Dr Warren Kaplan

Chief of Informatics

Conjoint/Adjunct Role(s)

Conjoint Lecturer, St Vincent's Clinical School, Faculty of Medicine, UNSW Australia

I am the Chief of Informatics at the Garvan Institute. Having completed a PhD (Wits University, South Africa, 1998) I joined Entigen a bioinformatics startup company, before moving to Garvan’s newly established Peter Wills Bioinformatics Centre in 2002. As bioinformatics head of the Centre my role included collaborative research and the provision of core services and infrastructure through grant funding. In my role within Garvan's Kinghorn Centre for Clinical Genomics I oversees the Centre's clinical grade genome sequencing software and informatics implementations, and manage projects relating to informatics, compute and data with partnering organisations. 

Research Interests

Genomics
Transcriptomics
High performance computing
Cloud computing
Big data
Big data analytics

Education

1998 - PhD, University of the Witwatersrand (Wits) - South Africa

Selected Publications

Tellam JT, Zhong J, Lekieffre L, Bhat P, Martinez M, et al. mRNA Structural constraints on EBNA1 synthesis impact on in vivo antigen presentation and early priming of CD8+ T cells. PLoS Pathog. 2014 Oct;10(10):e1004423. PubMed PMID: 25299404; PubMed Central PMCID: PMC4192603.

Ma X, Yang P, Kaplan WH, Lee BH, Wu LE, et al. ISL1 regulates peroxisome proliferator-activated receptor γ activation and early adipogenesis via bone morphogenetic protein 4-dependent and -independent mechanisms. Mol Cell Biol. 2014 Oct 1;34(19):3607-17. PubMed PMID: 25047837; PubMed Central PMCID: PMC4187726.

Suryani S, Carol H, Chonghaile TN, Frismantas V, Sarmah C, et al. Cell and molecular determinants of in vivo efficacy of the BH3 mimetic ABT-263 against pediatric acute lymphoblastic leukemia xenografts. Clin Cancer Res. 2014 Sep 1;20(17):4520-31. PubMed PMID: 25013123; PubMed Central PMCID: PMC4154988.

Nair R, Roden DL, Teo WS, McFarland A, Junankar S, et al. c-Myc and Her2 cooperate to drive a stem-like phenotype with poor prognosis in breast cancer. Oncogene. 2014 Jul 24;33(30):3992-4002. PubMed PMID: 24056965.

Mattick JS, Dziadek MA, Terrill BN, Kaplan W, Spigelman AD, et al. The impact of genomics on the future of medicine and health. Med J Aust. 2014 Jul 7;201(1):17-20. PubMed PMID: 24999876.

Warton K, Lin V, Navin T, Armstrong NJ, Kaplan W, Ying K, Gloss B, Mangs H, Nair SS, Hacker NF, Sutherland RL, Clark SJ, Samimi G. Methylation-capture and next-generation sequencing of free circulating DNA from human plasma. BMC Genomics. 2014 Jun 15;15(1):476. PubMed PMID: 24929644. 

Sutherland GT, Sheedy D, Sheahan PJ, Kaplan W, Kril JJ. Comorbidities, confounders, and the white matter transcriptome in chronic alcoholism. Alcohol Clin Exp Res. 2014 Apr;38(4):994-1001. doi: 10.1111/acer.12341. PubMed PMID: 24460866

Shaw AD, Tiwari Y, Kaplan W, Heath A, Mitchell PB, Schofield PR, Fullerton JM. Characterisation of genetic variation in ST8SIA2 and its interaction region in NCAM1 in patients with bipolar disorder. PLoS One. 2014 Mar 20;9(3):e92556. doi: 10.1371/journal.pone.0092556. eCollection 2014. PubMed PMID: 24651862

Nair R, Roden DL, Teo WS, McFarland A, Junankar S, Ye S, Nguyen A, Yang J, Nikolic I, Hui M, Morey A, Shah J, Pfefferle AD, Usary J, Selinger C, Baker LA, Armstrong N, Cowley MJ, Naylor MJ, Ormandy CJ, Lakhani SR, Herschkowitz JI, Perou CM, Kaplan W, O'Toole SA, Swarbrick A. c-Myc and Her2 cooperate to drive a stem-like phenotype with poor prognosis in breast cancer. Oncogene. 2013 Sep 23. doi: 10.1038/onc.2013.368. PubMed PMID: 24056965

Apte MV, Yang L, Phillips PA, Xu Z, Kaplan W, Cowley M, Pirola RC, Wilson JS. Extracellular matrix composition significantly influences pancreatic stellate cell gene expression pattern: role of transgelin in PSC function. Am J Physiol Gastrointest Liver Physiol. 2013 Sep 15;305(6):G408-17. doi: 10.1152/ajpgi.00016.2013. Epub 2013 Jul 18. PubMed PMID: 23868411

