Alicia Oshlack

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

Abstract Structural DNA variants can modify gene function by altering transcript sequences, and have been shown to be drivers in b..

Detecting copy number alterations in RNA-Seq using SuperFreq

Christoffer Flensburg, Alicia Oshlack, Ian Majewski

Journal article  |  2020

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

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..

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..

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

Andreas Halman, Alicia Oshlack

Journal article  |  2020

Abstract Background Short tandem repeats are important source of genetic variation, they are highly mutable and repeat expansions ..

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 ..

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..

Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk

Alexander N Combes, Belinda Phipson, Kynan T Lawlor, Aude Dorison, Ralph Patrick, Luke Zappia, Richard P Harvey, Alicia Oshlack, Melissa H Little

Journal article  |  2019  |  Development

Direct reprogramming to human nephron progenitor-like cells using inducible piggyBac transposon expression of SNAI2-EYA1-SIX1

Jessica M Vanslambrouck, Lauren E Woodard, Norseha Suhaimi, Felisha M Williams, Sara E Howden, Sean B Wilson, Andrew Lonsdale, Pei X Er, Joan Li, Jovana Maksimovic, Alicia Oshlack, Matthew H Wilson, Melissa H Little

Journal article  |  2019  |  Kidney International

Using equivalence class counts for fast and accurate testing of differential transcript usage

Marek Cmero, Nadia M Davidson, Alicia Oshlack

Journal article  |  2019  |  F1000Research

Background: RNA sequencing has enabled high-throughput and fine-grained quantitative analyses of the transcriptome. While differen..

Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data

Simon P Sadedin, Alicia Oshlack

Journal article  |  2019  |  Genome Biology

Pooled-parent exome sequencing to prioritise de novo variants in genetic disease

Harriet Dashnow, Katrina Bell, Zornitza Stark, Tiong Tan, Susan White, Alicia Oshlack

Journal article  |  2019

Abstract In the clinical setting, exome sequencing has become standard-of-care in diagnosing rare genetic disorders, however many ..

Kidney micro-organoids in suspension culture as a scalable source of human pluripotent stem cell-derived kidney cells

Santhosh Kumar, Pei X Er, Kynan T Lawlor, Ali Motazedian, Michelle Scurr, Irene Ghobrial, Alexander N Combes, Luke Zappia, Alicia Oshlack, Edouard G Stanley, Melissa H Little

Journal article  |  2019  |  Development

Nephron progenitor commitment is a stochastic process influenced by cell migration

Kynan T Lawlor, Luke Zappia, James Lefevre, Joo-Seop Park, Nicholas A Hamilton, Alicia Oshlack, Melissa H Little, Alexander N Combes

Journal article  |  2019  |  eLife

Single-cell analysis reveals congruence between kidney organoids and human fetal kidney

Alexander N Combes, Luke Zappia, Pei Xuan Er, Alicia Oshlack, Melissa H Little

Journal article  |  2019  |  Genome Medicine

Fast and accurate differential transcript usage by testing equivalence class counts [version 1; peer review: 3 approved with reservations]

M Cmero, NM Davidson, A Oshlack

Journal article  |  2019  |  F1000Research

Background: RNA sequencing has enabled high-throughput and fine-grained quantitative analyses of the transcriptome. While differen..

Evaluation of variability in human kidney organoids

Belinda Phipson, Pei X Er, Alexander N Combes, Thomas A Forbes, Sara E Howden, Luke Zappia, Hsan-Jan Yen, Kynan T Lawlor, Lorna J Hale, Jane Sun, Ernst Wolvetang, Minoru Takasato, Alicia Oshlack, Melissa H Little

Journal article  |  2019  |  Nature Methods

3D organoid-derived human glomeruli for personalised podocyte disease model ling and drug screening

Lorna J Hale, Sara E Howden, Belinda Phipson, Andrew Lonsdale, Pei X Er, Irene Ghobrial, Salman Hosawi, Sean Wilson, Kynan T Lawlor, Shahnaz Khan, Alicia Oshlack, Catherine Quinlan, Rachel Lennon, Melissa H Little

Journal article  |  2018  |  Nature Communications

Different Classes of ABL1 Fusions Activate Different Downstream Signalling Nodes

Lauren M Brown, Hannah Huckstep, Jarrod Sandow, Ray C Bartolo, Nadia Davidson, Breon Schmidt, Stefan Bjelosevic, Ricky W Johnstone, Alicia Oshlack, Melissa Davis, Paul G Ekert

Conference Proceedings  |  2018  |  Blood

Bazam: A rapid method for read extraction and realignment of high throughput sequencing data

Simon Sadedin, Alicia Oshlack

Journal article  |  2018

Abstract Background As costs of high throughput sequencing have fallen, we are seeing vast quantities of short read genomic data b..

