Bioinformatics & Cellular Genomics

　　The Facility

　　St Vincent’s Institute (SVI) www.svi.edu.au is an internationally recognised independent research organization, based on the St Vincent’s Hospital Campus on the edge of Melbourne’s CBD. The Institute has a dedicated team of over 150 talented research staff and students, who are committed to improving the health and life-expectancy of Australians. We focus on common diseases that represent major health issues for Australians today, including diabetes, bone diseases, cancer, cardiovascular disease, obesity and Alzheimer’s disease.

　　The Laboratory

　　The Bioinformatics & Cellular Genomics Laboratory is a newly funded group at SVI, established to solve the challenges of analysing and interpreting the large-scale biological data generated from medical research activity. In a jointly funded arrangement between SVI and the Melbourne Integrative Genomics Group (part of Melbourne University School of Mathematics and Statistics) and under the direction of NHMRC Fellow and Oxford graduate Dr Davis McCarthy, the Bioinformatics & Cellular Genomics Laboratory is capable of using large-scale studies of DNA and single-cell genetics to drive future medical discoveries.

　　BRIEF SUMMARY

　　The Position

　　We are seeking a motivated and successful postdoctoral Researcher to manage an independent project in single-cell genetics, developing new computational methods and open-source software to enable cloud-scale analyses of single-cell data. You will implement statistical and machine learning approaches and coordinate the processing and analysis of ‘omic data, identifying opportunities to customise more efficient workflows and methods where warranted.

　　The position also plays an important role in the overall performance and scientific activities of the laboratory as you will contribute to publications, assist in the supervision of students and present at seminars and lab meetings. The researcher will also have an organisation-wide responsibility in collaborating closely with the researchers of the wet-lab laboratories, providing computational expertise on experimental design and data analysis.

　　The successful incumbent will have a PhD (or equivalent) in a computational discipline relevant to bioinformatics and cellular genomics (bioinformatics, statistics, machine learning, computer science, applied mathematics, physics or similar) and possess advanced skills in using computer programming and scripting in R or Python and, ideally, familiarity with one or more of C++, Go, Nim, Rust, Java, Perl or SQL programming languages. You will have a demonstrated ability in the use of Unix-based systems, computing clusters and related queueing systems and in large-scale data analysis and management. Ideally you will have prior experience working in high-performance computing environments, including academic and/or commercial cloud computing platforms and experience using bioinformatics workflow management software (e.g. Snakemake, Nextflow, CWL). Your track record in bioinformatics, genomics, computational biology or other relevant quantitative fields will be evidenced by high-quality publications. Demonstrated experience developing open-source software and reproducible data analyses will be highly regarded.

　　Salary commensurate with qualifications and experience, ranging from AUD 83,000 – $90,000 per annum, plus:

　　9.5% superannuation

　　generous $15,900 FBT exempt salary packaging

　　Applications addressed to Dr Davis McCarthy should include the following:

　　Current CV

　　Covering letter addressing selection criteria, as outlined on the Position Description

　　Enquiries Dr Davis McCarthy dmccarthy@svi.edu.au

　　Application Email Address : hr313@svi.edu.au

　　MAIN JOB PURPOSE

　　The goal of SVI’s Bioinformatics and Cellular Genomics lab is to solve the challenges of analysing and interpreting large-scale biological data. We are broadly interested in the use of computational approaches to drive biological discovery and develop methods and software for the analysis of data produced by modern sequencing technologies, particularly single-cell genomic data. Further, we are interested in studying the effects of changes in DNA on gene expression in individual cells and in developing the necessary computational toolkits to enable large-scale studies of single-cell genetics.

　　The roles of a Research Officer are: 1) to conduct research on a defined project(s) within the overall interests of the laboratory; 2) to assist with the supervision of students; 3) to contribute to the overall maintenance of the laboratory, to 4) to participate in associated scientific activities, including institutional seminars, committees, etc.

　　KEY RESPONSIBILITIES

　　1. Manage an independent project and conduct computational analyses and methods development.

　　Develop computational methods, approaches, and software to enable single-cell genetics.

　　Adapt and/or develop original computational and analytical methods in support of existing and future research.

