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Select Publications

By Conjoint Professor Paul Ekert

Preprints

Lonsdale A; Halman A; Brown L; Kosasih H; Ekert P; Oshlack A, 2022, Toblerone: detecting exon deletion events in cancer using RNA-seq, http://dx.doi.org/10.1101/2022.10.27.514132

Schmidt B; Cmero M; Ekert P; Davidson N; Oshlack A, 2021, Slinker: Visualising novel splicing events in RNA-Seq data, http://dx.doi.org/10.12688/f1000research.74836.1

Mayoh C; Gifford AJ; Terry R; Lau LM; Wong M; Rao P; Shai-Hee T; Saletta F; Khuong-Quang D-A; Qin V; Mateos M; Meyran D; Miller KE; Yuksel A; Mould EV; Bowen-James R; Govender D; Senapati A; Zhukova N; Omer N; Dholaria H; Alvaro F; Tapp H; Diamond Y; Pozza LD; Moore AS; Nicholls W; Gottardo NG; McCowage G; Hansford JR; Khaw S-L; Wood PJ; Catchpoole D; Cottrell CE; Mardis ER; Marshall GM; Tyrrell V; Haber M; Ziegler DS; Vittorio O; Trapani JA; Cowley MJ; Neeson PJ; Ekert PG, A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer, http://dx.doi.org/10.1101/2022.09.16.508179

Brown L; Tax G; Mateos PA; de Weck A; Foresto S; Robertson T; Jalud F; Ajuyah P; Barahona P; Mao J; Dolman ME; Wong M; Mayoh C; Cowley M; Lau L; Sadras T; Ekert P, A novel TRKB-activating internal tandem duplication characterizes a new mechanism of receptor tyrosine kinase activation, http://dx.doi.org/10.21203/rs.3.rs-5472548/v1

Schmidt B; Brown LM; Ryland GL; Lonsdale A; Kosasih HJ; Ludlow LE; Majewski IJ; Blombery P; Ekert PG; Davidson NM; Oshlack A, ALLSorts: a RNA-Seq classifier for B-Cell Acute Lymphoblastic Leukemia, http://dx.doi.org/10.1101/2021.08.01.454393

Brown LM; Mayoh C; Camper KA; Tax G; Mateos PA; Li W; El-Kamand S; Sullivan P; Bradley J; Thompson PI; Chen J; Sadras T; Salomon R; Wong M; Cowley MJ; de Weck A; Lau LMS; Manoharan N; Ekert PG, CBL mutations in pediatric solid and CNS tumors are a marker of receptor tyrosine kinase activation and a potential therapeutic target, http://dx.doi.org/10.64898/2025.12.02.691063

Schmidt BM; Davidson NM; Hawkins AD; Bartolo R; Majewski IJ; Ekert PG; Oshlack A, Clinker: visualising fusion genes detected in RNA-seq data, http://dx.doi.org/10.1101/218586

Maksimovic J; Streeton-Cook V; Grima CV; Hanna D; Tawfic N; Ludlow LE; Brown LM; Ekert PG; Alaei S; Yoannidis D; Kosasih HJ; White DL; Ahn A; Goel S; Khaw SL; Oshlack A; Sadras T, Closing the fusion-detection gap in single-cell RNA-seq with a scalable, probe-based workflow, http://dx.doi.org/10.64898/2026.08.26.747171

Fordham AM; Brown LM; Mayoh C; Salib A; Barger ZA; Wong M; Sian TCCLK; Xie J; Gunther K; Trebilcock P; Terry RL; Barahona P; Ajuyah P; Sherstyuk A; Avila A; Cadiz R; Perkins CM; Gifford AJ; Mao J; Zhao A; O’Regan LP; Gorgels D; Lau LM; Ziegler DS; Haber M; Tyrrell V; Lock RB; Cowley MJ; Nicholls W; Daly RJ; Ekert PG; Fleuren ED, Comprehensive multi-platform tyrosine kinase profiling reveals novel actionable FGFR aberrations across pediatric and AYA sarcomas, http://dx.doi.org/10.1101/2023.07.19.548825

Kan WL; Dhagat U; Hercus TR; Kaufmann KB; Nero TL; Zeng AGX; Toubia J; Barry EF; Broughton SE; Gomez GA; Dottore M; Cheung Tung Shing KS; Thomas D; Benard B; Simpson KJ; Schoof E; Goodall GJ; Begley CG; Ekert PG; Tvorogov D; D'Andrea RJ; Dick JE; Parker MW; Lopez A, Distinct Assemblies of Heterodimeric Cytokine Receptors Govern Stemness Programs in Leukemia, http://dx.doi.org/10.2139/ssrn.3707264

Mayoh C; Barahona P; Lin A; Cui L; Ajuyah P; Altekoester A; Lau LM; Khuong-Quang D-A; Sullivan P; Senapati A; Nagabushan S; Sullivan A; Omer N; Moore AS; Nicholls W; Endersby R; Gottardo NG; McCowage G; Pozza LD; Hansford JR; Khaw S-L; Wood PJ; Trahair TN; Marshall GM; Ziegler DS; Tyrrell V; Haber M; Wong M; Ekert PG; Cowley MJ, Expanding the utility of transcriptome analysis for mutation detection in high-risk childhood precision oncology, http://dx.doi.org/10.1101/2025.06.25.661445

