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

Pavey S, Pinder A, Fernando W, D'Arcy N, Matigian N, Skalamera D, Lê Cao KA, Loo-Oey D, Hill MM, Stark M, Kimlin M, Burgess A, Cloonan N, Sturm RA, Gabrielli B.

Mol Oncol. 2019 Nov 16. doi: 10.1002/1878-0261.12601. [Epub ahead of print]


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

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

Animal. 2019 Oct 30:1-14. doi: 10.1017/S1751731119002453. [Epub ahead of print]


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

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

Nat Methods. 2019 Jun;16(6):479-487. doi: 10.1038/s41592-019-0425-8. Epub 2019 May 27.


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

Asquith M, Sternes PR, Costello ME, Karstens L, Diamond S, Martin TM, Li Z, Marshall MS, Spector TD, le Cao KA, Rosenbaum JT, Brown MA.

Arthritis Rheumatol. 2019 Oct;71(10):1642-1650. doi: 10.1002/art.40917. Epub 2019 Aug 12.


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

Watts MP, Spurr LP, Lê Cao KA, Wick R, Banfield JF, Moreau JW.

Water Res. 2019 Jul 1;158:106-117. doi: 10.1016/j.watres.2019.02.058. Epub 2019 Mar 23.


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

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

Ann Rheum Dis. 2019 Apr;78(4):494-503. doi: 10.1136/annrheumdis-2018-214381. Epub 2019 Jan 30.


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

Singh A, Shannon CP, Gautier B, Rohart F, Vacher M, Tebbutt SJ, Lê Cao KA.

Bioinformatics. 2019 Sep 1;35(17):3055-3062. doi: 10.1093/bioinformatics/bty1054.


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

Buchanan K, Mehdi AM, Hughes I, Cotterill A, Le Cao KA, Thomas R, Harris M.

Pediatr Diabetes. 2019 Mar;20(2):166-171. doi: 10.1111/pedi.12808. Epub 2019 Jan 8.


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

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

MBio. 2018 Oct 9;9(5). pii: e01432-18. doi: 10.1128/mBio.01432-18.


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

D'Arcy N, Matigian N, Lê Cao KA, Gabrielli B.

Pigment Cell Melanoma Res. 2019 Mar;32(2):336-338. doi: 10.1111/pcmr.12740. Epub 2018 Oct 22. No abstract available.


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

Mehdi AM, Hamilton-Williams EE, Cristino A, Ziegler A, Bonifacio E, Le Cao KA, Harris M, Thomas R.

JCI Insight. 2018 Mar 8;3(5). pii: 98212. doi: 10.1172/jci.insight.98212.


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

Hervé MR, Nicolè F, Lê Cao KA.

J Chem Ecol. 2018 Mar;44(3):215-234. doi: 10.1007/s10886-018-0932-6. Epub 2018 Feb 25.


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

Bradbury LA, Hollis KA, Gautier B, Shankaranarayana S, Robinson PC, Saad N, Lê Cao KA, Brown MA.

J Rheumatol. 2018 Jun;45(6):771-778. doi: 10.3899/jrheum.170312. Epub 2018 Feb 15.


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

Hanson AL, Cuddihy T, Haynes K, Loo D, Morton CJ, Oppermann U, Leo P, Thomas GP, Lê Cao KA, Kenna TJ, Brown MA.

Arthritis Rheumatol. 2018 Feb;70(2):255-265. doi: 10.1002/art.40369. Epub 2017 Dec 29.


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

Rohart F, Gautier B, Singh A, Lê Cao KA.

PLoS Comput Biol. 2017 Nov 3;13(11):e1005752. doi: 10.1371/journal.pcbi.1005752. eCollection 2017 Nov.


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

Watts MP, Gan HM, Peng LY, Lê Cao KA, Moreau JW.

Environ Sci Technol. 2017 Nov 21;51(22):13353-13362. doi: 10.1021/acs.est.7b04152. Epub 2017 Nov 8.


Human hepatocellular carcinomas with a periportal phenotype have the lowest potential for early recurrence after curative resection.

Désert R, Rohart F, Canal F, Sicard M, Desille M, Renaud S, Turlin B, Bellaud P, Perret C, Clément B, Lê Cao KA, Musso O.

Hepatology. 2017 Nov;66(5):1502-1518. doi: 10.1002/hep.29254. Epub 2017 Sep 26.


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

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

BMC Bioinformatics. 2017 Feb 27;18(1):128. doi: 10.1186/s12859-017-1553-8.


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

Patrick R, Kobe B, Lê Cao KA, Bodén M.

Bioinformatics. 2017 Jun 15;33(12):1773-1781. doi: 10.1093/bioinformatics/btx072.


