Alicia Oshlack

Human yolk sac-like haematopoiesis generates RUNX1-, GFI1- and/or GFI1B-dependent blood and SOX17-positive endothelium

Freya F Bruveris, Elizabeth S Ng, Ana Rita Leitoguinho, Ali Motazedian, Katerina Vlahos, Koula Sourris, Robyn Mayberry, Penelope McDonald, Lisa Azzola, Nadia M Davidson, Alicia Oshlack, Edouard G Stanley, Andrew G Elefanty

Journal article  |  2020  |  Development (Cambridge)

The genetic regulatory network controlling early fate choices during human blood cell development are not well understood. We used..

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

Ralph Patrick, David T Humphreys, Vaibhao Janbandhu, Alicia Oshlack, Joshua WK Ho, Richard P Harvey, Kitty K Lo

Journal article  |  2020  |  Genome Biology

High-throughput single-cell RNA-seq (scRNA-seq) is a powerful tool for studying gene expression in single cells. Most current scRN..

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

Marek Cmero, Breon Schmidt, Ian Majewski, Paul Ekert, Alicia Oshlack, Nadia Davidson

Journal article  |  2020

Genomic rearrangements can modify gene function by altering transcript sequences, and have been shown to be drivers in both cancer..

Detecting copy number alterations in RNA-Seq using SuperFreq

Christoffer Flensburg, Alicia Oshlack, Ian Majewski

Journal article  |  2020

Calling copy number alterations (CNAs) from RNA-Seq is challenging, because differences in gene expression mean that read depth ac..

The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia

Lauren M Brown, Andrew Lonsdale, Andrea Zhu, Nadia M Davidson, Breon Schmidt, Anthony Hawkins, Elise Wallach, Michelle Martin, Francoise M Mechinaud, Seong Lin Khaw, Ray C Bartolo, Louise EA Ludlow, Jackie Challis, Ian Brooks, Vida Petrovic, Nicola C Venn, Rosemary Sutton, Ian J Majewski, Alicia Oshlack, Paul G Ekert

Journal article  |  2020  |  Blood Advances

Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy, and implementation of risk-adapted therapy has been in..

SuperFreq: Integrated mutation detection and clonal tracking in cancer

Christoffer Flensburg, Tobias Sargeant, Alicia Oshlack, Ian J Majewski

Journal article  |  2020  |  PLoS Computational Biology

Analysing multiple cancer samples from an individual patient can provide insight into the way the disease evolves. Monitoring the ..

Accuracy of short tandem repeats genotyping tools in whole exome sequencing data.

Andreas Halman, Alicia Oshlack

Journal article  |  2020  |  F1000Research

Background: Short tandem repeats are an important source of genetic variation. They are highly mutable and repeat expansions are a..

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

Ralph Patrick, David Humphreys, Vaibhao Janbandhu, Alicia Oshlack, Joshua WK Ho, Richard Harvey, Kitty Lo

Journal article  |  2019

Abstract High-throughput single-cell RNA-seq (scRNA-seq) is a powerful tool for studying gene expression in single cells. Most cur..

The role of cardiac transcription factor NKX2-5 in regulating the human cardiac miRNAome

Deevina Arasaratnam, Katrina M Bell, Choon Boon Sim, Kathy Koutsis, David J Anderson, Elizabeth L Qian, Edouard G Stanley, Andrew G Elefanty, Michael M Cheung, Alicia Oshlack, Anthony J White, Charbel Abi Khalil, James E Hudson, Enzo R Porrello, David A Elliott

Journal article  |  2019  |  Scientific Reports

MicroRNAs (miRNAs) are translational regulatory molecules with recognised roles in heart development and disease. Therefore, it is..

Targeted therapy and disease monitoring in CNTRL-FGFR1-driven leukaemia

Lauren M Brown, Ray C Bartolo, Nadia M Davidson, Breon Schmidt, Ian Brooks, Jackie Challis, Vida Petrovic, Dong-Anh Khuong-Quang, Francoise Mechinaud, Seong L Khaw, Ian J Majewski, Alicia Oshlack, Paul G Ekert

Journal article  |  2019  |  Pediatric Blood & Cancer

We report two patients with leukaemia driven by the rare CNTRL-FGFR1 fusion oncogene. This fusion arises from a t(8;9)(p12;q33) tr..