MCM3AP in recessive axonal neuropathy and mild intellectual disability

E Ylikallio, R Woldegebriel, M Tumiati, P Isohanni, MM Ryan, Z Stark, W Maie, SL Sawyer, KM Bell, A Oshlack, PL Lockhart, M Shcherbii, A Estrada-Cuzcano, D Atkinson, T Hartley, M Tetreault, I Cuppen, WL van der Pol, A Candayan, E Battaloglu, et al.

Conference Proceedings  |  2018  |  EUROPEAN JOURNAL OF HUMAN GENETICS

Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period

Ramona H Krauss, Belinda Phipson, Alicia Oshlack, Nikita Prasad-Gupta, Michael M Cheung, Joseph J Smolich, Salvatore Pepe

Journal article  |  2018  |  PLOS ONE

Ximmer: a system for improving accuracy and consistency of CNV calling from exome data

Simon P Sadedin, Justine A Ellis, Seth L Masters, Alicia Oshlack

Journal article  |  2018  |  GigaScience

STRetch: detecting and discovering pathogenic short tandem repeat expansions

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

Journal article  |  2018  |  Genome Biology

SuperFreq: Integrated mutation detection and clonal tracking in cancer

Christoffer Flensburg, Tobias Sargeant, Alicia Oshlack, Ian Majewski

Journal article  |  2018

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

Clustering trees: a visualization for evaluating clusterings at multiple resolutions

Luke Zappia, Alicia Oshlack

Journal article  |  2018  |  GigaScience

Clustering techniques are widely used in the analysis of large datasets to group together samples with similar properties. For exa..

Clinker: visualizing fusion genes detected in RNA-seq data

Breon M Schmidt, Nadia M Davidson, Anthony DK Hawkins, Ray Bartolo, Ian J Majewski, Paul G Ekert, Alicia Oshlack

Journal article  |  2018  |  GigaScience

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

Luke Zappia, Belinda Phipson, Alicia Oshlack

Journal article  |  2018  |  PLOS Computational Biology

Patient-iPSC-Derived Kidney Organoids Show Functional Validation of a Ciliopathic Renal Phenotype and Reveal Underlying Pathogenetic Mechanisms

Thomas A Forbes, Sara E Howden, Kynan Lawlor, Belinda Phipson, Jovana Maksimovic, Lorna Hale, Sean Wilson, Catherine Quinlan, Gladys Ho, Katherine Holman, Bruce Bennetts, Joanna Crawford, Peter Trnka, Alicia Oshlack, Chirag Patel, Andrew Mallett, Cas Simons, Melissa H Little

Journal article  |  2018  |  The American Journal of Human Genetics

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis

Nadia M Davidson, Alicia Oshlack

Journal article  |  2018  |  GigaScience

Background: RNA sequencing (RNA-seq) analyses can benefit from performing a genome-guided and de novo assembly, in particular for ..

Cord Blood CD8( ) T Cells Have a Natural Propensity to Express IL-4 in a Fatty Acid Metabolism and Caspase Activation-Dependent Manner

Yuxia Zhang, Jovana Maksimovic, Bing Huang, David Peter De Souza, Gaetano Naselli, Huan Chen, Li Zhang, Kai Weng, Hanquan Liang, Yanhui Xu, John M Wentworth, Nicholas D Huntington, Alicia Oshlack, Sitang Gong, Axel Kallies, Peter Vuillermin, Min Yang, Leonard C Harrison

Journal article  |  2018  |  Frontiers in Immunology

NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network

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, et al.

Journal article  |  2018  |  Nature Communications

Clustering trees: a visualisation for evaluating clusterings at multiple resolutions

Luke Zappia, Alicia Oshlack

Journal article  |  2018

Abstract Clustering techniques are widely used in the analysis of large data sets to group together samples with similar propertie..

