Kim-Anh Le Cao

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

Journal article  |  2020  |  animal

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

Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition

Simon Poirier, Sébastien Déjean, Cédric Midoux, Kim-Anh Lê Cao, Olivier Chapleur

Journal article  |  2020

Abstract Anaerobic digestion (AD) is a microbial process that can efficiently degrade organic waste into renewable energies such a..

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

Paul Angel, Nadia Rajab, Yidi Deng, Chris Pacheco, Tyrone Chen, Kim-Anh Lê Cao, Jarny Choi, Christine Wells

Journal article  |  2020

ABSTRACT Gene expression atlases have transformed our understanding of the development, composition and function of human tissues...

The role of gut microbiota and gastrointestinal dysfunction in a mouse model of Huntington's disease

Carolina Gubert, Geraldine Kong, Jamie JM Liew, Chloe Love, Yiwen Wang, Kim-Anh Le Cao, Thibault Renoir, Anthony J Hannan

Conference Proceedings  |  2020  |  NEUROGASTROENTEROLOGY AND MOTILITY

Integrative analyses to investigate the link between microbial activity and metabolites degradation during anaerobic digestion

Laetitia Cardona, Kim Anh Lê Cao, Francesc Puig-Castellví, Chrystelle Bureau, Céline Madigou, Laurent Mazéas, Olivier Chapleur

Journal article  |  2020

Abstract Anaerobic digestion (AD) is a promising biological process which converts waste into sustainable energy. To fully exploit..

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

Journal article  |  2020  |  Neurobiology of Disease

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

Journal article  |  2019  |  Scientific Reports

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

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

Sandra Pavey, Alex Pinder, Winnie Fernando, Nicholas D'Arcy, Nicholas Matigian, Dubravka Skalamera, Kim-Anh Le Cao, Dorothy Loo-Oey, Michelle M Hill, Mitchell Stark, Michael Kimlin, Andrew Burgess, Nicole Cloonan, Richard A Sturm, Brian Gabrielli

Journal article  |  2019  |  Molecular Oncology

Ultraviolet radiation-induced DNA mutations are a primary environmental driver of melanoma. The reason for this very high level of..

Managing batch effects in microbiome data.

Yiwen Wang, Kim-Anh LêCao

Journal article  |  2019  |  Briefings in Bioinformatics

Microbial communities have been increasingly studied in recent years to investigate their role in ecological habitats. However, mi..

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

Antoine Bodein, Olivier Chapleur, Arnaud Droit, Kim-Anh Le Cao

Journal article  |  2019  |  Frontiers in Genetics

Statistical analysis of microbiome data with R. YinglinXia, JunSun, Ding‐GenChen. (2018). Singapore: Springer. 505 pages, ISBN: 978‐981‐13‐1533‐6

Kim‐Anh Lê Cao

Journal article  |  2019  |  Biometrical Journal

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

Journal article  |  2019  |  Bioinformatics

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

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

Journal article  |  2019  |  Scientific Reports

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

Mark Asquith, Peter R Sternes, Mary-Ellen Costello, Lisa Karstens, Sarah Diamond, Tammy M Martin, Zhixiu Li, Mhairi S Marshall, Timothy D Spector, Le Cao Kim-Anh, James T Rosenbaum, Matthew A Brown

Journal article  |  2019  |  Arthritis & Rheumatology

OBJECTIVE: HLA alleles affect susceptibility to more than 100 diseases, but the mechanisms that account for these genotype-disease..

iMAC: An interactive atlas to explore phenotypic differences between in vivo, ex vivo and in vitro-derived myeloid cells in the Stemformatics platform

Nadia Rajab, Paul Angel, Mariola Kurowska-Stolarska, Simon Milling, Chris Pacheco, Matt Rutar, Jarny Choi, Christine Wells

Journal article  |  2019

Summary Macrophages isolated from different tissues have distinct niche roles that maintain tissue homeostasis, as well as providi..

