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  1. Article

    Open Access

    CAMPAREE: a robust and configurable RNA expression simulator

    The accurate interpretation of RNA-Seq data presents a moving target as scientists continue to introduce new experimental techniques and analysis algorithms. Simulated datasets are an invaluable tool to accura...

    Nicholas F. Lahens, Thomas G. Brooks, Dimitra Sarantopoulou in BMC Genomics (2021)

  2. Article

    Open Access

    Comparative evaluation of full-length isoform quantification from RNA-Seq

    Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA...

    Dimitra Sarantopoulou, Thomas G. Brooks, Soumyashant Nayak in BMC Bioinformatics (2021)

  3. Article

    Open Access

    A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression

    Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability of Ion Torrent has left scientists wondering which platform is most effective for differential gene expression (DGE) analy...

    Nicholas F. Lahens, Emanuela Ricciotti, Olga Smirnova, Erik Toorens in BMC Genomics (2017)

  4. Article

    Open Access

    IVT-seq reveals extreme bias in RNA sequencing

    RNA-seq is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the proliferation of library construction meth...

    Nicholas F Lahens, Ibrahim Halil Kavakli, Ray Zhang, Katharina Hayer in Genome Biology (2014)