Statistical and Computational Methods for High-Throughput Sequencing Data Analysis of Alternative Splicing (Q30668937)

4 November 2017

Statistical and Computational Methods for High-Throughput Sequencing Data Analysis of Alternative Splicing (English)

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alternative mRNA splicing, via spliceosome

4 November 2017

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based on heuristic

inferred from title

high-throughput sequencing

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Liang Chen

1

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4 November 2017

1 May 2013

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Statistics in biosciences

4 November 2017

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4 November 2017

5

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4 November 2017

1

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4 November 2017

138-155

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https://scigraph.springernature.com/pub.10.1007/s12561-012-9064-7

4 November 2017

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cites work

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

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Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

20 June 2018

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Summarizing and correcting the GC content bias in high-throughput sequencing

20 June 2018

1 reference

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Estimation of alternative splicing variability in human populations

20 June 2018

1 reference

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HITS-CLIP: panoramic views of protein-RNA regulation in living cells

20 June 2018

1 reference

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SpliceTrap: a method to quantify alternative splicing under single cellular conditions

20 June 2018

1 reference

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Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

20 June 2018

1 reference

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Bias detection and correction in RNA-Sequencing data

20 June 2018

1 reference

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Improving RNA-Seq expression estimates by correcting for fragment bias

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Analysis and design of RNA sequencing experiments for identifying isoform regulation

20 June 2018

1 reference

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Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads

20 June 2018

1 reference

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De novo assembly and analysis of RNA-seq data.

20 June 2018

1 reference

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MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls

20 June 2018

1 reference

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

TassDB2 - A comprehensive database of subtle alternative splicing events

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Biases in Illumina transcriptome sequencing caused by random hexamer priming

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Detection of splice junctions from paired-end RNA-seq data by SpliceMap.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Understanding mechanisms underlying human gene expression variation with RNA sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Transcriptome genetics using second generation sequencing in a Caucasian population

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Alternative splicing: good and bad effects of translationally silent substitutions.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

RNA-Seq gene expression estimation with read mapping uncertainty

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Fine-scale variation and genetic determinants of alternative splicing across individuals

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

H-DBAS: human-transcriptome database for alternative splicing: update 2010

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

De novo transcriptome assembly with ABySS.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

SOAP2: an improved ultrafast tool for short read alignment

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Fast and accurate short read alignment with Burrows-Wheeler transform

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Transcript length bias in RNA-seq data confounds systems biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

TopHat: discovering splice junctions with RNA-Seq

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Statistical inferences for isoform expression in RNA-Seq

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

A large genome center's improvements to the Illumina sequencing system

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Alternative isoform regulation in human tissue transcriptomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Mapping short DNA sequencing reads and calling variants using mapping quality scores

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Mapping and quantifying mammalian transcriptomes by RNA-Seq

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Splicing in disease: disruption of the splicing code and the decoding machinery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Heritability of alternative splicing in the human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Splicing regulation in neurologic disease

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

HOLLYWOOD: a comparative relational database of alternative splicing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

ASD: a bioinformatics resource on alternative splicing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

SpliceInfo: an information repository for mRNA alternative splicing in human genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

DEDB: a database of Drosophila melanogaster exons in splicing graph form

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

The Alternative Splicing Gallery (ASG): bridging the gap between genome and transcriptome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

CLIP identifies Nova-regulated RNA networks in the brain

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

Analysis of canonical and non-canonical splice sites in mammalian genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3776476

10.1007/S12561-012-9064-7

20 June 2018

Identifiers

DOI

1 reference

PMCID

3776476

Dimensions Publication ID

4 November 2017

0 references

1 reference

4 November 2017

1 reference

PMCID

3776476