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 If you are a potential supervisor, [[supervisor_instructions:click here]]
+=== The Barrier Atlas: Cross-Tissue Insights into Homeostasis and Dysfunction ===
+Contact: Amanda Oliver (Amanda.Oliver@qimrb.edu.au)
+Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of human tissue biology, revealing cellular diversity across organs and disease states. Building on existing datasets profiling millions of cells, this project aims to construct a unified single-cell atlas of barrier tissues, including the lung and gut, to uncover shared and tissue-specific mechanisms that maintain immune balance at the body’s environmental interfaces. The student will develop and apply computational pipelines for large-scale data integration, quality control, cell type annotation, and spatial and microbial mapping across millions of cells and thousands of samples. Advanced methods such as gene regulatory network inference, deep learning, and foundation models will be used to explore cross-tissue immune regulation and barrier dysfunction. By combining single-cell, spatial, and microbiome data, the project will deliver the first cross-tissue atlas of barrier biology, providing new insights into diseases such as inflammatory bowel disease and chronic respiratory disorders.
+Suitable for Masters, or PhD students. Strong bioinformatics skills using Python or R are essential; experience with single-cell or spatial transcriptomics and knowledge of immunology or barrier tissue biology is highly desirable.
+=== The Escape of Human Genomic Data into Public Repositories ===
+Contact: Michael Hall (michael.hall1@uq.edu.au)
+Public sequencing repositories (e.g. SRA) are growing rapidly, but many studies involving human clinical samples may inadvertently include identifiable host DNA—even when ethics approvals explicitly prohibit this. This project investigates the extent and implications of such data leakage.
+Objectives:
+	•	Identify publicly available datasets from clinical pathogen/metagenomic sequencing studies
+	•	Quantify residual human genomic content using a variety of approaches and references
+	•	Benchmark human read detection approaches (e.g. host depletion vs k-mer-based methods)
+	•	Assess potential identifiability using forensic markers (e.g. Illumina Infinium SNPs, CODIS loci)
+	•	Explore the role of ethics language, technical variability, and population bias (e.g. African vs European genomes) in leakage rates
+Skills you’ll gain:
+	•	Handling and processing large sequencing datasets
+	•	Working knowledge of alignment and k-mer classification tools (e.g. minimap2, kraken) and human read detection pipelines
+	•	Experience in reproducible bioinformatics analysis and privacy-aware genomic research
+	•	Insight into the intersection of ethics, bioinformatics, and public data governance
+This project is ideal for students interested in clinical genomics, privacy, ethics, or data-driven policy impact. Familiarity with the command line is necessary. Knowledge of Python would be great, but not required—we can build those skills as you go!
+=== Decoding the relationships between DNA replication, genome architecture, chromatin organisation ===
+Contact: Dr Mathew Jones (mathew.jones@uq.edu.au)
+The human genome is packaged into chromatin and assembled into 3D self-interacting chromatin domains that regulate gene expression and coordinate the process of DNA replication. Understanding the relationships between genome structure and function is one of the outstanding challenges in modern biology. Changes in the 3D structure of the genome can cause copying errors (genetic mutations) during DNA replication that results in diseases such as cancer and advanced aging. Decoding the relationships between the genomic landscape and cellular processes such as DNA replication has the potential to inform the development of novel treatments that can treat cancer and extend longevity.
+In this project we are seeking talented and enthusiastic postgraduate students to tackle two fundamental questions: 1. How does the epigenome and the 3D organisation of the genome regulate DNA replication? 2. How are these processes disrupted in cancer and impacted by cancer therapies. The project will assess the impact of genomic features on replication using nanopore sequencing data generated by the Jones lab’s and their artificial intelligence assay for assessing DNA replication in human cells (https://doi.org/10.1101/2022.09.22.509021) and publicly available Hi-C, Repli-Seq, CUT & RUN, ChIP-seq, scSeq, datasets (e.g., GEO, ENCODE).
+Bioinformatics and Computer Science students with skills in R, Python and C++ that are familiar with software suites for the comparison, manipulation and annotation of genomic features are encouraged to contact Dr Mathew Jones (mathew.jones@uq.edu.au) to learn more about the projects available.
+=== Pangenomes to predict bacterial transmission in healthcare settings ===
+Contacts: Leah Roberts l.roberts3@uq.edu.au, Michael Hall michael.hall2@unimelb.edu.au
+Predicting whether two bacterial isolates are the same (and thereby inferring if transmission has occurred) has traditionally been performed by identifying and counting single nucleotide variants (SNVs). To do this, a reference genome is usually selected, and isolate reads are mapped to the reference to identify SNVs in regions shared between all isolates. However, for large datasets of very diverse bacterial strains, a single reference genome is usually insufficient, as the shared regions between the strains becomes a very small proportion of the total genomic content.
+We propose a novel method using pangenome reference graphs to better identify and discriminate transmission of bacterial pathogens. This project would start to build test datasets and develop novel workflows for predicting transmission from pangenome graphs.
+This project is suitable for an honours, Masters, or PhD student. Background in command line, HPC and python is highly desirable. This project will be based at UQCCR (Herston Campus) and co-supervised by Dr Michael Hall (University of Melbourne).
 === Investigation of the effect of the circadian rhythm on the genetic control of gene expression ===
-Sonia shah <sonia.shah@imb.uq.edu.au>, Solal Chauquet <uqschauq@uq.edu.au >
+Contact: Sonia shah <sonia.shah@imb.uq.edu.au>, Solal Chauquet <uqschauq@uq.edu.au >
 The circadian rhythm reflects the daily cycle of behaviours and metabolic processes organisms exhibit. A 24-hour gene expression pattern occurs at the molecular level, with genes activated either during the day or night. Different tissues all display circadian control, with some more affected than others. Within the liver, for example, 3000 genes are subjected to circadian control. This regulation is orchestrated by a small group of CLOCK genes, establishing feedback loops that result in rhythmic gene expression in every tissue.