PhD recruitment - Efficient construction and visualisation of pangenomes for crops with large genomes @ The University of Adelaide - Analytics for the Australian Grain Industry (AAGI)

Employer :  The University of Adelaide - Analytics for the Australian Grain Industry (AAGI)

Closing date:  Open until filled
Brief position description:  

The Analytics for the Australian Grains Industry (AAGI) initiative is a five-year strategic partnership to enhance the profitability and global competitiveness of the Australian grains sector through advanced analytics. The University of Adelaide, in collaboration with Curtin University, the University of Queensland and other research institutions, is leveraging machine learning, data fusion, and statistics to support grain growers in making data-driven decisions.

We are recruiting one PhD candidate for the project "Efficient construction and visualisation of pangenomes for crops with large genomes." Pangenomes are highly relevant for grain RD&E pre-breeding research because they capture the full spectrum of genetic diversity within a species, going beyond the limitations of single-reference genomes. By integrating multiple genomes from different individuals or populations, pangenomes provide a more comprehensive understanding of gene presence/absence, structural variations, and evolutionary dynamics. 

In this project we will aim to develop novel dynamic programming computational methods for pangenome assembly of diploid and polyploid crop species and benchmark them against other methods such as graph-based methods. This project will combine algorithm development and computational programming with large population genomes. Candidates will work within a vibrant cutting-edge analytics team that delivers technologies back to the Australian grains industry research to maximise benefits for farmers and growers. This research project will also be highly collaborative with major partners, Curtin University and the University of Western Australia. Through these linkages, there will also be an opportunity to develop the research further into a practical web-based visualisation tool to represent pangenome and structural variations.

Job website: http://scholarships.adelaide.edu.au/Scholarships/postgraduate-research/faculty-of-sciences-engineering-and-technology-set/analytics

Contact name:   Sandy Khor

Contact email:  sandy.khor@adelaide.edu.au

CSIRO Industry PhD - Prediction of molecular interactions with RNA using AI for basic research and therapeutic discovery @ ANU - CSIRO - RNAfold.ai

Employer : ANU - CSIRO - RNAfold.ai

Closing date:  Open until filled
Brief position description:  

This project aims to develop advanced deep-learning models to predict interactions between ribonucleic acid (RNA) and other molecules. These models will help decode RNA interaction networks involved in fundamental cellular processes and disease mechanisms and identify novel therapeutic strategies. The outcomes will enable more precise design of RNA-targeting drugs, accelerating the development of next-generation therapeutics.

Job website:  http://science.anu.edu.au/study/research/iPhD

Contact name:     Eduardo Eyras

Contact email:   eduardo.eyras@anu.edu.au

Laboratory Head @ WEHI

Employer : WEHI 

Closing date:  16/6/2025
Brief position description:  

Brief position description: WEHI is seeking innovative and driven researchers from around the world to lead the next generation of scientific discovery. If you are passionate about advancing knowledge and making a tangible impact on health and disease, we invite you to join our world-class research institute.

We are seeking emerging leaders in biomedical research who are:

Discovery-driven: Committed to pushing the boundaries of knowledge and scientific advancement.
Recognised experts: Demonstrating excellence and leadership in their field.
Impact-focused: Passionate about translating research into benefits for national and global communities.
Collaborative and inclusive: Dedicated to fostering a diverse and supportive research culture.
Our research strengths

WEHI’s research programs span a broad range of disciplines, including:

Bioinformatics, Computational Biology and AI
Cancer
Omics Technology
Drug Discovery
Immunology
Infection and Global Health
Inflammation
Structural Biology
Genetics and Gene Regulation
Ubiquitin Signalling

Job website:  https://www.wehi.edu.au/careers/make-your-future-melbourne/
Contact name:  Pauline Mooney

Contact email:     mooney.p@wehi.edu.au

PhD Student @ The University of Queensland

Employer : The University of Queensland

Closing date:  30/11/2025
Brief position description:  

Brief position description: PhD position to decipher the gene regulatory code and epigenetic mechanisms governing developmental processes and aging, and their links to disease. 

