PhD Scholarship - Targeting transposable elements in cancer @ SAiGENCI and University of Adelaide

Employer:  SAiGENCI

Closing date:   30/09/2024

Brief position description:
Transposable elements (TEs), also known as “jumping genes” are repetitive genomic elements that represent almost half of the human genome. While the majority of TEs in the human genome have lost the ability to transpose, their sequences hold a significant regulatory potential. TEs contain binding sites for transcription factors (TFs), enabling them to function as alternative promoters or enhancers regulating the gene expression. TEs are frequently activated during tumorigenesis, promoting oncogenic gene expression. While some TEs have been previously documented to contribute to gene deregulation in cancer, a comprehensive view of the regulatory landscape of TEs in cancer remains incomplete. This project will leverage large pan-cancer transcriptome, epigenome, and 3D genome datasets to carry out a comprehensive study of the contribution of TEs to the regulatory cancer genome. 

Ideally, we are seeking a candidate with prior research experience in NGS data processing and analyses, and knowledge of at least one computational language (e.g., Python, R). Datasets you will have access to include ATAC-seq, RNA-seq Hi-C, ChIP-seq/CUT&RUN, Nanopore, and single-cell data. We have access to HPC to streamline any large data processing and machine learning applications.

Interested candidates, please email a cover letter explaining your interest in the position and relevant experience along with a CV and transcripts to joanna.achinger@adelaide.edu.au.

Job website: https://smex-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=http%3a%2f%2fachingerlab.com&umid=a8c4442d-db60-4c38-ac21-33995073cbac&auth=2af5473c4b03509246eb08bd803a6cf835f69953-f842cca45072ae94ad95be57bead415989e40ebd

Contact name: Joanna Achinger-Kawecka

Contact email:  joanna.achinger@adelaide.edu.au

PhD Scholarship - Improving molecular and phenotypic predictions through network-based prior knowledge and AI @ University of Queensland

Employer:   University of Queensland (ARC Centre of Excellence for Plant Success in Nature and Agriculture)

Closing date:   15/08/2024

Brief position description:
Are you interested in applying graph theory and AI algorithms to practical biological problems? If so, this PhD opportunity might be for you! This project, supervised by Dr. David Kainer at The University of Queensland, will develop and apply machine learning and AI approaches for network-assisted analyses that can improve crop development, including prediction of:
- gene-to-gene relationships
- gene editing outcomes 
- phenotypes

As part of the ARC Centre of Excellence for Plant Success in Nature and Agriculture, you will be part of a highly talented and diverse team of researchers in biology, maths, computer science and agriculture.

Job website:   https://study.uq.edu.au/study-options/phd-mphil-professional-doctorate/projects/improving-molecular-and-phenotypic-predictions-through-network-based-prior-knowledge-and-ai

Contact name: David Kainer

Contact email:  d.kainer@uq.edu.au

2 year full-time Post Doc - Bioinformatics (Multiple Sclerosis) @ University of Newcastle

Employer:  University of Newcastle

Closing date:   16/08/2024

Brief position description:
As the Bioinformatics Post-doctoral Fellow you will help generate, analyse and interpret "multi-omic" data (eg. genomic, epigenomic, transcriptomic) using a variety of biocomputational approaches that include conventional and novel approaches (eg. machine learning). 

Your responsibilities in this role will include:
-Analysis of genomics and multi-omics datasets.
-Support training of PhD and undergraduate students.
-Contribute to grant and paper writing.
-Attend regular study meetings to discuss findings.
-Attend and present at local, national or international conferences.