Kalyuga M, Gallego-Ortega D, Lee HJ, Roden DL, Cowley MJ, Caldon CE, Stone A, Allerdice SL, Valdes-Mora F, Launchbury R, Statham AL, Armstrong N, Alles MC, Young A, Egger A, Au W, Piggin CL, Evans CJ, Ledger A, Brummer T, Oakes SR, Kaplan W, Gee JM, Nicholson RI, Sutherland RL, Swarbrick A, Naylor MJ, Clark SJ, Carroll JS, Ormandy CJ. ELF5 Suppresses Estrogen Sensitivity and Underpins the Acquisition of Antiestrogen Resistance in Luminal Breast Cancer. PLoS Biol. 2012 Dec;10(12) PMID: 23300383

Cantley J, Walters SN, Jung MH, Weinberg A, Cowley MJ, Whitworth PT, Kaplan W, Hawthorne WJ, O'Connell PJ, Weir G, Grey ST. A Pre-Existent Hypoxic Gene Signature Predicts Impaired Islet Graft Function And Glucose Homeostasis. Cell Transplant. 2012 Oct 31. PMID: 23127310

Biankin AV, Waddell N, Kassahn KS, Gingras MC, Muthuswamy LB, Johns AL, Miller DK, Wilson PJ, Patch AM, Wu J, Chang DK, Cowley MJ, Gardiner BB, Song S, Harliwong I, Idrisoglu S, Nourse C, Nourbakhsh E, Manning S, Wani S, Gongora M, Pajic M, Scarlett CJ, Gill AJ, Pinho AV, Rooman I, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu C, Nones K, Lynn Fink J, Christ A, Bruxner T, Cloonan N, Kolle G, Newell F, Pinese M, Scott Mead R, Humphris JL, Kaplan W, Jones MD, Colvin EK, Nagrial AM, Humphrey ES, Chou A, Chin VT, Chantrill LA, Mawson A, Samra JS, Kench JG, Lovell JA, Daly RJ, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N; Australian Pancreatic Cancer Genome Initiative; The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Biankin AV, Johns AL, Mawson A, Chang DK, Scarlett CJ, Brancato MA, Rowe SJ, Simpson SL, Martyn-Smith M, Thomas MT, Chantrill LA, Chin VT, Chou A, Cowley MJ, Humphris JL, Jones MD, Scott Mead R, Nagrial AM, Pajic M, Pettit J, Pinese M, Rooman I, Wu J, Tao J, Dipietro R, Watson C, Wong R, Pinho AV, Giry-Laterriere M, Daly RJ, Musgrove EA, Sutherland RL; Queensland Center for Medical Genomics, Institute for Molecular Bioscience, Grimmond SM, Waddell N, Kassahn KS, Miller DK, Wilson PJ, Patch AM, Song S, Harliwong I, Idrisoglu S, Nourse C, Nourbakhsh E, Manning S, Wani S, Gongora M, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu C, Nones K, Lynn Fink J, Christ A, Bruxner T, Cloonan N, Newell F, Pearson JV; Royal North Shore Hospital, Samra JS, Gill AJ, Pavlakis N, Guminski A, Toon C; Bankstown Hospital, Biankin AV, Asghari R, Merrett ND, Chang DK, Pavey DA, Das A; Liverpool Hospital, Cosman PH, Ismail K, O'Connor C; Westmead Hospital, Lam VW, McLeod D, Pleass HC, Richardson A, James V; Royal Prince Alfred Hospital, Kench JG, Cooper CL, Joseph D, Sandroussi C, Crawford M, Gallagher J; Fremantle Hospital, Texler M, Forrest C, Laycock A, Epari KP, Ballal M, Fletcher DR, Mukhedkar S; Sir Charles Gairdner Hospital, Spry NA, Deboer B, Chai M; St John of God Healthcare, Zeps N, Beilin M, Feeney K; Royal Adelaide Hospital, Nguyen NQ, Ruszkiewicz AR, Worthley C, Tan CP, Debrencini T; Flinders Medical Centre, Chen J, Brooke-Smith ME, Papangelis V; Greenslopes Private Hospital, Tang H, Barbour AP; Envoi Pathology, Clouston AD, Martin P; Princess Alexandria Hospital, O'Rourke TJ, Chiang A, Fawcett JW, Slater K, Yeung S, Hatzifotis M, Hodgkinson P; Austin Hospital, Christophi C, Nikfarjam M, Mountain Victorian Cancer Biobank A; Johns Hopkins Medical Institutes, Eshleman JR, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Schulick RD, Wolfgang CL, Morgan RA, Hodgin MB; ARC-NET Center for Applied Research on Cancer, Scarpa A, Lawlor RT, Capelli P, Beghelli S, Corbo V, Scardoni M, Pederzoli P, Tortora G, Bassi C; University of California, San Francisco, Tempero MA, Kakkar N, Zhao F, Qing Wu Y, Wang M, Muzny DM, Fisher WE, Charles Brunicardi F, Hodges SE, Reid JG, Drummond J, Chang K, Han Y, Lewis LR, Dinh H, Buhay CJ, Beck T, Timms L, Sam M, Begley K, Brown A, Pai D, Panchal A, Buchner N, De Borja R, Denroche RE, Yung CK, Serra S, Onetto N, Mukhopadhyay D, Tsao MS, Shaw PA, Petersen GM, Gallinger S, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Schulick RD, Wolfgang CL, Morgan RA, Lawlor RT, Capelli P, Corbo V, Scardoni M, Tortora G, Tempero MA, Mann KM, Jenkins NA, Perez-Mancera PA, Adams DJ, Largaespada DA, Wessels LF, Rust AG, Stein LD, Tuveson DA, Copeland NG, Musgrove EA, Scarpa A, Eshleman JR, Hudson TJ, Sutherland RL, Wheeler DA, Pearson JV, McPherson JD, Gibbs RA, Grimmond SM. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature. 2012 Oct 24. PMID: 23103869

