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List of works by Kim-Anh Lê Cao

A Generic Multivariate Framework for the Integration of Microbiome Longitudinal Studies With Other Data Types

scientific article published on 07 November 2019

A Linear Mixed Model Spline Framework for Analysing Time Course 'Omics' Data

scientific article

A Natural History of Actinic Keratosis and Cutaneous Squamous Cell Carcinoma Microbiomes

scientific article published on 09 October 2018

A field guide to cultivating computational biology

scientific article published on 08 October 2021

A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy

scientific article

A molecular classification of human mesenchymal stromal cells

scientific article published on 24 March 2016

A new method for integrated analysis applied to gene expression and cytokines secretion in response to LIPO-5 vaccine in HIV-negative volunteers.

scientific article published on 13 September 2012

A novel approach for biomarker selection and the integration of repeated measures experiments from two assays

scientific article

A peripheral blood transcriptomic signature predicts autoantibody development in infants at risk of type 1 diabetes.

scientific article published on 8 March 2018

A pilot study on transcriptome data analysis of folliculogenesis in pigs.

scientific article

A retrospective analysis of clinical features of oral malignant and potentially malignant disorders with and without oral epithelial dysplasia

scientific article published on 18 October 2013

A simple, scalable approach to building a cross-platform transcriptome atlas

scientific article published on 28 September 2020

A small set of extra-embryonic genes defines a new landmark for bovine embryo staging.

scientific article published on 6 October 2010

A sparse PLS for variable selection when integrating omics data

scientific article

An mRNA atlas of G protein-coupled receptor expression during primary human monocyte/macrophage differentiation and lipopolysaccharide-mediated activation identifies targetable candidate regulators of inflammation.

scientific article

Analysis of a simulated microarray dataset: comparison of methods for data normalisation and detection of differential expression (open access publication).

scientific article

Analysis of the real EADGENE data set: comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (open access publication)

scientific article

Analysis of the real EADGENE data set: multivariate approaches and post analysis (open access publication)

scientific article

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

scientific article published on 27 May 2019

Citrullinated peptide dendritic cell immunotherapy in HLA risk genotype–positive rheumatoid arthritis patients

article

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

scientific article

Determinants of body fat in infants of women with gestational diabetes mellitus differ with fetal sex.

scientific article published on 12 October 2011

Dietary intake influences gut microbiota development of healthy Australian children from the age of one to two years

scientific article published on 28 August 2019

Diffusion-weighted Imaging Is a Sensitive and Specific Magnetic Resonance Sequence in the Diagnosis of Ankylosing Spondylitis

scientific article published on 15 February 2018

Disease surveillance based on Internet-based linear models: an Australian case study of previously unmodeled infection diseases

scientific article

DynOmics to identify delays and co-expression patterns across time course experiments

scientific article published on 09 January 2017

Dynamic molecular changes during the first week of human life follow a robust developmental trajectory

scientific article published on 12 March 2019

Effect of Perioperative Opioids on Cancer-Relevant Circulating Parameters: Mu Opioid Receptor and Toll-Like Receptor 4 Activation Potential, and Proteolytic Profile

scientific article published on 6 March 2018

Epistatic interactions between killer immunoglobulin-like receptors and human leukocyte antigen ligands are associated with ankylosing spondylitis

scientific article published on 17 August 2020

Genetic Variants in ERAP1 and ERAP2 Associated With Immune-Mediated Diseases Influence Protein Expression and the Isoform Profile.

scientific article

Genome-resolved metagenomics of an autotrophic thiocyanate-remediating microbial bioreactor consortium

scientific article published on 23 March 2019

Genome-wide characterization of the routes to pluripotency.

scientific article published on December 2014

HLA Alleles Associated With Risk of Ankylosing Spondylitis and Rheumatoid Arthritis Influence the Gut Microbiome

scientific article published on 12 August 2019

Human Hepatocellular Carcinomas with a Periportal Phenotype Have the Lowest Potential for Early Recurrence after Curative Resection

scientific article

IL-23 favours outgrowth of spondyloarthritis-associated pathobionts and suppresses host support for homeostatic microbiota

scientific article published on 30 January 2019

IL-6-driven STAT signalling in circulating CD4+ lymphocytes is a marker for early anticitrullinated peptide antibody-negative rheumatoid arthritis

scientific article published on 3 February 2015

In Situ Stimulation of Thiocyanate Biodegradation through Phosphate Amendment in Gold Mine Tailings Water.

scientific article

In vivo gene expression in granulosa cells during pig terminal follicular development.

scientific article

Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets

scientific article

Integrative mixture of experts to combine clinical factors and gene markers.

scientific article published on 11 March 2010

MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms

scientific article

Malignant transformation of oral epithelial dysplasia: a real-world evaluation of histopathologic grading

scientific article

Managing batch effects in microbiome data

scientific article published on 28 November 2019

Mapping the stabilome: a novel computational method for classifying metabolic protein stability

scientific article

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities

scientific article

Multiple interaction nodes define the postreplication repair response to UV-induced DNA damage that is defective in melanomas and correlated with UV signature mutation load

scientific article published on 19 December 2019

Novel multivariate methods for integration of genomics and proteomics data: applications in a kidney transplant rejection study

scientific article

Pathway dysregulation analysis of the nucleotide excision repair mechanisms reveals it is not a common feature of melanomas

scientific article published on 22 October 2018

Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer.

scientific article published on 26 September 2015

PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation

scientific article

PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events

scientific article published on 9 October 2014

Predicting qualitative phenotypes from microarray data - the Eadgene pig data set.

scientific article

Prediction of kinase-specific phosphorylation sites through an integrative model of protein context and sequence

scientific article

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

scientific article published on 9 March 2015

Ratios of T-cell immune effectors and checkpoint molecules as prognostic biomarkers in diffuse large B-cell lymphoma: a population-based study

scientific article published on October 2015

Sorting the nuclear proteome

scientific article published on July 2011

Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems ⬇️

scientific article published on June 22, 2011

Sparse canonical methods for biological data integration: application to a cross-platform study.

scientific article

Taxonomic and functional assessment using metatranscriptomics reveals the effect of Angus cattle on rumen microbial signatures

scientific article published on 30 October 2019

Temporal development of the oral microbiome and prediction of early childhood caries

scientific article published on 24 December 2019

The EADGENE Microarray Data Analysis Workshop (open access publication).

scientific article

The T-cell Receptor Repertoire Influences the Tumor Microenvironment and Is Associated with Survival in Aggressive B-cell Lymphoma.

scientific article published on 20 September 2016

The surprising benefit of passive-aggressive behaviour at Christmas parties: being crowned king of the crackers

scientific article published on December 2014

Uncoupled embryonic and extra-embryonic tissues compromise blastocyst development after somatic cell nuclear transfer.

scientific article

Variable selection for generalized canonical correlation analysis.

scientific article

Visualising associations between paired ‘omics’ data sets ⬇️

scientific article published on November 13, 2012

YuGene: a simple approach to scale gene expression data derived from different platforms for integrated analyses

scientific article

integrOmics: an R package to unravel relationships between two omics datasets

scientific article published on 25 August 2009

mixOmics: An R package for 'omics feature selection and multiple data integration

scientific article published on 3 November 2017

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