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

Rohart F, Milinovich GJ, Avril SM, Lê Cao KA, Tong S, Hu W.

Sci Rep. 2016 Dec 20;6:38522. doi: 10.1038/srep38522.


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

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

Sci Rep. 2016 Sep 26;6:34000. doi: 10.1038/srep34000.


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

Keane C, Gould C, Jones K, Hamm D, Talaulikar D, Ellis J, Vari F, Birch S, Han E, Wood P, Le-Cao KA, Green MR, Crooks P, Jain S, Tobin J, Steptoe RJ, Gandhi MK.

Clin Cancer Res. 2017 Apr 1;23(7):1820-1828. doi: 10.1158/1078-0432.CCR-16-1576. Epub 2016 Sep 20.


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

Lê Cao KA, Costello ME, Lakis VA, Bartolo F, Chua XY, Brazeilles R, Rondeau P.

PLoS One. 2016 Aug 11;11(8):e0160169. doi: 10.1371/journal.pone.0160169. eCollection 2016.


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

Shah AK, Lê Cao KA, Choi E, Chen D, Gautier B, Nancarrow D, Whiteman DC, Baker PR, Clauser KR, Chalkley RJ, Saunders NA, Barbour AP, Joshi V, Hill MM.

Data Brief. 2016 Apr 1;7:1058-62. doi: 10.1016/j.dib.2016.03.081. eCollection 2016 Jun.


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

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

Pigment Cell Melanoma Res. 2016 Jul;29(4):444-52. doi: 10.1111/pcmr.12489.


A molecular classification of human mesenchymal stromal cells.

Rohart F, Mason EA, Matigian N, Mosbergen R, Korn O, Chen T, Butcher S, Patel J, Atkinson K, Khosrotehrani K, Fisk NM, Lê Cao KA, Wells CA.

PeerJ. 2016 Mar 24;4:e1845. doi: 10.7717/peerj.1845. eCollection 2016.


Identifying Molecular Mechanisms of the Late-Phase Asthmatic Response by Integrating Cellular, Gene, and Metabolite Levels in Blood.

Singh A, Shannon CP, Kim YW, DeMarco ML, Gauvreau GM, FitzGerald JM, Boulet LP, O'Byrne PM, Le Cao KA, Tebbutt SJ.

Ann Am Thorac Soc. 2016 Mar;13 Suppl 1:S98. doi: 10.1513/AnnalsATS.201510-694MG.


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

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

Mol Oncol. 2016 Jan;10(1):179-93. doi: 10.1016/j.molonc.2015.09.007. Epub 2015 Sep 26.


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

Straube J, Gorse AD; PROOF Centre of Excellence Team, Huang BE, Lê Cao KA.

PLoS One. 2015 Aug 27;10(8):e0134540. doi: 10.1371/journal.pone.0134540. eCollection 2015.


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

Benham H, Nel HJ, Law SC, Mehdi AM, Street S, Ramnoruth N, Pahau H, Lee BT, Ng J, Brunck ME, Hyde C, Trouw LA, Dudek NL, Purcell AW, O'Sullivan BJ, Connolly JE, Paul SK, Lê Cao KA, Thomas R.

Sci Transl Med. 2015 Jun 3;7(290):290ra87. doi: 10.1126/scitranslmed.aaa9301.


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

Anderson AE, Pratt AG, Sedhom MA, Doran JP, Routledge C, Hargreaves B, Brown PM, Lê Cao KA, Isaacs JD, Thomas R.

Ann Rheum Dis. 2016 Feb;75(2):466-73. doi: 10.1136/annrheumdis-2014-205850. Epub 2015 Feb 3.


Genome-wide characterization of the routes to pluripotency.

Hussein SM, Puri MC, Tonge PD, Benevento M, Corso AJ, Clancy JL, Mosbergen R, Li M, Lee DS, Cloonan N, Wood DL, Munoz J, Middleton R, Korn O, Patel HR, White CA, Shin JY, Gauthier ME, Lê Cao KA, Kim JI, Mar JC, Shakiba N, Ritchie W, Rasko JE, Grimmond SM, Zandstra PW, Wells CA, Preiss T, Seo JS, Heck AJ, Rogers IM, Nagy A.

Nature. 2014 Dec 11;516(7530):198-206. doi: 10.1038/nature14046. Erratum in: Nature. 2015 Jul 30;523(7562):626.


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

Huang BE, Clifford D, Lê Cao KA.

Med J Aust. 2014 Dec 11;201(11):694-6.


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

Günther OP, Shin H, Ng RT, McMaster WR, McManus BM, Keown PA, Tebbutt SJ, Lê Cao KA.

OMICS. 2014 Nov;18(11):682-95. doi: 10.1089/omi.2014.0062.


