Research Topics
| Alicia OshlackSummaryAffiliation: The Walter and Eliza Hall Institute of Medical Research Country: Australia Publications
| Collaborators
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Detail Information
Publications
From RNA-seq reads to differential expression resultsAlicia Oshlack
Bioinformatics Division, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville 3052, Australia
Genome Biol 11:220. 2010..Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression...- Gene ontology analysis for RNA-seq: accounting for selection biasMatthew D Young
Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3052, Australia
Genome Biol 11:R14. 2010..Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more consistent with the known biology... - Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basisAndrew J Holloway
Ian Potter Foundation Centre for Cancer Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, St Andrew s Place, East Melbourne, Victoria 3002, Australia
BMC Bioinformatics 7:511. 2006.... - Normalization of boutique two-color microarrays with a high proportion of differentially expressed probesAlicia Oshlack
Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria, Australia
Genome Biol 8:R2. 2007..Specifically, this can occur when specialized boutique arrays are constructed that contain a subset of genes selected to test particular biological functions... - Using DNA microarrays to study gene expression in closely related speciesAlicia Oshlack
Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3050, Australia
Bioinformatics 23:1235-42. 2007..Here, we use data collected using a multi-primate cDNA array to evaluate the reliability of each approach... - Transcript length bias in RNA-seq data confounds systems biologyAlicia Oshlack
Walter and Eliza Hall Institute of Medical Research, Parkville, Vic, Australia
Biol Direct 4:14. 2009..As yet, a rigorous analysis methodology has not been developed and we are still in the stages of exploring the features of the data... - A scaling normalization method for differential expression analysis of RNA-seq dataMark D Robinson
Bioinformatics Division, Walter and Eliza Hall Institute, 1G Royal Parade, Parkville, Australia
Genome Biol 11:R25. 2010..We outline a simple and effective method for performing normalization and show dramatically improved results for inferring differential expression in simulated and publicly available data sets... - Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChipsWei Shi
The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
Nucleic Acids Res 38:e204. 2010..The use of control probes as part of the background correction and normalization strategy is shown to achieve the lowest FDR for a given bias... - ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activityMatthew D Young
Walter and Eliza Hall Institute, 1G Royal Parade, Parkville 3052, Australia
Nucleic Acids Res 39:7415-27. 2011..The data analysis techniques developed here will be useful for the identification of common enrichment profiles for other histone modifications that have important consequences for transcriptional regulation... - Segmental duplications contribute to gene expression differences between humans and chimpanzeesRan Blekhman
Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
Genetics 182:627-30. 2009..Accordingly, we show that species-specific segmental duplications are enriched with genes that are differentially expressed between humans and chimpanzees... - Natural selection on gene expressionYoav Gilad
Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
Trends Genet 22:456-61. 2006..An important implication is that mutations affecting gene expression will often be deleterious and might underlie many human diseases... - Expression profiling in primates reveals a rapid evolution of human transcription factorsYoav Gilad
Department of Genetics, Yale University, New Haven, Connecticut 06510, USA
Nature 440:242-5. 2006..Among the gene set with a human-specific increase in expression, there is an excess of transcription factors; the same is not true for genes with increased expression in chimpanzee... - Array-based gene discovery with three unrelated subjects shows SCARB2/LIMP-2 deficiency causes myoclonus epilepsy and glomerulosclerosisSamuel F Berkovic
Department of Medicine, Austin Health and Northern Health, Heidelberg, Victoria 3081, Australia
Am J Hum Genet 82:673-84. 2008..The heterogeneous pathology in the kidney and brain suggests that SCARB2/Limp2 has pleiotropic effects that may be relevant to understanding the pathogenesis of other forms of glomerulosclerosis or collapse and myoclonic epilepsies... - A comparison of background correction methods for two-colour microarraysMatthew E Ritchie
Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
Bioinformatics 23:2700-7. 2007..Different estimators of background, and various model-based processing methods, are compared in this study in search of the best option for differential expression analyses of small microarray experiments...