Solutions Architect Genomics Machine Learning @ CSIRO

Employer:  CSIRO

Closing date: 12 May 2024, 11:00pm AEST

Brief position description: 
Acknowledgement of Country
CSIRO acknowledges the Traditional Owners of the land, sea and waters, of the area that we live and work on across Australia. We acknowledge their continuing connection to their culture and pay our respects to their Elders past and present. View our vision towards reconciliation

Child safety
CSIRO is committed to the safety and wellbeing of all children and young people involved in our activities and programs. View our Child Safe Policy.

The opportunity
Lead the technical development of the VariantSpark platform and clinical pathology applications
Use your cloud-based, high-performance computing & machine learning expertise to bring IT solutions to human health applications
Flexible work arrangements! Mix of home and office

Many of CSIRO's innovations were once considered impossible. Fast WiFi, Aerogard insect repellent and the plastic Australian banknote, to name a few. Until someone, just like you, joined us and took on the challenge. We’re recruiting inventors, innovators and change makers. Join Team CSIRO and help make the impossible possible.

CSIRO's AEHRC (The Australian e-Health Research Centre) is the leading national research facility applying information and communication technology to improve health services and clinical treatment for Australians. AEHRC is a world-wide unique trailblazer of advanced digital solutions and covers the full spectrum from basic science to mobile technologies and digital healthcare services that are applied in clinical practice.


The Solutions Architect Genomic Machine Learning will work with scientists from the high-performing Transformational Bioinformatics Team to develop novel digital services that join genomics and medical information to empower clinicians. The role will lead the technical development of the VariantSpark platform, as well as clinical pathology applications. Envisioned as a point-of-care solution, the technology needs to build on the latest in cloud services and cloud computing technology to deliver speed and accuracy on unprecedented data volumes. You will use your software engineering expertise and demonstrated knowledge in cloud-based distributed or high-performance computing as well as machine learning skills to help us bring advanced IT solutions to human health applications.


This position is advertised across two competency levels and the successful candidate will be appointed at the level commensurate with their skills and experience. More detail around the difference between the two levels is outlined in the position description.

Your duties will include:
In collaboration with scientists, design and implement innovative cloud architecture to carry out impactful research and cater for the challenges in the health and life science domain (fast turn-around-time and large volumes of data).
Implement ML solutions to biological research questions; Explore novel ML methodological approaches to research questions.
Be knowledgeable about cloud services across multiple vendors (specifically AWS, Azure, GCP). 
Prepare appropriate documentation through repositories (e.g. bitbucket), project boards (e.g. trello), online communities (e.g. gist) and contribute to reports, scientific papers, blog-posts and videos.


Higher level duties:
Develop novel ML algorithms, tailored for genomic problems.
Stay on top of newly released cloud services across multiple vendors (specifically AWS, Azure, GCP) and take ownership in applying them effectively to the scientific applications developed by the team.
Identify market-gaps and lead development of tailored solutions to commercial impact and be involved in grant applications.

Location: Sydney NSW preferred; Open to other major cities like Melbourne and Brisbane

Salary: *AU$93k - AU$119k plus up to 15.4% superannuation

Tenure: Specified term of 3 years / Full-time

Reference: 95944

* Applications are invited across two capability levels (CSOF4 & CSOF5) detailed in the position description for each of the levels and the successful candidate will be appointed at the level that commensurate with their skills and experience. 

To be considered you will need:
A bachelor’s degree (or will shortly satisfy the requirements of a bachelor’s degree) or equivalent relevant work experience in a relevant discipline area, such as Information Technology, Bioinformatics, Electrical Engineering, Data Science.
Evidence of experience with cloud-based distributed or high-performance computing (e.g. EMR, HDInsight, Dataproc) as well as more than one language relevant for cloud services (e.g. Python, NodeJS, Scala, BASH).
Proven impact from developing web services on more than one cloud vendor (e.g. AWS, GCP, Azure).
Experience and passion for designing and implementing machine learning solutions (SVM, RF, DeepLearning) and deep knowledge of statistics.

For appointment at the higher competence and salary level, additional skills and experience is required, as outlined in the position description.