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

Mathew P Watts, Liam P Spurr, Kim-Anh Le Cao, Ryan Wick, Jillian F Banfield, John W Moreau

Journal article  |  2019  |  Water Research

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

Journal article  |  2019  |  Nature Methods

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

Syeda F Zahir, Alison Griffin, J Lennert Veerman, Dianna J Magliano, Jonathan E Shaw, Le Cao Kim-Anh, Ahmed M Mehdi

Journal article  |  2019  |  Diabetologia

Ecological consequences of abrupt temperature changes in anaerobic digesters

Celine Madigou, Kim-Anh Le Cao, Chrystelle Bureau, Laurent Mazeas, Sebastien Dejean, Olivier Chapleur

Journal article  |  2019  |  Chemical Engineering Journal

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

Journal article  |  2019  |  Annals of the Rheumatic Diseases

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

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, et al.

Journal article  |  2019  |  Nature Communications

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

An improved clinical model to predict stimulated C-peptide in children with recent-onset type 1 diabetes.

Kerry Buchanan, Ahmed M Mehdi, Ian Hughes, Andrew Cotterill, Kim-Anh Le Cao, Ranjeny Thomas, Mark Harris

Journal article  |  2019  |  Pediatric Diabetes

BACKGROUND: Stimulated C-peptide measurement after a mixed meal tolerance test (MMTT) is the accepted gold standard for assessing ..

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

Nicholas D'Arcy, Nicholas Matigian, Kim-Anh Le Cao, Brian Gabrielli

Journal article  |  2019  |  Pigment Cell & Melanoma Research

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

Journal article  |  2018  |  Molecular & Cellular Proteomics

Taxonomic and functional assessment reveals specific rumen microbial species and gene families associated with feed efficiency in Angus cattle

A Neves, K Le Cao, S Mandal, T Sharpton, T McAllister, L Guan

Conference Proceedings  |  2018  |  JOURNAL OF ANIMAL SCIENCE

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

Report  |  2018

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

Intestinal Metaproteomics Reveals Host-Microbiota Interactions in Subjects at Risk for Type 1 Diabetes

Patrick G Gavin, Jane A Mullaney, Dorothy Loo, Kim-Anh Le Cao, Peter A Gottlieb, Michelle M Hill, Danny Zipris, Emma E Hamilton-Williams

Journal article  |  2018  |  Diabetes Care

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

Journal article  |  2018  |  mBio

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

Linda A Bradbury, Kelly A Hollis, Benoit Gautier, Sateesh Shankaranarayana, Philip C Robinson, Nivene Saad, Kim-Anh Le Cao, Matthew A Brown

Journal article  |  2018  |  The Journal of Rheumatology

OBJECTIVE: We tested the discriminatory capacity of diffusion-weighted magnetic resonance imaging (DWI) and its potential as an ob..

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

Nan Xie, Nicholas Matigian, Tharindu Vithanage, Kye Gregory, Zeyad D Nassar, Peter J Cabot, Paul N Shaw, Carl MJ Kirkpatrick, Le Cao Kim-Anh, David Sturgess, Marie-Odile Parat

Journal article  |  2018  |  Clinical Cancer Research

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

Ahmed M Mehdi, Emma E Hamilton-Williams, Alexandre Cristino, Anette Ziegler, Ezio Bonifacio, Kim-Anh Le Cao, Mark Harris, Ranjeny Thomas

Journal article  |  2018  |  JCI Insight

Multivariate Analysis of Multiple Datasets: a Practical Guide for Chemical Ecology

Maxime R Herve, Florence Nicole, Kim-Anh Le Cao

Journal article  |  2018  |  Journal of Chemical Ecology

Chemical ecology has strong links with metabolomics, the large-scale study of all metabolites detectable in a biological sample. C..

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

Aimee L Hanson, Thomas Cuddihy, Katelin Haynes, Dorothy Loo, Craig J Morton, Udo Oppermann, Paul Leo, Gethin P Thomas, Le Cao Kim-Anh, Tony J Kenna, Matthew A Brown

Journal article  |  2018  |  Arthritis & Rheumatology

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

Mathew P Watts, Han M Gan, Lee Y Peng, Kim-Anh Le Cao, John W Moreau

Journal article  |  2017  |  Environmental Science & Technology

Human Hepatocellular Carcinomas With a Periportal Phenotype Have the Lowest Potential for Early Recurrence After Curative Resection

Romain Desert, Florian Rohart, Frederic Canal, Marie Sicard, Mireille Desille, Stephanie Renaud, Bruno Turlin, Pascale Bellaud, Christine Perret, Bruno Clement, Kim-Anh Le Cao, Orlando Musso

Journal article  |  2017  |  Hepatology

Hepatocellular carcinomas (HCCs) exhibit a diversity of molecular phenotypes, raising major challenges in clinical management. HCC..

