A5006353479- Single-cell and spatial transcriptomics
- Gene expression and cancer classification
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Genetic Syndromes and Imprinting
- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- Cell Image Analysis Techniques
- Cancer Cells and Metastasis
- Cell death mechanisms and regulation
- Respiratory and Cough-Related Research
- Immune Cell Function and Interaction
- T-cell and B-cell Immunology
- Ubiquitin and proteasome pathways
- Lymphoma Diagnosis and Treatment
- Congenital heart defects research
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Wnt/β-catenin signaling in development and cancer
- Phagocytosis and Immune Regulation
- Invertebrate Immune Response Mechanisms
The University of Melbourne
2016-2025
Walter and Eliza Hall Institute of Medical Research
2016-2025
SIB Swiss Institute of Bioinformatics
2014-2016
University of Zurich
2014-2016
QIMR Berghofer Medical Research Institute
2011
limma is an R/Bioconductor software package that provides integrated solution for analysing data from gene expression experiments. It contains rich features handling complex experimental designs and information borrowing to overcome the problem of small sample sizes. Over past decade, has been a popular choice discovery through differential analyses microarray high-throughput PCR data. The particularly strong facilities reading, normalizing exploring such Recently, capabilities have...
Abstract New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean-variance relationship of log-counts, generates a precision weight each observation and enters these into limma empirical Bayes analysis pipeline. This opens access analysts to large body methodology developed microarrays. Simulation studies show that performs as well or better than count-based methods even when data generated according...
<ns3:p>The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with counts summarised at gene-level, typical analysis involves pre-processing, exploratory analysis, differential expression testing pathway results obtained informing future experiments validation studies. In this workflow article, we from mouse mammary gland, demonstrating use popular <ns3:bold>edgeR</ns3:bold> package import, organise, filter normalise data,...
The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with counts summarised at gene-level, typical analysis involves pre-processing, exploratory analysis, differential expression testing pathway results obtained informing future experiments validation studies. In this workflow article, we from mouse mammary gland, demonstrating use popular edgeR package import, organise, filter normalise data, followed by limma its voom...
A modified Chromium 10x droplet-based protocol that subsamples cells for both short-read and long-read (nanopore) sequencing together with a new computational pipeline (FLAMES) is developed to enable isoform discovery, splicing analysis, mutation detection in single cells. We identify thousands of unannotated isoforms find conserved functional modules are enriched alternative transcript usage different cell types species, including ribosome biogenesis mRNA splicing. Analysis at the level...
Abstract Motivation Summary graphics for RNA-sequencing and microarray gene expression analyses may contain upwards of tens thousands points. Details about certain genes or samples interest are easily obscured in such dense summary displays. Incorporating interactivity into plots would enable additional information to be displayed on demand facilitate intuitive data exploration. Results The open-source Glimma package creates interactive exploring analysis with a few simple R commands. It...
RNA-seq has been a boon to the quantitative analysis of transcriptomes. A notable application is detection changes in transcript usage between experimental conditions. For example, discovery pathological alternative splicing may allow development new treatments or better management patients. From an perspective, there are several ways approach data unravel differential usage, such as annotation-based exon-level counting, percentage spliced in, assembled transcripts. The goal this research...
<ns3:p>The ability to easily and efficiently analyse RNA-sequencing data is a key strength of the Bioconductor project. Starting with counts summarised at gene-level, typical analysis involves pre-processing, exploratory analysis, differential expression testing pathway results obtained informing future experiments validation studies. In this workflow article, we from mouse mammary gland, demonstrating use popular <ns3:bold>edgeR</ns3:bold> package import, organise, filter normalise data,...
Although gene set enrichment analysis has become an integral part of high-throughput expression data analysis, the assessment methods remains rudimentary and ad hoc. In absence suitable gold standards, evaluations are commonly restricted to selected datasets biological reasoning on relevance resulting enriched sets.We develop extensible framework for reproducible benchmarking based defined criteria applicability, prioritization detection relevant processes. This incorporates a curated...