Eligibility
Applications for this position are open to Australian/New Zealand Citizens and Australian Permanent Residents only. Appointment to this role is subject to provision of a national police check and may be subject to other security/medical/character requirements.

Flexible working arrangements
We work flexibly at CSIRO, offering a range of options for how, when and where you work. 

Diversity and inclusion
We are working hard to recruit people representing the diversity across our society, and ensure that all our people feel supported to do their best work and feel empowered to let their ideas flourish. 

About CSIRO
At CSIRO Australia's national science agency, we solve the greatest challenges through innovative science and technology. We put the safety and wellbeing of our people above all else and earn trust everywhere because we only deal in facts. We collaborate widely and generously and deliver solutions with real impact. 


CSIRO is committed to values-based leadership to inspire performance and unlock the potential of our people.

Join us and start creating tomorrow today!


How to apply
Please apply on-line and provide a cover letter and CV that best demonstrate your motivation and ability to meet the requirements of this role.

Applications close
12 May 2024, 11:00pm AEST.

Job website:   Solutions Architect Genomics Machine Learning (csiro.au)

Contact name:  Shree Chattopodhyay

Contact email:  careers.online@csiro.au

Post Doctoral Fellow @ University of Colorado Anschutz Medical Campus

Employer:  Dashnow Lab, University of Colorado Anschutz Medical Campus

Closing date: until filled

Brief position description: The Dashnow Lab in the Department of Biomedical Informatics at the University of Colorado Anschutz Medical Campus is seeking a computational Postdoctoral Fellow with a background in human genomics, bioinformatics, computational biology, or related fields. Individuals from diverse backgrounds are strongly encouraged to apply.

The Dashnow Lab develops computational genomics methods to understand the genetic underpinnings of rare diseases and increase diagnoses. We have particular expertise in difficult-to-genotype repetitive regions. We develop and apply these methods at scale to current and emerging DNA sequencing technologies. Our research directly impacts individuals with rare diseases and their families, giving them answers and hope for treatment after a long diagnostic odyssey. The lab has strong national and international collaborations, including with large rare disease and population consortiums and with industry.

Current project funding supports new approaches for diagnosis and gene discovery for short tandem repeat diseases, computational methods development for both short and long-read sequencing technologies, and population genetics.

The postdoc and PI will jointly envision projects tailored to the fellow’s skillset and long-term career goals. Postdocs will be expected to carry out computational research, analyze data, and disseminate their findings, software, and data to the biomedical community.

https://smex-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fdashnowlab.org&umid=28cb69d0-a8a6-4042-b4d4-d7d30eee1f41&auth=2af5473c4b03509246eb08bd803a6cf835f69953-f93247b12bc58ed03fb08aa321bae0cc1c4c28c8

Job website:   http://cu.taleo.net/careersection/2/jobdetail.ftl?job=33187&lang=en

Contact name:  Harriet Dashnow 

Contact email: harriet.dashnow@cuanschutz.edu

Postdoctoral Computational Biologist @ Melanoma Institute Australia

Employer:  Melanoma Institute Australia

Closing date: 26 April 2024

Brief position description: Melanoma Institute Australia (MIA) is a world-leading melanoma research non-profit organisation. Led by current joint Australians of the Year Professor Georgina Long AO and Professor Richard Scolyer AO, our mission is to reach zero deaths from melanoma this decade. The Melanoma Translational Research Group is a diverse team of researchers, located at the University of Sydney, that works alongside our MIA clinical oncology, surgical, pathology and biostatistics teams to investigate the biology of melanoma development, risk stratification and response to systemic therapies. The group is highly successful with major resources in human clinical tissue samples, including molecular and imaging data, spanning whole genome and increasing single cell sequencing datasets, transcriptomics, multiplex immunohistochemistry, and spatial biology.
MIA is seeking a driven postdoctoral computational biologist that will leverage the vast resources available for the discovery and validation of tools that improve diagnosis, prognosis, and treatment of melanoma patients. Through impactful translational research, the role will work alongside computational biologists, pathologists and clinicians to interrogate multi-omics datasets, imaging data and other resources available at MIA. 
Responsibilities: 
- To lead and contribute to a portfolio of projects with a focus on discovery and validation of diagnostic and prognostic tools.
- Use deep learning to analyze histopathological images of melanoma and related tumours.
- Conduct analyses and experimentation to answer scientific hypotheses.
- Refine data analysis pipeline in the multi-omics and imaging space for reproducible experimentation for various projects in the laboratory.
- Publish research in high impact journals and present at international conferences.
- Mentor and supervise students to develop bioinformatics talent with a focus on clinical significance.
- Attend clinical and collaborative research meetings to co-develop clinical questions and the possible implications of research findings.
- Comply with the Institute’s policy for handling information.

