open_projects
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| If you are a potential supervisor, [[supervisor_instructions: | If you are a potential supervisor, [[supervisor_instructions: | ||
| - | === Decoding the relationships between DNA replication, | + | === Decoding the relationships between DNA replication, |
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| + | 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. | 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? | + | 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? |
| 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. | 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. | ||
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| === De novo identification of insertion sequences with De Bruijn graphs === | === De novo identification of insertion sequences with De Bruijn graphs === | ||
| - | Leah Roberts: l.roberts3@uq.edu.au, | + | Contacts: |
| Insertion sequences (IS) are small DNA elements that can replicate and move throughout a bacterial genome independently. This ability often results in their insertion upstream of or within genes, which consequently leads to large effects on gene expression within the bacteria. These changes in expression can affect a multitude of phenotypes, including resistance to antibiotics and virulence. As such, is it necessary that we characterise where these IS move to within the genome. | Insertion sequences (IS) are small DNA elements that can replicate and move throughout a bacterial genome independently. This ability often results in their insertion upstream of or within genes, which consequently leads to large effects on gene expression within the bacteria. These changes in expression can affect a multitude of phenotypes, including resistance to antibiotics and virulence. As such, is it necessary that we characterise where these IS move to within the genome. | ||
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| === Machine Learning to predict plasmids from bacterial isolates === | === Machine Learning to predict plasmids from bacterial isolates === | ||
| - | Leah Roberts: l.roberts3@uq.edu.au, | + | Contacts: |
| Plasmids play a key role in gene exchange between bacteria and often carry gene conferring resistance to antibiotics and survival in hospital environments. However, they are difficult to fully characterise from short-read whole genome sequencing data alone. This is because plasmids are typically full of repeat sequences which can cause problems for short-reads assemblers. Long-read sequencing can solve this issue, however this technology is currently not routinely used in healthcare settings. | Plasmids play a key role in gene exchange between bacteria and often carry gene conferring resistance to antibiotics and survival in hospital environments. However, they are difficult to fully characterise from short-read whole genome sequencing data alone. This is because plasmids are typically full of repeat sequences which can cause problems for short-reads assemblers. Long-read sequencing can solve this issue, however this technology is currently not routinely used in healthcare settings. | ||
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| This project is suitable for an honours or Masters student. Background in command line, HPC and python is highly desirable. This project will be based at UQCCR (Herston Campus) and co-supervised by Prof Zamin Iqbal (University of Bath, UK). | This project is suitable for an honours or Masters student. Background in command line, HPC and python is highly desirable. This project will be based at UQCCR (Herston Campus) and co-supervised by Prof Zamin Iqbal (University of Bath, UK). | ||
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| === Pangenomes to predict bacterial transmission in healthcare settings === | === Pangenomes to predict bacterial transmission in healthcare settings === | ||
| - | Leah Roberts: l.roberts3@uq.edu.au, | + | Contacts: |
| 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, | 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, | ||
open_projects.1740721075.txt.gz · Last modified: 2025/02/28 16:37 by project