Job website:   http://www.seek.com.au/job/77471655?savedSearchID=237ec23c-e02d-456c-9d79-1dc28ea8b146&tracking=JMC-SavedSearch-anz-1

Contact name: Rodney Lea 

Contact email:   rodney.lea@newcastle.edu.au

Senior Bioinformatician, Bioinformatics Training @ The University of Melbourne

Employer: The University of Melbourne

Closing date:   02/08/24

Brief position description:
Job no: 0062191
Location: Parkville
Role type: Full-time
Faculty: Medicine, Dentistry and Health Sciences
Department: Melbourne Bioinformatics
Salary: Level C – $146,050 - $168,403 p.a. plus 17% super

Oversee and organise the development and delivery of the bioinformatics training program to empower life scientists.
Opportunity to shape and lead education initiatives within a dynamic research environment containing a team of highly skilled bioinformaticians.
Salary packaging, subsidised health and wellbeing services, fitness and cultural clubs, Myki discounts, and a 25% discount on graduate courses to our staff and their immediate families!
About the Role
The purpose of the role within Melbourne Bioinformatics is to lead the training operations, overseeing a team of trainers and contributing to the development and delivery of bioinformatics content. This involves creating new training materials, delivering workshops, and establishing an online repository for easy access to resources. The Senior Bioinformatician will collaborate with external partners to enhance expertise and align training with national initiatives, ensuring content is comprehensive and of high quality. They will provide strategic oversight to ensure training targets are met effectively and efficiently.

Your responsibilities will include:

Lead the development and provision of local bioinformatics training content, including in-person workshops and stand-alone online content.
Identify high-quality training content from external sources that should be linked to our local training repository.
Oversee the organisation of our local training repository.
Develop new training materials in accordance with community needs, as determined through consultation with our local users and the national training network.
Who We Are Looking For
You will thrive in this role if you possess strong communication, leadership, and networking abilities, coupled with adept stakeholder management and attention to detail. Your demonstrated capacity to work both independently and collaboratively within a team, combined with excellent organisational and leadership skills, will ensure successful project outcomes

You will also have:

A PhD or equivalent experience or over 2 years working in bioinformatics or a closely related field.
A passion for transferring knowledge and the ability to apply highly technical skills and content within a training environment.
The ability to assess the effectiveness of existing and new training courses and make modifications to course content.
Demonstrated knowledge of current tools, standards, and methods in bioinformatics.
For further information regarding responsibilities and requirements, please refer to the attached PD.
Your New Team – Melbourne Bioinformatics
Melbourne Bioinformatics, nestled within the vibrant hub of Australia's life sciences, empowers researchers with cutting-edge tools and expertise. From software development to bioinformatics training, it accelerates scientific discovery and fosters collaboration. Since its inception, Melbourne Bioinformatics has propelled Victoria to the forefront of life sciences, generating impactful insights that benefit health, agriculture, and engineering, enriching both academia and industry alike.

What We Offer You!
In addition, we offer the opportunity to be part of a vibrant community and enjoy a range of benefits, including generous leave provisions, salary packaging, health and well-being services and discounts on graduate courses. For more information, check out our benefits page!

About the University of Melbourne
We’re tightly connected with the community, both at home and abroad. We take pride in our people, who all contribute to our mission to benefit society through the transformative impact of education and research. Discover more via our website and stay connected with our stories and people on LinkedIn.   

Be Yourself
The University of Melbourne values the unique backgrounds, experiences and contributions that each person brings to our community and welcomes and celebrates diversity.  First Nations people, those identifying as LGBTQIA+, parents, carers, people of all ages, abilities and genders, and people of diverse ethnicity, nationality and faith are encouraged to apply. Our aim is to create a workforce that reflects the diversity of the community in which we live. For more information please visit our Diversity and Inclusion page.

We are dedicated to ensuring barrier free and inclusive practices to recruit the most talented candidates. If you require reasonable adjustments, please contact Kim Groizard at hr-careers@unimelb.edu.au, with an email containing your name and contact details for a confidential discussion. Please ensure your email is titled "Reasonable Adjustments Request".

Aboriginal and Torres Strait Islander Applicants
We aspire to be the University of choice for Indigenous Australians, with unprecedented investment to attract, nurture and retain Aboriginal and Torres Strait Islander students and staff. Tangible support through a range of programs and initiatives will ensure that you personally succeed and flourish while at the University of Melbourne.