　　Implement statistical and machine learning approaches for genomics data analysis in open-source software.

　　Coordinate the processing and analysis of ‘omic data.

　　Implement and develop efficient pipelines for the pre-processing and analysis of a wide range of multi-omics data and where necessary develop new custom bioinformatics methods and/or pipelines.

　　Organise data, research, and analysis procedures.

　　Collaborate with wet-lab biologists, provide expertise on experimental design and manage the collaboration

　　Analyse the results of experiments conducted by collaborators and keep records of experimental and analytical results.

　　Maintain knowledge of relevant scientific literature, techniques/technologies and issues

　　Undertake research in a transparent and documented manner, in accordance with the Australian Code for Responsible Conduct in Research and SV’s Research and Governance guidelines

　　Performance measures

　　Data analyses are designed carefully and performed competently, efficiently and accurately

　　Methods and software development is carried out competently, efficiently and accurately, adhering to the Lab’s ethos of open and reproducible science

　　Projects are completed with the responsible management of resources and consumables

　　Knowledge is kept up to date through regular reading of literature to support all aspects of the research and to contribute to defining new directions

　　2. Contribute to laboratory publications:

　　Provide analysis of data from specific collaborative projects

　　Assemble data and results into figures for manuscripts and grant applications

　　Write manuscripts for publication in consultation with the Lab Head

　　Performance measures

　　Data analyses are completed with minimal delay

　　Preparation/contribution to publications, grant applications, etc

　　3. Contribute to laboratory administration/maintenance:

　　Maintain detailed (electronic) laboratory notebooks (or equivalent), digital data servers, documentation of code repositories, descriptions of computational analyses and other records

　　Provide technical expertise in the development and management of scientific computing environments to support the work of the laboratory (e.g. some light sys admin work).

　　Contribute to the maintenance of the laboratory’s repositories of data and of computer code.

　　Develop procedures to support reproducible research in the lab and Institute.

　　Performance measures

　　Laboratory notebooks (electronic notebooks or equivalent) and digital records are up to date

　　Datasets and code repositories are well-documented and well-maintained

　　Data analyses are well-documented and fully reproducible

　　4. Present at laboratory and unit meetings:

　　Attend and participate at regular laboratory and unit meetings

　　Prepare data and analyses, and present at these meetings

　　Performance measures

　　Active participation and professional contribution at all meetings

　　5. Supervision and teamwork

　　Contribute to the mentoring/supervision of undergraduate and/or graduate students

　　Provide training to laboratory assistants and students in specific methods/approaches/techniques

　　Make a positive contribution to the effectiveness of, and positive working relationships within, the laboratory group.

　　Provide collaborative support to others in the group and assist in the smooth running of projects.

　　Provide training and assistance with bioinformatics analyses to other members of the laboratory, as well as external collaborators as appropriate.

　　Collaborate with other SVI and University of Melbourne groups to provide bioinformatics support and identify experimental design/data analysis issues that would benefit from bioinformatics expertise.

　　Work with external collaborators.

　　Performance measures

　　Strong, harmonious and effective working relationships are developed and maintained with other members of the laboratory and collaborators within SVI and at other institutions

　　Knowledge and expertise is shared with team members and collaborators

　　6. Participate in activities within the institute and broader scientific community:

　　Attend regular the weekly institute seminars and make a contribution to the discussion

　　Engage with the SVI Postdoctoral Association

　　Engage with the Australian Bioinformatics and Computational Biology Society and/or Statistical Society of Australia and/or EMBL Australia

　　Attend and present (when the project is at an acceptably mature stage) at the national scientific meetings of the above societies as well as other local symposia/meetings and, where possible, international meetings

　　Performance measures

　　*Active participation with the SVI Postdoctoral Association and relevant scientific societies

　　Presentation of seminars

　　7. Occupational health and safety

　　SVI has a duty of care to all employees to provide a safe work environment. All employees must also take responsibility for their own safety, and that of fellow workmates, and should apply a common-sense approach to work methods to minimize risk to themselves and others.

　　Performance measures

　　Adherence to SVI Occupational Health & Safety guidelines, including the wearing of personal protective equipment as provided

　　Use equipment in compliance with manufacturers’ or relevant guidelines

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