Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems (Q34740039)

4 August 2017

title

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems (English)

1 reference

alternative mRNA splicing, via spliceosome

4 August 2017

1 reference

1 reference

1 reference

Julie A Dickerson

3

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Ann E. Loraine

series ordinal

2

1 reference

4 August 2017

Ruolin Liu

1

1 reference

4 August 2017

publication date

16 December 2014

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4 August 2017

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4 August 2017

volume

15

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4 August 2017

page(s)

364

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Creative Commons Attribution 4.0 International

4 August 2017

copyright license

start time

1 December 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

1 reference

Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Methods to study splicing from high-throughput RNA sequencing data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Assessment of transcript reconstruction methods for RNA-seq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Accurate detection of differential RNA processing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

SplicingCompass: differential splicing detection using RNA-seq data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Modelling and simulating generic RNA-Seq experiments with the flux simulator

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Alternative splicing in plants--coming of age.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Detecting differential usage of exons from RNA-seq data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Intron-mediated alternative splicing of Arabidopsis P5CS1 and its association with natural variation in proline and climate adaptation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Localization and dynamics of nuclear speckles in plants.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

FDM: a graph-based statistical method to detect differential transcription using RNA-seq data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

The developmental transcriptome of Drosophila melanogaster

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Analysis and design of RNA sequencing experiments for identifying isoform regulation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Conservation of an RNA regulatory map between Drosophila and mammals

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Alternative splicing and evolution: diversification, exon definition and function

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Fast and SNP-tolerant detection of complex variants and splicing in short reads

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Statistical inferences for isoform expression in RNA-Seq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Alternative splicing of pre-messenger RNAs in plants in the genomic era.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Genomewide comparative analysis of alternative splicing in plants

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

The evolving roles of alternative splicing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

RIKEN Arabidopsis full-length (RAFL) cDNA and its applications for expression profiling under abiotic stress conditions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Mechanisms of alternative pre-messenger RNA splicing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271460

Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants.

7 July 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12859-014-0364-4

Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12859-014-0364-4

Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12859-014-0364-4

Temperature-dependent regulation of flowering by antagonistic FLM variants.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12859-014-0364-4

Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25511303

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Stress-induced alternative splicing provides a mechanism for the regulation of microRNA processing in Arabidopsis thaliana

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25511303

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifying differentially spliced genes from two groups of RNA-seq samples

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25511303

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S12859-014-0364-4

1 reference

4 August 2017

DBLP publication ID

journals/bmcbi/LiuLD14

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

4 August 2017

1 reference