Ageing is the number risk factor of disease. Here we hypothesized that an improved understanding of the regulatory logic of enhancers gaining or losing activity during ageing might unlock a better understanding of the mechanisms that predispose to disease. 

Therefore, we wish to decipher at base-pair resolution the regulatory lexicon of age-affected gene regulatory elements across cell-types and study their link to healthspan and disease susceptibility. 

The project aims to:

1. Apply Convolutional Neural Networks (CNNS) (https://smex-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fkipoi.org&umid=ead86e2d-3110-4736-8b11-653b7f78697c&auth=6ee66d642a212b82964c9073f0dd934b55317413-a650930ae1631338f53f8b55d69a7ae9db6fe061) and other strategies to decode the grammar of gene regulatory elements with activity changes in ageing. 
2. Evaluate cross-species conservation of this regulatory grammar (e.g., mouse, dog and human) and our ability to predict age-susceptible gene regulatory elements.
3. Assess the impact of genetic mutations in gene regulatory elements with age-altered activity on disease susceptibility using genome-wide association study (GWAS) data.

Job website:  http://study.uq.edu.au/study-options/phd-mphil-professional-doctorate/projects/deciphering-gene-regulatory-code-ageing-set-stage-therapeutic-interventions

Contact name:  Marina Naval Sanchez 

Contact email:     m.navalsanchez@imb.uq.edu.au

Rare Disease Bioinformatician @ Centre for Population Genomics (MCRI/Garvan)

Employer : Centre for Population Genomics (MCRI/Garvan)

Closing date:  24/04/2025
Brief position description:  

The CPG Rare Disease Program is seeking a bioinformatician to join our growing team and contribute to developing tools, pipelines and processes for scalable analysis of genomic data from undiagnosed families affected by rare genetic disorders. You will join a highly collaborative and integrated team of clinical analysts, computational biologists, bioinformaticians and software engineers who together support Australia's largest rare disease research platform.

The primary focus of this role will be improving and extending the team's capability to interrogate WGS, long read, RNA-seq and other genomic data sets from rare disease patients and their family members, to improve the diagnosis of severe genetic diseases. The duties of this role will include a combination of iterative refinement of existing analysis pipelines, and the development of novel analysis tools and pipelines.

While this position will involve cutting-edge genomic science, the measures of success and promotion will be on developing and deploying complex analysis methods at scale, and not on traditional academic metrics such as leading publications. This role is best suited to individuals with a strong track record of scientific output who are interested in continuing to contribute to impactful science but not in the traditional academic career track.

The CPG is geographically distributed and operates under a fully-remote model. However, office space is available at both the Garvan Institute in Sydney and the MCRI in Melbourne. In-person events are held multiple times per year to ensure regular opportunities for in-person interaction.

Job website:  https://career10.successfactors.com/career?career%5fns=job%5flisting&company=C0007531036P&navBarLevel=JOB%5fSEARCH&rcm%5fsite%5flocale=en%5fGB&career_job_req_id=42637&selected_lang=en_GB&jobAlertController_jobAlertId=&jobAlertController_jobAlertName=&browserTimeZone=Pacific/Auckland&_s.crb=XmvoHGOCOCBraS5yC1ZiR%2fXlCDCQoUa8wyL41KfMhic%3d

Contact name:  Matthew Welland

Contact email:    matthew.welland@populationgenomics.org.au

Postdoctoral Fellow (Bioinformatics & Computational Biology) @ Peter MacCallum Cancer Centre

Employer : Peter MacCallum Cancer Centre

Closing date:  04/04/2025
Brief position description:  

