VCFG publications and other resources

Key publications

Chan KT, Blake B, Zhu H, Kang J, Trigos AS, Madhamshettiwar PB, Diesch J, Paavolainen L, Horvath P, Hannan RD, George AJ, Sanij E, Hannan KM, Simpson KJ and Pearson RB. A functional genetic screen defines the AKT-induced senescence signaling network. Cell Death and Differentiation. 2019.

Ma X, Zhang L, Song J, Nguyen E, Lee RS, Rodgers SJ, Li F, Huang C, Schittenhelm RB, Chan H, Cheang C, Wu J, Brown KK, Mitchell CA, Simpson KJ, Daly RJ. Characterization of the Src-regulated kinome identifies SGK1 as a key mediator of Src-induced transformation. Nature Communications Jan 17, 2019

Zoranovic T, Manent J, Willoughby L, Matos de Simoes R, La Marca JE, Golenkina S, Cuiping X, Gruber S, Angjeli B, Kanitz EE, Cronin SJF, Neely GG, Wernitznig A, Humbert PO, Simpson KJ, Mitsiades CS, Richardson HE, Penninger JM.  A genome-wide Drosophila epithelial tumorigenesis screen identifies Tetraspanin 29Fb as an evolutionarily conserved suppressor of Ras-driven cancer. PLoS Genet. 2018 Oct 16;14(10):e1007688.

Lin HM, Nikolic I, Yang J, Castillo L, Deng N, Chan CL, Yeung NK, Dodson E, Elsworth B, Spielman C, Lee BY, Boyer Z, Simpson KJ, Daly RJ, Horvath LG, Swarbrick A. MicroRNAs as potential therapeutics to enhance chemosensitivity in advanced prostate cancer.  Scientific Reports 2018 May 18;8(1):7820

Pearson H, Jason J, Meniel V, Fennell C, Waring P, Montgomery K, Rebello R, Macpherson A, Koushyar S, Furic L, Cullinane C, Clarkson R, Smalley M, Simpson KJ, Phesse T, Shepherd P, Humbert P, Sansom O and Phillips W. Identification of Pik3ca mutation as a genetic driver of prostate cancer that cooperates with Pten loss to accelerate progression and castration-resistant growth. Cancer Discovery 2018 Jun; 8(6):764-779

Darby WG, Grace MS, Simpson KJ, Woodman OL and McIntyre P. A functional kinase short interfering ribonucleic acid screen using protease-activated receptor 2-dependent opening of transient receptor potential vanilloid-4. ASSAY Drug Development Technologies, 2017 Nov 17

Cluse L.A. Nikolic I, Knight D, Madhamshettiwar PB, Luu J, Cowley KJ, Semple T, Mir Arnau G, Shortt J, Johnstone RW and Simpson KJ. (2018) A Comprehensive Protocol Resource for Performing Pooled shRNA and CRISPR Screens. In: Jenkins B. (eds) Inflammation and Cancer. Methods in Molecular Biology, vol 1725. Humana Press, New York, NY

Nikolic I, Elsworth B, Dodson E, Wu SZ, Gould CM, Mestdagh P, Marshall GM, Horvath LG, Simpson KJ, Swarbrick A. Discovering cancer vulnerabilities using high-throughput micro-RNA screening. Nucleic Acids Research. 2017 Nov 16.

Williams SP, Odell AF, Karnezis T, Farnsworth RH, Gould CM, Li J, Paquet-Fifield S, Harris NC, Walter A, Gregory JL, Lamont SF, Liu R, Takano EA, Nowell CJ, Bower NI, Resnick D, Smyth GK, Coultas L, Hogan Bm, Fox SB, Mueller SN, Simpson KJ, Achen MG, Stacker SA. Genome-wide functional analysis reveals central signaling regulators of lymphatic endothelial cell migration and remodeling. Science Signaling. 2017 Oct 3;10(499)

Manent J, Banerjee S, de Matos Simoes R, Zoranovic T, Mitsiades C, Penninger JM, Simpson KJ, Humbert PO, Richardson HE. Autophagy suppresses Ras-driven epithelial tumourigenesis by limiting the accumulation of reactive oxygen species. Oncogene. June 5, 2017.

Preston S, Jiao Y, Baell JB, Keiser J, Crawford S, Koehler AV, Wang T, Simpson MM, Kaplan RM, Cowley KJ, Simpson KJ, Hofmann A, Jabbar A, Gasser RB. Screening of the 'Open Scaffolds' collection from Compounds Australia identifies a new chemical entity with anthelmintic activities against different developmental stages of the barber's pole worm and other parasitic nematodes. International Journal Parasitology Drugs Drug Resistance. 2017 May 28;7(3):286-294.

