Alicia Oshlack

ResearcherID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2016-2023
Publications (10 Years): 28

Top Venues

Genome biology

Nature communications

F1000Research

Blood advances

Peter MacCallum Cancer Centre

University of Melbourne (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Peter MacCallum Cancer Centre Nov 12 2019

Australia

Program (co)Head :: Computational Biology

Murdoch Childrens Research Institute Apr 11 2011 - Nov 11 2019

Australia

Head of Bioinformatics :: Bioinformatics

Education History

University of Melbourne - Mar 09 2003

Australia

PHD :: Physics

Publications

Allen Gu, Breon M Schmidt, Andrew Lonsdale, Roshan Niloofa, Hansen J Kosasih, Lauren M Brown, Teresa Sadras, Paul G Ekert, Alicia Oshlack
TALLSorts: a T-cell acute lymphoblastic leukemia subtype classifier using RNA-seq expression data. Blood advances (2023)
Teresa Sadras, Fatimah B Jalud, Hansen J Kosasih, Christopher R Horne, Lauren M Brown, Sam El-Kamand, Charles E de Bock, Lachlan McAloney, Ashley P Ng, Nadia M Davidson, Louise E A Ludlow, Alicia Oshlack, Mark J Cowley, Seong L Khaw, James G Murphy, Paul G Ekert
Unusual PDGFRB fusion reveals novel mechanism of kinase activation in Ph-like B-ALL. Leukemia (2023)
Katie L Ayers, Stefanie Eggers, Ben N Rollo, Katherine R Smith, Nadia M Davidson, Nicole A Siddall, Liang Zhao, Josephine Bowles, Karin Weiss, Ginevra Zanni, Lydie Burglen, Shay Ben-Shachar, Jenny Rosensaft, Annick Raas-Rothschild, Anne Jørgensen, Ralf Bernd Schittenhelm, Cheng Huang, Gorjana Robevska, Jocelyn van den Bergen, Franca Casagranda, Justyna Cyza, Svenja Pachernegg, David K Wright, Melanie Bahlo, Alicia Oshlack, Terrence J O'Brien, Patrick Kwan, Peter Koopman, Gary R Hime, Nadine Girard, Chen Hoffmann, Yuval Shilon, Amnon Zung, Enrico Bertini, Mathieu Milh, Bochra Ben Rhouma, Neila Belguith, Anu Bashamboo, Kenneth MacElreavey, Ehud Banne, Naomi Weintrob, Bruria BenZeev, Andrew H Sinclair
Variants in SART3 cause a spliceosomopathy characterised by failure of testis development and neuronal defects. Nature communications 14 (1) (2023)
Andrew Lonsdale, Andreas Halman, Lauren Brown, Hansen J Kosasih, Paul Ekert, Alicia Oshlack
Toblerone: detecting exon deletion events in cancer using RNA-seq. F1000Research 12 (2023)
Katie L Ayers, Stefanie Eggers, Ben N Rollo, Katherine R Smith, Nadia M Davidson, Nicole A Siddall, Liang Zhao, Josephine Bowles, Karin Weiss, Ginevra Zanni, Lydie Burglen, Shay Ben-Shachar, Jenny Rosensaft, Annick Raas-Rothschild, Anne Jørgensen, Ralf Bernd Schittenhelm, Cheng Huang, Gorjana Robevska, Jocelyn van den Bergen, Franca Casagranda, Justyna Cyza, Svenja Pachernegg, David K Wright, Melanie Bahlo, Alicia Oshlack, Terrence J O'Brien, Patrick Kwan, Peter Koopman, Gary R Hime, Nadine Girard, Chen Hoffmann, Yuval Shilon, Amnon Zung, Enrico Bertini, Mathieu Milh, Bochra Ben Rhouma, Neila Belguith, Anu Bashamboo, Kenneth McElreavey, Ehud Banne, Naomi Weintrob, Bruria BenZeev, Andrew H Sinclair
Author Correction: Variants in SART3 cause a spliceosomopathy characterised by failure of testis development and neuronal defects. Nature communications 14 (1) (2023)
