Threshold-seq: a tool for determining the threshold in short RNA-seq datasets. - Rogan Magee; Phillipe Loher; Eric Londin; Isidore Rigoutsos (Bioinform., 2017)

MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. - Venetia Pliatsika; Phillipe Loher; Rogan Magee; Aristeidis G. Telonis; Eric Londin; Megumi Shigematsu; Yohei Kirino; Isidore Rigoutsos (Nucleic Acids Res., 2018)

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. - Thomas Desvignes; Phillipe Loher; Karen Eilbeck; Jeffery Ma; Gianvito Urgese; Bastian Fromm; Jason Sydes; Ernesto Aparicio-Puerta; Víctor Barrera; Roderic Espín; Florian Thibord; Xavier Bofill-De Ros; et al. (Bioinform., 2020)

IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets. - Phillipe Loher; Nestoras Karathanasis; Eric Londin; Paul F. Bray; Venetia Pliatsika; Aristeidis G. Telonis; Isidore Rigoutsos (Bioinform., 2021)