Haploinsufficiency for the Six2 gene increases nephron progenitor proliferation promoting branching and nephron number

Alexander N Combes, Sean Wilson, Belinda Phipson, Brandon B Binnie, Adler Ju, Kynan T Lawlor, Cristina Cebrian, Sarah L Walton, Ian M Smyth, Karen M Moritz, Raphael Kopan, Alicia Oshlack, Melissa H Little

Journal article  |  2018  |  Kidney International

SHRNA SCREEN FOR NOVEL EPIG ENETIC REGULATORS OF Gamma-GLOBIN SILENCING

Betty Kao, Bradley McColl, Shian Su, Matthew Ritchie, L Jamie Gearing, Miha Pakusch, Tracy Willson, Jovana Maksimovic, Alicia Oshlack, Marnie Blewitt, Jim Vadolas

Conference Proceedings  |  2018  |  JOURNAL OF GENE MEDICINE

OPTIMISATION OF KIDNEY ORGANOIDS AS A REPRODUCIBLE AND DEVELOPMENTALLY ACCURATE MODEL OF HUMAN KIDNEY DEVELOPMENT AND DISEASE

Melissa H Little, Pei X Er, Belinda Phipson, Jessica Vanslambrouck, Sara Howden, Lorna Hale, Minoru Takasato, A Oshlack

Conference Proceedings  |  2018  |  JOURNAL OF GENE MEDICINE

Clinker: visualising fusion genes detected in RNA-seq data

Breon Schmidt, Nadia Davidson, Anthony DK Hawkins, Ray Bartolo, Ian Majewski, Paul Ekert, Alicia Oshlack

Journal article  |  2017

ABSTRACT Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes, and many are emerging as important th..

A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data

Zornitza Stark, Harriet Dashnow, Sebastian Lunke, Tiong Y Tan, Alison Yeung, Simon Sadedin, Natalie Thorne, Ivan Macciocca, Clara Gaff, Alicia Oshlack, Susan M White, Paul A James

Journal article  |  2017  |  European Journal of Human Genetics

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

Luke Zappia, Belinda Phipson, Alicia Oshlack

Journal article  |  2017

Abstract As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse th..

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis

Nadia Davidson, Alicia Oshlack

Journal article  |  2017

Abstract Background RNA-Seq analyses can benefit from performing a genome-guided and de novo assembly, in particular for species w..

Splatter: simulation of single-cell RNA sequencing data

Luke Zappia, Belinda Phipson, Alicia Oshlack

Journal article  |  2017  |  Genome Biology

Diagnostic Impact and Cost-effectiveness of Whole-Exome Sequencing for Ambulant Children With Suspected Monogenic Conditions

Tiong Yang Tan, Oliver James Dillon, Zornitza Stark, Deborah Schofield, Khurshid Alam, Rupendra Shrestha, Belinda Chong, Dean Phelan, Gemma R Brett, Emma Creed, Anna Jarmolowicz, Patrick Yap, Maie Walsh, Lilian Downie, David J Amor, Ravi Savarirayan, George McGillivray, Alison Yeung, Heidi Peters, Susan J Robertson, et al.

Journal article  |  2017  |  JAMA Pediatrics

Transcriptional profiles for distinct aggregation states of mutant Huntingtin exon 1 protein unmask new Huntington's disease pathways

Nagaraj S Moily, Angelique R Ormsby, Aleksandar Stojilovic, Yasmin M Ramdzan, Jeannine Diesch, Ross D Hannan, Michelle S Zajac, Anthony J Hannan, Alicia Oshlack, Danny M Hatters

Journal article  |  2017  |  Molecular and Cellular Neuroscience

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

Nadia M Davidson, Anthony DK Hawkins, Alicia Oshlack

Journal article  |  2017  |  Genome Biology

MCM3AP in recessive Charcot-Marie-Tooth neuropathy and mild intellectual disability

Emil Ylikallio, Rosa Woldegebriel, Manuela Tumiati, Pirjo Isohanni, Monique M Ryan, Zornitza Stark, Maie Walsh, Sarah L Sawyer, Katrina M Bell, Alicia Oshlack, Paul J Lockhart, Mariia Shcherbii, Alejandro Estrada-Cuzcano, Derek Atkinson, Taila Hartley, Martine Tetreault, Inge Cuppen, W Ludo van der Pol, Ayse Candayan, Esra Battaloglu, et al.