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

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

Journal article  |  2017  |  PLOS Computational Biology

Streptococcus Species Enriched in the Oral Cavity of RA Patients: A Persistent Source of Peptidoglycan-Polysaccharide Polymers Which Drive Disseminated Synovial Inflammation

Rabia Moentadj, Linda Rehaume, Paraic O Cuiv, Kate Ormerod, Muralidhara Maradana, Vanessa Anne Lakis, Mark Morrison, Philip Hugenholtz, Helen Benham, Kim-Anh Le Cao, Ranjeny Thomas

Conference Proceedings  |  2017  |  ARTHRITIS & RHEUMATOLOGY

IL-23 Promotes Fecal Microbiota Dysbiosis Associated with Susceptibility to Spondyloarthritis and Ileitis in ZAP-70 Mutant SKG Mice

Linda Rehaume, Nicholas Matigian, Kate Ormerod, Alicia Kang, Richard Linedale, Olga Zbarskaya, Kristine Kikly, Joshua Daly, Nancy Lachner, Philip Hugenholtz, Mark Morrison, Kim-Anh Le Cao, Ranjeny Thomas

Conference Proceedings  |  2017  |  ARTHRITIS & RHEUMATOLOGY

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

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

Journal article  |  2017  |  Bioinformatics

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

Colm Keane, Clare Gould, Kimberley Jones, David Hamm, Dipti Talaulikar, Jonathan Ellis, Frank Vari, Simone Birch, Erica Han, Peter Wood, Kim-Anh Le-Cao, Michael R Green, Pauline Crooks, Sanjiv Jain, Josh Tobin, Raymond J Steptoe, Maher K Gandhi

Journal article  |  2017  |  Clinical Cancer Research

Purpose: To investigate the relationship between the intra-tumoral T-cell receptor (TCR) repertoire and the tumor microenvironment..

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

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

Journal article  |  2017  |  Scientific Reports

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

Florian Rohart, Aida Eslami, Nicholas Matigian, Stéphanie Bougeard, Kim-Anh Lê Cao

Journal article  |  2017  |  BMC Bioinformatics

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

mixOmics: an R package for ‘omics feature selection and multiple data integration

Florian Rohart, Benoît Gautier, Amrit Singh, Kim-Anh Lê Cao

Journal article  |  2017

Abstract The advent of high throughput technologies has led to a wealth of publicly available ‘omics data coming from different so..

Multi-Omic Biomarker Signatures Are Predictive Of The Allergen-Induced Late Phase Asthmatic Response

A Singh, CP Shannon, Y Kim, M DeMarco, K-A Le Cao, G Gauvreau, JM Fitzgerald, L-P Boulet, P O'Byrne, SJ Tebbutt

Conference Proceedings  |  2017  |  AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

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

Journal article  |  2016  |  Scientific Reports

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

Journal article  |  2016  |  Clinical Proteomics

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

Journal article  |  2016  |  Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

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

Journal article  |  2016  |  Scientific Reports

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

Journal article  |  2016  |  PLOS ONE

DIABLO: from multi-omics assays to biomarker discovery, an integrative approach

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

Journal article  |  2016

Abstract Systems biology approaches, leveraging multi-omics measurements, are needed to capture the complexity of biological netwo..

HLA-B27 HAS MAJOR EFFECTS ON THE INTESTINAL MICROBIOME

ME Costello, M Asquith, KA Le Cao, S Diamond, T Martin, JT Rosenbaum, MA Brown

Conference Proceedings  |  2016  |  CLINICAL AND EXPERIMENTAL RHEUMATOLOGY

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

Journal article  |  2016  |  Pigment Cell & Melanoma Research

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

KILLER IMMUNOGLOBULIN-LIKE RECEPTORS ARE ASSOCIATED WITH ANKYLOSING SPONDYLITIS

AL Hanson, KA Le Cao, TJ Kenna, MA Brown

Conference Proceedings  |  2016  |  CLINICAL AND EXPERIMENTAL RHEUMATOLOGY

Glyco-centric lectin magnetic bead array (LeMBA) proteomics dataset of human serum samples from healthy, Barrett's esophagus and esophageal adenocarcinoma individuals