Shunsuke Kimura, Lindsey E Montefiori, Ilaria Iacobucci, Yaqi Zhao, Qingsong Gao, Elisabeth M Paietta, Claudia Haferlach, A Douglas Laird, Paul E Mead, Zhaohui Gu, Wendy Stock, Mark R Litzow, Jacob M Rowe, Selina M Luger, Stephen P Hunger, Georgina L Ryland, Breon Schmidt, Paul G Ekert, Alicia Oshlack, Sean M Grimmond, Jacqueline A Rehn, James Breen, David T O Yeung, Deborah L White, Ibrahim Aldoss, Elias J Jabbour, Ching-Hong Pui, Manja Meggendorfer, Wencke Walter, Wolfgang Kern, Torsten Haferlach, Samuel Brady, Jinghui Zhang, Kathryn G Roberts, Piers Blombery, Charles G Mullighan
Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia. Blood 139 (24) (2022)
Andreas Halman, Egor Dolzhenko, Alicia Oshlack
STRipy: A graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data. Human mutation 43 (7) (2022)
Nadia M Davidson, Ying Chen, Teresa Sadras, Georgina L Ryland, Piers Blombery, Paul G Ekert, Jonathan Göke, Alicia Oshlack
JAFFAL: detecting fusion genes with long-read transcriptome sequencing. Genome biology 23 (1) (2022)
Lauren M Brown, Soroor Hediyeh-Zadeh, Teresa Sadras, Hannah Huckstep, Jarrod J Sandow, Ray C Bartolo, Hansen J Kosasih, Nadia M Davidson, Breon Schmidt, Stefan Bjelosevic, Ricky Johnstone, Andrew Ian Webb, Seong L Khaw, Alicia Oshlack, Melissa J Davis, Paul G Ekert
SFPQ-ABL1 and BCR-ABL1 use different signaling networks to drive B-cell acute lymphoblastic leukemia. Blood advances 6 (7) (2022)
Breon Schmidt, Lauren M Brown, Georgina L Ryland, Andrew Lonsdale, Hansen J Kosasih, Louise E Ludlow, Ian J Majewski, Piers Blombery, Paul G Ekert, Nadia M Davidson, Alicia Oshlack
ALLSorts: an RNA-Seq subtype classifier for B-cell acute lymphoblastic leukemia. Blood advances 6 (14) (2022)
Breon Schmidt, Marek Cmero, Paul Ekert, Nadia Davidson, Alicia Oshlack
Slinker: Visualising novel splicing events in RNA-Seq data. F1000Research 10 (2021)
Marek Cmero, Breon Schmidt, Ian J Majewski, Paul G Ekert, Alicia Oshlack, Nadia M Davidson
MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data. Genome biology 22 (1) (2021)
Christoffer Flensburg, Tobias Sargeant, Alicia Oshlack, Ian J Majewski
SuperFreq: Integrated mutation detection and clonal tracking in cancer. PLoS computational biology 16 (2) (2020)
Andreas Halman, Alicia Oshlack
Accuracy of short tandem repeats genotyping tools in whole exome sequencing data. F1000Research 9 (2020)
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
The role of cardiac transcription factor NKX2-5 in regulating the human cardiac miRNAome. Scientific reports 9 (1) (2019)
Marek Cmero, Nadia M Davidson, Alicia Oshlack
Using equivalence class counts for fast and accurate testing of differential transcript usage. F1000Research 8 (2019)
Simon P Sadedin, Alicia Oshlack
Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data. Genome biology 20 (1) (2019)
Kynan T Lawlor, Luke Zappia, James Lefevre, Joo-Seop Park, Nicholas A Hamilton, Alicia Oshlack, Melissa H Little, Alexander N Combes
Nephron progenitor commitment is a stochastic process influenced by cell migration. eLife 8 (2019)
Alexander N Combes, Belinda Phipson, Kynan T Lawlor, Aude Dorison, Ralph Patrick, Luke Zappia, Richard P Harvey, Alicia Oshlack, Melissa H Little
Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk. Development (Cambridge, England) 146 (12) (2019)
Deevina Arasaratnam, Katrina M Bell, Choon Boon Sim, Kathy Koutsis, David J Anderson, Elizabeth L Qian, Edouard G Stanley, Edouard G Stanley, Michael M Cheung, Alicia Oshlack, Anthony J White, Charbel Abi Khalil, James E Hudson, Enzo R Porrello, David A Elliott
Publisher Correction: The role of cardiac transcription factor NKX2-5 in regulating the human cardiac miRNAome. Scientific reports 9 (1) (2019)
Marek Cmero, Nadia M Davidson, Alicia Oshlack
Fast and accurate differential transcript usage by testing equivalence class counts. F1000Research (2019)
David J Anderson, David I Kaplan, Katrina M Bell, Katerina Koutsis, John M Haynes, Richard J Mills, Dean G Phelan, Elizabeth L Qian, Ana Rita Leitoguinho, Deevina Arasaratnam, Tanya Labonne, Elizabeth S Ng, Richard P Davis, Simona Casini, Robert Passier, James E Hudson, Enzo R Porrello, Mauro W Costa, Arash Rafii, Clare L Curl, Lea M Delbridge, Richard P Harvey, Alicia Oshlack, Michael M Cheung, Christine L Mummery, Stephen Petrou, Andrew G Elefanty, Edouard G Stanley, David A Elliott
NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network. Nature communications 9 (1) (2018)
Harriet Dashnow, Monkol Lek, Belinda Phipson, Andreas Halman, Simon Sadedin, Andrew Lonsdale, Mark Davis, Phillipa Lamont, Joshua S Clayton, Nigel G Laing, Daniel G MacArthur, Alicia Oshlack
STRetch: detecting and discovering pathogenic short tandem repeat expansions. Genome biology 19 (1) (2018)
Lorna J Hale, Sara E Howden, Belinda Phipson, Andrew Lonsdale, Pei X Er, Irene Ghobrial, Salman Hosawi, Sean B Wilson, Kynan T Lawlor, Shahnaz Khan, Alicia Oshlack, Catherine Quinlan, Rachel Lennon, Melissa H Little
3D organoid-derived human glomeruli for personalised podocyte disease modelling and drug screening. Nature communications 9 (1) (2018)
Luke Zappia, Belinda Phipson, Alicia Oshlack
Splatter: simulation of single-cell RNA sequencing data. Genome biology 18 (1) (2017)
Nadia M Davidson, Anthony D K Hawkins, Alicia Oshlack
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes. Genome biology 18 (1) (2017)
Peter G Farlie, Nadia M Davidson, Naomi L Baker, Mai Raabus, Kelly N Roeszler, Claire Hirst, Andrew Thomas Major, Mylene M Mariette, David M Lambert, Alicia Oshlack, Craig A Smith
Co-option of the cardiac transcription factor Nkx2.5 during development of the emu wing. Nature communications 8 (1) (2017)
Elizabeth S Ng, Lisa Azzola, Freya F Bruveris, Vincenzo Calvanese, Belinda Phipson, Katerina Vlahos, Claire Hirst, Vanta J Jokubaitis, Qing C Yu, Jovana Maksimovic, Simone Liebscher, Vania Januar, Zhen Zhang, Brenda Williams, Aude Conscience, Jennifer Durnall, Steven Jackson, Magdaline Costa, David Elliott, David N Haylock, Susan K Nilsson, Richard Saffery, Katja Schenke-Layland, Alicia Oshlack, Hanna K A Mikkola, Edouard G Stanley, Andrew G Elefanty
Differentiation of human embryonic stem cells to HOXA+ hemogenic vasculature that resembles the aorta-gonad-mesonephros. Nature biotechnology 34 (11) (2016)

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Publication Activity (10 Years)

Top Topics

Top Venues

Alicia Oshlack