Journal article  |  2017  |  Brain

Co-option of the cardiac transcription factor Nkx2.5 during development of the emu wing

Peter G Farlie, Nadia M Davidson, Naomi L Baker, Mai Raabus, Kelly N Roeszler, Claire Hirst, Andrew Major, Mylene M Mariette, David M Lambert, Alicia Oshlack, Craig A Smith

Journal article  |  2017  |  Nature Communications

STRetch: detecting and discovering pathogenic short tandem repeat expansions

Harriet Dashnow, Monkol Lek, Belinda Phipson, Andreas Halman, Simon Sadedin, Andrew Lonsdale, Mark Davis, Phillipa Lamont, Joshua Clayton, Nigel Laing, Daniel MacArthur, Alicia Oshlack

Journal article  |  2017

Abstract Short tandem repeat (STR) expansions have been identified as the causal DNA mutation in dozens of Mendelian diseases. His..

Splatter: simulation of single-cell RNA sequencing data

Luke Zappia, Belinda Phipson, Alicia Oshlack

Journal article  |  2017

Abstract As single-cell RNA sequencing technologies have rapidly developed, so have analysis methods. Many methods have been teste..

Diagnostic and cost utility of whole exome sequencing in peripheral neuropathy

Maie Walsh, Katrina M Bell, Belinda Chong, Emma Creed, Gemma R Brett, Kate Pope, Natalie P Thorne, Simon Sadedin, Peter Georgeson, Dean G Phelan, Timothy Day, Jessica A Taylor, Adrienne Sexton, Paul J Lockhart, Lynette Kiers, Michael Fahey, Ivan Macciocca, Clara L Gaff, Alicia Oshlack, Eppie M Yiu, et al.

Journal article  |  2017  |  Annals of Clinical and Translational Neurology

Gene length and detection bias in single cell RNA sequencing protocols

Belinda Phipson, Luke Zappia, Alicia Oshlack

Journal article  |  2017  |  F1000Research

Background: Single cell RNA sequencing (scRNA-seq) has rapidly gained popularity for profiling transcriptomes of hundreds to thous..

Functionally distinct roles for different miR-155 expression levels through contrasting effects on gene expression, in acute myeloid leukaemia

N Narayan, L Morenos, B Phipson, SN Willis, G Brumatti, S Eggers, N Lalaoui, LM Brown, HJ Kosasih, RC Bartolo, L Zhou, D Catchpoole, R Saffery, A Oshlack, GJ Goodall, PG Ekert

Journal article  |  2017  |  Leukemia

Gene length and detection bias in single cell RNA sequencing protocols

Belinda Phipson, Luke Zappia, Alicia Oshlack

Journal article  |  2017

Abstract Single cell RNA sequencing (scRNA-seq) has rapidly gained popularity for profiling transcriptomes of hundreds to thousand..

Limb patterning genes and heterochronic development of the emu wing bud

Craig A Smith, Peter G Farlie, Nadia M Davidson, Kelly N Roeszler, Claire Hirst, Alicia Oshlack, David M Lambert

Journal article  |  2016  |  EvoDevo

Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort

Stefanie Eggers, Simon Sadedin, Jocelyn A van den Bergen, Gorjana Robevska, Thomas Ohnesorg, Jacqueline Hewitt, Luke Lambeth, Aurore Bouty, Ingrid M Knarston, Yang Tan Tiong, Fergus Cameron, George Werther, John Hutson, Michele O'Connell, Sonia R Grover, Yves Heloury, Margaret Zacharin, Philip Bergman, Chris Kimber, Justin Brown, et al.

Journal article  |  2016  |  Genome Biology

A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders

Zornitza Stark, Tiong Y Tan, Belinda Chong, Gemma R Brett, Patrick Yap, Maie Walsh, Alison Yeung, Heidi Peters, Dylan Mordaunt, Shannon Cowie, David J Amor, Ravi Savarirayan, George McGillivray, Lilian Downie, Paul G Ekert, Christiane Theda, Paul A James, Joy Yaplito-Lee, Monique M Ryan, Richard J Leventer, et al.

