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About

A core area of interest for the Davidson laboratory is developing computational methods that capture novel transcripts beyond those documented in the annotation of the human reference genome. Our research is applied to cancer, where disease-causing variants – both structural rearrangements and small mutations – can alter gene structure to produce novel splicing, fusion genes or other rearrangements in the RNA.

We are exploring how advanced sequencing technologies such as long-read and single-cell, as well as large cohorts of sequencing data from cancer patients, can be used to identify and profile transcribed structural variants that drive cancer.

The computational methods we develop are shared with the medical research community as open source software. In addition to developing new bioinformatics tools, our laboratory is involved in collaborative projects that utilise high throughput sequencing with other groups within and external to WEHI.

Publications

Selected publications from Dr Nadia Davidson

Massey S, Ang C-S, Davidson NM, Quigley A, Rollo B, Harris AR, Kapsa RMI, Christodoulou J, Van Bergen NJ. Correction: Novel CDKL5 targets identified in human iPSC-derived neurons. Cellular and Molecular Life Sciences. 2024;81(1):10.1007/s00018-024-05421-x

Massey S, Ang C-S, Davidson NM, Quigley A, Rollo B, Harris AR, Kapsa RMI, Christodoulou J, Van Bergen NJ. Novel CDKL5 targets identified in human iPSC-derived neurons. Cellular and Molecular Life Sciences. 2024;81(1):10.1007/s00018-024-05389-8

Cheng O, Ling MH, Wang C, Wu S, Ritchie ME, Göke J, Amin N, Davidson NM. Flexiplex: a versatile demultiplexer and search tool for omics data. Bioinformatics. 2024;40(3):10.1093/bioinformatics/btae102

Chua CC, Anstee N, Flensburg C, Teh C, Ivey A, Amin N, Thijssen R, Bohlander SK, Kakadia PM, Xu Z, Fong CY, Ting S, Loo S, Tiong IS, Gray D, Fleming S, Davidson N, Roberts AW, Majewski I, Wei AH, Brown FC. Venetoclax Has Potent Efficacy in NPM1 mutated AML with Acquired Resistance Associated with Either Perturbed Pro-Survival Signalling or NPM1 wild-Type Populations. Blood. 2023;142(Supplement 1):10.1182/blood-2023-185321

Ayers KL, Eggers S, Rollo BN, Smith KR, Davidson NM, Siddall NA, Zhao L, Bowles J, Weiss K, Zanni G, Burglen L, Ben-Shachar S, Rosensaft J, Raas-Rothschild A, Jørgensen A, Schittenhelm RB, Huang C, Robevska G, van den Bergen J, Casagranda F, Cyza J, Pachernegg S, Wright DK, Bahlo M, Oshlack A, O’Brien TJ, Kwan P, Koopman P, Hime GR, Girard N, Hoffmann C, Shilon Y, Zung A, Bertini E, Milh M, Ben Rhouma B, Belguith N, Bashamboo A, McElreavey K, Banne E, Weintrob N, BenZeev B, Sinclair AH. Variants in SART3 cause a spliceosomopathy characterised by failure of testis development and neuronal defects. Nature Communications. 2023;14(1):10.1038/s41467-023-39040-0

Sadras T, Jalud FB, Kosasih HJ, Horne CR, Brown LM, El-Kamand S, de Bock CE, McAloney L, Ng AP, Davidson NM, Ludlow LEA, Oshlack A, Cowley MJ, Khaw SL, Murphy JM, Ekert PG. Unusual PDGFRB fusion reveals novel mechanism of kinase activation in Ph-like B-ALL. Leukemia. 2023;37(4):10.1038/s41375-023-01843-x

Schmidt B, Brown LM, Ryland GL, Lonsdale A, Kosasih HJ, Ludlow LE, Majewski IJ, Blombery P, Ekert PG, Davidson NM, Oshlack A. ALLSorts: an RNA-Seq subtype classifier for B-cell acute lymphoblastic leukemia. Blood Advances. 2022;6(14):10.1182/bloodadvances.2021005894

Brown LM, Hediyeh-zadeh S, Sadras T, Huckstep H, Sandow JJ, Bartolo RC, Kosasih HJ, Davidson NM, Schmidt B, Bjelosevic S, Johnstone R, Webb AI, Khaw SL, Oshlack A, Davis MJ, Ekert PG. SFPQ-ABL1 and BCR-ABL1 use different signaling networks to drive B-cell acute lymphoblastic leukemia. Blood Advances. 2022;6(7):10.1182/bloodadvances.2021006076

Davidson NM, Chen Y, Sadras T, Ryland GL, Blombery P, Ekert PG, Göke J, Oshlack A. JAFFAL: detecting fusion genes with long-read transcriptome sequencing. Genome Biology. 2022;23(1):10.1186/s13059-021-02588-5

Cmero M, Schmidt B, Majewski IJ, Ekert PG, Oshlack A, Davidson NM. MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data. Genome Biology. 2021;22(1):10.1186/s13059-021-02507-8

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