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