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- A new regulator of stemness to create dendritic cell factories for immunotherapy
- Advanced methods for genomic rearrangement detection
- Control of cytokine signaling by SOCS1
- Defining the protein modifications associated with respiratory disease
- Delineating the pathways driving cancer development and therapy resistance
- Developing a new drug that targets plasmacytoid dendritic cells for the treatment of lupus
- Development and mechanism of action of novel antimalarials
- Development of a novel particle-based malaria vaccine
- Development of tau-specific therapeutic and diagnostic antibodies
- Discovering novel therapies for major human pathogens
- Dissecting host cell invasion by the diarrhoeal pathogen Cryptosporidium
- Epigenetic biomarkers of tuberculosis infection
- Essential role of glycobiology in malaria parasites
- Evolution of haematopoiesis in vertebrates
- Human lung protective immunity to tuberculosis
- Identifying novel treatment options for ovarian carcinosarcoma
- Interaction with Toxoplasma parasites and the brain
- Interactions between tumour cells and their microenvironment in non-small cell lung cancer
- Investigating the role of mutant p53 in cancer
- Microbiome strain-level analysis using long read sequencing
- Minimising rheumatic adverse events of checkpoint inhibitor cancer therapy
- Modelling spatial and demographic heterogeneity of malaria transmission risk
- Naturally acquired immune response to malaria parasites
- Predicting the effect of non-coding structural variants in cancer
- Structural basis of catenin-independent Wnt signalling
- Structure and biology of proteins essential for Toxoplasma parasite invasion
- T lymphocytes: how memories are made
- TICKER: A cell history recorder for longitudinal patient monitoring
- Targeting host pathways to develop new broad-spectrum antiviral drugs
- Targeting post-translational modifications to disrupting the function of secreted proteins
- Targeting the epigenome to rewire pro-allergic T cells
- Targeting the immune microenvironment to treat KRAS-mutant adenocarcinoma
- The E3 ubiquitin ligase Parkin and mitophagy in Parkinson’s disease
- The molecular controls on dendritic cell development
- Understanding malaria infection dynamics
- Understanding the genetics of neutrophil maturation
- Understanding the neuroimmune regulation of innate immunity
- Understanding the proteins that regulate programmed cell death at the molecular level
- Using cutting-edge single cell tools to understand the origins of cancer
- When healthy cells turn bad: how immune responses can transition to lymphoma
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Gordon Smyth-projects
Researcher:
Analysis of RNA sequencing data
We have developed the limma and edgeR software packages that are widely used around the world for analyzing gene expression experiments. The edgeR package implements exact tests and generalized linear models for RNA-seq counts based on the negative binomial distribution. The limma package implements linear modelling and gene set testing approaches. Both the limma and edgeR packages implement empirical Bayes for borrowing strength between genes in genomic experiments.
Team members: Yunshun Chen, Wei Shi, Yang Liao, Yifang Hu
Sequence read alignment and quantification
Next generation sequencing produces huge numbers of DNA or RNA sequence reads. We have developed a read aligner called Subread, which works well for mapping of short or long reads. It has many applications, but is especially fast and robust relative to alternatives when applied to RNA-seq data. We have also developed a summarisation tool, called featureCounts, which is useful for quantifying abundances of genomic features such as genes, exons and promoters.
Team members: Wei Shi, Yang Liao
Analysis of ChIP sequencing data
We have developed methods for assessing differential binding of epigenetic histone marks and of transcription factors. We are currently developing methods for detecting DNA-DNA interactions using for Hi-C and Chia-PET data.
Team members: Aaron Lun, Wei Shi
Expression signature analysis applied to stem cells, breast cancer and lung cancer
We have developed a number of gene set test methods for assessing the behavior of co-regulated sets of genes representing higher level biological processes. We have collaborated extensively with the Visvader/Lindeman laboratory for nearly a decade and have successfully applied gene signature analyses to study adult stem cells and the origins of breast cancer.
Team members: Göknur Giner, Yunshun Chen, Yifang Hu