ABLeS participants

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.

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.

There are a wide range of applications of agentic AI that are emerging but questions of deployment, security and value are common amongst all types of users. This project seeks to investigate a number of applications of agentic AI in bioinformatics, understand the value of this applications to the end user compared to more manual alternatives and in the process understand the technical challenges and limitations of running these via locally deployable models.

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

This project develops and benchmarks a novel, groundbreaking mathematical framework that leverages topological data analysis and optimal transport to align disparate spatial modalities while strictly preserving full tissue mass and cellular topology across severe physical deformations.

We will use protein mass spectrometry and transcriptomics to identify the constituent proteins of platypus venom. Candidate proteins identified will then be analysed and screened in assays, to determine their function, associated envenomation symptoms, and potential as novel therapeutics.

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.

The project aims to investigate the roles of human endogenous retrovirus in motor neuron disease using multi-omics analysis.

A national collaborative project, which aims to develop foundational genomic data for priority animal pathogens and parasites, supporting national efforts in disease understanding, detection, surveillance and control.

The Dinoflagellate Genomics and Toxin Discovery Project is a collaborative national initiative focused on generating genomic resources and analytical capability for priority dinoflagellate species associated with harmful algal blooms and marine biotoxin production.

The Avian Genomics Initiative will fill genomic data gaps for investigating and managing unique Australian bird species.

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.

The Australian Fish Genomics Initiative seeks to address critical deficiencies in available genomic data for Australian fishes. By generating high-quality genomic data, this work will provide a foundation for improved population monitoring, environmental assessment, and the sustainable management of fisheries and aquatic 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).

MicrobialExplorer is an interactive R Shiny web application for exploratory analysis and visualisation of microbiome sequencing data, supporting researchers without bioinformatics expertise to interrogate their own datasets.

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.

AAGI and CCDM are advancing crop resilience and disease management by integrating genomics, pangenomics, structural bioinformatics, and advanced omics technologies to uncover genetic and molecular mechanisms underlying adaptation, virulence, and host defence in crops, pathogens, and pests.

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.

Small-molecule splicing modulators compounds may interact with recurrent AML mutations in spliceosome proteins like SF3B1, SRSF2, U2AF1, and cause synthetic lethality, killing mutant cells but spare healthy ones. In this project we will characterize the effect of 15 novel small-molecule splicing modulators compounds in the transcriptomes and RNA processing of cells using Nanopore single-molecule multimodal timing of in vivo mRNA synthesis protocol (https://www.biorxiv.org/content/10.1101/2025.04.27.650906v1.full.pdf).

The gut-brain axis is a bidirectional communication network linking neural function with the gut microenvironment and is increasingly implicated in neuropsychiatric and neurodegenerative conditions. We are conducting a large scale meta analysis of thousands of human metagenomes to identify consistent disease associated signatures.

The TCGA Prostate Adenocarcinoma (PRAD) cohort, with its rich germline SNP-array data linked to detailed clinical outcomes, offers a unique opportunity to investigate how germline variation influences both cancer biology and treatment response. By integrating SNP-based genome-wide risk profiling with high-resolution HLA imputation, we can build genetic models that not only improve prediction of prostate cancer recurrence and survival, but also reveal how inherited variation interacts with tumor subtypes, immune features, and treatment modalities such as surgery, radiation, or ADT.

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.

Molecular Dynamics Studies of Horse Prion Protein S167D-Variant and Wild-Type, and Other PrPC Proteins and PrPScs.

Computational Studies of Parkinson's Diseases, MD of alpha-synuclein WT and Variants.

FHMRI Bioinformatics is a new bioplatform to support bioinformatics analyses for research groups in the College of Medicine and Public Health at Flinders University.

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.

This project develops a novel approach using high-resolution confocal imaging of chromatin and epigenetics in single cells to derive cell-type-specific signatures of cellular identity and state, such as biological age, and to approximate organ and organism function. The predictive value of these signatures, demonstrated in mice, is now being expanded to human tissues.

This project will generate processed data products (FASTQ, unaligned/aligned modBAM, and VCF) from the raw signal-level nanopore data of the 1KGP-ONT cohort replicated at NCI (de95), enabling downstream analyses of human genetic variation and base modifications.

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.

Viviparity is thought to have originated as many as 115 times in squamates (snakes and lizards). However, we know very little about how natural selection acts on protein coding genes to dictate these transitions. Our study utilized over 30 genomes of snakes and lizards to investigate how diversifying selection has shaped the evolution of reproductive modes in squamates.

