DEVELOPMENT OF STATISTICAL METHODOLOGIES AND APPLICATION TO CLINICAL CANCER STUDIES

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

ALA Neves, Y Chen, K-A Le Cao, S Mandal, TJ Sharpton, T McAllister, LL Guan

2020-04-01

A greater understanding of the rumen microbiota and its function may help find new strategies to improve feed efficiency in cattle..

Microbiome profiling reveals gut dysbiosis in a transgenic mouse model of Huntington's disease

Geraldine Kong, Le Cao Kim-Anh, Louise M Judd, ShanShan Li, Thibault Renoir, Anthony J Hannan

2020-02-01

Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a trinucleotide repeat expansion in the huntingtin..

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

SG Dashper, HL Mitchell, K-A Le Cao, L Carpenter, MG Gussy, H Calache, SL Gladman, DM Bulach, B Hoffmann, D Catmull, S Pruilh, S Johnson, L Gibbs, E Amezdroz, U Bhatnagar, T Seemann, G Mnatzaganian, DJ Manton, EC Reynolds

2019-12-24

Human microbiomes are predicted to assemble in a reproducible and ordered manner yet there is limited knowledge on the development..

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

Misa Matsuyama, Mark Morrison, Kim-Anh Le Cao, Solange Pruilh, Peter SW Davies, Clare Wall, Amy Lovell, Rebecca J Hill

2019-08-28

Early life nutrition is a vital determinant of an individual's life-long health and also directly influences the ecological and fu..

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

Luyi Tian, Xueyi Dong, Saskia Freytag, Kim-Anh Le Cao, Shian Su, Abolfazl JalalAbadi, Daniela Amann-Zalcenstein, Tom S Weber, Azadeh Seidi, Jafar S Jabbari, Shalin H Naik, Matthew E Ritchie

2019-06-01

Single cell RNA-sequencing (scRNA-seq) technology has undergone rapid development in recent years, leading to an explosion in the ..

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

Linda M Rehaume, Nicholas Matigian, Ahmed M Mehdi, Nancy Lachner, Kate L Bowerman, Joshua Daly, Kim-Anh Le Cao, Philip Hugenholtz, Ranjeny Thomas

2019-04-01

OBJECTIVES: Certain gut bacterial families, including Bacteroidaceae, Porphyromonadaceae and Prevotellaceae, are increased in peop..

Evaluation of Serum Glycoprotein Biomarker Candidates for Detection of Esophageal Adenocarcinoma and Surveillance of Barrett's Esophagus

Alok K Shah, Gunter Hartel, Ian Brown, Clay Winterford, Renhua Na, Kim-Anh Le Cao, Bradley A Spicer, Michelle Dunstone, Wayne A Phillips, Reginald V Lord, Andrew P Barbour, David I Watson, Virendra Joshi, David C Whiteman, Michelle M Hill

2018-12-01

Esophageal adenocarcinoma (EAC) is thought to develop from asymptomatic Barrett's esophagus (BE) with a low annual rate of convers..

scRNA-seq mixology: towards better benchmarking of single cell RNA-seq analysis methods

Luyi Tian, Xueyi Dong, Saskia Freytag, Kim-Anh Lê Cao, Shian Su, Abolfazl JalalAbadi, Daniela Amann-Zalcenstein, Tom Weber, Azadeh Seidi, Jafar Jabbari, Shalin Naik, Matthew Ritchie

2018-10-03

Single cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years, bringing with new challenges in..

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

David LA Wood, Nancy Lachner, Jean-Marie Tan, Stephanie Tang, Nicola Angel, Antonia Laino, Richard Linedale, Kim-Anh Le Cao, Mark Morrison, Ian H Frazer, H Peter Soyer, Philip Hugenholtz

2018-09-01

Cutaneous squamous cell carcinoma (SCC) is the second-most-common cancer in Australia. The majority of SCCs progress from premalig..

