Category Archives: Publications

Microbial network inference for longitudinal microbiome studies with LUPINE

Our latest method based on PLS to infer microbial networks across time is now in preprint! LUPINE is a PLS-based method that combines dimension reduction, and partial correlations to infer associations between taxa. LUPINE takes into account information across time … Continue reading

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Our book is out!

We are excited to announce that our book is out, along with several case studies and R scripts available online. Check out this page. It’s been a very (very) long term project, and a great collaboration with Zoe Welham whose … Continue reading

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Multi-omics data integration: method and showcase applications

Lê Cao team and collaborators from University of British Columbia (Vancouver, Canada) have published their first method to integrate multiple omics data from the same set of biospecimens or individuals (e.g. transcriptomics, proteomics). Their method adopts a systems biology holistic approach by statistically … Continue reading

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New publication with multiple integration

Our paper ‘Novel Multivariate Methods for Integration of Genomics and Proteomics Data: Applications in a Kidney Transplant Rejection Study‘ has just been accepted in OMICS: a journal of integrative Biology, from a collaboration with scientists from the PRevention Of Organ Failure … Continue reading

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Article published explaining correlation circle plots, relevance networks and CIM

Our manuscript ‘Insightful graphicalt outputs to explore relationships between two “omics” data sets has been published and explains how to interpret Correlation Circle plots, how relevance networks and CIM are generated from rCCA and sPLS. Check this very colourful manuscript[intlink … Continue reading

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Another presentation about mixOmics

Another general presentation of mixOmics dating Dec 2012, which presents some preliminary but exciting results about time course data and the generalisation of PLS to multi block data sets using the approach of our collaborator Arthur Tenenhaus and colleagues. Go[intlink … Continue reading

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General presentation about mixOmics

A new general presentation about mixOmics is available (and should be updated for major update of the package) in the [intlink id=”204″ type=”page”]Presentation Section[/intlink]. Lê Cao K.-A. Unravelling `omics’ data with the mixOmics R package, Illustration on several studies. General presentation on mixOmics … Continue reading

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(s)IPCA

Independent Principal Component Analysis (IPCA) In some case studies, we have identified some limitations when using PCA: PCA assumes that gene expression follows a multivariate normal distribution and recent studies have demonstrated that microarray gene expression measurements follow instead a … Continue reading

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New methods: multilevel analyses

A multilevel approach has been added for cross-over design experiments (up to two cross factors), in collaboration with A/Prof B. Liquet (Universite de Bordeaux, France).  This approach takes into account the complex structure of repeated measurements from different assays, where different treatments are applied … Continue reading

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Web-interface

R package and Methods: IPCA and sparse IPCA functions have been implemented (as well as their associated S3 functions). IPCA stands for Principal Component Analysis with Independent Loadings. It is a combination of the advantages of both PCA and Independent … Continue reading

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