For further information, including our 2023-2027 Indigenous strategy please visit -https://about.unimelb.edu.au/reconciliation/murmuk-djerring

Join Us!
If you feel this role is right for you, please apply with the following documents: 

Resume
Cover Letter outlining your interest and experience
The responses against the Selection Criteria^ (found in the Position Description)
Please note: As part of the interview process, you will be requested to deliver a 20-minute presentation demonstrating bioinformatics training, details of this to be provided once shortlisted candidates are finalised.

For information to help you with compiling short statements to answer the selection criteria and competencies, please go to http://about.unimelb.edu.au/careers/selection-criteria

If you have any questions regarding the recruitment process, please feel free to contact Brett Verity via email at hr-careers@unimelb.edu.au, ensuring that you include the Position Number and the Job Title as the subject. Please do not share your application to this email address.

If you have any particular questions regarding the job please follow the details listed on the Position Description.

Applications close: 2 August 2024 11:55 PM Australian Eastern Daylight Time (AEDT) / Melbourne time zone. 

Please note that in the event of sourcing a suitable candidate, the closing date for applications may be brought forward, and the job vacancy may be closed. Therefore, we encourage interested individuals to submit their applications promptly.

Job website:   http://jobs.unimelb.edu.au/caw/en/job/917735?lApplicationSubSourceID=

Contact name:  Brett Verity

Contact email: brett.verity@unimelb.edu.au

Research Officer/Postdoctoral Fellow in Bioinformatics/Computational Biology @ SAHMRI

Employer:  South Australian Health & Medical Research Institute (SAHMRI)

Closing date:   18th July 2024

Brief position description:
 We are seeking an experienced Research Officer/Postdoctoral Fellow in Bioinformatics/Computational Biology to support projects within the cancer systems biology and systems immunology areas. Prior experience in at least some of the following areas is essential: analysis of next generation sequencing (NGS) data; multi-omics data integration, network and pathway biology; cancer systems biology; and/or machine learning methods. Active collaboration and the ability to manage multiple different projects simultaneously is essential. Reporting to the Director Computational & Systems Biology Program, the position will also work closely in collaboration with other researchers including the Prostate Cancer Group at SAHMRI. 

Job website:https://smex-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fsahmri.org.au%2fcareers%2dand%2dstudy%2fworking%2dat%2dsahmri%2fvacancies%2fresearch%2dofficer%2dpostdoctoral%2dfellow%2din%2dbioinformatics%2dcomputational%2dbiology&umid=91739ab2-bf5b-44cf-b39d-60d7d275018c&auth=2af5473c4b03509246eb08bd803a6cf835f69953-abc7ebf474a0da355c625dea592402037538a685

Contact name: David Lynn

Contact email:  david.lynn@sahmri.com

Postdoc position: AI large-language models of single-cell data for cancer immunogenomics @ Adelaide University

Employer:  SAiGENCI (Adelaide University)

Closing date:   18 July 2024

Brief position description:
  **Develop AI-driven digital tissue models for precision oncology, harnessing a multidisciplinary approach to tailor immunotherapy across diverse demographic profiles.**

**(Level B) $107,276 to $126,894 per annum plus an employer contribution of 17% superannuation applies.**

Fixed term, full time position available for 24 months.

The South Australian Immunogenomics Cancer Institute (SAiGENCI) is embarking on a ground-breaking project to create a digital tissue AI model for precision oncology. This role offers an exciting opportunity to be part of a multidisciplinary team that combines expertise in AI, bioinformatics, clinical oncology, and cancer immunology. As a key team member, you will contribute to advancing our understanding and implementation of immunotherapy tailored to demographic specificities such as age and sex. The role involves the development and refinement of AI-driven tissue models (e.g. large-language models) and the analysis of extensive single-cell data across a wide demographic spectrum.