Journal article  |  2016  |  Genetics in Medicine

Differentiation of human embryonic stem cells to HOXA( ) hemogenic vasculature that resembles the aorta-gonad-mesonephros

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, et al.

Journal article  |  2016  |  Nature Biotechnology

SuperTranscript: a data driven reference for analysis and visualisation of transcriptomes

Nadia Davidson, Anthony DK Hawkins, Alicia Oshlack

Journal article  |  2016

Abstract Numerous methods have been developed to analyse RNA sequencing data, but most rely on the availability of a reference gen..

missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform

Belinda Phipson, Jovana Maksimovic, Alicia Oshlack

Journal article  |  2016  |  Bioinformatics

A cross-package Bioconductor workflow for analysing methylation array data.

Jovana Maksimovic, Belinda Phipson, Alicia Oshlack

Journal article  |  2016  |  F1000Research

Methylation in the human genome is known to be associated with development and disease. The Illumina Infinium methylation arrays a..

Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data

Jovana Maksimovic, Johann A Gagnon-Bartsch, Terence P Speed, Alicia Oshlack

Journal article  |  2015  |  Nucleic Acids Research

Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq

Katie L Ayers, Luke S Lambeth, Nadia M Davidson, Andrew H Sinclair, Alicia Oshlack, Craig A Smith

Journal article  |  2015  |  BMC Genomics

Cpipe: a shared variant detection pipeline designed for diagnostic settings

Simon P Sadedin, Harriet Dashnow, Paul A James, Melanie Bahlo, Denis C Bauer, Andrew Lonie, Sebastian Lunke, Ivan Macciocca, Jason P Ross, Kirby R Siemering, Zornitza Stark, Susan M White, Graham Taylor, Clara Gaff, Alicia Oshlack, Natalie P Thorne

Journal article  |  2015  |  Genome Medicine

Purification and Transcriptomic Analysis of Mouse Fetal Leydig Cells Reveals Candidate Genes for Specification of Gonadal Steroidogenic Cells

Kathryn S McClelland, Katrina Bell, Christian Larney, Vincent R Harley, Andrew H Sinclair, Alicia Oshlack, Peter Koopman, Josephine Bowles

Journal article  |  2015  |  Biology of Reproduction

JAFFA: High sensitivity transcriptome-focused fusion gene detection

Nadia M Davidson, Ian J Majewski, Alicia Oshlack

Journal article  |  2015  |  Genome Medicine

Jarid2 regulates hematopoietic stem cell function by acting with polycomb repressive complex 2

Sarah A Kinkel, Roman Galeev, Christoffer Flensburg, Andrew Keniry, Kelsey Breslin, Omer Gilan, Stanley Lee, Joy Liu, Kelan Chen, Linden J Gearing, Darcy L Moore, Warren S Alexander, Mark Dawson, Ian J Majewski, Alicia Oshlack, Jonas Larsson, Marnie E Blewitt

Journal article  |  2015  |  Blood

A comparison of control samples for ChIP-seq of histone modifications

Christoffer Flensburg, Sarah A Kinkel, Andrew Keniry, Marnie E Blewitt, Alicia Oshlack

Journal article  |  2014  |  Frontiers in Genetics

The polycomb repressive complex 2 governs life and death of peripheral T cells

Yuxia Zhang, Sarah Kinkel, Jovana Maksimovic, Esther Bandala-Sanchez, Maria C Tanzer, Gaetano Naselli, Jian-Guo Zhang, Yifan Zhan, Andrew M Lew, John Silke, Alicia Oshlack, Marnie E Blewitt, Leonard C Harrison

Journal article  |  2014  |  Blood

Identification, Expression, and Regulation of Anti-Mullerian Hormone Type-II Receptor in the Embryonic Chicken Gonad

Andrew D Cutting, Katie Ayers, Nadia Davidson, Alicia Oshlack, Tim Doran, Andrew H Sinclair, Mark Tizard, Craig A Smith

Journal article  |  2014  |  Biology of Reproduction

Susceptibility to Acute Rheumatic Fever Based on Differential Expression of Genes Involved in Cytotoxicity, Chemotaxis, and Apoptosis