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

Florian Rohart, Benoit Gautier, Amrit Singh, Kim-Anh Le Cao

2017-11-01

The advent of high throughput technologies has led to a wealth of publicly available 'omics data coming from different sources, su..

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

Ralph Patrick, Bostjan Kobe, Kim-Anh Le Cao, Mikael Boden

2017-06-15

Motivation: Genome-wide association studies are identifying single nucleotide variants (SNVs) linked to various diseases, however ..

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

Florian Rohart, Aida Eslami, Nicholas Matigian, Stephanie Bougeard, Kim-Anh Le Cao

2017-02-27

BACKGROUND: Molecular signatures identified from high-throughput transcriptomic studies often have poor reliability and fail to re..

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

Jasmin Straube, Bevan Emma Huang, Kim-Anh Le Cao

2017-01-09

Dynamic changes in biological systems can be captured by measuring molecular expression from different levels (e.g., genes and pro..

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

Florian Rohart, Gabriel J Milinovich, Simon MR Avril, Kim-Anh Le Cao, Shilu Tong, Wenbiao Hu

2016-12-20

Effective disease surveillance is critical to the functioning of health systems. Traditional approaches are, however, limited in t..

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

Ralph Patrick, Coralie Horin, Bostjan Kobe, Kim-Anh Lê Cao, Mikael Bodén

2016-11-01

Identifying kinase substrates and the specific phosphorylation sites they regulate is an important factor in understanding protein..

Integrating Multi-omics Data to Dissect Mechanisms of DNA repair Dysregulation in Breast Cancer.

Chao Liu, Florian Rohart, Peter T Simpson, Kum Kum Khanna, Mark A Ragan, Kim-Anh Lê Cao

2016-09-26

DNA repair genes and pathways that are transcriptionally dysregulated in cancer provide the first line of evidence for the altered..

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

Kim-Anh Le Cao, Mary-Ellen Costello, Vanessa Anne Lakis, Francois Bartolo, Xin-Yi Chua, Remi Brazeilles, Pascale Rondeau

2016-08-11

Culture independent techniques, such as shotgun metagenomics and 16S rRNA amplicon sequencing have dramatically changed the way we..

Multiparameter analysis of naevi and primary melanomas identifies a subset of naevi with elevated markers of transformation.

Carly Fox, Duncan Lambie, James S Wilmott, Alex Pinder, Sandra Pavey, Kim-Anh Lê Cao, Taner Akalin, Isil Kilinc Karaarslan, Fezal Ozdemir, Richard A Scolyer, Miko Yamada, H Peter Soyer, Helmut Schaider, Brian Gabrielli

2016-07-01

Here we have carried out a multiparameter analysis using a panel of 28 immunohistochemical markers to identify markers of transfor..

Implementation and evaluation of amyloidosis subtyping by laser-capture microdissection and tandem mass spectrometry.

Peter Mollee, Samuel Boros, Dorothy Loo, Jayde E Ruelcke, Vanessa A Lakis, Kim-Anh Lê Cao, Patricia Renaut, Michelle M Hill

2016-01-01

BACKGROUND: Correct identification of the amyloidosis-causing protein is crucial for clinical management. Recently the Mayo Clinic..

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

Chao Liu, Sriganesh Srihari, Samir Lal, Benoit Gautier, Peter T Simpson, Kum Kum Khanna, Mark A Ragan, Kim-Anh Le Cao

2016-01-01

The Homologous Recombination (HR) pathway is crucial for the repair of DNA double-strand breaks (DSBs) generated during DNA replic..

Ratios of T-cell immune-effectors with tumour associated macrophages and PD-1/PD-L1 axis immune-checkpoint molecules, add to the predictive power of conventional prognosticators in diffuse large B cell lymphoma

C Keane, F Vari, M Hertzberg, K LE CAO, MR Green, E Han, JF Seymour, RJ Hicks, D Gill, P Crooks, C Gould, K Jones, LR Griffiths, D Talaulikar, S Jain, J Tobin, MK Gandhi

2015-01-01