This research focuses on long-read RNA sequencing and proteogenomics analysis to develop sample-specific protein databases from RNA-seq data.

Develop scalable nanopore DNA barcoding and phylogenetic workflows capable of processing thousands of Australian invertebrate specimens for biodiversity, conservation, and invasive species research.

We aim to generate genomic data for each of the ~2000 terrestrial invertebrate species on Lord Howe Island. This will provide baseline information for conservation of the biodiversity of this World Heritage Listed area.

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.

The proposed project will investigate the genomic architecture, evolutionary history and population structure of multiple Blattodean species. This has substantial implications for our understanding of chromosome evolution, inbreeding and parallel evolution, as well as useful results for the conservation of insect biodiversity in Australia and Japan.

Development of a workflow for Structural variation detection and filtration.

The Omics Accelerator is a NCRIS funded node that aims to develop and deploy multi-omic diagnostics for Australian industry. The requested project will utilize supercomputing resources for Omics accelerator and Metabolomics Australia method development.

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

This project trains and evaluates sparse autoencoders on single cell foundation model (scFM)'s token embeddings to test whether they encode discriminative biological signals that can be faithfully recovered.

This multidimensional approach will provide a comprehensive exploration of TEs as potential drivers of both metastasis and therapeutic escape in melanoma. By generating high-resolution maps of TE insertions and methylation status, we aim to uncover how TEs contribute to disease evolution to allow the discovery of predictive biomarkers for therapy response or disease progression and novel therapeutic targets to overcome resistance.

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

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

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.

We are performing method development and validation for surveillance traps designed to attract exotic flies before they become a major issue for Australian Agriculture and exports.

This project uses variants in different mouse genetic backgrounds to identify putative genetic modifiers of abdominal aortic aneurysm that could be used for diagnosis, risk prediction or therapeutic interventions.

This project is an integrative meta-analysis of preexisting scRNA-seq datasets from humans with abdominal aortic aneurysm (AAA) and mouse models of AAA.

Quantify how drought (rainfed) vs irrigation shapes the functional capacity of wheat-field soil microbiomes at global scale, and then “zoom in” on a deep-sequenced Australian transect to resolve fine-grained pathways, genomes (MAGs), and ecological indicators.

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

This project aims to identify candidate chickpea defense response (R) genes that interact with effector proteins secreted by Ascochyta rabiei, a fungal pathogen causing the chickpea Ascochyta blight disease. The analysis will be performed using dedicated NextFlow version of an AlphaPulldown-style workflow (wisps), which was developed to run on the NCI HPC.

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.

An observational, longitudinal study to investigate how environmental microbial diversity (e.g., from green spaces) might influence the human commensal microbiota and immune responses, and thereby reduce allergy/asthma risk.

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.

This project develops GPU-accelerated, uncertainty-aware deep learning models for multimodal medical image segmentation by integrating imaging data with clinical signals and text using large language models (LLMs) and vision–language models (VLMs). The goal is to improve robustness, interpretability, and clinical reliability in computer-assisted diagnosis.

Applying single cell RNA sequencing to understand the immune landscape of thyroid cancer, with the goal of identifying therapeutic targets and biomarkers.

This project aims to contribute to the improvement of hemp as a crop, particularly in terms of seed production, through quantitative genetic and functional genomic techniques.

This project is to generate a new, comprehensive database of DNA reference sequences for Southern Ocean marine life, collating existing and newly generated reference sequences. It will map existing ancient DNA records from around Antarctica against this new database to improve palaeo-environmental reconstructions.

The dysregulation of splicing is a hallmark of cancer. Comparing local RNA-seq cohort data to large-scale global splicing databases remains challenging due to incompatible and specialised processing pipelines. This project aims to uniformly process local reference cohort data to allow efficient comparison with major international pre-computed datasets.

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

The project involves development of agentic workflows to autonomously test bioinformatic tools, and subsequently construct novel agentic workflows to answer unexplored biomedical questions.

This project aims to build a unified AI-assisted workflow that takes a single genetic variant and limited, non-identifiable patient information as input and returns curated, evidence-backed report to guide rare disease research. Over 12 months, we will evaluate at least 50 rare disease variants and release the workflow, examples and benchmark for reuse by Australian life science researchers.

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

Bioinformatics analyses for the Threatened Species Initiative.

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.