Kim-Anh Le Cao

MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis

Babak Shaban, Mar Quiroga, Robert Turnbull, Edoardo Tescari, Kim-Anh Lê Cao, Heroen Verbruggen

Journal article  |  2023  |  Journal of Open Source Software

MetaGenePipe (MGP) is an efficient, flexible, portable, and scalable metagenomics pipeline that uses performant bioinformatics sof..

MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis

BABAK SHABAN, Maria del Mar Quiroga, Robert Turnbull, EDOARDO TESCARI, KIM-ANH LE CAO, HEROEN VERBRUGGEN

Software / Code  |  2023

MetaGenePipe (MGP) is an efficient, flexible, portable, and scalable metagenomics pipeline that uses performant bioinformatics sof..

PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data

Yiwen Wang, Kim-Anh Le Cao

Journal article  |  2023  |  BRIEFINGS IN BIOINFORMATICS

Microbial communities are highly dynamic and sensitive to changes in the environment. Thus, microbiome data are highly susceptible..

Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples.

Chloe J Love, Carolina Gubert, Saritha Kodikara, Geraldine Kong, Kim-Anh Lê Cao, Anthony J Hannan

Journal article  |  2022  |  STAR Protoc

Fecal samples are frequently used to characterize bacterial populations of the gastrointestinal tract. A protocol is provided to p..

Randomized phase I trial of antigen-specific tolerizing immunotherapy with peptide/calcitriol liposomes in ACPA rheumatoid arthritis.

Amee Sonigra, Hendrik J Nel, Pascale Wehr, Nishta Ramnoruth, Swati Patel, Karin A van Schie, Maxwell W Bladen, Ahmed M Mehdi, Joanne Tesiram, Meghna Talekar, Jamie Rossjohn, Hugh H Reid, Frederik E Stuurman, Helen Roberts, Phillip Vecchio, Ian Gourley, Mark Rigby, Stephane Becart, Rene Em Toes, Hans Ulrich Scherer, et al.

Journal article  |  2022  |  JCI Insight

BACKGROUNDAntigen-specific regulation of autoimmune disease is a major goal. In seropositive rheumatoid arthritis (RA), T cell hel..

Statistical challenges in longitudinal microbiome data analysis.

Saritha Kodikara, Susan Ellul, Kim-Anh Lê Cao

Journal article  |  2022  |  Brief Bioinform

The microbiome is a complex and dynamic community of microorganisms that co-exist interdependently within an ecosystem, and intera..

Faecal microbiota transplant ameliorates gut dysbiosis and cognitive deficits in Huntington's disease mice

Carolina Gubert, Jocelyn M Choo, Chloe J Love, Saritha Kodikara, Bethany A Masson, Jamie JM Liew, Yiwen Wang, Geraldine Kong, Vinod K Narayana, Thibault Renoir, Kim-Anh Le Cao, Geraint B Rogers, Anthony J Hannan

Journal article  |  2022  |  BRAIN COMMUNICATIONS

Huntington's disease is a neurodegenerative disorder involving psychiatric, cognitive and motor symptoms. Huntington's disease is ..

Modèles multivariés pour l’intégration de données et la sélection de biomarqueurs dans les données omiques

Sébastien DÉJEAN, Kim-Anh LÊ CAO

Book Chapter  |  2022

Les méthodes multivariées linéaires présentées permettent : l’exploration d’un seul jeu de données (ACP), la discrimination (PLS-D..

Alterations in the Gut Fungal Community in a Mouse Model of Huntington's Disease

Geraldine Kong, Kim-Anh Le Cao, Anthony J Hannan

Journal article  |  2022  |  MICROBIOLOGY SPECTRUM

Huntington's disease (HD) is a neurodegenerative disorder caused by a trinucleotide expansion in the HTT gene, which is expressed ..

Sincast: a computational framework to predict cell identities in single-cell transcriptomes using bulk atlases as references

Yidi Deng, Jarny Choi, Kim-Anh Le Cao

Journal article  |  2022  |  BRIEFINGS IN BIOINFORMATICS

Characterizing the molecular identity of a cell is an essential step in single-cell RNA sequencing (scRNA-seq) data analysis. Nume..