Alok K Shah, Kim-Anh Le Cao, Eunju Choi, David Chen, Benoit Gautier, Derek Nancarrow, David C Whiteman, Peter R Baker, Karl R Clauser, Robert J Chalkley, Nicholas A Saunders, Andrew P Barbour, Virendra Joshi, Michelle M Hill

Journal article  |  2016  |  Data in Brief

A molecular classification of human mesenchymal stromal cells

Florian Rohart, Elizabeth A Mason, Nicholas Matigian, Rowland Mosbergen, Othmar Korn, Tyrone Chen, Suzanne Butcher, Jatin Patel, Kerry Atkinson, Kiarash Khosrotehrani, Nicholas M Fisk, Kim-Anh Le Cao, Christine A Wells

Journal article  |  2016  |  PeerJ

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

Amy E Anderson, Arthur G Pratt, Mamdouh AK Sedhom, John Paul Doran, Christine Routledge, Ben Hargreaves, Philip M Brown, Kim-Anh Le Cao, John D Isaacs, Ranjeny Thomas

Journal article  |  2016  |  Annals of the Rheumatic Diseases

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

Journal article  |  2016  |  Molecular Oncology

Serum Glycoprotein Biomarker Discovery and Qualification Pipeline Reveals Novel Diagnostic Biomarker Candidates for Esophageal Adenocarcinoma

Alok K Shah, Kim-Anh Le Cao, Eunju Choi, David Chen, Benoit Gautier, Derek Nancarrow, David C Whiteman, Nicholas A Saunders, Andrew P Barbour, Virendra Joshi, Michelle M Hill

Journal article  |  2015  |  Molecular & Cellular Proteomics

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

Colm Keane, Frank Vari, Mark Hertzberg, Kim-Anh Le Cao, Michael R Green, Erica Han, John F Seymour, Rodney J Hicks, Devinder Gill, Pauline Crooks, Clare Gould, Kimberley Jones, Lyn R Griffiths, Dipti Talaulikar, Sanjiv Jain, Josh Tobin, Maher K Gandhi

Journal article  |  2015  |  The Lancet Haematology

Diffusion Weighted Imaging Is a Sensitive and Specific MRI Protocol for the Diagnosis and Assessment of Disease Severity in Ankylosing Spondylitis

Linda A Bradbury, Kelly A Hollis, Benoit Gautier, Sateesh Shankaranarayana, Philip Robinson, Nivene Saad, Kim-Anh Le Cao, Matthew A Brown

Conference Proceedings  |  2015  |  ARTHRITIS & RHEUMATOLOGY

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

Jasmin Straube, Alain-Dominique Gorse, Bevan Emma Huang, Kim-Anh Le Cao

Journal article  |  2015  |  PLOS ONE

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

Helen Benham, Hendrik J Nel, Soi Cheng Law, Ahmed M Mehdi, Shayna Street, Nishta Ramnoruth, Helen Pahau, Bernett T Lee, Jennifer Ng, Marion EG Brunck, Claire Hyde, Leendert A Trouw, Nadine L Dudek, Anthony W Purcell, Brendan J O'Sullivan, John E Connolly, Sanjoy K Paul, Kim-Anh Le Cao, Ranjeny Thomas

Journal article  |  2015  |  Science Translational Medicine

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

Michael B Clark, Tim R Mercer, Giovanni Bussotti, Tommaso Leonardi, Katelin R Haynes, Joanna Crawford, Marion E Brunck, Kim-Anh Le Cao, Gethin P Thomas, Wendy Y Chen, Ryan J Taft, Lars K Nielsen, Anton J Enright, John S Mattick, Marcel E Dinger

Journal article  |  2015  |  Nature Methods

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

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

Journal article  |  2015  |  Bioinformatics

Analysing delays between time course gene expression data and biomarkers

J Straube, A Bernard, BE Huang, KA Le Cao

Conference Proceedings  |  2015  |  CEUR Workshop Proceedings

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

Journal article  |  2015  |  Lancet Haematology

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

B Emma Huang, David Clifford, Kim-Anh Le Cao

Journal article  |  2014  |  Medical Journal of Australia

Genome-wide characterization of the routes to pluripotency

Samer MI Hussein, Mira C Puri, Peter D Tonge, Marco Benevento, Andrew J Corso, Jennifer L Clancy, Rowland Mosbergen, Mira Li, Dong-Sung Lee, Nicole Cloonan, David LA Wood, Javier Munoz, Robert Middleton, Othmar Korn, Hardip R Patel, Carl A White, Jong-Yeon Shin, Maely E Gauthier, Kim-Anh Le Cao, Jong-Il Kim, et al.

