2019

• DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays
  A. Singh, C. P. Shannon, B. Gautier, F. Rohart, M. Vacher, S.J. Tebbutt, K-A. Le Caô
  Bioinformatics. [Bioinformatics] [PubMed].
  

2017

• mixOmics: an R package for 'omics feature selection and multiple data integration
  F. Rohart, B. Gautier, A. Singh, K-A. Le Caô
  PLOS Computational Biology. [PLOS Computational Biology] [PubMed].
  
• Human Hepatocellular Carcinomas with a Periportal Phenotype Have the Lowest Potential for Early Recurrence after Curative Resection
  R. Désert, F. Rohart, F. Canal, M. Sicard, S. Merbarki, M. Desille, S. Renaud, B. Turlin, P. Bellaud, D. Bergeat, L. Sulpice, C. Perret, B. Clèment, K-A. Le Caô, O. Musso
  Hepatology, doi: 10.1002/hep.29254 [PubMed] [onlinelibrary.wiley.com].
  
• MINT: A multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms
  F. Rohart, A. Eslami, N. Matigian, S. Bougeard and K-A. Le Caô
  BMC Bioinformatics, doi: 10.1186/s12859-017-1553-8. [PubMed] [BMC Bioinformatics].
  

2016

• Disease surveillance based on Internet-based linear models: an Australian case study of previously unmodeled infection diseases
  F. Rohart*, G. Milinovich* (co-first author), S. Avril, K-A. Le Caô, Sh Tong, W. Hu.
  Scientific Reports, doi:10.1038/srep38522 [PubMed]
• Integrating Multi-omics Data to Dissect Mechanisms of DNA repair Dysregulation in Breast Cancer
  Ch. Liu, F. Rohart, P. Simpson, K. K. Khanna, M. Ragan and K-A. Le Caô.
  Scientific Reports, doi:10.1038/srep34000 [PubMed]
• Multiple Hypotheses Testing For Variable Selection
  F. Rohart
  Australian & New Zealand Journal of Statistics, doi:10.1111/anzs.12157. [onlinelibrary.wiley.com].
  
• A Molecular Classification of Human Mesenchymal Stromal Cells
  F. Rohart, E. Mason, N. Matigian, R. Mosbergen, O. Korn, T. Chen, S. Butcher, J. Patel, K. Atkinson, K. Khosrotehrani, N. Fisk, K-A. Le Caô and C-A. Wells.
  PeerJ, DOI 10.7717/peerj.1845 [PubMed] [PeerJ]

2015

• Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds.
  M. SanCristobal, F. Rohart , C. Lascor, M. Bouffaud, L. Trouilh, P. Martin, Y. Lippi, T. Tribout, T. Faraut, M.J. Mercat, D. Milan and L. Liaubet.
  BMC Genomics, 16:1055. DOI: 10.1186/s12864-015-2259-9 [PubMed] [BMC Genomics]

2014

• Selection of fixed effects in high dimensional linear mixed models using a multicycle ECM algorithm.
  F. Rohart, M. SanCristobal and B. Laurent.
  Computational Statistics & Data Analysis. DOI: 10.1016/j.csda.2014.06.022 [pdf] [ScienceDirect]
• YuGene: a simple approach to scale gene expression data derived from different platforms for integrated analyses.
  K-A. Le Caô*, F. Rohart* (co-first author), L. McHugh, O. Korn and C-A. Wells.
  Genomics, 2014 Apr;103(4):239-51. [ScienceDirect]

2012

• Phenotypic Prediction Based on Metabolomic Data on the Growing Pig from three main European Breeds.
  F. Rohart, A. Paris, B. Laurent, C. Canlet, J. Molina, M.J. Mercat, T. Tribout, N. Muller, N. Iannucelli, N. Villa-Vialaneix, L. Liaubet, D. Milan and M. SanCristobal.
  Journal of Animal Science 2012 Dec;90(13):4729-40.

R Packages

• mixOmics (Exploration and Integration of 'Omics datasets). K-A. Le Caô, F. Rohart, I. González, S. Déjean, B. Gautier, F. Bartolo, and others
  mixOmics is a R-package available on CRAN. See mixomics.org for a full description of this package.


• bootsPLS (bootstrapped Partial Least Squares). F. Rohart
  bootsPLS is a R-package available on CRAN (based on the paper ` A Molecular Classification of Human Mesenchymal Stromal Cells'). It calls the mixOmics package and perform subsampling to identify a stable signature.
  Here is a reproducible Rmd file (as well as the html output) on a baby dataset that shows a bit more how the package works (I hope)


• mht (multiple hypotheses testing). F. Rohart
  mht is a R-package available on CRAN (based on the paper `Multiple Hypotheses Testing For Variable Selection'). The main function is mht, two-steps procedure that performs variable selection in high dimensional linear models. Other functions are also available.


• MMS (Mixed Models Selection). F. Rohart
  MMS is a R-package available on CRAN (based on the paper `Selection of fixed effects in high dimensional linear mixed models using a multicycle ECM algorithm'). The main functions are mhtp and lassop, performing fixed effects selection in high dimensional linear mixed models. Other functions are also available.


• YuGene. F. Rohart, K-A. Le Caô, L. McHugh, O. Korn and C-A Wells
  YuGene is a R-package available on CRAN (based on the paper `YuGene: a simple approach to scale gene expression data derived from different platforms for integrated analyses'). The main function is YuGene, cross-platform normalization method. Other functions are also available.