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Transcriptome analysis

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

Learning smoothing models of copy number profiles using breakpoint annotations

Toby Dylan Hocking, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Valentina Boeva, Julie Cappo, Olivier Delattre, Francis Bach, Jean-Philippe Vert BMC Bioinformatics 2013, 14:164 (22 May 2013)

Abstract | Provisional PDF

2.

Methodology article   Open Access Highly Accessed

Iterative rank-order normalization of gene expression microarray data

Eric A Welsh, Steven A Eschrich, Anders E Berglund, David A Fenstermacher BMC Bioinformatics 2013, 14:153 (7 May 2013)

Abstract | Full text | PDF | ePUB | PubMed

3.

Software   Open Access

A metadata-aware application for remote scoring and exchange of tissue microarray images

Lorna Morris, Andrew Tsui, Charles Crichton, Steve Harris, Peter H Maccallum, William J Howat, Jim Davies, James D Brenton, Carlos Caldas BMC Bioinformatics 2013, 14:147 (1 May 2013)

Abstract | Full text | PDF | PubMed

4.

Research article   Open Access Highly Accessed

Empirical Bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution

Thomas J Hardcastle, Krystyna A Kelly BMC Bioinformatics 2013, 14:135 (23 April 2013)

Abstract | Full text | PDF | PubMed

5.

Methodology article   Open Access Highly Accessed

How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis

Robert Lehmann, Rainer Machné, Jens Georg, Manuela Benary, Ilka Axmann, Ralf Steuer BMC Bioinformatics 2013, 14:133 (21 April 2013)

Abstract | Provisional PDF | PubMed

6.

Research article   Open Access Highly Accessed

The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis

Xing Qiu, Hulin Wu, Rui Hu BMC Bioinformatics 2013, 14:124 (11 April 2013)

Abstract | Full text | PDF | PubMed

7.

Methodology article   Open Access Highly Accessed

Differential expression analysis for paired RNA-seq data

Lisa M Chung, John P Ferguson, Wei Zheng, Feng Qian, Vincent Bruno, Ruth R Montgomery, Hongyu Zhao BMC Bioinformatics 2013, 14:110 (27 March 2013)

Abstract | Provisional PDF | PubMed

8.

Methodology article   Open Access Highly Accessed

LASAGNA: A novel algorithm for transcription factor binding site alignment

Chih Lee, Chun-Hsi Huang BMC Bioinformatics 2013, 14:108 (24 March 2013)

Abstract | Provisional PDF | PubMed

9.

Research article   Open Access

SMOTE for high-dimensional class-imbalanced data

Rok Blagus, Lara Lusa BMC Bioinformatics 2013, 14:106 (22 March 2013)

Abstract | Full text | PDF | ePUB | PubMed

10.

Methodology article   Open Access Highly Accessed

Adaptive filtering of microarray gene expression data based on Gaussian mixture decomposition

Michal Marczyk, Roman Jaksik, Andrzej Polanski, Joanna Polanska BMC Bioinformatics 2013, 14:101 (20 March 2013)

Abstract | Full text | PDF | ePUB | PubMed

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