Sullivan AJ; Khuong-Quang D-A; Villani A; Wong-Erasmus M; Trinder S; Lau LMS; Barahona P; Altekoester A-K; Rumford M; Dias K; Mayoh C; Fuentes-Bolanos NA; Courtney EK; El-Kamand S; Cui L; Lin A; Davidson S; Yuki KE; Sanders N; Staunton J; Jessop S; Sriharan S; Alvaro F; Anazodo A; Bhatia K; Campbell M; Foresto S; Gottardo NG; Kirby M; Khaw SL; Manoharan N; McCowage G; Moore AS; Nicholls W; O’Connor M; Padhye B; Ryan AL; Super L; Wood PJ; Davies J; D’Arcy C; Gifford AJ; Rodriguez M; Tucker KM; Pinese M; Ekert PG; Haber M; Tyrrell V; Trahair TN; Marshall GM; Shlien A; Cowley MJ; Ziegler DS, High clinical utility of comprehensive multi-omic molecular profiling of rare and hard-to-diagnose pediatric tumors, http://dx.doi.org/10.21203/rs.3.rs-10108527/v1

Fuentes-Bolanos NA; Courtney E; Mayoh C; Warby M; Lau LMS; Wong-Erasmus M; Khuong-Quang D-A; Barahona P; Padhye B; El-Kamand S; Nunag S; Ajuyah P; Sherstyuk A; Altekoester A-K; Sullivan A; Poplawski N; Kiraly-Borri C; O’Sullivan S; Marfan H; Alli R; Curnow L; Bhatia K; Anazodo A; Trahair TN; Mateos M; Hansford JR; Dholaria H; Josephi-Taylor S; Moore AS; Nicholls W; Gottardo NG; Downie P; Khaw S-L; Tapp H; McCowage G; Dalla-Pozza L; Alvaro F; Wood PJ; Tyrrell V; Haber M; Cowley MJ; Ekert PG; Marshall GM; Kirk J; Tucker K; Pinese M; Ziegler DS, Integrated germline and somatic molecular profiling to detect cancer predisposition has a high clinical impact in poor-prognosis paediatric cancer, http://dx.doi.org/10.1101/2024.08.08.24311493

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, http://dx.doi.org/10.1101/2021.04.26.441398

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, http://dx.doi.org/10.1101/2020.06.03.131532

Shembrey C; Yang R; Casan J; Hu W; Sadras T; Prasad K; Shortt J; Johnstone RW; Trapani JA; Ekert PG; Fareh M, Molecular principles of CRISPR-Cas13 mismatch intolerance enable selective silencing of point-mutated oncogenic RNA with single-base precision, http://dx.doi.org/10.1101/2023.09.26.557083

Ziegler D; Lau L; Khuong-Quang D-A; Mayoh C; Wong M; Barahona P; Ajuyah P; Senapati A; Nagabushan S; Sherstyuk A; Altekoester A-K; Fuentes-Bolanos N; Yeung V; Sullivan A; Diamond Y; Omer N; Jessop S; Battaglia L; Zhukova N; Cui L; Lin A; Gifford A; Fleuren E; Dalla-Pozza L; Moore A; Khaw S; Eisenstat D; Gottardo N; Wood P; Tapp H; Alvaro F; McCowage G; Nicholls W; Hansford J; Manoharan N; Kotecha R; Mateos M; Lock R; Tyrrell V; Haber M; Trahair T; Cowley M; Ekert P; Marshall G, Precision-guided treatment improves outcomes for children with high-risk cancers, http://dx.doi.org/10.21203/rs.3.rs-3376668/v1

Fareh M; Zhao W; Hu W; Casan JM; Kumar A; Symons J; Voskoboinik I; Ekert PG; Rudraraju R; Lewin SR; Trapani JA, Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance, http://dx.doi.org/10.1101/2020.11.18.389312

Hu W; Kumar A; Qi S; Sadras T; Casan J; Ma D; Brown L; Haber M; Voskoboinik I; Trapani J; Ekert P; Fareh M, Single-base precision design of CRISPR-Cas13b enables systematic silencing of oncogenic fusions, http://dx.doi.org/10.21203/rs.3.rs-1714034/v1

Hu W; Kumar A; Qi S; Sadras T; Casan JM; Ma D; Brown LM; Haber M; Voskoboinik I; Trapani JA; Ekert PG; Fareh M, Single-base precision design of CRISPR-Cas13b enables systematic silencing of oncogenic fusions, http://dx.doi.org/10.1101/2022.06.22.497105

Mayoh C; Li W; Toumari M; Bazaz SR; Gerard A-L; Lowe A; Barahona P; Lau LM; Staunton J; Jacobson E; Nagabushan S; Manoharan N; Mitchell R; Ong F; Wong-Erasmus M; Ekert PG; Tyrrell V; Haber M; Ziegler DS; Cowley MJ; Mateos MK; Salomon R, Single-cell RNA-sequencing of cerebral spinal fluid identifies circulating tumour cells in children with brain cancer, http://dx.doi.org/10.64898/2025.12.18.694991

Hu W; Chen H; Casan JM; Shembrey C; He S; Brown LM; Hughes TP; White DL; De Weck A; Voskoboinik I; Trapani JA; Ekert PG; Sadras T; Fareh M, Systematic silencing of oncogenic fusion transcripts with ultra-precise CRISPR-Cas13b, http://dx.doi.org/10.1101/2025.02.10.637348

Gu A; Schmidt B; Lonsdale A; Brown LM; Sadras T; Ekert PG; Oshlack A, TALLSorts: a T-cell acute lymphoblastic leukaemia subtype classifier using RNA-seq expression data, http://dx.doi.org/10.1101/2023.04.05.535648

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