Software Developer, Monash University

Employer: Monash University

Closing date: 28th August 2018

Brief position description: The successful applicant will work with a diverse team of researchers to develop a graphical user interface (GUI) for constructing, performing, displaying, analysing and organising chemical simulations. The GUI will utilise existing scientific software that can perform each of these steps individually, and offer a common interface that will provide a coherent, streamlined process and make it accessible to those without specific knowledge of each individual software package.

Job website: http://careers.pageuppeople.com/513/cw/en/job/580782/software-developer

Contact name: Nicki Penny

Contact email: nicki.penny@monash.edu

 

Honours project – Spermtyping – Single cell analysis of the generation of genetic diversity via DNA repair pathways

Employer: St Vincent's Institute of Medical Research

Closing date: 05/10/2018

Brief position description: Spermtyping – Single cell analysis of the generation of genetic diversity via DNA repair pathways
Supervisors: Dr Wayne Crismani and Dr Davis McCarthy
Available for: Honours/Masters
Location: St Vincent’s Institute of Medical Research (through the University of Melbourne) 

Are you different from your brothers and sisters but have the same parents? Why is it that two parents can create children that are genetically unique? The answer is meiosis. We are seeking an enthusiastic bioinformatician or scientist with an interest in genetics and evolution, to uncover how DNA repair pathways regulate generation of diversity during meiosis. 
In our bodies, DNA double-strand breaks are incredibly dangerous and must be repaired. Nonetheless, there are natural processes that actively generate DNA double strand breaks in their hundreds during meiosis, to allow genetic recombination, or the reshuffling of genetic material between related chromosomes. This process is tightly regulated by mechanisms that are widely conserved in eukaryotes. We previously showed that mutants of the gene FANCM cause a huge increase in meiotic recombination in plants (eg Crismani et al, Science 2012). A related gene has the same effect in yeast. We have now generated FANCM-deficient mice to determine if the same process governs genetic diversity in mammals. This research has potential implications for our understanding and treatment of infertility in humans.

Your project will take place in a dynamic young team of experts skilled in genetics and single-cell genomics. You will learn and use a diverse set of bioinformatics techniques, which span; single cell sequencing, next generation bulk sequence analysis, haplotype analysis, analysis of recombination frequencies, mouse genetics and general analysis of meiosis. This project will see you develop significant computational novelty. The project will work towards uncovering how the generation of genetic diversity is regulated, and potentially affected in human disease such as certain types of infertility. 
The project may be adapted to include some wet-lab experiments if there is a strong desire to do so.

Requirements – a degree in bioinformatics or similar
Preferable – an understanding of molecular biology, particularly genetics.

$5,000 Honours and Masters scholarships are available to a limited number of outstanding candidates. Scholarships are awarded on a competitive basis and at the discretion of SVI.

Background reading
1. Crismani et al 2012. FANCM limits meiotic crossovers. Science
2. Kasak et al 2018. Bi-allelic Recessive Loss-of-Function Variants in FANCM Cause Non-obstructive Azoospermia. American Journal of Human Genetics

Want to know more? wcrismani@svi.edu.au

Job website: http://www.svi.edu.au/research_themes/research_staff/dr_wayne_crismani

Contact name: Wayne Crismani

Contact email: wcrismani@svi.edu.au

 

PhD/Masters Student in Bioinformatics, Melbourne

Employer: The University of Melbourne - Peter MacCallum Cancer Centre

Closing date: 01/11/2018

Brief position description: Evolution of breast cancer: understanding critical genomic and immune alterations in primary and metastatic breast cancer.

Understanding the cancer genome is seen as a key step in improving outcomes for cancer patients. However evolution of the cancer genome and how it evades host immunity during the natural history of lethal breast cancer is largely unknown. Some patients also have outstanding and long term responses to therapies= the biological basis behind this is also unknown. My lab is studying in detail tumour, tumor immune infiltrates and blood samples from human patients with primary and advanced breast cancers to understand these questions. We use a wide variety of cutting edge genomic techniques including next generation sequencing as well as single cell sequencing technologies. Validation of results may also occur, in vivo or in vitro as well as examining and developing novel therapeutics. I am looking for highly motivated students (Masters, PhD) interested in cancer research and improving patient outcomes from cancer: these projects may be focused on specific areas such as bioinformatics (honours and post graduate) or broadly encompass bioinformatics, immunology and molecular biology.

