Spinal Cord Tissue, PLoS One, 7, 10.1371/journal.pone.0044184
Picardi, 2014, Uncovering RNA editing sites in long non-coding RNAs, Front Bioeng Biotechnol, 2, 64, 10.3389/fbioe.2014.00064
Ramaswami, 2014, RADAR: a rigorously annotated database of A-to-I RNA editing, Nucleic Acids Res., 42, D109, 10.1093/nar/gkt996
Rudinger, 2009, RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal, Mol. Genet. Genom., 281, 473, 10.1007/s00438-009-0424-z
Samuel, 1959, Some studies in machine learning using the game of checkers, IBM J. Res. Dev., 3, 210, 10.1147/rd.33.0210
Small, 2000, The PPR motif - a TPR-related motif prevalent in plant organellar proteins, Trends Biochem. Sci., 25, 46, 10.1016/S0968-0004(99)01520-0
Sosso, 2012, PPR2263, a DYW-Subgroup Pentatricopeptide repeat protein, is required for mitochondrial nad5 and cob transcript editing, mitochondrion biogenesis, and maize growth, Plant Cell, 24, 676, 10.1105/tpc.111.091074
Sun, 2016, The unexpected diversity of plant organelle RNA editosomes, Trends Plant Sci., 21, 962, 10.1016/j.tplants.2016.07.005
Sun, 2016, RED: a java-MySQL software for identifying and visualizing RNA editing sites using rule-based and statistical filters, PLoS One, 11, e0150465, 10.1371/journal.pone.0150465
Takenaka, 2013, RNA editing in plants and its evolution, Annu. Rev. Genet., 47, 335, 10.1146/annurev-genet-111212-133519
Takenaka, 2019, RNA editing mutants as surrogates for mitochondrial SNP mutants, Plant Physiol. Biochem., 135, 310, 10.1016/j.plaphy.2018.12.014
Tang, 2010, The mitochondrial PPR protein LOVASTATIN INSENSITIVE 1 plays regulatory roles in cytosolic and plastidial isoprenoid biosynthesis through RNA editing, Plant J., 61, 456, 10.1111/j.1365-313X.2009.04082.x
Thompson, 2006, Genetic algorithm learning as a robust approach to RNA editing site prediction, BMC Bioinf., 7, 145, 10.1186/1471-2105-7-145
Tillich, 2006, The evolution of chloroplast RNA editing, Mol. Biol. Evol., 1912, 10.1093/molbev/msl054
Vapnik, 1995, 188
Wang, 2016, RES-Scanner: a software package for genome-wide identification of RNA-editing sites, GigaScience, 5, 37, 10.1186/s13742-016-0143-4
Wu, 2016, GMAP and GSNAP for genomic sequence alignment: enhancements to speed, accuracy, and functionality, Methods Mol. Biol., 1418, 283, 10.1007/978-1-4939-3578-9_15
Wu, 2018, REDO: RNA editing detection in plant organelles based on variant calling results, J. Comput. Biol., 25, 509, 10.1089/cmb.2017.0214
Xiong, 2017, RNA editing responses to oxidative stress between a wild abortive type male-sterile line and its maintainer line, Front. Plant Sci., 8, 2023, 10.3389/fpls.2017.02023
Yuan, 2012, Functional disruption of the pentatricopeptide protein SLG1 affects mitochondrial RNA editing, plant development, and responses to abiotic stresses in Arabidopsis, Plant J., 70, 432, 10.1111/j.1365-313X.2011.04883.x
Yura, 2009, RESOPS: a database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures, Plant Cell Physiol., 50, 1865, 10.1093/pcp/pcp132