hLGDB: a database of human lysosomal genes and their regulation. - Alessandro Brozzi; Lorena Urbanelli; Pierre-Luc Germain; Alessandro Magini; Carla Emiliani (Database J. Biol. Databases Curation, 2013)

Living Instruments and Theoretical Terms: Xenografts as Measurements in Cancer Research. - Pierre-Luc Germain (New Directions in the Philosophy of Science, 2014)

Streamlining differential exon and 3′ UTR usage with diffUTR. - Stefan Gerber; Gerhard Schratt; Pierre-Luc Germain (BMC Bioinform., 2021)

scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction. - Michael Soutschek; Fridolin Gross; Gerhard Schratt; Pierre-Luc Germain (Bioinform., 2022)

enrichMiR predicts functionally relevant microRNAs based on target collections. - Michael Soutschek; Tomás Germade; Pierre-Luc Germain; Gerhard Schratt (Nucleic Acids Res., 2022)

On the identification of differentially-active transcription factors from ATAC-seq data. - Felix Ezequiel Gerbaldo; Emanuel Sonder; Vincent Fischer 005; Selina Frei; Jiayi Wang; Katharina Gapp; Mark D. Robinson; Pierre-Luc Germain (PLoS Comput. Biol., 2024)

Ten simple rules for computational biologists collaborating with wet lab researchers. - Mark D. Robinson; Peiying Cai; Martin Emons; Reto Gerber; Pierre-Luc Germain; Samuel Gunz; Siyuan Luo; Giulia Moro; Emanuel Sonder; Anthony Sonrel; Jiayi Wang; David Wissel; et al. (PLoS Comput. Biol., 2024)