ABLeS participants

This project aims to advance sedimentary ancient DNA (sedaDNA) research in Australia by developing an automated bioinformatics pipeline for efficient and validated taxonomic profiling of modern and ancient target taxa in sediment samples.

This project aims to understand how tumour cells and the microenvironment adapt and co-evolve as an ecosystem to drive cancer progression, resistance and metastasis using a combination of multi-omics, microscopy and imaging data.

Faster generation, publication and re-use of reference genomes for Australian species.

This project investigates drought tolerance in Australian wild cotton species through quantitative proteomics analysis, comparing protein expression under drought and normal conditions. We will annotate protein sequences for three species using publicly available genomic and transcriptomic data, aiding our understanding of their drought response mechanisms.

Initiated in 2023, this national genomics program aims to transform our understanding of Australia’s diverse insect populations and support data-informed integrated pest management (IPM) strategies. By generating omics data, the initiative will help sustainably manage insect pests, safeguard agriculture, and promote healthy ecosystems.

We aim to use the Angiosperms353 target capture methodology to sequence every native NSW flowering plant species during stage one of our Phylogenomic Flagship project (about 7000 species and subspecies).

Development of DMG ADvanced mAchine learning Precision Treatment Strategy (ADAPTS) platform. This project aims to model temporal tumour adaptations to therapy and predict targetable vulnerabilities, based on non-invasive blood profiling, for therapeutic adjustments of patients with DMG under treatment.

Analysis of the DNA methylation patterns of blood samples from 52 pregnant women. DNA methylation patterns will be assessed between women who were stratified into high and low alignment to a mediterranean diet throughout pregnancy.

This project will investigate the formation of unusual chains of chromosomes that are increasingly being found in various vertebrate and invertebrate taxa, using an organism in which they are most commonly found, termites. We will test the hypothesis that inbreeding drives the evolution of meiotic sex linked chromosomes.

OmniFold is an open-source replication and extension of Alphafold3. It is an artificial intelligence tool used to predict biomolecular structures of proteins, DNA, RNA and other molecules.

Development of genomics resources to enhance our understanding of the evolution and conservation of the unique Australian flora.

Genome Assembly and base calling for genomes genreated by GAP.

Oceans are changing. Coral reefs are wonders of high socio-economic value threatened by climate extremes. To urgently prepare against extinction, this project expects to deliver ground-breaking estimates of coral evolution by integrating genomics and innovative disease models. Expected outcomes include the discovery of reefs that can survive extremes and repopulate other reefs, providing benefits in optimized capabilities to protect resilient and vulnerable reefs to sustain future ecosystem services and boosting Australia as a global leader in the conservation genomics revolution.

Our research uses phylogenomics to describe and map species distribution patterns, origin and spread of a class of marine life (brittle-stars or ophiuroids) across global seafloors over the past 100 million years.

Salt extremophiles (plant halophytes) have unique salt tolerance mechanisms not found in food crops. New genomic, transcriptomic, proteomic and genetic resources are now unlocking genes and pathways that could be introduced to our food crops. At the same time, we are using these resources to guide our modern breeding leading to domesticated wild extremophiles as future food crops.

Development of a workflow for Structural variation detection and filtration.

Prenatal programming of respiratory epithelial progenitors and early postnatal respiratory disease.

Development of new molecular tools to enhance and expand the genomics-based therapeutic toolkit.

Investigate plant pathogen genomics, population genetics, virulence evolution, fungicide resistance evolution, and diagnostics

This project aims to establish a robust metagenome assembled genome (MAG) database specifically focussing on bacterial communities from freshwater and wastewater ecosystems. Development of comprehensive metagenome assembled genome (MAG) database can provide essential insights into these ecosystems, ultimately supporting/allowing researchers to easily access and utilize the genomic data for their studies and decision-making.

Development of a scalable DIA-NN workflow for the processing of scanning SWATH mass spectra.

The project aims to first support and then accelerate nanopore basecalling on multiple GPU architectures from different vendors.

This project aims to create a compositional, gene expression and cell-communication map and uncover significant diversity in immunotherapy targets across ages and sex.

Analysis for NVIDIA Parabricks and GATK benchmarking for RNA-Seq, based on NVIDIA recommendations as well as for designing probes for an amplicon-based SNP array genotyping platform.

Explore software and hardware efficiencies in the current deep learning revolution in computational structural biology.

A portable genomics workflow for pond side sequencing of bacterial pathogens for sustainable aquaculture

Bioinformatics analyses for the Australian Amphibian and Reptile Genomics initiative.

Produce reference genomes for several grapevine varieties and to provide these as foundational datasets for further work.

A shared repository for bioinformatics tools, workflows, databases, and containers.

Workflow consolidation, testing and implementation for Rare Disease Genetics and Functional Genomics managed by the Harry Perkins Institute of Medical Research.

Bioinformatics analyses for the Threatened Species Initiative.

Analysis of high-risk paediatric children enrolled in the Zero Childhood Cancer initiative.

Defining accurate strain-specific germline references is an essential tool for understanding the development of B and T cells during immune responses. We are producing a haplotype-resolved Immunoglobulin and T cell receptor germline reference assembly using high-fidelity whole genome sequencing on BALB/c and B10.BR mice, followed by de-novo reference assembly, contig-alignment and annotation.

The project will analyse Tasmanian Devil genome to shed light on causes of Tasmanian Devil facial tumour disease (DFTD) disease.

Haemosphere is a publicly available resource of transcriptional data for human and mouse blood cells. This allows researchers around the world to access the expression data for their genes of interest, and identify novel genes that are interesting in their field of study.

Analysis of a large number of healthy and tumour samples by the Zero Childhood Cancer initiative.

Bioinformatics analyses by Crismani Bioinformatics.

Janis is an open-source Python tool that has been developed to assist with the translation between bioinformatics workflow specifications.

ONTViSc is a Nextflow-based end-to-end bioinformatics pipeline designed to help diagnostics of viruses and viroid pathogens for biosecurity.

This project involves investigating a novel neural network architecture for predicting protein-ligand binding affinity constants with potentially improved accuracy and generalisation compared to previous methods.

Unravel the spatial signalling ecosystem of cancer cells versus normal tissues through integrated analysis of single-cell and spatial transcriptomics data.

Impact of structural variants on the evolution of parity modes in Lerista bougainvillii, a reproductively bimodal lizard

This project will help life-science researchers improve the estimation of their grants and compute resources by creating a portable and rerunnable pipeline that benchmarks commonly used life-science analysis software.

Recovering reference microbial genomes from public metagenomes. We hope to recover taxonomically novel genomes, using Bin Chicken to decide which public metagenomes to analyse together.