Production Bioinformatics Engineer - Core Facility, Sydney

Employer: Garvan Institute of Medical Research

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

Brief position description: The Garvan Institute of Medical Research is one of Australia’s leading medical research institutes, with over 600 scientists, students and support staff. At Garvan our research is focused upon understanding the role of genes and molecular and cellular processes in health and disease as the basis for developing future preventions, treatments and cures. Our scientists are researchers who work towards making significant breakthroughs in scientific discovery to positively impact human health.

Our research support teams are no different. Like our scientists, we only recruit the best professionals in our Core Facilities which include Clinical Genomics, Flow Cytometry, Molecular Genetics, Histopathology and Microscopy. Our support teams are experts in their fields and are driven by the dynamic culture, innovation and cutting-edge research that Garvan offers. At Garvan no two days are the same. 

The Opportunity

Garvan has established the Kinghorn Centre for Clinical Genomics (KCCG) Core Facility to be at the forefront of translational advancements in DNA sequencing from research into the clinic and improve future patient care. 

We’re currently looking for a talented and motivated bioinformatics software engineer with a strong background in computer science, next-generation sequencing data analysis and a passion for learning about genomics to join the Production Bioinformatics team. Bioinformaticians and Software Engineers at all levels of experience are welcome to apply for this 1-year position with the possibility of extension.

Reporting to the Bioinformatics Manager, the key responsibilities are:
• Develop, implement and maintain automated high-throughput production for research and clinical genome sequencing pipelines.
• Design and implement pipelines to run on the internal and external high performance compute infrastructure and commercial clouds (AWS, GCP, Azure).
• Provide bioinformatics support to customers of the sequencing facility.
• Development of dashboards to proactively monitor process performance and sequencing quality.
• Take cutting edge bioinformatics research tools and implement them into production to support the development of new NGS based services.

About You

You will have the following key skills and attributes:

Essential
• Bachelor’s degree (or higher) in Bioinformatics, Computer Science or related fields
• Experience with analysis of next-generation sequencing data
• Experience with Linux command line and scripting languages (Python, Bash, R or other)
• Experience with source code management tools (git preferred) 
• Excellent problem solving abilities and strong attention to detail
• Ability to work independently
• Excellent verbal and written communication skills

Desirable
• Understanding of genomics, transcriptomics and epigenetics
• Experience with testing frameworks across languages, including unit, integration and acceptance testing
• Experience with cluster computing, e.g. Sun Grid Engine, Torque, PBS
• Experience with cloud computing platforms, e.g. Amazon Web Services
• Experience in a NATA accredited laboratory environment
• Experience with laboratory information management systems (LIMS)

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/GC201896 

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.

Job website: http://garvan.applynow.net.au/jobs/GC201896

Contact name: Human Resources

Contact email: hr@garvan.org.au

Biostatistician Proteogenomics, Sydney

Employer: Children's Medical Research Institute

Closing date: 14th September 2018

Brief position description: A Biostatistician position is available in the ProCan Cancer Data Science Group, led by Dr. Qing Zhong. ProCan (the ACRF International Centre for the Proteome of Human Cancer) is a world-first initiative developed and launched in September 2016 by Professors Phil Robinson and Roger Reddel, and established with a $10 million grant from the Australian Cancer Research Foundation (ACRF).

Job website: http://www.cmri.org.au/getattachment/About-Us/Job-Vacancies-and-Careers/JOB-Ad-PV1808_Biostatistician-readvertised.pdf.aspx?lang=en-AU

Contact name: Paulina Baranowski

Contact email: pbaranowski@cmri.org.au

Research Scientist - Bioinformatics, CSL

Employer: CSL Limited

Closing date: 21 September 2018

Brief position description: We have an opportunity available for a Research Scientist – Bioinformatics to provide scientific and technical expertise to help answer biomedical questions at the pre-clinical stage of the drug development pipeline using computational methods. In this position, you will expand CSL’s Research capability to mine genomic variants to characterize cell lines as well as to enable patient stratification for better design of clinical trials. Furthermore, you will devise an integrative approach to analyze multiple types of data obtained from in-house and external resources in order to answer key questions in the areas of biomarker discovery and understanding of mechanisms of action of targets, drug candidates and diseases of interest.

You will work closely with Bioinformatics Group members and other Research colleagues to set project objectives and to determine and implement data generation, analysis and software development strategies. You will also work alongside CSL’s external collaborators including spending time in their research laboratories as required to enable alignment of objectives and strategies for computational methods.

Additional Responsibilities include:

Provide input in the design of next-generation sequencing experiments including RNA-seq, DNA-seq, Rep-seq, etc.

