MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. - Laurent Gatto; Kathryn S. Lilley (Bioinform., 2012)

Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata. - Laurent Gatto; Lisa M. Breckels; Samuel Wieczorek; Thomas Burger; Kathryn S. Lilley (Bioinform., 2014)

Chapter 14. R for Proteomics. - Lisa M. Breckels; Sebastian Gibb; Vladislav A. Petyuk; Laurent Gatto (Proteome Informatics, 2016)

A Bioconductor workflow for processing and analysing spatial proteomics data. - Lisa M. Breckels; Claire M. Mulvey; Kathryn S. Lilley; Laurent Gatto (F1000Research, 2016)

Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics. - Lisa M. Breckels; Sean B. Holden; David Wojnar; Claire M. Mulvey; Andy Christoforou; Arnoud Groen; Matthew W. B. Trotter; Oliver Kohlbacher; Kathryn S. Lilley; Laurent Gatto (PLoS Comput. Biol., 2016)

Ten Simple Rules for Taking Advantage of Git and GitHub. - Yasset Pérez-Riverol; Laurent Gatto; Rui Wang; Timo Sachsenberg; Julian Uszkoreit; Felipe da Veiga Leprevost; Christian Fufezan; Tobias Ternent; Stephen J. Eglen; Daniel S. Katz; Tom J. Pollard; Alexander Konovalov 001; et al. (PLoS Comput. Biol., 2016)

BioContainers: an open-source and community-driven framework for software standardization. - Felipe da Veiga Leprevost; Björn A. Grüning; Saulo Aflitos; Hannes L. Röst; Julian Uszkoreit; Harald Barsnes; Marc Vaudel; Pablo A. Moreno; Laurent Gatto; Jonas Weber; Mingze Bai; Rafael C. Jiménez; et al. (Bioinform., 2017)

DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics. - Samuel Wieczorek; Florence Combes; Cosmin Lazar; Quentin Giai Gianetto; Laurent Gatto; Alexia Dorffer; Anne-Marie Hesse; Yohann Couté; Myriam Ferro; Christophe Bruley; Thomas Burger (Bioinform., 2017)

A Bayesian mixture modelling approach for spatial proteomics. - Oliver M. Crook; Claire M. Mulvey; Paul D. W. Kirk; Kathryn S. Lilley; Laurent Gatto (PLoS Comput. Biol., 2018)

ensembldb: an R package to create and use Ensembl-based annotation resources. - Johannes Rainer; Laurent Gatto; Christian X. Weichenberger (Bioinform., 2019)

A Bioconductor workflow for the Bayesian analysis of spatial proteomics. - Oliver M. Crook; Lisa M. Breckels; Kathryn S. Lilley; Paul D. W. Kirk; Laurent Gatto (F1000Research, 2019)

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection. - Oliver M. Crook; Aikaterini Geladaki; Daniel J. H. Nightingale; Owen L. Vennard; Kathryn S. Lilley; Laurent Gatto; Paul D. W. Kirk (PLoS Comput. Biol., 2020)

Exploiting the DepMap cancer dependency data using the depmap R package. - Theo Killian; Laurent Gatto (F1000Research, 2021)

Curated single cell multimodal landmark datasets for R/Bioconductor. - Kelly B. Eckenrode; Dario Righelli; Marcel Ramos; Ricard Argelaguet; Christophe Vanderaa; Ludwig Geistlinger; Aedín C. Culhane; Laurent Gatto; Vincent J. Carey; Martin Morgan; Davide Risso; Levi Waldron (PLoS Comput. Biol., 2023)

Learning and teaching biological data science in the Bioconductor community. - Jenny Drnevich; Frederick J. Tan; Fabricio Almeida-Silva; Robert Castelo; Aedín C. Culhane; Sean Davis 001; Maria A. Doyle; Susan P. Holmes; Leo Lahti; Alexandru Mahmoud; Kozo Nishida; Marcel Ramos; et al. (CoRR, 2024)

CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data. - Philippe Hauchamps; Babak Bayat; Simon Delandre; Mehdi Hamrouni; Marie Toussaint; Stephane Temmerman; Dan Lin; Laurent Gatto (BMC Bioinform., 2024)

Learning and teaching biological data science in the Bioconductor community. - Jenny Drnevich; Frederick J. Tan; Fabricio Almeida-Silva; Robert Castelo; Aedín C. Culhane; Sean R. Davis; Maria A. Doyle; Ludwig Geistlinger; Andrew R. Ghazi; Susan P. Holmes; Leo Lahti; Alexandru Mahmoud; et al. (PLoS Comput. Biol., 2025)