Key Selection Criteria 
To be successful in this role you will have:
Essential:
- A PhD in a relevant discipline such as Computational Biology, Machine learning or a closely related field. 
- A passion to understand the underlying molecular mechanisms that drive melanoma and other cancers.
- Experience processing and analysing multi-omics and/or imaging datasets. 
- Ability to use methods to easily convey complex data into visuals, such as multi-omics and image analyses (e.g. heatmaps/graphs) 
- Demonstrated skills in UNIX/Linux environments.
- Proven ability to execute jobs in high performance computing clusters environments e.g. via torque/slurm workload manager.
- Experienced in at least one programming language (preferably python). 
- Proven ability to work across diverse groups of staff within multidisciplinary teams.
- Excellent communication skills, both written and oral. 

Preferred:

- Experience in melanoma research, cancer research and biomarker development.
- Experience with analysis from omics data generated from formalin-fixed paraffin-embedded derived tissue samples.
- Experience with mIHC imaging and analysis techniques, e.g. HALO®, Phenocycler-Fusion®, QuPath
- Experience with machine learning techniques applied to image analysis.

Please apply by submitting your cover letter and resume to careers@melanoma.org.au
Addressing the selection criteria is mandatory and your application will not be considered if not answered.

Only applicants with full working rights within Australia should apply. Only successful applicants will be contacted. Please no recruitment agencies. This is a full-time role. We will consider applicants who apply by 26/04/2024.

We pay our respects to the Traditional Custodians of the lands on which Melanoma Institute Australia works, and their Elders both past and present, and acknowledge the deep, continuing connection of Aboriginal and Torres Strait Islander peoples to the land, waters, and sky.

Job website:   https://melanoma.org.au/

Contact name: Kylie Scott

Contact email: kylie.scott@melanoma.org.au

Postdoctoral Research Fellow (Level A or Level B) @ Monash University

Employer:  Monash University

Closing date: 14 April 2024

Brief position description: We are looking for a highly motivated postdoctoral scientist with advanced skills in computational biology. Additional laboratory-based skills in flow-cytometry are highly desirable (immunophenotyping and cell sorting). The successful applicant will undertake single and multi-omic analyses (Genetic, epigenetic, transcriptomic) of data derived from deeply phenotyped people with Multiple Sclerosis or related disorders.
This exciting position within the MS and Neuroimmunology Genomics and Prognostics team in the Department of Neuroscience, Monash University, will see you work with world leaders in MS prognostics and outcomes research.
Projects will be focussed on a number of different areas including:
• Precision medicine (pharmacogenomics)
• Prognostics
• Women’s Health

Applicants to this role should provide a covering letter outlining relative key skills and experience to assist us with our assessment.

Job website:   http://careers.pageuppeople.com/513/cw/en/job/663726/research-fellow-ms-and-neuroimmunology-genomics-and-prognostics-team

Contact name: Vilija Jokubaitis 

Contact email: vilija.jokubaitis@monash.edu

Genomics Senior Research Fellow @ Baker Heart and Diabetes Institute

Employer: Baker Heart and Diabetes Institute

Closing date:  8 April 2024

Brief position description: This postdoctoral post is a collaborative project with the Epigenetics in Human Health and Disease Team. This work focuses on characterizing the functional roles of regulatory proteins critical in gene transcription and examine the link to human disease using genetic, epigenomic and molecular approaches. The program is interested in understanding the transcriptional components in the regulation of metabolic memory and cardiac disease and further extend our understanding epigenetics in pre-clinical studies with a focus on cohort populations. This research will potentially provide tools for novel therapies. These key areas of therapeutic interest emphasising human studies have led to publications of high impact and international recognition.