Journal article  |  2014  |  Nature

Novel Multivariate Methods for Integration of Genomics and Proteomics Data: Applications in a Kidney Transplant Rejection Study

Oliver P Guenther, Heesun Shin, Raymond T Ng, W Robert McMaster, Bruce M McManus, Paul A Keown, Scott J Tebbutt, Kim-Anh Le Cao

Journal article  |  2014  |  OMICS: A Journal of Integrative Biology

Multiple Mechanisms of Tolerance Characterize the Immune Response to Autologous Modified Dendritic Cells Exposed to Citrullinated Peptides in Patients with Rheumatoid Arthritis.

Soi-Cheng Law, Hendrik Nel, Ahmed Mehdi, Kim-Anh Le Cao, Ranjeny Thomas

Conference Proceedings  |  2014  |  ARTHRITIS & RHEUMATOLOGY

RNA SEQUENCING IN ANKYLOSING SPONDYLITIS IDENTIFIES A NOVEL DISEASE-SPECIFIC TRANSCRIPTOME AND SPLICE VARIANTS

KH Haynes, T Cuddihy, K Le Cao, L Bradbury, MA Brown, GP Thomas

Conference Proceedings  |  2014  |  CLINICAL AND EXPERIMENTAL RHEUMATOLOGY

PTRF/cavin-1 neutralizes non-caveolar caveolin-1 microdomains in prostate cancer

H Moon, CS Lee, KL Inder, S Sharma, E Choi, DM Black, K-A Le Cao, C Winterford, JI Coward, MT Ling, DJ Craik, RG Parton, PJ Russell, MM Hill

Journal article  |  2014  |  Oncogene

Variable selection for generalized canonical correlation analysis

Arthur Tenenhaus, Cathy Philippe, Vincent Guillemot, Kim-Anh Le Cao, Jacques Grill, Vincent Frouin

Journal article  |  2014  |  Biostatistics

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

Kim-Anh Le Cao, Florian Rohart, Leo McHugh, Othmar Korn, Christine A Wells

Journal article  |  2014  |  Genomics

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

F Dost, K Le Cao, PJ Ford, C Ades, CS Farah

Journal article  |  2014  |  Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology

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

Chao Liu, Sriganesh Srihari, Kim-Anh Le Cao, Georgia Chenevix-Trench, Peter T Simpson, Mark A Ragan, Kum Kum Khanna

Journal article  |  2014  |  Nucleic Acids Research

The statistician's guide to a cracking good Christmas party

D Clifford, BE Huang, KA Lê Cao

Journal article  |  2014  |  Significance

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

Fatima Dost, Kim-Anh Le Cao, Pauline J Ford, Camile S Farah

Journal article  |  2013  |  Oral Surgery, Oral Medicine, Oral Pathology and Oral Radiology

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

Daniel M Hohenhaus, Kolja Schaale, Kim-Anh Le Cao, Vernon Seow, Abishek Iyer, David P Fairlie, Matthew J Sweet

Journal article  |  2013  |  Immunobiology

Abstract 2499: Diagnostic serum biomarkers for canine hemangiosarcoma: a potential model of human angiosarcoma.

