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Transcriptome analysis Section edited by Adam Olshen

This section incorporates all aspects of transcriptomic analysis including but not limited to: methods and applications for the analysis of microarray and RNA-seq data.

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1.

Research article   Open Access

Drug repositioning for orphan genetic diseases through Conserved Anticoexpressed Gene Clusters (CAGCs)

Ivan Molineris, Ugo Ala, Paolo Provero, Ferdinando Di Cunto BMC Bioinformatics 2013, 14:288 (2 October 2013)

Abstract | Provisional PDF

2.

Research article   Open Access

Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

Juliane Charlotte Thøgersen, Morten Mørup, Søren Damkiær, Søren Molin, Lars Jelsbak BMC Bioinformatics 2013, 14:279 (23 September 2013)

Abstract | Provisional PDF | PubMed

3.

Software   Open Access Highly Accessed

MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates

Caroline Bérard, Michael Seifert, Tristan Mary-Huard, Marie-Laure Martin-Magniette BMC Bioinformatics 2013, 14:271 (9 September 2013)

Abstract | Full text | PDF | PubMed

4.

Research article   Open Access Highly Accessed

μHEM for identification of differentially expressed miRNAs using hypercuboid equivalence partition matrix

Sushmita Paul, Pradipta Maji BMC Bioinformatics 2013, 14:266 (4 September 2013)

Abstract | Full text | PDF | ePUB | PubMed

5.

Methodology article   Open Access Highly Accessed

Ontology based molecular signatures for immune cell types via gene expression analysis

Terrence F Meehan, Nicole A Vasilevsky, Christopher J Mungall, David S Dougall, Melissa A Haendel, Judith A Blake, Alexander D Diehl BMC Bioinformatics 2013, 14:263 (30 August 2013)

Abstract | Full text | PDF | PubMed

6.

Software   Open Access Highly Accessed

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data

Yingtao Bi, Ramana V Davuluri BMC Bioinformatics 2013, 14:262 (27 August 2013)

Abstract | Full text | PDF | PubMed

7.

Methodology article   Open Access Highly Accessed

A balanced iterative random forest for gene selection from microarray data

Ali Anaissi, Paul J Kennedy, Madhu Goyal, Daniel R Catchpoole BMC Bioinformatics 2013, 14:261 (27 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

8.

Methodology article   Open Access Highly Accessed

Differential expression analysis with global network adjustment

Jonathan A Gelfond, Joseph G Ibrahim, Mayetri Gupta, Ming-Hui Chen, Jannine D Cody BMC Bioinformatics 2013, 14:258 (23 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

9.

Methodology article   Open Access Highly Accessed

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments

Mikel Esnaola, Pedro Puig, David Gonzalez, Robert Castelo, Juan R Gonzalez BMC Bioinformatics 2013, 14:254 (21 August 2013)

Abstract | Full text | PDF | PubMed

10.

Research article   Open Access Highly Accessed

Hierarchical Bayesian modelling of gene expression time series across irregularly sampled replicates and clusters

James Hensman, Neil D Lawrence, Magnus Rattray BMC Bioinformatics 2013, 14:252 (20 August 2013)

Abstract | Full text | PDF | PubMed

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