Job website: http://www.petermac.org/users/prof-sherene-loi

Contact name: Sherene Loi

Contact email: sherene.loi@petermac.org

 

Senior Research Fellow in Bioinformatics/Computational Biology, Southern Cross Uni

Employer: Southern Cross University

Closing date: 27th August 2018

Brief position description: Working with the Director, Southern Cross Plant Science, the Director for the Centre of Organics Research and other senior research colleagues, this role has primary responsibility for conducting research in computational biology and bioinformatics approaches, particularly as it applies to plant comparative genomic analysis, and contributing to the development of international quality research programs and projects. As senior researcher this role will be responsible for preparing and publishing high quality refereed research publications, developing proposals, and securing external project funding. Whilst research focused, this role will also contribute to the development of curriculum and teaching in the area of bioinformatics and computational biology.

Job website: https://www.scu.edu.au/about/jobsscu/vacancies/academic-vacancies/senior-research-fellow-in-bioinformaticscomputational-biology.php

Contact name: Prof. Graham King

Contact email: graham.king@scu.edu.au

 

Summer scholarship program for undergraduate students in STEM, Melbourne

Employer: Peter MacCallum Cancer Centre

Closing date: August 6

Brief position description: This program is open to undergraduate students in STEM to undertake a 6-week research project using data science, computer science algorithms, modeling, statistics and/or maths to answer questions in cancer using big data from genomics. 

You will work on a specific research project alongside senior scientists and other students, giving you the opportunity to apply and expand your skillset to investigate how cancer forms and help find more effective therapies for cancer. This scholarship program is a great way to gain experience in the application of STEM in real-life health sciences research.

These are paid placements for six weeks, or 30 days full-time to undertake during the summer holidays 2018-2019. You must have completed a minimum of 1 year of your undergraduate degree and be returning to undergraduate studies in 2019 to be eligible.

For further information please contact: Research.EducationAdmin@petermac.org

Job website: https://petermac.mercury.com.au/ViewPosition.aspx?id=Yo0PSgOPo7A=&jbc=ere

Contact name: Caroline Owen

Contact email: Research.EducationAdmin@petermac.org

Production Bioinformatician at Garvan Institute of Medical Research

Employer: Garvan Institute of Medical Research

Closing date: Open until filled

Brief position description: In 2017, the Garvan Weizmann Centre for Cellular Genomics (GWCCG) was formed, bringing together the Garvan Institute of Medical Research and The Weizmann Institute of Science to build Australia’s first Centre for Cellular Genomics.

The Garvan and the Weizmann Institutes have harnessed their synergistic strengths (in cytometry, genomics, informatics, and data visualisation) to enable cellular and single cell genomics to become routine tools for clinical and scientific analysis of many disease states. The Centre has a specific focus on 1) application of genomics (including DNA, transcriptomics, and epigenomics) to understand the cellular processes of the brain, immune system, and cancer; 2) the diagnosis of genetic diseases, stratification of cancers, and avoidance of adverse drug reactions; 3) the advancement of personal genetic health; and 4) the development of an improved health system that uses targeted information at cellular level to improve outcomes for patients and to better focus healthcare expenditure.

The Opportunity
The Production Bioinformatician will oversee the development, implementation and support of software and computational pipelines to translate raw single cell sequence data through to researchers. The role will focus on supporting robust and production scale pipelines that run on either local or national HPC systems, as well as cloud services.
Reporting to the Head of GWCCG Dr Joseph Powell, the key responsibilities include:
• Develop, implement and maintain the computational infrastructures required to support the analysis of high-throughput single cell sequencing data.
• Support the translation of new computational techniques from a research setting to production scale tools
• Work closely with Garvan’s Data Intensive Computer Engineering (DICE) group regarding the building of software pipelines that will run on DICE’s HPC and OpenStack computing environment, Australia’s supercomputing facility, the National Computational Infrastructure (NCI), as well as on commercial clouds (AWS, Google, and Azure)
• Identify areas of improvement in the GWCCG computational techniques and ensure the centre is adopting global best practices
• Assist collaborators in data analysis and to check the validity of experimental results
• Create computational solutions to generate automated reports from raw high-throughput single cell sequence data
• Establish and maintain excellent records of the computational analysis and techniques for all projects in GWCCG
• Represent GWCCG at national and international conferences, engaging with the research and clinical community, and promote the expansion of GWCCG through participation outreach initiatives

This role is offered on a full-time basis for 2 years in the first instance. 

