Blar i University of Bergen Library på tidsskrift "BMC Bioinformatics"

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    • Detecting diferentially methylated regions using a fast wavelet‑based approach to functional association analysis 

      Denault, William Robert Paul; Jugessur, Astanand (Journal article; Peer reviewed, 2021)
      Background We present here a computational shortcut to improve a powerful wavelet-based method by Shim and Stephens (Ann Appl Stat 9(2):665–686, 2015. https://doi.org/10.1214/14-AOAS776) called WaveQTL that was originally ...

    • A Graph Feature Auto-Encoder for the Prediction of Unobserved Node Features on Biological Networks 

      Hasibi, Ramin; Michoel, Tom (Journal article; Peer reviewed, 2021)
      Background Molecular interaction networks summarize complex biological processes as graphs, whose structure is informative of biological function at multiple scales. Simultaneously, omics technologies measure the variation ...

    • MOCCA: a fexible suite for modelling DNA sequence motif occurrence combinatorics 

      Bredesen, Bjørn André; Rehmsmeier, Marc (Journal article; Peer reviewed, 2021)
      Background Cis-regulatory elements (CREs) are DNA sequence segments that regulate gene expression. Among CREs are promoters, enhancers, Boundary Elements (BEs) and Polycomb Response Elements (PREs), all of which are ...

    • ORFik: a comprehensive R toolkit for the analysis of translation 

      Tjeldnes, Håkon; Labun, Kornel; Torres Cleuren, Yamila Nicole; Chyzynska, Katarzyna; Swirski, Michal; Valen, Eivind Dale (Journal article; Peer reviewed, 2021)
      Background With the rapid growth in the use of high-throughput methods for characterizing translation and the continued expansion of multi-omics, there is a need for back-end functions and streamlined tools for processing, ...

    • RASflow: an RNA-Seq analysis workflow with Snakemake 

      Zhang, Xiaokang; Jonassen, Inge (Journal article; Peer reviewed, 2020)
      Background With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq ...

    • Wavelet Screening: a novel approach to analyzing GWAS data 

      Denault, William Robert Paul; Gjessing, Håkon K.; Juodakis, Julius; Jacobsson, Bo; Jugessur, Astanand (Journal article; Peer reviewed, 2021)
      Background Traditional methods for single-variant genome-wide association study (GWAS) incur a substantial multiple-testing burden because of the need to test for associations with a vast number of single-nucleotide ...