Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion. - Carlos Pulido-Quetglas; Estel Aparicio-Prat; Carme Arnan; Taisia Polidori; Toni Hermoso; Emilio Palumbo; Julia V. Ponomarenko; Roderic Guigó; Rory Johnson (PLoS Comput. Biol., 2017)

LnCompare: gene set feature analysis for human long non-coding RNAs. - Joana Carlevaro-Fita; Leibo Liu; Yuan Zhou; Shan Zhang; Panagiotis Chouvardas; Rory Johnson; Jianwei Li (Nucleic Acids Res., 2019)

GENCODE reference annotation for the human and mouse genomes. - Adam Frankish; Mark Diekhans; Anne-Maud Ferreira; Rory Johnson; Irwin Jungreis; Jane E. Loveland; Jonathan M. Mudge; Cristina Sisu; James C. Wright; Joel Armstrong; If Barnes; Andrew E. Berry; et al. (Nucleic Acids Res., 2019)

CASPR, an analysis pipeline for single and paired guide RNA CRISPR screens, reveals optimal target selection for long non-coding RNAs. - Judith Bergadà-Pijuan; Carlos Pulido-Quetglas; Adrienne Vancura; Rory Johnson (Bioinform., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

GENCODE 2021. - Adam Frankish; Mark Diekhans; Irwin Jungreis; Julien Lagarde; Jane E. Loveland; Jonathan M. Mudge; Cristina Sisu; James C. Wright; Joel Armstrong; If Barnes; Andrew E. Berry; Alexandra Bignell; et al. (Nucleic Acids Res., 2021)

GENCODE: reference annotation for the human and mouse genomes in 2023. - Adam Frankish; Silvia Carbonell Sala; Mark Diekhans; Irwin Jungreis; Jane E. Loveland; Jonathan M. Mudge; Cristina Sisu; James C. Wright; Carme Arnan; If Barnes; Abhimanyu Banerjee; Ruth Bennett; et al. (Nucleic Acids Res., 2023)