Position title: Bioinformatician - Statewide Genomics
Employer: NSW Health Pathology
Closing date: 6/2/2022
Brief position description: NSW Health Pathology are looking for a Bioinformatician to contribute to the management and development of Statewide genome informatics system whilst collaborating and building effective working relationships with key stakeholders to support project development and implementation.
With flexibility on location between Newcastle and St Leonards you don’t want to miss out on this opportunity!
Job website: http://jobs.health.nsw.gov.au/nswhp/jobs/bioinformatician-statewide-genomics-132543
Contact name: Eva Chan
Contact email: eva.chan@health.nsw.gov.au
PhD Project: Bioinformatics analysis of tertiary phase glial in preterm brain injury @ VIC
Position title: PhD Project: Bioinformatics analysis of tertiary phase glial in preterm brain injury
Employer: RMIT University
Closing date: 28 February 2022
Brief position description: Permanent brain injury in babies can result from exposure to an inflammatory insult combined with being born preterm (<37 of 40 weeks’ gestation). Over their lifetime, these infants frequently struggle in academic and social settings due to cognitive and social deficits linked to their brain injuries. It is known that the cellular reactivity, termed the tertiary phase of injury persists into childhood and adolescence after early brain injury and is also observed after multiple other forms of brain injury. These changes involve dysfunction of astrocytes and microglia and sensitises the brain to further injury. By identifying these changes creates opportunities for novel therapeutic development.
This project would add to this field of research by identifying the signature of injury in a mouse model of preterm inflammatory brain injury. This would involve the bioinformatic analyses of novel RNA-seq data for cell-specific and temporal changes in a mouse model of human development and the thorough integration of existing data. Network exploration for pathway involvement in known pathways of cell function regulation will be key in identifying the nature of the changes. The identified glial signature will be validated at gene and protein levels in this lab to confirm and validate findings.
The preferred PhD candidate will have completed an Honours or Masters in bioinformatics, biostatistics, molecular biology, computer science, or a related discipline, and have a keen interest in neurobiology and development. This PhD position is supported by a scholarship.
Job website: https://www.rmit.edu.au/research/research-degrees/find-a-project
Contact name: Alice Johnstone
Contact email: alice.johnstone@rmit.edu.au
PhD Project: biomarker identification in lutetium PSMA-treated prostate cancer patients using circulating tumour DNA @ VIC
Position title: PhD Project: biomarker identification in lutetium PSMA-treated prostate cancer patients using circulating tumour DNA @ VIC
Employer: Peter MacCallum Cancer Centre
Closing date: 31/01/2022
Brief position description: Prostate-specific membrane antigen (PSMA) is a type 2 membrane glycoprotein overexpressed on prostate cancer cells that has emerged as a key therapeutic target in metastatic castration-resistant prostate cancer (mCRPC). Two landmark trials (including one led by Peter MacCallum Cancer Centre) have positioned lutetium PSMA radionuclide therapy (Lu-PSMA) as a highly effective new treatment option for mCRPC. Nevertheless, responses to Lu-PSMA treatment can be variable, and development of resistance remains inevitable. Identifying biomarkers linked to outcomes with Lu-PSMA is therefore a critical unmet need, in order to select patients most likely to benefit from treatment and to dissect mechanisms of therapeutic resistance.
As part of the newly opened Prostate Imaging and Theranostic Centre of Excellence (ProsTIC), we are running a series of investigator-led clinical trials with Lu-PSMA and other theranostics. Serial plasma samples collected as part of these trials represents a valuable world-first repository of biospecimens with which to perform biomarker discovery. Currently, these plasma samples are being utilised to generate targeted sequencing data from which somatic and germline mutations can be identified. As part of this fully-funded project, students will help to develop bioinformatics approaches to analyse and explore next-generation sequencing data to identify putative predictive and prognostic biomarkers for this novel radionuclide therapy that may be incorporated into future clinical trials here at Peter Mac. Students will receive training in clinical trial research, genomics, cancer biology, bioinformatics and biostatistics and will work with a team of wet-lab biologists and bioinformaticians. The candidate will require prior experience with unix-like operating systems, R and/or python programming languages. A background in mathematics or statistics is also highly desirable.
Job website:
Contact name: Heidi Fettke
Contact email: heidi.fettke@petermac.org
Bioinformatician - Cancer Research @ VIC
Position title: Bioinformatician - Cancer Research
Employer: Peter MacCallum Cancer Centre
Closing date: 19 Dec 2021
Brief position description: A professional bioinformatics role to support translational cancer immunotherapeutic research. Looking for candidates with 1 - 5 years of experience.
Job website: http://www.seek.com.au/job/55136586?type=standard#searchRequestToken=2446ba19-53d3-4d4a-8ead-6dfd7aa7de1d
Contact name: Jason Li
Contact email: jason.li@petermac.org
Bioinformatics Postdoctoral Researcher @ VIC
Position title: Bioinformatics Postdoctoral Researcher
Employer: Peter MacCallum Cancer Centre
Closing date: 24/01/2022
Brief position description: The Oshlack research group is offering an exciting opportunity to join the bioinformatics group in the Computational Biology Program at the Peter MacCallum Cancer Centre. The Oshlack group works on computational and statistical methods development as well as collaborative analysis with a strong focus on transcriptomics.
