UQCCR Genomics Subcommittee

UQCCR Genomics subcommittee is tasked to provide educational opportunities in the field of genomics. Specifically, facilitation and information regarding relevant workshops for both students and staff as well as the organisation of human-health genomics seminars with a focus on novel tools and applications.

Members

Chair: Dominic Guanzon - d.guanzon@uq.edu.au
Deputy Chair: Leah Roberts - l.roberts3@uq.edu.au
Member: Rhys Izuagbe - r.izuagbe@uq.edu.au
Member: Ella Trembizki - e.trembizki@uq.edu.au
Member: Brian Forde - b.forde@uq.edu.au
Member: Jun Yan - j.yan@uq.edu.au
Member: Kym Lowry - k.lowry@uq.edu.au
Member: Patrick Harris - p.harris@uq.edu.au
Member: Krispin Hajkowicz - k.hajkowicz@uq.edu.au

UQCCR genomic facilities and equipment

Illumina MiniSeq sequencer.
Oxford Nanopore – MinION and PromethION sequencers.
Forde cluster for microbial genomics analysis.

For the above resources, please feel free to contact the UQCCR Genomics subcommittee members or Kay Ramsay (Senior Lab Manager) for further details.

MGISP-960 High-throughput Automated Sample Preparation System. This system has a Temperature Control module, PCR module, Shaker and 2 x Magnetic frames for DeepWell plates. Some use cases for this machine include sequencing library preparation, nucleic acid extraction, bead-based cleanups and liquid handling in 96 well plate format.

For the MGISP-960, please feel free to contact Kym Lowry for futher details.

Genomic related resources

NCBI (National Center for Biotechnology Information)

Provides a wide range of resources including databases like PubMed, GenBank, BLAST, and various tools for sequence analysis, genome browsing, and more. Visit the NCBI website.

Ensembl

Offers genome databases and analysis tools for vertebrates and other eukaryotic species. It provides access to genomic data, gene annotation, comparative genomics, and more. Websites: useast.ensembl.org and asia.ensembl.org

UCSC Genome Browser

A widely used tool for visualizing and analyzing genomic data. It provides access to a large collection of genome assemblies and annotations from various organisms. Visit the UCSC Genome Browser website.

Galaxy Project

A platform for data-intensive biomedical research that provides a web-based interface for accessing a wide range of bioinformatics tools and workflows. Visit the Galaxy Project website.

Bioconductor

An open-source software project for the analysis and comprehension of genomic data, offering a wide range of packages for statistical analysis, visualization, and annotation. Visit the Bioconductor website.

EMBL-EBI (European Bioinformatics Institute)

Offers a suite of bioinformatics tools and databases, including resources for genomics, proteomics, and structural biology. Visit the EMBL-EBI website.

Genome Analysis Toolkit (GATK)

A software package developed by the Broad Institute for variant discovery in high-throughput sequencing data. It provides tools for variant calling, genotyping, and other genomic analyses. Websites: broadinstitute.org/scientific-community/software/genome-analysis-toolkit-gatk and gatk.broadinstitute.org/hc/en-us

STRING

A database of known and predicted protein-protein interactions, offering comprehensive coverage and various tools for network analysis. Visit the STRING website.

GenBank

The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. Visit the GenBank website.

ExPASy

Offers a wide range of tools and databases for proteomics research, including sequence analysis, protein structure prediction, and more. Visit the ExPASy website.