Carry out bioinformatic analyses on datasets generated in-house from different NGS and array experiments or collected from external databases and contribute to the interpretation and visualisation of the results.

Establish an in-house capability to utilize genetic and genomic variants in order to improve biomarker discovery, understanding of MoA, patient stratification strategies and prioritisation of indications for drug targets.

Establish an in-house capability to understand the immune repertoire dynamics by analysing Rep-seq datasets generated from patient samples.

Work with in-house software developers to develop fully automated workflows that assist in characterizing transgenic animal models and manufacturing/gene therapy cell lines.

Lead benchmarking and adaptation efforts for new sequencing technologies (e.g. long read and single cell sequencing) in CSL Research in order to answer relevant research questions across multiple drug discovery projects.

Lead efforts to integrate data from public databases (e.g., GTEx, ExAC, ENCODE, UK Biobank) inside CSL Research computational platform and improve upon current data mining practices.

Work with in-house data managers to devise new processes for managing big data and ensure compliance with CSL’s regulatory requirements.

Contribute to CSL’s growing collaboration network with academic laboratories and industry partners locally and globally.

Qualifications

PhD in computational biology, bioinformatics, computer science, biomedical informatics, informatics engineering, molecular biology, genomics or a related discipline with significant computational and biomedical components.

Bachelor’s or Master’s degree in biological sciences (e.g., computational biology, bioinformatics, molecular biology, translational sciences, genetics, etc.)

Essential

3+ years of post-doctoral experience in biomedical data analytics in a highly collaborative, interdisciplinary environment in academia and/or industry.

Demonstrated experience in working with genomic variants and genetic information to answer biomedical questions.

Demonstrated experience in eQTL analysis on patient cohorts and/or utilizing eQTL data from public databases to understand mechanism of action of targets, drug candidates or diseases.

Demonstrated experience in applying network biology and pathway analysis algorithms.

Demonstrated experience in using public databases to answer key research questions related to experimental design, biomarker discovery and patient stratification.

Demonstrated experience in working in a Unix-like and high-performance computing (HPC) environment.

Demonstrated experience in developing workflows using various programming languages, e.g., Python, R, CWL, etc.

High quality track record of publications and presentations at national and international conferences.

Desirable

Experience in applying bioinformatic techniques to enable target identification, biomarker discovery and understanding target/drug mechanism of action studies.

Experience in performing de novo genome assembly using short read and long read sequencing technologies.

Experience in applying machine learning algorithms to interrogate complex datasets.

Experience in developing software using various programming languages, e.g., Java, C++, etc.

Experience in developing web applications for data analytics purposes.

Experience in publishing software packages in open source community projects.

How to Apply:

Applications must address the selection criteria above and include a current CV and covering letter.

Applications close Friday, 21st September, 2018

Job website: http://www.linkedin.com/jobs/view/research-scientist-bioinformatics-at-csl-829445513/

Contact name: Sophie Saba

Research products database developer - Contract position

Employer: Jomar Life Research

Closing date: 30 Sept

Brief position description: Our company is a distributor of reagents and kits for biological research. Our catalog consists of hundreds of thousands of individual products. To assist our customers in identifying relevant products of interest, we are seeking to substantially improve our current product catalog and search tool. We wish to engage a contractor with strong coding and database management skills as well as familiarity with biological nomenclature to construct the architecture behind this search function. 

A suitable candidate should have very strong skills in Excel, including VBA coding, Microsoft access and database management. Additionally, it would be highly desirable if the candidate has experience with ecommerce platforms, ideally Magento. Lastly, understanding of biology and good familiarity with biological nomenclature is essential. Therefore it would be suitable to someone with a background in bioinformatics. 

We envision this position as initially being on a fixed-term contract basis, but possibly progressing to an on-going part-time role. This position may suit a current graduate student seeking to supplement their income. 

An attractive compensation will be offered for a suitable candidate.

If interested, please email a cover letter describing your relevant experience and CV to Alex Szabo at the address provided.

Job website: http://www.jlresearch.com.au

Contact name: Alexander Szabo

Contact email: alex.szabo@JLresearch.com.au

Senior Sales Specialist, Clinical Informatics, Illumina

Employer: Illumina

Closing date: 30/08/2018

Brief position description: The Senior Sales Specialist, Clinical Informatics will use their technical knowledge and expertize to provide pre-sales support to prospective customers and the sales organization on Illumina's Next Generation Sequencing data analysis pipelines and analysis applications primarily for use in clinical research or testing. This will be primarily through increasing awareness of the platforms and enabling customers to uptake new workflows and building a community of satisfied customers.

Job website: http://www.seek.com.au/job/36990915

Contact name: Zhiliang Chen

Contact email: zchen1@illumina.com

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