Penelope A Bryant, Gordon K Smyth, Travis Gooding, Alicia Oshlack, Zinta Harrington, Bart Currie, Jonathan R Carapetis, Roy Robins-Browne, Nigel Curtis

Journal article  |  2014  |  Infection and Immunity

DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging

Belinda Phipson, Alicia Oshlack

Journal article  |  2014  |  Genome Biology

Corset: enabling differential gene expression analysis for de novo assembled transcriptomes

Nadia M Davidson, Alicia Oshlack

Journal article  |  2014  |  Genome Biology

Cell-Type-Specific Transcriptional Profiles of the Dimorphic Pathogen Penicillium marneffei Reflect Distinct Reproductive, Morphological, and Environmental Demands

Shivani Pasricha, Michael Payne, David Canovas, Luke Pase, Nathamon Ngaosuwankul, Sally Beard, Alicia Oshlack, Gordon K Smyth, Sansanee C Chaiyaroj, Kylie J Boyce, Alex Andrianopoulos

Journal article  |  2013  |  G3: Genes, Genomes, Genetics

Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy

Mark N Cruickshank, Alicia Oshlack, Christiane Theda, Peter G Davis, David Martino, Penelope Sheehan, Yun Dai, Richard Saffery, Lex W Doyle, Jeffrey M Craig

Journal article  |  2013  |  Genome Medicine: medicine in the post-genomic era

Genome-wide DNA methylation analysis identifies hypomethylated genes regulated by FOXP3 in human regulatory T cells

Yuxia Zhang, Jovana Maksimovic, Gaetano Naselli, Junyan Qian, Michael Chopin, Marnie E Blewitt, Alicia Oshlack, Leonard C Harrison

Journal article  |  2013  |  Blood

Condensin I associates with structural and gene regulatory regions in vertebrate chromosomes

Ji Hun Kim, Tao Zhang, Nicholas C Wong, Nadia Davidson, Jovana Maksimovic, Alicia Oshlack, William C Earnshaw, Paul Kalitsis, Damien F Hudson

Journal article  |  2013  |  Nature Communications

Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing

Ian J Majewski, Lorenza Mittempergher, Nadia M Davidson, Astrid Bosma, Stefan M Willems, Hugo M Horlings, Iris de Rink, Liliana Greger, Gerrit KJ Hooijer, Dennis Peters, Petra M Nederlof, Ingrid Hofland, Jeroen de Jong, Jelle Wesseling, Roelof JC Kluin, Wim Brugman, Ron Kerkhoven, Frank Nieboer, Paul Roepman, Annegien Broeks, et al.

Journal article  |  2013  |  Journal of Pathology

miRNA-Seq normalization comparisons need improvement

Xiaobei Zhou, Alicia Oshlack, Mark D Robinson

Journal article  |  2013  |  RNA

RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome

Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Gruetzner, Andrew H Sinclair, Alicia Oshlack, Craig A Smith

Journal article  |  2013  |  Genome Biology

A 10-step guide to party conversation for bioinformaticians

Alicia Oshlack

Journal article  |  2013  |  Genome Biology

Sixty years of genome biology

W Ford Doolittle, Peter Fraser, Mark B Gerstein, Brenton R Graveley, Steven Henikoff, Curtis Huttenhower, Alicia Oshlack, Chris P Ponting, John L Rinn, Michael C Schatz, Jernej Ule, Detlef Weigel, George M Weinstock

Journal article  |  2013  |  Genome Biology

Bpipe: a tool for running and managing bioinformatics pipelines

Simon P Sadedin, Bernard Pope, Alicia Oshlack

Journal article  |  2012  |  Bioinformatics

Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design

Matthew D Young, Davis J McCarthy, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack, Mark D Robinson

Book Chapter  |  2012

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack

Journal article  |  2012  |  Genome Biology

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity

Matthew D Young, Tracy A Willson, Matthew J Wakefield, Evelyn Trounson, Douglas J Hilton, Marnie E Blewitt, Alicia Oshlack, Ian J Majewski

Journal article  |  2011  |  Nucleic Acids Research

Expression discordance of monozygotic twins at birth Effect of intrauterine environment and a possible mechanism for fetal programming