This 1.0EFT position is for a bioinformatics postdoctoral fellow to drive the computational aspects of a range of exciting projects, both new and ongoing, in the Dawson laboratory. The position will involve the analysis of large-scale single cell data through the application of best-practice bioinformatics workflows and the development of innovative methods as required. The position will require a highly motivated bioinformatician or computational biologist to build on innovative methods including SPLINTR (Fennell, Vassiliadis et al; Nature 2022; Holze et al Cell Reports Methods 2024; Guirguis et al Cancer Discovery 2023) – a cellular barcoding and lineage tracing technique. The role will include the analysis of various single cell sequencing data types, including scRNA-seq, scChIP-seq, scATAC-seq, spatial transcriptomics and other emerging single cell platforms. The role requires strong R programming skills as well as familiarity with additional programming languages such as Python and/or Perl. The position requires experience working on a high-performance computing cluster in a Linux environment and knowledge of shell scripting. Best practices in documentation and coding, particularly with respect to reproducible and transparent science are required. The individual will collaborate very closely with other bioinformaticians, as well as cell and molecular biologists and clinical fellows to advance joint initiatives. 

The successful applicant must have the ability to conduct research both independently and as part of a team, provide competent computational and analysis skills to the laboratory and be able to communicate results with research investigators.

This role is based within the Collaborative Centre for Genomic Cancer Medicine, a joint venture of the University of Melbourne and Peter MacCallum Cancer Centre seeking to improve the lives of people with cancer through equitable access to personalised treatment options and prevention strategies informed by the latest genomic tests and analysis. 

This role will contribute to the University of Melbourne's partnership with international genomics company Illumina by collaborating with The Advanced Genomics Collaboration, jointly fostering the development of world-leading genomics research and innovation activities and to accelerate the translation of these innovation through to adoption in the healthcare system.

Job website:  http://careers.petermac.org/job/MELBOURNE-Postdoctoral-Fellow-%28Bioinformatics-&-Computational-Biology%29-M-Dawson-Lab-VIC-3000/1062136466/

Contact name:  Enid Lam

Contact email:  enid.lam@petermac.org

Bioinformatics Post Doctoral Researcher @ Peter MacCallum Cancer Centre (Sarah-Jane Dawson Lab)

Employer :  Peter MacCallum Cancer Centre (Sarah-Jane Dawson Lab)

Closing date:  02/04/2025
Brief position description:  

Applications are invited to join an exciting research program within the Molecular Biomarkers and Translational Genomics Laboratory led by Sarah-Jane Dawson at the Peter MacCallum Cancer Centre (https://smex-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=www.thedawsonlab.com&umid=9efeec09-9974-4fda-8f5c-26d6018cc684&auth=6ee66d642a212b82964c9073f0dd934b55317413-00e91312fa2fe8056fa4c1e5f081ff87af2d8e09) and The University of Melbourne. The research will explore the use of circulating tumour DNA to study genomic and epigenomic evolution and provide insights into treatment response and resistance in cancer.

The position will involve the analysis of large-scale genomic data, with a focus on whole genome sequencing, through the application of best-practice bioinformatics workflows and the development of innovative new methods (e.g. Hollizeck and Wang et al, Nature Communications 2024). The individual will be responsible for driving their own specified projects, but will also collaborate very closely with cancer molecular biologists to work on joint initiatives.

The position will require a highly motivated and skilled bioinformatician or computational biologist with expertise in the analysis of next generation sequencing data, integration of genome-wide datasets, competency in programming languages R and Python and experience with working on a high-performance computing cluster. Applicants should have demonstrated experience developing and deploying bioinformatics analysis workflows. Experience working with containers and version-controlled pipelines as well as cloud computing is desirable but not required.

The position will be in a research environment that includes a large and interactive group of bioinformaticians and computational biologists within The Collaborative Centre for Genomic Cancer Medicine at the Peter MacCallum Cancer Centre and The University of Melbourne. The position will be initially for a fixed term of 12 months with the opportunity to extend. Remuneration will be commensurate with qualifications and experience.

This role will contribute to the University of Melbourne's partnership with international genomics company Illumina by collaborating with The Advanced Genomics Collaboration by jointly fostering the development of world-leading genomics research and innovation activities and to accelerate the translation of these innovation through to adoption in the healthcare system.

