Alicia Oshlack

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

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

Journal article  |  2021  |  GENOME BIOLOGY

Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using exist..

Detecting copy number alterations in RNA-Seq using SuperFreq.

Christoffer Flensburg, Alicia Oshlack, Ian J Majewski

Journal article  |  2021  |  Bioinformatics

MOTIVATION: Calling copy number alterations (CNAs) from RNA sequencing (RNA-Seq) is challenging, because of the marked variability..

Gene set enrichment analysis for genome-wide DNA methylation data

Jovana Maksimovic, Alicia Oshlack, Belinda Phipson

Journal article  |  2021  |  GENOME BIOLOGY

DNA methylation is one of the most commonly studied epigenetic marks, due to its role in disease and development. Illumina methyla..

JAFFAL: Detecting fusion genes with long read transcriptome sequencing

Nadia Davidson, Ying Chen, Teresa Sadras, Georgina Ryland, Piers Blombery, Paul Ekert, Paul Ekert, Jonathan Göke, Alicia Oshlack

Journal article  |  2021

Massively parallel short read transcriptome sequencing has greatly expanded our knowledge of fusion genes which are drivers of tum..

Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor

Choon Boon Sim, Belinda Phipson, Mark Ziemann, Haloom Rafehi, Richard J Mills, Kevin I Watt, Kwaku D Abu-Bonsrah, Ravi KR Kalathur, Holly K Voges, Doan T Dinh, Menno ter Huurne, Celine J Vivien, Antony Kaspi, Harikrishnan Kaipananickal, Alejandro Hidalgo, Leanne MD Delbridge, Rebecca L Robker, Paul Gregorevic, Cristobal G dos Remedios, Sean Lal, et al.

Journal article  |  2021  |  CIRCULATION

BACKGROUND: Despite in-depth knowledge of the molecular mechanisms controlling embryonic heart development, little is known about ..

MLL-TFE3: a novel and aggressive KMT2A fusion identified in infant leukemia

Hansen J Kosasih, Nadia M Davidson, Stefan Bjelosevic, Emma Morrish, Margs S Brennan, Alicia Oshlack, Ricky W Johnstone, Gabriela Brumatti, Seong L Khaw, Paul G Ekert

Journal article  |  2020  |  BLOOD ADVANCES

Key Points A novel KMT2A-rearrangement, MLL-TFE3, was identified in an infant leukemia patient. MLL-TFE3 expression..

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

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..