This program is focused on the epigenetic analyses of prominent international cohorts. We have collected patient material to assess epigenomic indices using ChIP-seq, RNA-seq and Methyl-seq. The project aims to characterize the epigenetic landscape with the progression and development of disease. The aim of the work is to bridge the clinical and preclinical research in our department. 

Job website:   http://www.seek.com.au/job/74186574

Contact name: Sam El-Osta

Contact email: sam.el-osta@baker.edu.au

Bioinformatics Research Officer / Senior Research Officer @ VIC

Employer: WEHI

Closing date: 2024/04/01

Brief position description:  An excellent opportunity is available for a Bioinformatics Research Officer / Senior Research Officer to work within the Advanced Genomics Facility on the analysis of spatial omics, Olink (proteomics), and single-cell data at Australia’s pre-eminent biomedical research institute.


This successful candidate analyse data from a variety of cutting edge spatial omics technologies, including Visium, Xenium, STOmics, MERSCOPE and more, as well as developing new analysis workflows for Olink protein-profiling data.
This is a great opportunity to analyse data from cutting edge technologies, collaborate with excellent biomedical scientists, and to work in a supportive team.

This position could lead to either fully research-driven or staff-scientist career pathways.

Job website:  https://wehi.wd3.myworkdayjobs.com/broadbean_external/job/Parkville-Victoria-Australia/Bioinformatics-Research-Officer---Senior-Research-Officer_JR2234-2

Contact name: Peter Hickey

Contact email: hickey@wehi.edu.au

Research Assistant (Bioinformatics & Computational Biology) @VIC

Employer: Peter MacCallum Cancer Centre

Closing date:  8 March 2024

Brief position description: Applications are invited to join an exciting multi-discliplinary research program within Mark Dawson’s Laboratory (https://smex-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=www.thedawsonlab.com&umid=de34786c-b3ea-4c7d-b51b-dcb7d64b3414&auth=4d41e25c5d761d3d9b3f3fb6ac781e525dd700b4-bb19eb3663de449407d29df43edfe9515cc2e7cc) at the Peter MacCallum Cancer Centre. The research will explore the molecular mechanisms of clonal dominance in normal development and in cancer biology to provide insights into cell fate decisions, normal and malignant stem cell renewal, treatment response and resistance in cancer.

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 provide support for a variety of projects that build on innovative methods including SPLINTR (Fennell, Vassiliadis et al; Nature 2022, Holze et al BioRxiv 2023) – a cellular barcoding and lineage tracing technique. The role will include the analysis of a range of next generation sequencing data, including scRNA-seq, scChIP-seq, scATAC-seq and spatial transcriptomics. The role will require proficiency in at least one relevant programming language (e.g. R/Python/Perl) and experience working on a high-performance computing cluster. The individual will collaborate very closely with other bioinformaticians, cancer cell and molecular biologists in the Dawson laboratory team to work on joint initiatives.

The position will be in a research environment that includes a large and interactive group of bioinformaticians and computational biologists in the Computational Cancer Biology Program and the Bioinformatics Core Facility. The position will be initially for a fixed term of 12 months with the opportunity to extend for up to 5 years. Remuneration will be commensurate with qualifications and experience.

Applicants to this role should provide a covering letter outlining relative key skills and experience to assist us with our assessment. 

Alternatively, please contact us using the information below for a confidential discussion.

Hiring Manager: Dane Vassiliadis and Enid Lam
Email: Dane.Vassiliadis@petermac.org and Enid.Lam@petermac.org

Job website:  http://careers.petermac.org/job/MELBOURNE-Research-Assistant-%28Bioinformatics-&-Computational-Biology%29-VIC-3000/948385710/

Contact name: Enid Lam

Contact email: enid.lam@petermac.org

Postdoctoral Fellow @ Monash Biomedicine Discovery Institute

Employer: Monash University

Closing date: Sunday 10th March 2024

Brief position description: We're seeking a talented Research Fellow to join our team under the guidance of Professor Diana Hansen. You will collaborate with multidisciplinary teams across Indonesia and Japan, participating in international consortiums to investigate immune responses to dengue virus. Utilizing a systems biology approach, you'll identify correlates of protection from severe illness and biomarkers to predict dengue fever outcomes in endemic areas.

