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1
RASER: reads aligner for SNPs and editing sites of RNA.
Bioinformatics. 2015 Dec 15;31(24):3906-13. doi: 10.1093/bioinformatics/btv505. Epub 2015 Aug 30.
2
ASElux: an ultra-fast and accurate allelic reads counter.
Bioinformatics. 2018 Apr 15;34(8):1313-1320. doi: 10.1093/bioinformatics/btx762.
3
RNASequel: accurate and repeat tolerant realignment of RNA-seq reads.
Nucleic Acids Res. 2015 Oct 15;43(18):e122. doi: 10.1093/nar/gkv594. Epub 2015 Jun 16.
4
AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.
PLoS Comput Biol. 2016 Oct 5;12(10):e1005096. doi: 10.1371/journal.pcbi.1005096. eCollection 2016 Oct.
5
Fast and SNP-aware short read alignment with SALT.
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6
STAR: ultrafast universal RNA-seq aligner.
Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.
7
RES-Scanner: a software package for genome-wide identification of RNA-editing sites.
Gigascience. 2016 Aug 18;5(1):37. doi: 10.1186/s13742-016-0143-4.
8
iMapSplice: Alleviating reference bias through personalized RNA-seq alignment.
PLoS One. 2018 Aug 10;13(8):e0201554. doi: 10.1371/journal.pone.0201554. eCollection 2018.
9
OSA: a fast and accurate alignment tool for RNA-Seq.
Bioinformatics. 2012 Jul 15;28(14):1933-4. doi: 10.1093/bioinformatics/bts294. Epub 2012 May 15.
10
Using RNA-Seq to Discover Genetic Polymorphisms That Produce Hidden Splice Variants.
Methods Mol Biol. 2017;1648:129-142. doi: 10.1007/978-1-4939-7204-3_10.

引用本文的文献

1
ncRNA Editing: Functional Characterization and Computational Resources.
Methods Mol Biol. 2025;2883:455-495. doi: 10.1007/978-1-0716-4290-0_20.
4
A-to-I RNA Editing in Cancer: From Evaluating the Editing Level to Exploring the Editing Effects.
Front Oncol. 2021 Feb 11;10:632187. doi: 10.3389/fonc.2020.632187. eCollection 2020.
5
EndoVIPER-seq for Improved Detection of A-to-I Editing Sites in Cellular RNA.
Curr Protoc Chem Biol. 2020 Jun;12(2):e82. doi: 10.1002/cpch.82.
6
Selective Enrichment of A-to-I Edited Transcripts from Cellular RNA Using Endonuclease V.
J Am Chem Soc. 2020 Mar 18;142(11):5241-5251. doi: 10.1021/jacs.9b13406. Epub 2020 Mar 5.
7
Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins.
High Throughput. 2019 Nov 29;8(4):19. doi: 10.3390/ht8040019.
8
Regulation of RNA editing by RNA-binding proteins in human cells.
Commun Biol. 2019 Jan 14;2:19. doi: 10.1038/s42003-018-0271-8. eCollection 2019.
9
Widespread RNA editing dysregulation in brains from autistic individuals.
Nat Neurosci. 2019 Jan;22(1):25-36. doi: 10.1038/s41593-018-0287-x. Epub 2018 Dec 17.
10
Single-nucleotide variants in human RNA: RNA editing and beyond.
Brief Funct Genomics. 2019 Feb 14;18(1):30-39. doi: 10.1093/bfgp/ely032.

本文引用的文献

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Genome sequence-independent identification of RNA editing sites.
Nat Methods. 2015 Apr;12(4):347-50. doi: 10.1038/nmeth.3314. Epub 2015 Mar 2.
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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18.
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Systematic evaluation of spliced alignment programs for RNA-seq data.
Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3.
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RADAR: a rigorously annotated database of A-to-I RNA editing.
Nucleic Acids Res. 2014 Jan;42(Database issue):D109-13. doi: 10.1093/nar/gkt996. Epub 2013 Oct 25.
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GIIRA--RNA-Seq driven gene finding incorporating ambiguous reads.
Bioinformatics. 2014 Mar 1;30(5):606-13. doi: 10.1093/bioinformatics/btt577. Epub 2013 Oct 11.
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Whole transcriptome RNA-Seq allelic expression in human brain.
BMC Genomics. 2013 Aug 22;14:571. doi: 10.1186/1471-2164-14-571.
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Identifying RNA editing sites using RNA sequencing data alone.
Nat Methods. 2013 Feb;10(2):128-32. doi: 10.1038/nmeth.2330. Epub 2013 Jan 6.
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STAR: ultrafast universal RNA-seq aligner.
Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635. Epub 2012 Oct 25.

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