Studies using refgenie

Here are some studies we have found that make use of refgenie in some way:

  • Dozmorov et al. (2021). Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines
    GigaScience. DOI: /10.1093/gigascience/giab022
  • Leal-Calvo et al. (2021). A new paradigm for leprosy diagnosis based on host gene expression
    bioRxiv. DOI: 10.1101/2021.07.30.454441
  • Rauscher et al. (2021). Patient-derived gene and protein expression signatures of NGLY1 deficiency
    bioRxiv. DOI: 10.1101/2021.07.28.453930
  • Gudukbay et al. (2021). GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping
    DOI: 10.1109/ipdpsw52791.2021.00037
  • Kupkova et al. (2021). Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests one-carbon metabolite insufficiency
    medRxiv. DOI: 10.1101/2021.06.11.21258783
  • Toulmin et al. (2021). Type II alveolar cell MHCII improves respiratory viral disease outcomes while exhibiting limited antigen presentation
    Nature Communications. DOI: 10.1038/s41467-021-23619-6
  • Gerber et al. (2021). Streamlining differential exon and 3′ UTR usage with diffUTR
    BMC Bioinformatics. DOI: 10.1186/s12859-021-04114-7
  • Hasegawa et al. (2021). Clonal inactivation of telomerase promotes accelerated stem cell differentiation
    bioRxiv. DOI: 10.1101/2021.04.28.441728
  • Mölder et al. (2021). Sustainable data analysis with Snakemake
    F1000Research. DOI: 10.12688/f1000research.29032.2
  • Smith et al. (2021). PEPPRO: quality control and processing of nascent RNA profiling data
    Genome Biology. DOI: 10.1186/s13059-021-02349-4
  • Smith et al. (2020). PEPATAC: An optimized ATAC-seq pipeline with serial alignments
    bioRxiv. DOI: 10.1101/2020.10.21.347054
  • VijayKrishna et al. (2020). Expanding the Galaxy's reference data
    bioRxiv. DOI: 10.1101/2020.10.09.327114
  • Zhou et al. (2020). CATA: a comprehensive chromatin accessibility database for cancer
    bioRxiv. DOI: 10.1101/2020.05.16.099325