Lavinia Gordon, Ji-Hoon E Joo, Roberta Andronikos, Miina Ollikainen, Euan M Wallace, Mark P Umstad, Michael Permezel, Alicia Oshlack, Ruth Morley, John B Carlin, Richard Saffery, Gordon K Smyth, Jeffrey M Craig

Journal article  |  2011  |  Epigenetics

Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips

Wei Shi, Alicia Oshlack, Gordon K Smyth

Journal article  |  2010  |  Nucleic Acids Research

Gene ontology analysis for RNA-seq: accounting for selection bias

Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack

Journal article  |  2010  |  Genome Biology

A scaling normalization method for differential expression analysis of RNA-seq data

Mark D Robinson, Alicia Oshlack

Journal article  |  2010  |  Genome Biology

From RNA-seq reads to differential expression results

Alicia Oshlack, Mark D Robinson, Matthew D Young

Journal article  |  2010  |  Genome Biology

Segmental Duplications Contribute to Gene Expression Differences Between Humans and Chimpanzees

Ran Blekhman, Alicia Oshlack, Yoav Gilad

Journal article  |  2009  |  Genetics

Transcript length bias in RNA-seq data confounds systems biology

Alicia Oshlack, Matthew J Wakefield

Journal article  |  2009  |  Biology Direct

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

Ran Blekhman, Alicia Oshlack, Adrien E Chabot, Gordon K Smyth, Yoav Gilad

Journal article  |  2008  |  PLoS Genetics

Array-based gene discovery with three unrelated subjects shows SCARB2/LIMP-2 deficiency causes myoclonus epilepsy and glomerulosclerosis

Samuel E Berkovic, Leanne M Dibbens, Alicia Oshlack, Jeremy D Silver, Marina Katerelos, Danya F Vears, Renate Luellmann-Rauch, Judith Blanz, Ke Wei Zhang, Jim Stankovich, Renate M Kalnins, John P Dowling, Eva Andermann, Frederick Andermann, Enrico Faldini, Rudi D'Hooge, Lata Vadlamudi, Richard A Macdonell, Bree L Hodgson, Marta A Bayly, et al.

Journal article  |  2008  |  American Journal of Human Genetics

A Combination of Genomic Approaches Reveals the Role of FOXO1a in Regulating an Oxidative Stress Response Pathway

Paola de Candia, Ran Blekhman, Adrien E Chabot, Alicia Oshlack, Yoav Gilad

Journal article  |  2008  |  PLoS ONE

A comparison of background correction methods for two-colour microarrays

Matthew E Ritchie, Jeremy Silver, Alicia Oshlack, Melissa Holmes, Dileepa Diyagama, Andrew Holloway, Gordon K Smyth

Journal article  |  2007  |  BIOINFORMATICS

Using DNA microarrays to study gene expression in closely related species

Alicia Oshlack, Adrien E Chabot, Gordon K Smyth, Yoav Gilad

Journal article  |  2007  |  Bioinformatics

Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes

Alicia Oshlack, Dianne Emslie, Lynn M Corcoran, Gordon K Smyth

Journal article  |  2007  |  Genome Biology

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

Andrew J Holloway, Alicia Oshlack, Dileepa S Diyagama, David DL Bowtell, Gordon K Smyth

Journal article  |  2006  |  BMC BIOINFORMATICS

Natural selection on gene expression

Yoav Gilad, Alicia Oshlack, Scott A Rifkin

Journal article  |  2006  |  Trends in Genetics

The spectral energy distribution of PKS 2004-447: a compact steep-spectrum source and possible radio-loud narrow-line Seyfert 1 galaxy

LC Gallo, PG Edwards, E Ferrero, J Kataoka, DR Lewis, SP Ellingsen, Z Misanovic, WF Welsh, M Whiting, Th Boller, W Brinkmann, J Greenhill, A Oshlack

Journal article  |  2006  |  Monthly Notices of the Royal Astronomical Society

Expression profiling in primates reveals a rapid evolution of human transcription factors

Y Gilad, A Oshlack, GK Smyth, TP Speed, KP White

Journal article  |  2006  |  Nature

A very radio loud narrow-line Seyfert 1: PKS 2004-447

AYKN Oshlack, RL Webster, MT Whiting

Journal article  |  2001  |  Astrophysical Journal