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. Methodology Article

    Mapping eQTL by leveraging multiple tissues and DNA methylation

    DNA methylation is an important tissue-specific epigenetic event that influences transcriptional regulation of gene expression. Differentially methylated CpG sites may act as mediators between genetic variatio...

    Chaitanya R. Acharya, Kouros Owzar and Andrew S. Allen

    BMC Bioinformatics 2017 18:455

    Published on: 18 October 2017

  2. Software

    Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data

    Although ultrahigh-throughput RNA-Sequencing has become the dominant technology for genome-wide transcriptional profiling, the vast majority of RNA-Seq studies typically profile only tens of samples, and most ...

    Joseph N. Paulson, Cho-Yi Chen, Camila M. Lopes-Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass and John Quackenbush

    BMC Bioinformatics 2017 18:437

    Published on: 3 October 2017

  3. Software

    SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines

    The evolution of next-generation sequencing (NGS) technologies has led to increased focus on RNA-Seq. Many bioinformatic tools have been developed for RNA-Seq analysis, each with unique performance characteris...

    Jérôme Audoux, Mikaël Salson, Christophe F. Grosset, Sacha Beaumeunier, Jean-Marc Holder, Thérèse Commes and Nicolas Philippe

    BMC Bioinformatics 2017 18:428

    Published on: 29 September 2017

  4. Software

    mmquant: how to count multi-mapping reads?

    RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previou...

    Matthias Zytnicki

    BMC Bioinformatics 2017 18:411

    Published on: 15 September 2017

  5. Software

    BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets

    A group of miRNAs can regulate a biological process by targeting genes involved in the process. The unbiased miRNA functional enrichment analysis is the most precise in silico approach to predict the biological p...

    Konstantinos Zagganas, Thanasis Vergoulis, Maria D. Paraskevopoulou, Ioannis S. Vlachos, Spiros Skiadopoulos and Theodore Dalamagas

    BMC Bioinformatics 2017 18:399

    Published on: 6 September 2017

  6. Software

    ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data

    Given the development of high-throughput experimental techniques, an increasing number of whole genome transcription profiling time series data sets, with good temporal resolution, are becoming available to re...

    Giorgos Minas, Hiroshi Momiji, Dafyd J. Jenkins, Maria J. Costa, David A. Rand and Bärbel Finkenstädt

    BMC Bioinformatics 2017 18:316

    Published on: 26 June 2017

  7. Methodology Article

    A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays

    Alternative gene splicing is a common phenomenon in which a single gene gives rise to multiple transcript isoforms. The process is strictly guided and involves a multitude of proteins and regulatory complexes....

    Marijke Van Moerbeke, Adetayo Kasim, Willem Talloen, Joke Reumers, Hinrick W. H. Göhlmann and Ziv Shkedy

    BMC Bioinformatics 2017 18:273

    Published on: 25 May 2017

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