McCormack A, Kaplan W, Gill AJ, Little N, Cook R, Robinson B, Clifton-Bligh R. MGMT expression and pituitary tumours: relationship to tumour biology. Pituitary. 2012 Jul 15. PMID: 22797801

Holt LJ, Turner N, Mokbel N, Trefely S, Kanzleiter T, Kaplan W, Ormandy CJ, Daly RJ, Cooney GJ. Grb10 regulates the development of fiber number in skeletal muscle. FASEB J. 2012 May 23.

Swaminathan S, Suzuki K, Seddiki N, Kaplan W, Cowley MJ, Hood CL, Clancy JL, Murray DD, Méndez C, Gelgor L, Anderson B, Roth N, Cooper DA, Kelleher AD. Differential Regulation of the Let-7 Family of MicroRNAs in CD4+ T Cells Alters IL-10 Expression. J Immunol. 2012 Jun 15;188(12):6238-46.

Cowley MJ, Weinberg A, Zammit N, Walters SN, Hawthorne WJ, Loudovaris T, Thomas H, Kay T, Gunton JE, Alexander SI, Kaplan W, Chapman J, O'Connell PJ, Grey ST. Human Islets Express A Marked Pro-Inflammatory Molecular Signature Prior To Transplantation. Cell Transplant. 2012

Bhadri VA, Cowley MJ, Kaplan W, Trahair TN, Lock RB. Evaluation of the NOD/SCID xenograft model for glucocorticoid-regulated gene expression in childhood B-cell precursor acute lymphoblastic leukemia. BMC Genomics. 2011

Vu TT, Gatto D, Turner V, Funnell AP, Mak KS, Norton LJ, Kaplan W, Cowley MJ, Agenès F, Kirberg J, Brink R, Pearson RC, Crossley M. Impaired B cell development in the absence of Krüppel-like factor 3. J Immunol. 2011

Jankova L, Chan C, Fung CL, Song X, Kwun SY, Cowley MJ, Kaplan W, Dent OF, Bokey EL, Chapuis PH, Baker MS, Robertson GR, Clarke SJ, Molloy MP. Proteomic comparison of colorectal tumours and non-neoplastic mucosa from paired patient samples using iTRAQ mass spectrometry. Mol Biosyst. 2011

Zhao JT, Cowley MJ, Lee P, Birzniece V, Kaplan W, Ho KK. Identification of novel GH-regulated pathway of lipid metabolism in adipose tissue: a gene expression study in hypopituitary men. J Clin Endocrinol Metab. 2011

Hilton HN, Kalyuga M, Cowley MJ, Alles MC, Lee HJ, Caldon CE, Blazek K, Kaplan W, Musgrove EA, Daly RJ, Naylor MJ, Graham JD, Clarke CL, Ormandy CJ. The antiproliferative effects of progestins in T47D breast cancer cells are tempered by progestin induction of the ETS transcription factor Elf5. Mol Endocrinol. 2010

Li J, Sze DM, Brown RD, Cowley MJ, Kaplan W, Mo SL, Yang S, Aklilu E, Kabani K, Loh YS, Yamagishi T, Chen Y, Ho PJ, Joshua DE. Clonal expansions of cytotoxic T cells exist in the blood of patients with Waldenstrom macroglobulinemia but exhibit anergic properties and are eliminated by nucleoside analogue therapy. Blood. 2010

Coolen MW, Stirzaker C, Song JZ, Statham AL, Kassir Z, Moreno CS, Young AN, Varma V, Speed TP, Cowley M, Lacaze P, Kaplan W, Robinson MD, Clark SJ. Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol. 2010

Mitchell CJ, Nelson AE, Cowley MJ, Kaplan W, Stone G, Sutton SK, Lau A, Lee CM, Ho KK. Detection of growth hormone doping by gene expression profiling of peripheral blood. J Clin Endocrinol Metab. 2009

Dr Warren Kaplan