This position will allow you to explore and develop new methodologies that integrate detailed cellular and molecular data to enhance the precision of established therapies and uncover new treatment avenues. We are looking for experienced individuals who are passionate about using their skills to make a tangible impact in medical research. You will be part of a team that values collaboration, innovation, and the pursuit of excellence. If you are driven to be at the cutting edge of technology and healthcare, we would like to hear from you.

Key responsibilities: Develop and apply advanced AI large-language models to analyse large-scale single-cell datasets; Contribute to the expansion and refinement of our large-scale single-cell database; and collaborate with a multidisciplinary team to advance the field of precision oncology.

To be successful you will need: 

- Explicitly address each selection criteria below

- PhD in Computational Biology, Bioinformatics, Computer Science, or a closely related field with a strong focus on machine learning and deep learning applications.

- Demonstrable experience in developing and implementing deep learning tools, particularly in the context of large-language models.

- Proficiency in programming languages commonly used in computational biology and data science, such as Python and R, with the ability to handle complex data analysis tasks. Please provide publicly available examples.

- A strong record of research, evidenced by publications in peer-reviewed journals or presentations at significant conferences, particularly in areas related to AI, language modelling, computational biology, bioinformatics, or immunogenomics.

**Enjoy an outstanding career environment**

We embrace flexibility as a key principle to allow our people to manage the changing demands of work, personal and family life.

We offer a wide range of attractive staff benefits. These include: salary packaging; flexible work arrangements; high-quality professional development programs and activities; and an on-campus health clinic, gym and other fitness facilities. 

Job website: http://careers.adelaide.edu.au/cw/en/job/514185/ai-largelanguage-models-of-singlecell-data-for-cancer-immunogenomics

Contact name: Stefano Mangiola

Contact email:    stefano.mangiola@adelaide.edu.au

Postdoc position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis @ Adelaide University

Employer:  SAiGENCI (Adelaide University)

Closing date:   18 July 2024

Brief position description:
 Advance cancer diagnosis by analysing immune system responses and treatment efficacy using spatial and single-cell computational immunogenomics.

**(Level A) $75,888 to $102,040 per annum plus an employer contribution of 17% superannuation applies.**

The position is for a postdoctoral fellow in spatial and single-cell computational immunogenomics for cancer diagnosis. This position will advance cancer diagnosis by analysing immune responses and treatment efficacy through data-driven research and a multi-omic approach. Exploring the dynamics of circulating immune cells in blood reveals crucial insights into the immune system's response, its efficacy against metastatic cancer, and its reaction to treatments. Profiling peripheral blood immune single cells and circulating cytokines, we uncovered patterns of immune cell communication and composition linked to metastatic progression (Mangiola et al. 2024). 

This exciting position aims to expand this research to study the local tumour microenvironment and apply this approach to identify individual immune characteristics influencing immunotherapy success. We aim to employ a multiomic approach, analysing extensive patient data across all stages of disease progression. This research will utilise state-of-the-art facilities, including 10x Xenium, 10x CITE-seq, Milliplex and proteomics. We are searching for a dynamic individual for the Computational Biologist/Bioinformatician/Biostatistician role. Managing personal research funds is a possibility depending on the appointment level and the candidate's experience.

Key responsibilities: Develop and apply advanced AI large-language models to analyse large-scale single-cell datasets; Contribute to the expansion and refinement of our large-scale single-cell database; and collaborate with a multidisciplinary team to advance the field of precision oncology.

**To be successful you will need:** 

- Explicitly address each selection criteria

- PhD in Computational Biology, Bioinformatics, Computer Science, or a
closely related field with a strong focus on machine learning and
deep learning applications.

- Demonstrable experience in analysing large-scale single-cell genomic
data.

- Proficiency in programming languages commonly used in computational
biology and data science, such as Python and R, with the ability to
handle complex data analysis tasks. Please provide publicly available
examples.

- A strong record of research, evidenced by publications in
peer-reviewed journals or presentations at significant conferences,
particularly in areas related to AI, language modelling,
computational biology, bioinformatics, or immunogenomics. 