Eunju Choi, David Chen, Kim-Anh Lê Cao, Helle Bielefeldt-Ohmann, Caroline A O'Leary, Michelle M Hill

Journal article  |  2013  |  Cancer Chemistry

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

Benoit Liquet, Kim-Anh Le Cao, Hakim Hocini, Rodolphe Thiebaut

Journal article  |  2012  |  BMC Bioinformatics

Visualising associations between paired 'omics' data sets

Ignacio Gonzalez, Kim-Anh Le Cao, Melissa J Davis, Sebastien Dejean

Journal article  |  2012  |  BMC BioData Mining

Ski Overexpression in Skeletal Muscle Modulates Genetic Programs That Control Susceptibility to Diet-Induced Obesity and Insulin Signaling

Marianne Diaz, Nick Martel, Rebecca L Fitzsimmons, Natalie A Eriksson, Gary J Cowin, Gethin P Thomas, Kim-Anh Le Cao, George EO Muscat, Gary M Leong

Journal article  |  2012  |  Obesity

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

R Thiebaut, B Liquet, H Hocini, S Hue, L Richert, M Raimbault, K Le Cao, Y Levy

Journal article  |  2012  |  Retrovirology

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

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

Journal article  |  2012  |  BMC SYSTEMS BIOLOGY

Uncoupled Embryonic and Extra-Embryonic Tissues Compromise Blastocyst Development after Somatic Cell Nuclear Transfer

Severine A Degrelle, Florence Jaffrezic, Evelyne Campion, Kim-Anh Le Cao, Daniel Le Bourhis, Christophe Richard, Nathalie Rodde, Renaud Fleurot, Robin E Everts, Jerome Lecardonnel, Yvan Heyman, Xavier Vignon, Xiangzhong Yang, Xiuchun C Tian, Harris A Lewin, Jean-Paul Renard, Isabelle Hue

Journal article  |  2012  |  PLoS ONE

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

Kate Schroder, Katharine M Irvine, Martin S Taylor, Nilesh J Bokil, Kim-Anh Le Cao, Kelly-Anne Masterman, Larisa I Labzin, Colin A Semple, Ronan Kapetanovic, Lynsey Fairbairn, Altuna Akalin, Geoffrey J Faulkner, John Kenneth Baillie, Milena Gongora, Carsten O Daub, Hideya Kawaji, Geoffrey J McLachlan, Nick Goldman, Sean M Grimmond, Piero Carninci, et al.

Journal article  |  2012  |  Proceedings of the National Academy of Sciences

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

Fangzhou Yao, Jeff Coquery, Kim-Anh Le Cao

Journal article  |  2012  |  BMC Bioinformatics

Determinants of Body Fat in Infants of Women With Gestational Diabetes Mellitus Differ With Fetal Sex

Barbara E Lingwood, Alexandra M Henry, Michael C d'Emden, Amanda-Mei Fullerton, Robin H Mortimer, Paul B Colditz, Kim-Anh Le Cao, Leonie K Callaway

Journal article  |  2011  |  Diabetes Care

Sorting the nuclear proteome

Denis C Bauer, Kai Willadsen, Fabian A Buske, Kim-Anh Le Cao, Timothy L Bailey, Graham Dellaire, Mikael Boden

Journal article  |  2011  |  Bioinformatics

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

Kim-Anh Le Cao, Simon Boitard, Philippe Besse

Journal article  |  2011  |  BMC Bioinformatics

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

Severine A Degrelle, Kim-Anh Le Cao, Yvan Heyman, Robin E Everts, Evelyne Campion, Christophe Richard, Celine Ducroix-Crepy, X Cindy Tian, Harris A Lewin, Jean-Paul Renard, Christele Robert-Granie, Isabelle Hue

Journal article  |  2011  |  REPRODUCTION

Integrative mixture of experts to combine clinical factors and gene markers

Kim-Anh Le Cao, Emmanuelle Meugnier, Geoffrey J McLachlan

Journal article  |  2010  |  Bioinformatics

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

Kim-Anh Le Cao, Ignacio Gonzalez, Sebastien Dejean

Journal article  |  2009  |  Bioinformatics

Multiclass classification and gene selection with a stochastic algorithm

Kim-Anh Le Cao, Agnes Bonnet, Sebastien Gadat

Journal article  |  2009  |  Computational Statistics & Data Analysis

A pilot study on transcriptome data analysis of folliculogenesis in pigs

G Tosser-Klopp, K-A Le Cao, A Bonnet, N Gobert, F Hatey, C Robert-Granie, S Dejean, J Antic, L Baschet, M SanCristobal

