Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis (Q26782685)

Computational and Structural Biotechnology Journal

Constance Ciaudo

series ordinal

2

0 references

language of work or name

English

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publication date

2015

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published in

1 reference

describes a project that uses

Crossref

volume

13

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page(s)

469-77

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Cytoscape

Cytoscape

2 references

Europe PubMed Central

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

edgeR

edgeR

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CZ Software Mentions: A large dataset of software mentions in the biomedical literature

DESeq2

DESeq

DESeq2

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

DESeq2

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28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Model-based method for transcription factor target identification with limited data.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation).

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Comprehensive analysis of microRNA-mRNA co-expression in circadian rhythm

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Clustering time-series gene expression data using smoothing spline derivatives.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Clustering short time series gene expression data

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Clustering of time-course gene expression data using a mixed-effects model with B-splines

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Normalization and noise reduction for single cell RNA-seq experiments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Comparison of software packages for detecting differential expression in RNA-seq studies

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Good laboratory practice for clinical next-generation sequencing informatics pipelines.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Detecting time periods of differential gene expression using Gaussian processes: an application to endothelial cells exposed to radiotherapy dose fraction.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Next generation sequencing technology: Advances and applications.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

TimeClust: a clustering tool for gene expression time series.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

The External RNA Controls Consortium: a progress report.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4564389

Temporal aggregation bias and inference of causal regulatory networks

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26430493

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A tiling resolution DNA microarray with complete coverage of the human genome

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26430493

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.CSBJ.2015.08.004

1 reference

1117436

1117436

1 reference

1 reference

1 reference