integrOmics: an R package to unravel relationships between two omics datasets. - Kim-Anh Lê Cao; Ignacio González; Sébastien Déjean (Bioinform., 2009)

Sparse canonical methods for biological data integration: application to a cross-platform study. - Kim-Anh Lê Cao; Pascal G. P. Martin; Christèle Robert-Granié; Philippe Besse (BMC Bioinform., 2009)

Multiclass classification and gene selection with a stochastic algorithm. - Kim-Anh Lê Cao; Agnès Bonnet; Sébastien Gadat (Comput. Stat. Data Anal., 2009)

Integrative mixture of experts to combine clinical factors and gene markers. - Kim-Anh Lê Cao; Emmanuelle Meugnier; Geoffrey J. McLachlan (Bioinform., 2010)

Sorting the nuclear proteome. - Denis C. Bauer; Kai Willadsen; Fabian A. Buske; Kim-Anh Lê Cao; Timothy L. Bailey; Graham Dellaire; Mikael Bodén (Bioinform., 2011)

Sparse PLS Discriminant Analysis: biologically relevant feature selection and graphical displays for multiclass problems. - Kim-Anh Lê Cao; Simon Boitard; Philippe Besse (BMC Bioinform., 2011)

Visualising associations between paired 'omics' data sets. - Ignacio González; Kim-Anh Lê Cao; Melissa J. Davis; Sébastien Déjean (BioData Min., 2012)

A novel approach for biomarker selection and theintegration of repeated measures experiments from two assays. - Benoit Liquet; Kim-Anh Lê Cao; Hakim Hocini; Rodolphe Thiébaut (BMC Bioinform., 2012)

Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets. - Fangzhou Yao; Jeff Coquery; Kim-Anh Lê Cao (BMC Bioinform., 2012)

Mapping the stabilome: a novel computational method for classifying metabolic protein stability. - Ralph Patrick; Kim-Anh Lê Cao; Melissa J. Davis; Bostjan Kobe; Mikael Bodén (BMC Syst. Biol., 2012)

PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events. - Ralph Patrick; Kim-Anh Lê Cao; Bostjan Kobe; Mikael Bodén (Bioinform., 2015)

PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation. - Ralph Patrick; Bostjan Kobe; Kim-Anh Lê Cao; Mikael Bodén (Bioinform., 2017)

MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms. - Florian Rohart; Aida Eslami; Nicholas Matigian; Stéphanie Bougeard; Kim-Anh Lê Cao (BMC Bioinform., 2017)

mixOmics: An R package for 'omics feature selection and multiple data integration. - Florian Rohart; Benoît Gautier; Amrit Singh; Kim-Anh Lê Cao (PLoS Comput. Biol., 2017)

DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays. - Amrit Singh; Casey P. Shannon; Benoît Gautier; Florian Rohart; Michaël Vacher; Scott J. Tebbutt; Kim-Anh Lê Cao (Bioinform., 2019)

Managing batch effects in microbiome data. - Yiwen Wang; Kim-Anh Lê Cao (Briefings Bioinform., 2020)

A simple, scalable approach to building a cross-platform transcriptome atlas. - Paul W. Angel; Nadia Rajab; Yidi Deng; Chris M. Pacheco; Tyrone Chen; Kim-Anh Lê Cao; Jarny Choi; Christine A. Wells (PLoS Comput. Biol., 2020)

A multi-modal data harmonisation approach for discovery of COVID-19 drug targets. - Tyrone Chen; Melcy Philip; Kim-Anh Lê Cao; Sonika Tyagi (Briefings Bioinform., 2021)

A field guide to cultivating computational biology. - Anne E. Carpenter; Casey S. Greene; Piero Carnici; Benilton S. Carvalho; Michiel de Hoon; Stacey D. Finley; Kim-Anh Lê Cao; Jerry S. H. Lee; Luigi Marchionni; Suzanne Sindi; Fabian J. Theis; Gregory P. Way; et al. (CoRR, 2021)

multiomics: A user-friendly multi-omics data harmonisation R pipeline. - Tyrone Chen; Al J. Abadi; Kim-Anh Lê Cao; Sonika Tyagi (F1000Research, 2021)

Sincast: a computational framework to predict cell identities in single-cell transcriptomes using bulk atlases as references. - Yidi Deng; Jarny Choi; Kim-Anh Lê Cao (Briefings Bioinform., 2022)

Statistical challenges in longitudinal microbiome data analysis. - Saritha Kodikara; Susan Ellul; Kim-Anh Lê Cao (Briefings Bioinform., 2022)

timeOmics: an R package for longitudinal multi-omics data integration. - Antoine Bodein; Marie-Pier Scott-Boyer; Olivier Périn; Kim-Anh Lê Cao; Arnaud Droit (Bioinform., 2022)

PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data. - Yiwen Wang; Kim-Anh Lê Cao (Briefings Bioinform., 2023)

MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis. - Babak Shaban; Maria Mar del Quiroga; Robert Turnbull; Edoardo Tescari; Kim-Anh Lê Cao; Heroen Verbruggen (J. Open Source Softw., 2023)

Semisynthetic simulation for microbiome data analysis. - Kris Sankaran; Saritha Kodikara; Jingyi Jessica Li; Kim-Anh Lê Cao (Briefings Bioinform., 2024)