Jiao Y, Preston S, Koehler AV, Stroehlein AJ, Chang BCH, Simpson KJ, Cowley KJ, Palmer MJ, Laleu B, Wells TNC, Jabbar A, Gasser RB. Screening of the 'Stasis Box' identifies two kinase inhibitors under pharmaceutical development with activity against Haemonchus contortus. Parasitology Vectors. 2017 Jul 5;10(1):323.

Hoffman AF, Simpson KJ, Horvath P, Lovitt C, Silvers S, Easton E, LaBarbera DV, Mendez M, Rothenberg ME, Seldin J, Wardwell-Swanson J, Fennell M.  HCS/HCA 3D Imaging: Best Practices and Unmet needs colloquium. ASSAY, Drug Development Technologies, Feb 2017

Simpson KJ, Smith JA. Knocking down the obstacles to functional genomics data sharing. Scientific DATA. 2017 Mar 1;4:170019.

Haqshenas G, Wu J, Simpson, KJ, Daly RJ, Netter HJ, Baumert TF, Doerig C. Signalome-wide assessment of host cell response to hepatitis C virus. Nature Communications. 2017 May 8;8:15158.

Williams SP, Gould CM, Nowell CJ, Karnezis T, Achen MG, Simpson KJ, Stacker SA. Systematic high content genome-wide RNAi screens of endothelial cell migration and morphology. Scientific DATA. 2017 Mar 1;4:170009.

Deffrasnes C, Marsh GA, Foo CH, Rootes CL, Gould CM, Grusovin J, Monaghan P, Lo MK, Tompkins SM, Adams TE, Lowenthal JW, Simpson KJ, Stewart CR, Bean AG, Wang LF. Genome-wide siRNA screening at biosafety level 4 reveals a crucial role for the nucleolar methyltransferase fibrillarin in henipavirus infection. PLoS Pathog. 2016; 12(3):e1005478.

Dutta B, Azhir A, Merino LH, Guo Y, Revanur S, Madhamshettiwar PB, Germain RN, Smith JA, Simpson KJ, Martin SE, Buehler E, Fraser ID. An interactive web-based application for Comprehensive Analysis of RNAi-screen Data. Nat Commun. 2016; 7:10578.

Eyre NS, Hampton-Smith RJ, Aloia AL, Eddes JS, Simpson KJ, Hoffmann P, Beard MR. Phosphorylation of NS5A Serine-235 is essential to hepatitis C virus RNA replication and normal replication compartment formation. Virology. 2016; 491:27-44.

Falkenberg KJ, Newbold A, Gould CM, Luu J, Trapani JA, Matthews GM, Simpson KJ, Johnstone RW. A genome scale siRNA screen reveals GLI1 as a novel gene regulating vorinostat sensitivity. Cell Death Differ. 2016; 23(7):1209-18.

Davis SJ, Sheppard KE, Anglesio MS, George J, Traficante N, Fereday S, Intermaggio MP, Menon U, Gentry-Maharaj A, Lubinksi J, Gronwald J, Pearce CL, Pikel MC, Wu A, Kommoss S, Pfisterer J, du Bois A, Hilpert F, Ramus SJ, Bowtell DDL, Huntsman DG, Pearson RB, Simpson KJ*, Campbell IG*, Gorringe KL*. Enhanced GAB2 expression is associated with improved survival in high-grade serous ovarian cancer and sensitivity to PI3K inhibition. Mol Cancer Ther. 2015; 14(6):1495-53. (*Equal senior author)

Fennell M, Simpson KJSociety of Biomolecular Imaging and Informatics Special Issue. Assay Drug Dev Technol. 2015; 13(9):507-8.

Bowman D, Fennell M, Simpson KJ. Colloquium: SBI2 HCS/HCA informatics and data analysis – best practices and unmet needs. September 15, 2015. Assay Drug Dev Technol. 2015; 13(9):509-14.

Fennell M, Simpson KJSociety of Biomolecular Imaging and Informatics special issueAssay Drug Dev Technol. 2015; 13(7):339-40.

Dagley MJ, Saunders EC, Simpson KJ*, McConville MJ*. High-content assay for measuring intracellular growth of Leishmania in human macrophages. Assay Drug Dev Technol. 2015; 13(7):389-401. (*Equal senior author)

Telford BJ, Chen A, Beethan H, Frick J, Brew TP, Gould CM, Single A, Godwin T, Simpson KJ, Guilford P. Synthetic lethal screens identify vulnerabilities in GPCR signaling and cytoskeletal organization in E-cadherin-deficient cells. Mol Cancer Ther. 2015; 14(5):1213-23.

Said Nur Akmarina BM, Gould CM, Lackovic K, Simpson KJ*, Williams ED*. Whole-genome multiparametric screening to identify modulators of epithelial-to-mesenchymal transition. Assay Drug Dev Technol. 2014; 12(7):385-94. (*Equal senior author)

Falkenberg KJ, Gould CM, Johnstone RW, Simpson KJ. Genome-wide functional genomic and transcriptomic analyses for genes regulating sensitivity to vorinostat. Sci Data. 2014; 1:140017.

