The Bioinformatics Hub has a keen interest in finding and supporting students with an interest in bioinformatics. Please contact us for information on any future projects.
Nhi Hin - PhD CandidateThe molecular signature of Alzheimer's disease
Principal Supervisor: Michael Lardelli, School of Biological Sciences
Alzheimer's disease is a complex neurodegenerative disease and the most prevalent form of dementia in Australia. Unfortunately, the causes and progression of Alzheimer's disease are still not well understood. Most patients with Alzheimer's disease have a form of the disease called 'sporadic Alzheimer's disease', meaning that there is no identifiable cause of the disease. This makes it difficult to study exactly why Alzheimer's disease arises, along with the molecular processes involved in its progression. However, a small subset of Alzheimer's disease patients have 'familial Alzheimer's disease' due to genetic mutations passed down through their families.
Many of these mutations have occurred in the PRESENILIN genes PSEN1 and PSEN2, which encode the Presenilins, proteins which are highly involved in the progression of Alzheimer's disease. Although most patients with Alzheimer's disease have the sporadic form, patients with either the sporadic or familial forms of Alzheimer's disease show highly similar brain pathology and clinical symptoms. Consequently, understanding the functions of genes like the _PRESENILIN_ genes in familial Alzheimer's disease is likely to impart valuable knowledge about the causes and progression of sporadic Alzheimer's disease.
My research involves comparing RNA-seq transcriptome data from two different zebrafish genetic models of familial Alzheimer's disease developed by the Alzheimer's Disease Genetics Laboratory. Each of these models has a different mutation in the zebrafish psen1 gene. Even though these mutations are different (one results in a truncated Presenilin protein while the other results in a small deletion which does not otherwise disrupt the protein), humans with either of these mutations would similarly develop (familial) Alzheimer's disease. By exploring the overlap between the dysregulated genes and molecular processes in both of these models, it may be possible to establish a molecular "signature" common to Alzheimer's disease cases.
Ning Liu - PhD CandidatInvestigating Three Dimensional Chromosome Structure in T Lymphocytes using High-Resolution Chromosome Conformation Capture Assays
Principal Supervisor: Dr. Jimmy Breen, Robinson Research Institute & SAHMRI
Co-Supervisors: Prof. Simon Barry, Robinson Research Institute & Women and Children Hospital; Dr. Rick Tearle, Davies Research Centre
Genome-wide association studies (GWAS) is able to identify genetic variation such as single nucleotide polymorphism (SNP) that is significantly associating with a specific phenotype (e.g. a type of diseases) in the human genome. However, most of the identified SNPs for diseases are located in non-coding regions, suggesting the mechanism of how they contribute to diseases are unknown. Here we hypotheses that these non-coding genetic variations are regulating gene expressions in three dimensional manner, resulted by the dynamic 3D chromosome conformation. In my PhD, I analyse HiC and HiChIP datasets of T cells generated by Simon's group, together with publicly available HiC and Capture-HiC datasets to identify significant 3D interactions and Topological Associated Domains (TADs) to construct high resolution chromosome conformation map of T cells. Additionally, I mined publicly available RNA-seq data to identify expression Quantitative trait loci (eQTL) of human T cells. Finally, by integrating 3D interactions, eQTLs, GWAS SNPs and other epigenomics data, I aim to link non-coding genetic variations to gene expression regulation using 3D interactions.
Weixiong He - Master of BiotechnologyCreating computational workflows and pipelines for methylation quantitative trait loci (meQTL) analyses in human placental data
Principal Supervisor: Dr Jimmy Breen, Robinson Research Institute
DNA methylation plays a crucial role in embryogenesis. Methylation quantitative trait loci (meQTL) are thought to response for the changes in DNA methylation pattern. meQTL analyses aim to identify the effect of genetic variants (commonly SNPs) on the methylation of nearby methylated sites. However, meQTLs are likely altered in the different population, developmental stages and tissues. For reproducible science, it is necessary to create a standardised workflow that can be applied in all meQTL analyses.
We currently have imputed genotypes and genome-wide DNA methylation profiles for maternal blood and feral placental tissue, as well as other potential datasets from Cerebral Palsy patients and publicly available data. This project would aim to test current meQTL pipelines created at the RRI and create a step-by-step instruction on how to identify methylation QTLs from DNA methylation and genotype data in reproductive tissues.
Guanchen Li - Master of BiotechnologyUsing SNP calling methods and Next-Generation Sequencing for identification of degraded human remains
Principal Supervisor: A/Prof Jeremy Austin, Australian Centre for Ancient DNA
Co-Supervisor: Steve Pederson
Over the past three decades, genetic identification of human individuals has made great strides due to the rapid development of DNA analysis technologies. DNA fingerprinting and STR (Short-Tandem Repeat) profiling which use repetitive DNA motifs with different repeat units to generate a unique DNA pattern for each person have been used to determine the identification of unknown individuals in many forensic cases.
While extracted DNA samples from degraded human remains are highly fragmented and they cannot be used to generate a DNA profile in DNA fingerprinting and STR profiling process. In our project, the single-nucleotide polymorphisms (SNPs) calling method which is another new human identification approach will be used for human identification. SNPs which are single-base variations among individuals have been considered as DNA markers and each SNP locus contains only two alleles. Extracted DNA from unknown individuals have been sequenced through NGS technology. Accurate SNPs in NGS-generated DNA reads will be identified by using bioinformatics tools. Finally, the found SNPs will be compared with genomics databases (such as GEDmatch) for identifying the unknown individuals or finding their close relatives.