Job website: https://careers.petermac.org/job/MELBOURNE-Bioinformatics-Post-Doctoral-Researcher-SJ-Dawson-VIC-3000/1058115966/

Contact name:   Dineika Chandrananda

Contact email:  Dineika.Chandrananda@petermac.org

2 PhD Scholarships, Animal Statistical Genetics, ARC Training Centre Predictive Breeding @ Agriculture Victoria Research and La Trobe University

Employer :  Agriculture Victoria Research and La Trobe University

Closing date:   Until filled
Brief position description:  

As part of the Australian Research Council training centre for predictive breeding (https://lnkd.in/gJvc6bB2), our Computational Biology Group / Genomics Cellular Sciences branch of Agriculture Victoria Research is looking for PhD candidates 👨‍🎓 👩‍🎓 . You will be in beautiful Melbourne Australia to work on exciting projects related to big data, health and environmental footprints of animals 🐄 🐄 . Students will work with amazing teams and facilities such as high-performance computer clusters. Each scholarship covers a stipend (~$37,000 annually) and includes travel funding and relocation assistance. Please check out the flyer for details and contacts, e.g., Kendra Whiteman [kendra.whiteman@agriculture.vic.gov.au]

Job website:https://www.linkedin.com/posts/ruidong-xiang-9945184a_as-part-of-the-australian-research-council-activity-7300137621890945025-s2kY?utm_source=share&utm_medium=member_desktop&rcm=ACoAAApmKIABmY_wtTy-X0q2v00eGM5I0TaWylkaustralia

Contact name:    Kendra Whiteman

Contact email:  kendra.whiteman@agriculture.vic.gov.au

Postdoctoral Research Fellow, Bioinformatics @ James Cook University - Cairns campus

Employer :  James Cook University - Cairns campus

Closing date:  26/03/25
Brief position description:  

An opportunity exists for an exceptional early career researcher to join the Field lab in Cairns. My lab develops bioinformatic software to support a variety of large genomics projects centered on the role of genetic variation in human disease and host/parasite interactions. This will build on recent work using high-throughput sequence data to elucidate the underlying genetic cause of autoimmune disease and to understand host/parasite interactions. We aim to develop robust software and computational workflows to study increasingly complex multi-omics datasets from a variety of technologies including short-read, long-read and single cell sequencing.

Note the job is currently listed until Dec 2026 however funds are available for possible extension.

Job website: https://careers.jcu.edu.au/jobs/postdoctoral-research-fellow-bioinformatics-cairns-qld-australia

Contact name:   Matt Field

Contact email:  matt.field@jcu.edu.au

Shariant Software Developer @ SA Health - Statewide Clinical Support Services

Employer :  SA Health - Statewide Clinical Support Services

Closing date:  10/03/2025
Brief position description:  

We are seeking a senior software developer or clinical bioinformatician with genomics expertise to join our dynamic team and play a pivotal role in driving the development of Shariant. 

Shariant is an Australian Genomics initiative, that operates in collaboration with SA Pathology, and enables real-time sharing of genetic variant knowledge and data among clinical genetic testing laboratories across Australia. With a track record of over 34,000 submissions from 15 labs, Shariant facilitates faster and more accurate diagnoses, benefiting patient care. 

In this role, you will be responsible for the implementation of genomic data platform functionalities, such as experimental assay evidence (RNA, functional), into Shariant for real-time use by laboratories. You will also lead improvements to variant standardisation and resolution pipelines integral to the platform, and contribute to developing additional functionality driven by Shariant user laboratories. 

The role is suited to an individual with demonstrated proficiency in using Python for development of genomic data platforms, to deliver a highly robust, sustainable and clinically essential platform.

Interstate applicants are welcome to apply, with flexible/remote working arrangements available.

Apply now to become a vital member of the Shariant Team and help shape the future of genomic data sharing!

Job website:  http://www.seek.com.au/shariant-jobs?jobId=82245524&type=standard

Contact name:   Matilda Jackson

Contact email:  Matilda.Jackson@sa.gov.au