Development of Statistical Methodologies and Application to Clinical Cancer Studies

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

G Kong, KAL Cao, LM Judd, SS Li, T Renoir, AJ Hannan

2020-02-01

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

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

ALA Neves, Y Chen, KA Lê Cao, S Mandal, TJ Sharpton, T McAllister, LL Guan

2020-01-01

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

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

M Matsuyama, M Morrison, KAL Cao, S Pruilh, PSW Davies, C Wall, A Lovell, RJ Hill

2019-12-01

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

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

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

2019-12-01

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

DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays.

Amrit Singh, Casey P Shannon, Benoît Gautier, Florian Rohart, Michaël Vacher, Scott J Tebbutt, Kim-Anh Lê Cao

2019-09-01

MOTIVATION: In the continuously expanding omics era, novel computational and statistical strategies are needed for data integratio..

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

L Tian, X Dong, S Freytag, KA Lê Cao, S Su, A JalalAbadi, D Amann-Zalcenstein, TS Weber, A Seidi, JS Jabbari, SH Naik, ME Ritchie

2019-06-01

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

Exploring the association between BMI and mortality in Australian women and men with and without diabetes: the AusDiab study

SF Zahir, A Griffin, JL Veerman, DJ Magliano, JE Shaw, KAL Cao, AM Mehdi

2019-05-01

Aims/hypothesis: There is conflicting evidence about the obesity paradox—the counterintuitive survival advantage of obesity among ..

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

LM Rehaume, N Matigian, AM Mehdi, N Lachner, KL Bowerman, J Daly, KA Lê Cao, P Hugenholtz, R Thomas

2019-04-01

Objectives Certain gut bacterial families, including Bacteroidaceae, Porphyromonadaceae and Prevotellaceae, are increased in peopl..

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

Amy H Lee, Casey P Shannon, Nelly Amenyogbe, Tue B Bennike, Joann Diray-Arce, Olubukola T Idoko, Erin E Gill, Rym Ben-Othman, William S Pomat, Simon D van Haren, Kim-Anh Lê Cao, Momoudou Cox, Alansana Darboe, Reza Falsafi, Davide Ferrari, Daniel J Harbeson, Daniel He, Cai Bing, Samuel J Hinshaw, Jorjoh Ndure

2019-03-12

Systems biology can unravel complex biology but has not been extensively applied to human newborns, a group highly vulnerable to a..

Evaluation of serum glycoprotein biomarker candidates for detection of esophageal adenocarcinoma and surveillance of barrett’s esophagus

AK Shah, G Hartel, I Brown, C Winterford, R Na, KA Lê Cao, BA Spicer, MA Dunstone, WA Phillips, RV Lord, AP Barbour, DI Watson, V Joshi, DC Whiteman, MM Hill

2018-12-01

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

A natural history of actinic keratosis and cutaneous squamous cell carcinoma microbiomes

DLA Wood, N Lachner, JM Tan, S Tang, N Angel, A Laino, R Linedale, KAL Cao, M Morrison, IH Frazer, HP Soyer, P 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

F Rohart, B Gautier, A Singh, KA Lê 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

R Patrick, B Kobe, KA Lê Cao, M Bodén

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

F Rohart, A Eslami, N Matigian, S Bougeard, KA Lê 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

J Straube, BE Huang, KAL 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

F Rohart, GJ Milinovich, SMR Avril, KA Lê Cao, S Tong, W 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

R Patrick, C Horin, B Kobe, KAL Cao, M Bodén

2016-11-01

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

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

P Mollee, S Boros, D Loo, JE Ruelcke, VA Lakis, KAL Cao, P Renaut, MM Hill

2016-10-27

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

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

C Liu, F Rohart, PT Simpson, KK Khanna, MA Ragan, KA 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

KAL Cao, ME Costello, VA Lakis, F Bartolo, XY Chua, R Brazeilles, P Rondeau

2016-08-01

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

C Fox, D Lambie, JS Wilmott, A Pinder, S Pavey, KA Lê Cao, T Akalin, IK Karaarslan, F Ozdemir, RA Scolyer, M Yamada, HP Soyer, H Schaider, B Gabrielli

2016-07-01

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

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

C Liu, S Srihari, S Lal, B Gautier, PT Simpson, KK Khanna, MA Ragan, KA Lê 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