About You
You will have the following key skills and experience:

• The Bioinformatician shall possess a MSc or higher degree in a relevant area of science or informatics (exceptional candidates with a BSc will be considered)
• Expertise in computational bioinformatics techniques, with a special focus on single cell transcriptomics, genomics and epigenetics
• Experience working in genome informatics in either a research or commercial setting is highly desirable
• Demonstrated experience in working in high performance computing environments
• Very strong programming skills in languages such as C/C++, Python, Perl, and R
• Demonstrated experience in using version control and software repositories
• Demonstrated experience in the development and implementation of new and cutting-edge bioinformatics tools
• Demonstrated experience in the development and implementation of training and education programs with a focus on bioinformatics techniques
• Demonstrated experience in project management methodology including planning, implementation and reporting, and the ability to assess priorities and manage competing deadlines.
• Excellent written and oral communication, representation and interpersonal skills essential for interaction with internal and external stakeholders, including GWCCG Executives

How to Apply
All applications must be submitted via the Garvan Careers site via the link below. Applications from other sites/channels will unfortunately not be considered.
http://garvan.applynow.net.au/jobs/GC201881

Your application should include: 
• A cover letter
• Your resume including at least 2 referees
• Copies of relevant qualifications / academic transcripts
Only applicants with full working rights in Australia are eligible to apply for this role.

Closing Date
As we are reviewing applications as they are received, we encourage you to submit your application as soon as possible.

Job website:http://garvan.applynow.net.au/jobs/GC201881

Contact name: Joseph Powell

Contact email:j.powell@garvan.org.au

Development Bioinformatician at Garvan Institute of Medical Research

Employer: Garvan Institute of Medical Research

Closing date: Open until filled

Brief position description: In 2017, the Garvan Weizmann Centre for Cellular Genomics (GWCCG) was formed, bringing together the Garvan Institute of Medical Research and The Weizmann Institute of Science to build Australia’s first Centre for Cellular Genomics.

The Garvan and the Weizmann Institutes have harnessed their synergistic strengths (in cytometry, genomics, informatics, and data visualisation) to enable cellular and single cell genomics to become routine tools for clinical and scientific analysis of many disease states. The Centre has a specific focus on 1) application of genomics (including DNA, transcriptomics, and epigenomics) to understand the cellular processes of the brain, immune system, and cancer; 2) the diagnosis of genetic diseases, stratification of cancers, and avoidance of adverse drug reactions; 3) the advancement of personal genetic health; and 4) the development of an improved health system that uses targeted information at cellular level to improve outcomes for patients and to better focus healthcare expenditure.

The Opportunity
The Development Bioinformatician will oversee the creation of new computational methods and tools to solve problems arising from new single cell assays being developed in GWCCG. There will be a particular focus on single cell DNA sequence data, as well as multi-level genomics data from individual cells. The role will also focus on supporting large-scale research activities undertaken by GWCCG researchers, or in collaboration with external researchers.
Reporting to the Head of GWCCG Dr Joseph Powell, the key responsibilities include:
• Development of new methods for processing and integrating high-throughput single cell sequence data generated from new molecular assays
• Work closely with the GWCCG Production Bioinformatician to help translate the new computational techniques from a research setting to production scale tools
• Work closely with Garvan’s Data Intensive Computer Engineering (DICE) group regarding the building of software pipelines that will run on DICE’s HPC and OpenStack computing environment, Australia’s supercomputing facility, the National Computational Infrastructure (NCI), as well as on commercial clouds (AWS, Google, and Azure)
• Take the lead in delivering research output and writing scientific papers arising from research conducted in GWCCG
• Play a role in writing funding and grant proposals
• Assist collaborators in data analysis and to check the validity of experimental design and results
• Represent GWCCG at national and international conferences, engaging with the research and clinical community, and promote the expansion of GWCCG through participation outreach initiatives

This role is offered on a full-time basis for 2 years in the first instance. 

