Between-group analysis of microarray data. - Aedín C. Culhane; Guy Perrière; Elizabeth C. Considine; Thomas G. Cotter; Desmond G. Higgins (Bioinform., 2002)

Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. - Aedín C. Culhane; Guy Perrière; Desmond G. Higgins (BMC Bioinform., 2003)

Expression Profiler: next generation - an online platform for analysis of microarray data. - Misha Kapushesky; Patrick Kemmeren; Aedín C. Culhane; Steffen Durinck; Jan Ihmels; Christine Körner; Meelis Kull; Aurora Torrente; Ugis Sarkans; Jaak Vilo; Alvis Brazma (Nucleic Acids Res., 2004)

MADE4: an R package for multivariate analysis of gene expression data. - Aedín C. Culhane; Jean Thioulouse; Guy Perrière; Desmond G. Higgins (Bioinform., 2005)

Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data. - Florent Baty; Michel P. Bihl; Guy Perrière; Aedín C. Culhane; Martin H. Brutsche (BMC Bioinform., 2005)

Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. - Ian B. Jeffery; Desmond G. Higgins; Aedín C. Culhane (BMC Bioinform., 2006)

Integrating transcription factor binding site information with gene expression datasets. - Ian B. Jeffery; Stephen F. Madden; Paul A. McGettigan; Guy Perrière; Aedín C. Culhane; Desmond G. Higgins (Bioinform., 2007)

AI Methods for Analyzing Microarray Data. - Amira Djebbari; Aedín C. Culhane; Alice Armstrong; John Quackenbush (Encyclopedia of Artificial Intelligence, 2009)

GeneSigDB - a curated database of gene expression signatures. - Aedín C. Culhane; Thomas Schwarzl; Razvan Sultana; Kermshlise C. Picard; Shaita C. Picard; Tim H. Lu; Katherine R. Franklin; Simon J. French; Gerald Papenhausen; Mick Correll; John Quackenbush (Nucleic Acids Res., 2010)

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models. - Markus S. Schröder; Aedín C. Culhane; John Quackenbush; Benjamin Haibe-Kains (Bioinform., 2011)

iBBiG: iterative binary bi-clustering of gene sets. - Daniel Gusenleitner; Eleanor Howe; Stefan Bentink; John Quackenbush; Aedín C. Culhane (Bioinform., 2012)

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. - Aedín C. Culhane; Markus S. Schröder; Razvan Sultana; Shaita C. Picard; Enzo N. Martinelli; Caroline Kelly; Benjamin Haibe-Kains; Misha Kapushesky; Anne-Alyssa St Pierre; William Flahive; Kermshlise C. Picard; Daniel Gusenleitner; et al. (Nucleic Acids Res., 2012)

Gene Expression Atlas update - a value-added database of microarray and sequencing-based functional genomics experiments. - Misha Kapushesky; Tomasz Adamusiak; Tony Burdett; Aedín C. Culhane; Anna Farne; Alexey Filippov; Ele Holloway; Andrey Klebanov; Nataliya Kryvych; Natalja Kurbatova; Pavel Kurnosov; James Malone; et al. (Nucleic Acids Res., 2012)

The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. - Shannan J. Ho Sui; Kimberly Begley; Dorothy Reilly; Brad Chapman; Ray McGovern; Philippe Rocca-Serra; Eamonn Maguire; Gabriel M. Altschuler; Terah A. A. Hansen; Ramakrishna Sompallae; Andrei Krivtsov; Ramesh A. Shivdasani; et al. (Nucleic Acids Res., 2012)

RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface. - Markus S. Schröder; Daniel Gusenleitner; John Quackenbush; Aedín C. Culhane; Benjamin Haibe-Kains (Bioinform., 2013)

Significance Analysis of Prognostic Signatures. - Andrew H. Beck; Nicholas W. Knoblauch; Marco M. Hefti; Jennifer Kaplan; Stuart J. Schnitt; Aedín C. Culhane; Markus S. Schröder; Thomas Risch; John Quackenbush; Benjamin Haibe-Kains (PLoS Comput. Biol., 2013)

A multivariate approach to the integration of multi-omics datasets. - Chen Meng; Bernhard Küster; Aedín C. Culhane; Amin Moghaddas Gholami (BMC Bioinform., 2014)

Integrative Exploratory Analysis of Two or More Genomic Datasets. - Chen Meng; Aedín C. Culhane (Statistical Genomics, 2016)

Public data and open source tools for multi-assay genomic investigation of disease. - Lavanya Kannan; Marcel Ramos; Angela Re; Nehme Hachem; Zhaleh Safikhani; Deena M. A. Gendoo; Sean Davis 001; David Gomez-Cabrero; Robert Castelo; Kasper D. Hansen; Vincent J. Carey; Martin Morgan; et al. (Briefings Bioinform., 2016)

Dimension reduction techniques for the integrative analysis of multi-omics data. - Chen Meng; Oana A. Zeleznik; Gerhard G. Thallinger; Bernhard Küster; Amin Moghaddas Gholami; Aedín C. Culhane (Briefings Bioinform., 2016)

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)

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)