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.


Selected publications from Dr Nadia Davidson

NM Davidson, Y Chen, GL Ryland, P Blombery, J Goeke and A Oshlack, JAFFAL: Detecting fusion genes with long read transcriptome sequencing, Genome Biology 23 (1) 2022. PMID: 34991664

B Schmidt, LM Brown, GL Ryland, ALonsdale, HJ Kosasih, LE Ludlow, IJ Majewski, P Blombery, PG Ekert, NM Davidson and A Oshlack, ALLSorts: an RNA-Seq subtype classifier for B-cell acute lymphoblastic leukemia, Blood advances, 6 (14), 2022, PMID: 35482550

M Cmero, B Schmidt, IJ Majewski, PG Ekert, A Oshlack and NM Davidson, MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data, Genome biology 22 (1), 296, 2021, PMID: 34686194

M Cmero, NM Davidson and A Oshlack, Using equivalence class counts for fast and accurate testing of differential transcript usage, F1000Research 8, 2019, PMID: 31143443

NM Davidson and A Oshlack, Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis, GigaScience 7 (5), giy045, 2018, PMID: 29722876

NM Davidson, ADK Hawkins and A Oshlack, SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes, Genome biology 18 (1), 148, 2017, PMID: 28778180

NM Davidson, IJ Majewski and A Oshlack, JAFFA: High sensitivity transcriptome-focused fusion gene detection, Genome medicine 7 (1), 1, 2015, PMID: 26019724

NM Davidson and A Oshlack, Corset: enabling differential gene expression analysis for de novo assembled transcriptomes, Genome Biology 15 (7), 410, 2014, PMID: 25063469

IJ Majewski, L Mittempergher, NM Davidson , A Bosma, SM Willems , HM Horlings, Id Rink, L Greger, GJK Hooijer, D Peters, PM Nederlof , I Hofland , J de Jong , J Wesseling , RJC Kluin , W Brugman , R Kerkhoven, R Nieboer , P Roepman, A Broeks, TR Muley , J Jassem, J Niklinski , N van Zandwijk, A Brazma, A Oshlack, M van den Heuvel , R Bernards ,Identification of recurrent FGFR3 fusion genes in lung cancer through kinome‐centred RNA sequencing, The Journal of pathology 230 (3), 270-276, 2013, PMID: 23661334

KL Ayers, NM Davidson, D Demiyah, KN Roeszler, F Grützner, AH Sinclair, A Oshlack and CA Smith, RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome, Genome biology 14 (3), R26, 2013, PMID: 23531366

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