Tianzhi Yu – Master of BiotechnologyRNA-Seq time course of mouse endometriosis model
Principal Supervisor: Steve Pederson, Bioinformatics Hub
Co-Supervisor: John Schjenken, Robinson Research Institute
Endometriosis is a gynaecological disease characterized by the growth of estrogen-responsive endometrial tissue (normally lined inside of the uterus) outside the uterine cavity. i.e. Endometriosis is characterized by endometrial tissue being ‘in the wrong place’. This disease affecting ~10% of reproductive-aged women worldwide. Despite its prevalence, the pathogenesis of endometriosis remains unclear. Most people believe that endometriosis is caused by the reflux of menstrual blood (containing endometrial fragments) into peritoneal cavity (having 85% of macrophages).
The presence of endometrial fragments leads to the recruitment of inflammatory cells, especially, a large number of macrophages. As macrophages arrive at the site, they can be then activated towards M1 subclass (classic activation) by exposing to inflammation-related cytokines. Studies demonstrated that M1 macrophages are highly specialized in removal of debris. So large amount of shed endometrial cells are cleaned and the level of pro-inflammatory cytokines are therefore reduced (i.e. the resolution of inflammatory). So, the recruited macrophages cannot become M1 in time; they don’t work properly to engulf the shed endometrial cells, and therefore, these endometrial cells will get a chance to stick to the surfaces/organs in the cavity. As the anti-inflammatory molecules increased, macrophages are polarized towards M2 subtype (alternative activation), helping the attached endometrial tissue to repair, proliferate, and eventually establish the lesions.
Previous studies have shown that miRNA-155 promotes M1 macrophage activation whereas miRNA-223 is involved in M2 macrophage polarization. Therefore, Robinson Research Institute developed miR-223-deficient and miR-155-deficient homologous mice models, in order to study the functional alteration of macrophages and the development of endometriotic lesions. The objective of my study is, to analyse the differential expression of mRNA in these miRNA-deficient mice models with the endometriotic-like disease and compare this mRNA expression profile to that in humans, by using mRNA-seq. In order to predict the pathways and gens associated with lesion development.
Jacqueline Rehn - Master of BiotechnologyThe role of DNA damage in ancient metagenomic studies
Co-Supervisor: Laura Weyrich, Australian Centre for Ancient DNA
Studies of the human microbiome have demonstrated that alterations in the diversity and distribution of bacterial populations in the body can result in dysbiosis and disease. While research in this field has helped to understand the aetiology of several complex disorders, questions about what constitutes a healthy microbiome and how modern lifestyles have affected these symbiotic relationships remain. Shotgun sequencing analysis of dental calculus taken from ancient remains can address some of these questions by providing a snapshot of the oral microbiome throughout time.
However, authentication of these results is difficult given the complexity of distinguishing between sequences of ancient bacteria trapped in dental plaque and modern environmental contaminants. Ancient DNA from mammals has been shown to have characteristic patterns of damage that can be identified using bioinformatics tools and used to authenticate DNA sequences as being ancient in origin. Bacteria are assumed to demonstrate similar patterns of damage but little research has been conducted to confirm that this is the case.
Furthermore, it is unclear how sequencing errors introduced due to the damaged nature of recovered DNA might affect the accuracy of taxonomic profiling. In our project, we aim to use simulated data to investigate the impact of DNA damage on accurate profiling of bacterial populations in metagenomic samples and investigate differences in the type of damage that accumulates in human and microbial genomes.
Kelly Ren - Master of BiotechnologyDNA-methylated differences in monozygotic twins discordant for unipolar and bipolar depression
Although monozygotic (MZ) twins share nearly all of their genetic variants, they can be discordant in some particular diseases, such as unipolar and bipolar depression. One possible contributor of this is DNA methylation, which is an epigenetic mechanism influenced by environmental, genetic and stochastic events. Here, our project focuses on the epigenetic analysis of a set of Infinium Human Methylation 450 BeadChip (450k) MZ twins data that has been provided by Flinders University.
This data has been obtained from blood samples collected from monozygotic twins aged between 22 to 60. Bioinformatic analysis of this data will hopefully help identify differences in the methylation patterns of depressed and healthy twins. Pathway analysis will then identify the genetic pathways that contribute to depression. Results will be meta-analysed with other MZ twin data from the Brisbane Older Ageing Twins Study with an average age of 70 and the Brisbane Longitudinal Twin Study with average age of 14, as well as similar published studies that are publicly available in order to further discover if age or other factors also play roles in disease progression.
Awais Choudhry - B.Sc (Honours)Aristaless related X-linked Intellectual Disability
Co-Supervisor: Cheryl Shoubridge
Intellectual disability (ID) affects between 1 to 3% of the population affecting individuals and their families. Males with ID usually contain a mutation in a gene located on the X chromosome. Aristaless (ARX) mutations is associated with X-linked ID. ARX is frequently mutated causing a variety of phenotypes ranging from severe X-linked lissencephaly with ambiguous gentialia to mild ID with no consistent clinical features. This range of symptoms depends on the location and severity of the mutation. ARX contains four separate poly-alanine (PA) tracts each of which when expanded causes different disease phenotypes.
PA1 and PA2 contains approximately 60% of mutations for disease causing mutations in ARX. ARX is a paired homeodomain transcription factor which represses over 800 genes directly. In diseased individuals containing mutations in ARX, over 200 genes are deregulated while many genes expressed regularly, the cause of this remains unknown. We suspect there maybe a correlation between the accessibility of the motif site and its ability to regulate gene expression. Using Hi-C data, Atac-seq and Chip-seq we will investigate the potential causes of certain genes being deregulated by ARX and others remaining functional.