MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data (Q34135283)

31 July 2017

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data (English)

1 reference

alternative mRNA splicing, via spliceosome

31 July 2017

0 references

1 reference

1 reference

Zhi-xiang Lu

5

0 references

Jian Huang

object named as

Jian Huang

3

0 references

author name string

Shihao Shen

1

1 reference

31 July 2017

Juw Won Park

2

1 reference

31 July 2017

Kimberly A Dittmar

4

1 reference

31 July 2017

Qing Zhou

6

1 reference

31 July 2017

Russ P Carstens

7

1 reference

31 July 2017

Yi Xing

8

1 reference

31 July 2017

language of work or name

English

0 references

publication date

20 January 2012

1 reference

31 July 2017

Nucleic Acids Research

1 reference

31 July 2017

40

1 reference

31 July 2017

8

1 reference

31 July 2017

e61

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

31 July 2017

start time

7 November 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Functional consequences of developmentally regulated alternative splicing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Sequencing technology does not eliminate biological variability

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Degrade, move, regroup: signaling control of splicing proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Improving RNA-Seq expression estimates by correcting for fragment bias

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Detection and removal of biases in the analysis of next-generation sequencing reads

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Widespread establishment and regulatory impact of Alu exons in human genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Context-dependent robustness to 5' splice site polymorphisms in human populations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Analysis and design of RNA sequencing experiments for identifying isoform regulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Conservation of an RNA regulatory map between Drosophila and mammals

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Alternative expression analysis by RNA sequencing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

An ESRP-regulated splicing programme is abrogated during the epithelial-mesenchymal transition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

rQuant.web: a tool for RNA-Seq-based transcript quantitation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Modeling non-uniformity in short-read rates in RNA-Seq data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Biases in Illumina transcriptome sequencing caused by random hexamer priming

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Alternative splicing and evolution: diversification, exon definition and function

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Regulation of alternative splicing by histone modifications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

RNA-Seq: a revolutionary tool for transcriptomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Alternative isoform regulation in human tissue transcriptomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Splicing regulation: from a parts list of regulatory elements to an integrated splicing code

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

SCNM1, a putative RNA splicing factor that modifies disease severity in mice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Tau gene mutations: dissecting the pathogenesis of FTDP-17.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Genome-wide detection of tissue-specific alternative splicing in the human transcriptome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

A genomic view of alternative splicing

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Alternative splicing: increasing diversity in the proteomic world

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss

5 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1291

Algorithm 778: L-BFGS-B: Fortran subroutines for large-scale bound-constrained optimization

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1291

A Limited Memory Algorithm for Bound Constrained Optimization

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1291

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR1291

Computational analysis and experimental validation of tumor-associated alternative RNA splicing in human cancer.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3333886

28 October 2018

Identifiers

DOI

10.1093/NAR/GKR1291

1 reference

31 July 2017

1 reference

31 July 2017

1 reference