Thomas DW, Gould CM, Handoko Y, Simpson KJ. Functional genomics down under: RNAi screening in the Victorian Centre for Functional Genomics. Comb Chem High Throughput Screen. 2014; 17(4):343-55.

Saunders DN, Falkenberg KJ, Simpson KJ. High-throughput approaches to measuring cell death. Cold Spring Harb Protoc. 2014; 2014(6):591-601.

Falkenberg KJ, Saunders DN, Simpson KJ. A high-throughput, multiplex cell death assay using an RNAi screening approach. Cold Spring Harb Protoc. 2014; 2014(6):663-76.

Brasacchio D, Noori T, House C, Brennan AJ, Simpson KJ, Susanto O, Bird PI, Johnstone RW, Trapani JA. A functional genomics screen identifies PCAF and ADA3 as regulators of human granzyme B-mediated apoptosis and Bid cleavageCell Death Differ. 2014; 21(5):748-60.

George AJ, Purdue BW, Gould CM, Thomas DW, Handoko Y, Qian H, Quaife-Ryan GA, Morgan KA, Simpson KJ, Thomas WG, Hannan RD. A functional siRNA screen identifies genes modulating angiotensin II-mediated EGFR transactivationJ Cell Sci. 2013; 126(Pt 23):5377-90.

Etemadmoghadam D, Weir BA, Au-Yeung G, Alsop K, Mitchell G, George J, Australian Ovarian Cancer Study Group, Davis S, D'Andrea AD, Simpson K, Hahn WC, Bowtell DDL. Synthetic lethality between CCNE1 amplification and loss of BRCA1Proc Natl Acad Sci USA. 2013; 110(48):19489-94.

Said Nur Akmarina BM, Simpson KJ*, Williams ED*. Strategies and challenges for systematically mapping biologically significant molecular pathways regulating carcinoma epithelial-mesenchymal transition. Cells Tissues Organs. 2013; 197(6):424-34. (*Equal senior author)

Davis SJ, Sheppard KE, Pearson RB, Campbell IG, Gorringe KL, Simpson KJ. Functional analysis of genes in regions commonly amplified in high-grade serous and endometrioid ovarian cancerClin Cancer Res. 2013; 19(6):1411-21.

Strezoska Ž, Licon A, Haimes J, Spayd KJ, Patel KM, Sullivan K, Jastrzebski K, Simpson KJ, Leake D, van Brabant Smith A, Vermeulen A. Optimized PCR conditions and increased shRNA fold representation improve reproducibility of pooled shRNA screensPLoS ONE. 2012; 7(8):e42341.

PUBLICATIONS of interest

Fuchs F, Pau G, Kranz D, Skylar O, Budjan C, Steinbrink S, Horn T, Pedal A, Huber W, Boutros M. Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Mol Syst Biol. 2010; 6:370.

Mullenders J, von der Saal W, van Dongene MM, Reiff U, van Willligen R, Beijersbergen RL, Tiefenthaler G, Klein C, Bernards R. Candidate biomarkers of response to an experimental cancer drug identified through a large-scale RNA interference genetic screen. Clin Cancer Res. 2009; 15(18):5811-9.

Birmingham A, Selfors LM, Forster T, Wrobel D, Kennedy CJ, Shanks E, Santoyo-Lopez J, Dunican DJ, Long A, Kelleher D, Smith Q, Beijersbergen RL, Ghazal P, Shamu CE. Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods. 2009; 6(8):569-75.

Gobeil S, Zhu X, Doillon CJ, Green MR. A genome-wide shRNA screen identifies GAS1 as a novel melanoma metastasis suppressor gene. Genes Dev. 2008; 22(21):2932-40.

Whitehurst AW, Bodermann CO, Cardenas J, Ferguson D, Girard L, Peyton M, Minna JD, Michnoff C, Hao W, Roth MG, Xie XJ, White MA. Synthetic lethal screen identification of chemosensitizer loci in cancer cells. Nature. 2007; 446(7137):815-9.

Other resources

Office of the Gene Technology Regulator

Australasian Genomic Technologies Association (AGTA)

Australian Cancer Research Foundation

Australian Phenomics Network (APN)

APN at the Harry Perkins Institute of Medical Research

Australian Government Education Investment Fund

The Jack Brockhoff Foundation

Society for Biomolecular Imaging and Informatics: first conference September 2014

RNAi Global Initiative: resources and information about RNAi

Thermo Scientific: Dharmacon RNAi reagent information

Victorian Department of Economic Development, Jobs, Transport and Resources

Victorian Platform Technologies Network (VPTN)

related experts

A/Prof Kaylene Simpson