Journal article  |  2009  |  animal

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

Kim-Anh Le Cao, Pascal GP Martin, Christele Robert-Granie, Philippe Besse

Journal article  |  2009  |  BMC Bioinformatics

Statistical Analysis on Microarray Data: Selection of Gene Prognosis Signatures

Kim-Anh Le Cao, Geoffrey J McLachlan

Book Chapter  |  2009

ofw: An R Package to Select Continuous Variables for Multiclass Classification with a Stochastic Wrapper Method

Kim-Anh Le Cao, Patrick Chabrier

Journal article  |  2008  |  JOURNAL OF STATISTICAL SOFTWARE

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

A Bonnet, KA Le Cao, M SanCristobal, F Benne, C Robert-Granie, G Law-So, S Fabre, P Besse, E De Billy, H Quesnel, F Hatey, G Tosser-Klopp

Journal article  |  2008  |  REPRODUCTION

A Sparse PLS for Variable Selection when Integrating Omics Data

Kim-Anh Le Cao, Debra Rossouw, Christele Robert-Granie, Philippe Besse

Journal article  |  2008  |  Statistical Applications in Genetics and Molecular Biology

Selection of biologically relevant genes with a wrapper stochastic algorithm

Kim-Anh Le Cao, Olivier Goncalves, Philippe Besse, Sebastien Gadat

Journal article  |  2007  |  STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY

The EADGENE microarray data analysis workshop (open access publication)

Dirk-Jan De Koning, Florence Jaffrezic, Mogens Sando Lund, Michael Watson, Caroline Channing, Ina Hulsegge, Marco H Pool, Bart Buitenhuis, Jakob Hedegaard, Henrik Hornshoj, Li Jiang, Peter Sorensen, Guillemette Marot, Celine Delmas, Kim-Anh Le Cao, Magali San Cristobal, Michael D Baron, Roberto Malinverni, Alessandra Stella, Ronald M Brunner, et al.

Journal article  |  2007  |  Genetics Selection Evolution

Analysis of the real EADGENE data set: Multivariate approaches and post analysis (Open Access publication)

Peter Sorensen, Agnes Bonnet, Bart Buitenhuis, Rodrigue Closset, Sebastien Dejean, Celine Delmas, Mylene Duval, Liz Glass, Jakob Hedegaard, Henrik Hornshoj, Ina Hulsegge, Florence Jaffrezic, Kirsty Jensen, Li Jiang, Dirk-Jan De Koning, Kim-Anh Le Cao, Haisheng Nie, Wolfram Petzl, Marco H Pool, Christele Robert-Granie, et al.

Journal article  |  2007  |  Genetics Selection Evolution

Analysis of a simulated microarray dataset: Comparison of methods for data normalisation and detection of differential expression (Open Access publication)

Michael Watson, Monica Perez Alegre, Michael Denis Baron, Celine Delmas, Peter Dovc, Mylene Duval, Jean Louis Foulley, Juan Jose Garrido Pavon, Ina Hulsegge, Florence Jaffrezic, Angeles Jimenez Marin, Miha Lavric, Kim Anh Le Cao, Guillemette Marot, DAphne Mouzaki, Marco H Pool, Christele Robert Granie, Magali San Cristobal, Gwenola Tosser Klopp, David Waddington, et al.

Journal article  |  2007  |  Genetics Selection Evolution

Analysis of the real EADGENE data set: Comparison of methods and guidelines for data normalisation and selection of diffrentially expressed genes (Open Access publication)

Florence Jaffrezic, Dirk-Jan De Koning, Paul J Boettcher, Agnes Bonnet, Bart Buitenhuis, Rodrigue Closset, Sebastien Dejean, Celine Delmas, Johanne C Detilleux, Peter Dovc, Mylene Duval, Jean-Louis Foulley, Jakob Hedegaard, Henrik Hornshoj, Ina Hulsegge, Luc Janss, Kirsty Jensen, Li Jiang, Miha Lavric, Kim-Anh Le Cao, et al.

Journal article  |  2007  |  Genetics Selection Evolution

ULTRASONOGRAPHIC EVALUATION OF PEYRONIES DISEASE

G BALCONI, E ANGELI, R NESSI, L DEFLAVIIS

Journal article  |  1988  |  Urologic radiology

High-resolution ultrasonography was performed on 58 patients with Peyronie's disease and on 6 healthy men; in 3 patients the exami..