Job website:  http://careers.adelaide.edu.au/cw/en/job/514184/spatial-singlecell-computational-immunogenomics-for-cancer-diagnosis

Contact name: Stefano Mangiola

Contact email:    stefano.mangiola@adelaide.edu.au

Postdoc/RA position: Software Engineer For R and High-Performance Computing @ Adelaide University

Employer:  SAiGENCI (Adelaide University)

Closing date:   18 July 2024

Brief position description:
 R software engineer for tidyomics ecosystem and highly-scalable single-cell and spatial omic pipelines

**(Level A) $75,888 to $102,040 per annum plus an employer contribution of 17% superannuation applies.**

The position is for a postdoctoral or research-assistant fellow in advanced R programming. Tidyomics (Nature Methods 2024) is an R software ecosystem that enhances the analysis and visualisation of high-dimensional omics data, applying the principles of tidy data analysis, a de facto standard in data science. Given its large adoption, we propose to improve the documentation, robustness, and interoperability of the Tidyomics ecosystem and extend it to spatial profiling technologies.

This exciting position also aims to develop high-performance single-cell and spatial analysis pipelines in R, for high-performance and cloud computing. These pipelines will serve our popular CuratedAtlasQuery database, which deploys the curated and annotated single-cell universe to researchers and institutions.

Key responsibilities: Develop and enhance the tidyomics ecosystem (GitHub: tidyomics), write documentation and create and deliver workshops nationally and internationally. Enhance the pipeline HPCell (GitHub: MangiolaLaboratory/HPCell) and the single-cell knowledge base CuartedAtlasQuery.

**To be successful you will need:** 

- Explicitly address each selection criteria below

- MSc/PhD in Computational Biology, Bioinformatics, Computer Science, or a closely related field with a strong focus on machine learning and deep learning applications.

- Proficiency R, with the ability to handle complex data analysis tasks. Please provide publicly available examples.

- A record of research, evidenced by publications in peer-reviewed journals or presentations at significant conferences, particularly in areas related to AI, language modelling, computational biology, bioinformatics, or immunogenomics.

- Demonstrable experience in analysing large-scale single-cell genomic data.

- Extensive experience in handling, processing, and interpreting large-scale biological datasets, including single-cell RNA-Seq data.

**Enjoy an outstanding career environment**

The University of Adelaide is a uniquely rewarding workplace. The size, breadth and quality of our education and research programs - including significant industry, government and community collaborations - offers you a vast scope and opportunity for a long, fulfilling career.

We embrace flexibility as a key principle to allow our people to manage the changing demands of work, personal and family life.

In addition, we offer a wide range of attractive staff benefits. These include: salary packaging; flexible work arrangements; high-quality professional development programs and activities; and an on-campus health clinic, gym and other fitness facilities.

Job website:  http://careers.adelaide.edu.au/cw/en/job/514194/grantfunded-researcher-a

Contact name: Stefano Mangiola

Contact email:    stefano.mangiola@adelaide.edu.au

mRNA Design Engineer - Computational Biology (Postdoctoral Fellow) @ Australian National University

Employer:  Australian National University

Closing date:   21 July 2024

Brief position description:
You will become a leading part of world-class industry-supported RNA research and development with immediate translational outcomes. You will be able to leverage the international standing of The Australian National University and connect with innovative RNA companies as part of the position. You will be mostly working on computational and bioinformatic R&D within RNA, transcriptomic, proteomic and genetic software and data. Talented, energetic and motivated scientists are sought to fulfill the position, capable of taking on highly dynamic research. The position may be extended, and commitment increased, depending on the success of its initial projects.

Job website: http://jobs.anu.edu.au/jobs/mrna-design-engineer-computational-biology-postdoctoral-fellow-canberra-act-act-australia

Contact name: Nikolay Shirokikh

Contact email:    nikolay.shirokikh@anu.edu.au