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List of works by Alicia Oshlack

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

scientific article published on March 2, 2010
Gene ontology analysis for RNA-seq: accounting for selection bias

scientific article
A comparison of background correction methods for two-colour microarrays

scientific article
SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips

scientific article
Transcript length bias in RNA-seq data confounds systems biology

scientific article published in 2009
From RNA-seq reads to differential expression results

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

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

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

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

scientific article
missMethyl: an R package for analyzing data from Illumina’s HumanMethylation450 platform

scientific article published on September 30, 2015
Natural selection on gene expression

scientific article published on 27 June 2006
Corset: enabling differential gene expression analysis for de novoassembled transcriptomes

scientific article published on July 26, 2014
A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders

scientific article published on 3 March 2016
Gene regulation in primates evolves under tissue-specific selection pressures

scientific article
Splatter: simulation of single-cell RNA sequencing data

scientific article published on 12 September 2017
Diagnostic Impact and Cost-effectiveness of Whole-Exome Sequencing for Ambulant Children With Suspected Monogenic Conditions.

scientific article
Bpipe: a tool for running and managing bioinformatics pipelines

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

scientific article published on 18 October 2013
Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing

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

scientific article published on 23 August 2013
Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort

scientific article
Using DNA microarrays to study gene expression in closely related species

scientific article published on 23 March 2007
Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes

scientific article published on January 2007
RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome

scientific article
Differentiation of human embryonic stem cells to HOXA+ hemogenic vasculature that resembles the aorta-gonad-mesonephros.

scientific article published on 17 October 2016
Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

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

scientific article
JAFFA: High sensitivity transcriptome-focused fusion gene detection

scientific article published on May 11, 2015
The polycomb repressive complex 2 governs life and death of peripheral T cells

scientific article published on 20 June 2014
A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway

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

scientific article
Expression discordance of monozygotic twins at birth: effect of intrauterine environment and a possible mechanism for fetal programming

scientific article published in May 2011
Cpipe: a shared variant detection pipeline designed for diagnostic settings

scientific article published on 10 July 2015
Evaluation of variability in human kidney organoids

scientific article published on 20 December 2018
Patient-iPSC-Derived Kidney Organoids Show Functional Validation of a Ciliopathic Renal Phenotype and Reveal Underlying Pathogenetic Mechanisms

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

scientific article published on September 23, 2014
STRetch: detecting and discovering pathogenic short tandem repeat expansions

scientific article published on 21 August 2018
3D organoid-derived human glomeruli for personalised podocyte disease modelling and drug screening

scientific article published in Nature Communications
Cell-type-specific transcriptional profiles of the dimorphic pathogen Penicillium marneffei reflect distinct reproductive, morphological, and environmental demands

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

scientific article published on 2 February 2015
Single-cell analysis reveals congruence between kidney organoids and human fetal kidney

scholarly article by Alexander N Combes et al published 23 January 2019 in Genome Medicine
SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

scientific article published on 04 August 2017
A cross-package Bioconductor workflow for analysing methylation array data

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

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

scientific article published on 14 October 2016
miRNA-Seq normalization comparisons need improvement

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

scientific article published on 16 September 2015
Clustering trees: a visualization for evaluating clusterings at multiple resolutions

scholarly article by Luke Zappia & Alicia Oshlack published 1 July 2018 in GigaScience
Segmental duplications contribute to gene expression differences between humans and chimpanzees

scientific article published on 30 March 2009

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