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Modeling non-uniformity in short-read rates in RNA-Seq data.
Genome Biol. 2010;11(5):R50. doi: 10.1186/gb-2010-11-5-r50. Epub 2010 May 11.
2
Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.
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3
Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation.
Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):19867-72. doi: 10.1073/pnas.1113972108. Epub 2011 Dec 1.
4
Towards reliable isoform quantification using RNA-SEQ data.
BMC Bioinformatics. 2010 Apr 29;11 Suppl 3(Suppl 3):S6. doi: 10.1186/1471-2105-11-S3-S6.
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WemIQ: an accurate and robust isoform quantification method for RNA-seq data.
Bioinformatics. 2015 Mar 15;31(6):878-85. doi: 10.1093/bioinformatics/btu757. Epub 2014 Nov 17.
6
Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq.
Bioinformatics. 2011 Feb 15;27(4):502-8. doi: 10.1093/bioinformatics/btq696. Epub 2010 Dec 17.
7
Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq.
J Bioinform Comput Biol. 2010 Dec;8 Suppl 1:177-92. doi: 10.1142/s0219720010005178.
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PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution.
Nucleic Acids Res. 2014 Feb;42(3):e20. doi: 10.1093/nar/gkt1304. Epub 2013 Dec 20.
10
A two-parameter generalized Poisson model to improve the analysis of RNA-seq data.
Nucleic Acids Res. 2010 Sep;38(17):e170. doi: 10.1093/nar/gkq670. Epub 2010 Jul 29.

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A duplex sequencing approach for high-sensitivity detection of genome-edited plants.
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Sources of non-uniform coverage in short-read RNA-Seq data.
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Artifacts and biases of the reverse transcription reaction in RNA sequencing.
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Nanopore microscope identifies RNA isoforms with structural colours.
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Polee: RNA-Seq analysis using approximate likelihood.
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8
Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing.
BMC Genomics. 2021 Jan 21;22(1):69. doi: 10.1186/s12864-021-07381-z.
9
AIDE: annotation-assisted isoform discovery with high precision.
Genome Res. 2019 Dec;29(12):2056-2072. doi: 10.1101/gr.251108.119. Epub 2019 Nov 6.
10
Modelling RNA-Seq data with a zero-inflated mixture Poisson linear model.
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本文引用的文献

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Biases in Illumina transcriptome sequencing caused by random hexamer priming.
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Statistical inferences for isoform expression in RNA-Seq.
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RNA-Seq: a revolutionary tool for transcriptomics.
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Cross-hybridization modeling on Affymetrix exon arrays.
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Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.
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An integrated software system for analyzing ChIP-chip and ChIP-seq data.
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Alternative isoform regulation in human tissue transcriptomes.
Nature. 2008 Nov 27;456(7221):470-6. doi: 10.1038/nature07509.
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Probe signal correction for differential methylation hybridization experiments.
BMC Bioinformatics. 2008 Oct 23;9:453. doi: 10.1186/1471-2105-9-453.
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Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications.
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SeqMap: mapping massive amount of oligonucleotides to the genome.
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