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

Patrick R, Lê Cao KA, Kobe B, Bodén M.

Bioinformatics. 2015 Feb 1;31(3):382-9. doi: 10.1093/bioinformatics/btu663. Epub 2014 Oct 9.


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

Lê Cao KA, Rohart F, McHugh L, Korn O, Wells CA.

Genomics. 2014 Apr;103(4):239-51. doi: 10.1016/j.ygeno.2014.03.001. Epub 2014 Mar 22.


Variable selection for generalized canonical correlation analysis.

Tenenhaus A, Philippe C, Guillemot V, Le Cao KA, Grill J, Frouin V.

Biostatistics. 2014 Jul;15(3):569-83. doi: 10.1093/biostatistics/kxu001. Epub 2014 Feb 17.


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

Dost F, Lê Cao K, Ford PJ, Ades C, Farah CS.

Oral Surg Oral Med Oral Pathol Oral Radiol. 2014 Mar;117(3):343-52. doi: 10.1016/j.oooo.2013.09.017. Epub 2013 Oct 17.


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

Dost F, Lê Cao KA, Ford PJ, Farah CS.

Oral Surg Oral Med Oral Pathol Oral Radiol. 2013 Dec;116(6):725-33. doi: 10.1016/j.oooo.2013.08.005. Epub 2013 Oct 18.


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.

Hohenhaus DM, Schaale K, Le Cao KA, Seow V, Iyer A, Fairlie DP, Sweet MJ.

Immunobiology. 2013 Nov;218(11):1345-53. doi: 10.1016/j.imbio.2013.07.001. Epub 2013 Jul 15.


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

Moon H, Lee CS, Inder KL, Sharma S, Choi E, Black DM, Lê Cao KA, Winterford C, Coward JI, Ling MT; Australian Prostate Cancer BioResource, Craik DJ, Parton RG, Russell PJ, Hill MM.

Oncogene. 2014 Jul 3;33(27):3561-70. doi: 10.1038/onc.2013.315. Epub 2013 Aug 12.


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

Liquet B, Lê Cao KA, Hocini H, Thiébaut R.

BMC Bioinformatics. 2012 Dec 6;13:325. doi: 10.1186/1471-2105-13-325.


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

Degrelle SA, Jaffrezic F, Campion E, Lê Cao KA, Le Bourhis D, Richard C, Rodde N, Fleurot R, Everts RE, Lecardonnel J, Heyman Y, Vignon X, Yang X, Tian XC, Lewin HA, Renard JP, Hue I.

PLoS One. 2012;7(6):e38309. doi: 10.1371/journal.pone.0038309. Epub 2012 Jun 6.


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

Schroder K, Irvine KM, Taylor MS, Bokil NJ, Le Cao KA, Masterman KA, Labzin LI, Semple CA, Kapetanovic R, Fairbairn L, Akalin A, Faulkner GJ, Baillie JK, Gongora M, Daub CO, Kawaji H, McLachlan GJ, Goldman N, Grimmond SM, Carninci P, Suzuki H, Hayashizaki Y, Lenhard B, Hume DA, Sweet MJ.

Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):E944-53. doi: 10.1073/pnas.1110156109. Epub 2012 Mar 26.


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

Yao F, Coquery J, Lê Cao KA.

BMC Bioinformatics. 2012 Feb 3;13:24. doi: 10.1186/1471-2105-13-24.


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

Lingwood BE, Henry AM, d'Emden MC, Fullerton AM, Mortimer RH, Colditz PB, Lê Cao KA, Callaway LK.

Diabetes Care. 2011 Dec;34(12):2581-5. doi: 10.2337/dc11-0728. Epub 2011 Oct 12.


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

Lê Cao KA, Boitard S, Besse P.

BMC Bioinformatics. 2011 Jun 22;12:253. doi: 10.1186/1471-2105-12-253.


Sorting the nuclear proteome.

Bauer DC, Willadsen K, Buske FA, Lê Cao KA, Bailey TL, Dellaire G, Bodén M.

Bioinformatics. 2011 Jul 1;27(13):i7-14. doi: 10.1093/bioinformatics/btr217.


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

Degrelle SA, Lê Cao KA, Heyman Y, Everts RE, Campion E, Richard C, Ducroix-Crépy C, Tian XC, Lewin HA, Renard JP, Robert-Granié C, Hue I.

Reproduction. 2011 Jan;141(1):79-89. doi: 10.1530/REP-10-0174. Epub 2010 Oct 6.


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

Lê Cao KA, Meugnier E, McLachlan GJ.

Bioinformatics. 2010 May 1;26(9):1192-8. doi: 10.1093/bioinformatics/btq107. Epub 2010 Mar 11.

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