Key Responsibilities:
1. Conducting cutting-edge research and publishing findings in conferences and journals
2. Supervising research-support staff and guiding junior members of the research team
3. Contributing to research proposal submissions and engaging in professional activities
4. Collaborating with geographically dispersed teams and managing projects effectively
5. Occasionally contributing to teaching programs within your research field
6. Co-supervising honours and postgraduate research project.
Key Selection Criteria:
• Doctoral qualification in immunology, microbiology, or public health
• Demonstrated experience in assessing immune responses to infection in humans
• Proficiency in techniques such as flow cytometry, CyTOF, ELISA, RNA-sequencing, and single-cell RNA-sequencing
• Basic coding skills in R or willingness to learn for high-dimensional cytometry analysis
• Strong statistical analysis skills and a record of research publications
• Experience in mentoring and supervising research staff and students
• Excellent communication and organizational skills
• Ability to work independently and collaboratively in a team environment

Job website: https://careers.pageuppeople.com/513/cw/en/job/661973/research-fellow-microbiology

Contact: Diana Hansen

Contact email: diana.hansen@monash.edu

Bioinformatician @ CSIRO

Employer: CSIRO

Closing date: Monday 19th February 2024

Brief position description: The role of a bioinformatician in CSIRO is to conduct innovative research leading to scientific achievements that are aligned with CSIRO’s strategies. 

Specifically, this role will deliver research outcomes to the CSIRO cotton breeding program, a breeding program with a research and development pipeline from understanding the molecular basis of traits of interest through to commercial variety delivery. 

As part of several industry-supported research projects, we are undertaking a large-scale genomic prediction and phenomic analysis of commercial cotton varieties across a suite of traits. 

We are looking for a computational biologist specialising in genome informatics that can develop and utilize computational approaches to analyse genomic and transcriptomic datasets, with a particular emphasis on next generation DNA and RNA sequencing, its application to genotype by sequencing, genome assembly and annotation , through to gene network-analysis and use in genomic prediction models for improving breeding accuracy

Job website: https://jobs.csiro.au/job-invite/95291/

Contact: Rad Suchecki or Warren Conaty via email at Rad.Suchecki@csiro.au  Warren.Conaty@csiro.au, respectively

Postdoctoral Fellow / Research Fellow @ ANU

Employer: National Centre for Indigenous Genomics, The Australian National University

Closing date: 25 Feb 2024

Brief position description: The National Centre for Indigenous Genomics (NCIG) is creating reference resources for Indigenous genomics to advance knowledge and healthcare utility for Indigenous Australians. Towards that, we are generating telomere-2-telomere reference genomes and population-scale variation catalogues in partnerships with multiple Indigenous Australian communities. We are conducting a major research project into Indigenous Pharmacogenomics funded by an MRFF grant titled “Advancing Health Equity for Indigenous Australians through Pharmacogenomics”.
As a postdoctoral or research fellow focusing on pharmacogenomic research, you will play a pivotal role in conducting discovery research, developing innovative algorithms and software solutions for genomic data analyses, and performing empirical evaluations and benchmarking experiments. Through your contributions, you will enhance the utility and impact of NCIG genomic resources for the benefit of Indigenous Australians.
We are seeking exceptional candidates with a track record of high-impact research in genomics, bioinformatics, and quantitative biology. You will have exceptional technical skills and be familiar with computational technologies, DNA sequencing platforms, and large-scale genomics data analysis. If you are passionate about using your expertise to improve Indigenous health outcomes in active partnerships with Indigenous communities, we invite you to apply for this challenging and rewarding position at NCIG. Join us in making a real impact on Indigenous health by pushing the boundaries of genomics research.

Job website: http://jobs.anu.edu.au/jobs/postdoctoral-fellow-research-fellow-canberra-act-act-australia-d4461721-a086-4e0c-9521-94b41db206f6

Contact name: Hardip Patel

Contact email: hardip.patel@anu.edu.au