About You
You will have the following key skills and experience:
• The Bioinformatician shall possess a PhD or higher degree in a relevant area of science or informatics (exceptional candidates with a MSc will be considered)
• Expertise in computational bioinformatics techniques, with a special focus on single cell transcriptomics, genomics and epigenetics
• Demonstrated experience in bioinformatics research and a proven track record in translating research through activities such as peer-reviewed publications
• Experience working in genome informatics in either a research or commercial setting is highly desirable
• Demonstrated experience in working in high performance computing environments
• Very strong programming skills in languages such as C/C++, Python, Perl, and R
• Demonstrated experience in using version control and software repositories
• Demonstrated experience in project management methodology including planning, implementation and reporting, and the ability to assess priorities and manage competing deadlines
• Excellent written and oral communication, representation and interpersonal skills essential for interaction with internal and external stakeholders, including GWCCG Executives

How to Apply
All applications must be submitted via the Garvan Careers site via the link below. Applications from other sites/channels will unfortunately not be considered.
http://garvan.applynow.net.au/jobs/GC201882

Your application should include: 
• A cover letter
• Your resume including at least 2 referees
• Copies of relevant qualifications / academic transcripts
Only applicants with full working rights in Australia are eligible to apply for this role.

Closing Date
As we are reviewing applications as they are received, we encourage you to submit your application as soon as possible.

Job website:http://garvan.applynow.net.au/jobs/GC201882

Contact name: Joseph Powell

Contact email:j.powell@garvan.org.au

Research Assistant / Research Associate / Research Fellow in Adelaide

Position title: Research Assistant / Research Associate / Research Fellow

Employer: Centre for Cancer Biology, and Alliance between SA Pathology and the University of South Australia

Closing date: 13/7/2018

Brief position description: We are advertising multiple research assistant/associate and research fellow positions in the Molecular Pathology and Lymphatic Development Research Laboratories of the Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia. These positions are full time 2-year and 1-year fixed term contracts and applications close July 13, 2018. Suitable applicants will have a background in genetics and/or bioinformatics and/or statistics and/or cell and molecular biology and/or developmental biology and/or biochemistry and/or immunology related disciplines.

For further information, see the job website or contact

Prof Hamish Scott (hamish.scott@sa.gov.au)
A/Prof Natasha Harvey (natasha.harvey@unisa.edu.au)

Job website: http://workingatunisa.nga.net.au/cp/index.cfm?event=jobs.checkJobDetailsNewApplication&returnToEvent=jobs.listJobs&jobid=47E466CE-A9C9-9120-96DD-A442E1EB8736&CurATC=External&CurBID=62AFB35D%2D9273%2D4A11%2D8DCC%2D9DB401354197&JobListID=22fc4f47%2De994%2D46a3%2Db8c9%2D9bc901269f43&jobsListKey=3febe8e3%2Db52a%2D4742%2Db254%2Defad071c15c5&persistVariables=CurATC,CurBID,JobListID,jobsListKey,JobID&lid=99635370108

Contact name: Andreas Schreiber

Contact email: andreas.schreiber@adelaide.edu.au

 

PhD scholarship – Computational and statistical models for single-cell multi-omics data in immunology, Sydney

Position title: PhD scholarship – Computational and statistical models for single-cell multi-omics data in immunology

Employer: UNSW Sydney

Closing date: 20/7/2018

Brief position description: Up to 2 PhD scholarships are available to undertake research on developing an applying cutting-edge statistical and computational models to learn the molecular pathways driving immune cells to a successful immune response against pathogens and cancer. This knowledge will inform novel immunotherapies for cancer and vaccines against significant pathogens affecting marginalised communities.

Job website: https://www.2025.unsw.edu.au/apply/scientia-phd-scholarships/computational-and-statistical-models-single-cell-multi-omics-data

Contact name: Fabio Luciani

Contact email: luciani@unsw.edu.au

Bioinformatician in Pathology at Peter Mac, Melbourne

Position title: Bioinformatician

Employer: Peter MacCallum Cancer Centre

Closing date: 23/07/2018

Brief position description: Peter Mac is one of a handful of integrated cancer research, education and treatment centres in the world. Each day our team strives to provide the very best in cancer care, even better treatments and potential cancer cures for all people affected by cancer.

The aim of this role is to provide bioinformatics support to the Pathology Department to develop a high-throughput diagnostic genomics assay for TMB/MSI assessment in cancer patients.

The role will involve designing the assay, interrogating public databases and manipulating large next generation sequencing (NGS) datasets in order to demonstrate the analytical validity of the assay.

Two main requirements for this position:
- PhD or MSc or equivalent in Bioinformatics, Computer Science or Computational Biology
- Prior full-time work experience (1-5 years) in a Bioinformatics, Computer Science or Computational Biology role

For further information about this opportunity, please review the position description or contact us for a confidential discussion.

Job website: http://petermac.mercury.com.au/ViewPosition.aspx?id=7Cm7btcr2bY=

Contact name: Andrew Fellowes

Contact email: andrew.fellowes@petermac.org