Case fatality rates for severe malaria remain high even in the best clinical settings because antimalarial drugs act against parasite without alleviating life-threatening inflammation. We assessed potential host-directed therapy of a new class anti-inflammatory drugs, innate defense regulator (IDR) peptides, based on host peptides. The Plasmodium berghei ANKA model experimental cerebral was adapted to use as preclinical screen by combining late-stage intervention established infections with...
Background Spatial transcriptomics allows gene expression to be measured within complex tissue contexts. Among the array of spatial capture technologies available is 10x Genomics’ Visium platform, a popular method which enables transcriptomewide profiling sections. offers range sample handling and library construction methods introduces need for benchmarking compare data quality assess how well technology can recover expected features biological signatures. Results Here we present...
Gene set enrichment analysis is a popular approach for prioritising the biological processes perturbed in genomic datasets. The Bioconductor project hosts over 80 software packages capable of gene analysis. Most these search enriched signatures amongst differentially regulated genes to reveal higher level themes that may be missed when focusing only on evidence from individual genes. With so many different methods offer, choosing best algorithm and visualization can challenging. EGSEA...
Differential expression analysis of genomic data types, such as RNA-sequencing experiments, use linear models to determine the size and direction changes in gene expression. For RNA-sequencing, there are several established software packages for this purpose accompanied with pipelines that well described. However, two crucial steps process can be a stumbling block many -- set up an appropriate model via design matrices comparisons interest contrast matrices. These particularly troublesome...
Abstract RNA-seq datasets can contain millions of intron reads per library that are typically removed from downstream analysis. Only overlapping annotated exons considered to be informative since mature mRNA is assumed the major component sequenced, especially for poly(A) RNA libraries. In this study, we show informative, and through exploratory data analysis read coverage signal representative both pre-mRNAs retention. We demonstrate how utilized in differential expression using our index...
Abstract Application of Oxford Nanopore Technologies’ long-read sequencing platform to transcriptomic analysis is increasing in popularity. However, such can be challenging due the high sequence error and small library sizes, which decreases quantification accuracy reduces power for statistical testing. Here, we report two nanopore RNA-seq datasets with goal obtaining gene- isoform-level differential expression information. A dataset synthetic, spliced, spike-in RNAs (‘sequins’) as well a...
Carefully designed control experiments provide a gold standard for benchmarking different genomics research tools. A shortcoming of many gene expression studies is that replication involves profiling the same reference RNA sample multiple times. This leads to low, pure technical noise atypical regular studies. To achieve more realistic structure, we generated RNA-sequencing mixture experiment using two cell lines cancer type. Variability was added by extracting from independent cultures and...
Group heteroscedasticity is commonly observed in pseudo-bulk single-cell RNA-seq datasets and its presence can hamper the detection of differentially expressed genes. Since most bulk methods assume equal group variances, we introduce two new approaches that account for heteroscedastic groups, namely voomByGroup voomWithQualityWeights using a blocked design (voomQWB). Compared to current gold-standard do not heteroscedasticity, show results from simulations various experiments demonstrate...
Spatial transcriptomics allows gene expression to be measured within complex tissue contexts. Among the array of spatial capture technologies available is 10x Genomics' Visium platform, a popular method which enables transcriptome-wide profiling sections. offers range sample handling and library construction methods introduces need for benchmarking compare data quality assess how well technology can recover expected features biological signatures. Here we present SpatialBenchVisium, unique...
Previous studies on the epigenetic regulator DNA methyltransferase 3-Like (DNMT3L), have demonstrated it is an essential of paternal imprinting and early male meiosis. Dnmt3L also a effect gene, i.e., wild type offspring heterozygous mutant sires display abnormal phenotypes suggesting inheritance aberrant marks chromosomes. In order to reveal mechanisms underlying these effects, we assessed X chromosome meiotic compaction, XY aneuploidy rates global transcription in haploid germ cells from...
Influenza A virus (IAV) is rapidly detected in the airways by immune system, with resident parenchymal cells and leukocytes orchestrating viral sensing induction of antiviral inflammatory responses. The are innervated heterogeneous populations vagal sensory neurons which also play an important role pulmonary defense. How these respond to IAV respiratory infection remains unclear. Here, we use a murine model provide first evidence that undergo significant transcriptional changes following...