The candidate will work on the analysis of data from cutting edge technologies, specifically long read sequencing, single cell sequencing technologies and the combination of the two. The position will involve understanding the strengths and limitations of the technologies and how to extract the most interesting information form the data. In addition, the candidate will likely develop computational and statistical approaches for data analysis which can be generalised in software. The position will involve the analysis of real data sets generated by collaborators within and outside the PeterMac. Analysis will have the aim of producing deeper insights and understanding into the drivers and outcomes in cancer development and progression. The successful candidate should hold a PhD in a quantitative field such as bioinformatics, computational biology, statistics, computer science, physics or mathematics. The candidate will be expected to have excellent organizational and time management skills, and a high level of interpersonal skills.
This position is an opportunity for the successful candidate to bring experience from a previous field and use it to further develop skills and knowledge in the computational biology field specifically related to cancer transcriptomics and tumour biology. The candidate will join a dynamic and supportive team of scientist within the research group and the institute.
This position is fixed term full-time for 24 months with the possibility of extension. Consideration will be given for suitable applicants looking for a part-time position.
Job website: https://petermac.mercury.com.au/ViewPosition.aspx?id=Exmt33nMdsM=&jbc=ere
Contact name: Alicia Oshlack
Contact email: alicia.oshlack@petermac.org
Sr Bioinformatics Scientist @ Illumina
Position title: Sr Bioinformatics Scientist
Employer: Illumina
Closing date: 31 Jan 2022
Brief position description: Our team develops Next Generation Sequencing (NGS) secondary analysis solutions used by researchers and clinicians worldwide, providing sample-to-answer pipelines with high reliability, speed, and accuracy of results.
We are responsible for the industry-leading FPGA-accelerated DRAGEN platform, high-performance software, and integration of pipelines into in the ICA Cloud and BSSH platforms for automation, scalability, and data interpretation. The platform caters to a wide variety of applications, from rare and undiagnosed inherited diseases, population-scale genetics, precision medicine, cancer research, COVID-19 testing, metagenomics, single-cell analysis, etc.
We are looking for a highly driven and talented bioinformatics scientist to join our methods development team to work on various aspects of secondary analysis pipelines, large variant calling (SV, CNV), small variant calling (SNV) or RNA. The ideal candidate will be able to contribute both to the algorithm design based on bioinformatics/algorithm/statistics background, and to the software code base, based on proficient C/C++ programming skills.
Responsibilities:
• Algorithm development – Design, develop, and maintain highly accurate computational algorithms for large-scale analysis of novel types of genomic data
• Data analysis – Lead investigation and resolution of technical problems, applying best practice statistical/computational methods
• Pipeline development – design and develop pipelines in production-grade C/C++ software
• Collaboration -- Closely interact with product owners, systems engineers, testers, and FPGA design teams.
• Support -- provide technical assistance to escalated production issues.
• Leadership -- Provide technical leadership to an Agile team if required. Maintain awareness of industry trends and evaluate applicability of new software technologies to platform development efforts.
Listed responsibilities are an essential, but not exhaustive list, of the usual duties associated with the position. Changes to individual responsibilities may occur due to business needs.
Required Skills and Experience:
• PhD with 5+ years’ experience in academic or industrial settings in Bioinformatics, Computational Biology, Biostatistics or Computer Science, or equivalent experience
• Experience developing next generation sequencing data analysis methods for DNA and/or RNA sequence
• Extensive experience in an object-oriented programming language; C++ preferred
• Strong background in computer science algorithms relevant to bioinformatics
• Strong communication skills and ability to describe complex analyses to audiences with diverse backgrounds
• Ability to contribute independently and collaboratively, take ownership of assigned tasks, and excel in a fast-paced environment
• Experience with using version control systems such as Git
Desired Skills and Experience:
• Experience with scripting languages, including Python and bash
• Experience with multi-threading and memory management techniques.
• Knowledge and experience with probability and statistics and/or machine learning
• Knowledge and experience with cloud application development, in particular AWS
• Knowledge and experience with a wide range of bioinformatics tools
• Familiarity with professional software development practices (testing, CICD, debugging, source control, etc.)
• Demonstrated success in collaborating in a team environment and delivering high-quality software products using agile development methodologies
Job website: http://illumina.wd1.myworkdayjobs.com/illumina-careers/job/Australia---Remote/Sr-Bioinformatics-Scientist_29812-JOB
Contact name: David Lin
Contact email: david.lin@illumina.com
Exploring Cutaneous Squamous Cell Carcinoma (cSCC) using integrated multi-omics approaches @ NSW
Position title: Exploring Cutaneous Squamous Cell Carcinoma (cSCC) using integrated multi-omics approaches
Employer: University of Wollongong
Closing date: 30 december 2021
Brief position description: Exploring the mutational landscape of Cutaneous Squamous Cell
Carcinoma (cSCC) using integrated multi-omics approaches.
Our group is working to decipher the driver mutations and molecular pathways that promote metastasis in cSCC using a multi-Omics (whole genome/transcriptome/methylome) approach. This information will also be used to facilitate the stratification of potential clinically important genes (biomarkers) as predictors of metastatic potential in primary cSCC and identify potential new therapeutic targets. This PhD project will provide the opportunity for a student to work on the integration and analysis of the multi-omics dataset being generated by the group. The student will join a collaborative team of clinicians and molecular and bioinformatics scientists exploring cSCC from the Illawarra Health and Medical Research Institute (located on the University of Wollongong campus), the Sydney Head Neck Cancer Institute and at the National Cancer Centre Singapore Scholarship Information
A PhD scholarship is available for commencement at the University of Wollongong, Australia.
Stipend: $28,597* non-taxable (maximum 3 years full time). Part-funded by Cancer Institute NSW, Translational Program Grant 2020/TPG2081
Entry Requirements
Outstanding applicants holding First Class Honours or a Master’s degree in a discipline relevant to the research topic such as bioinformatics and biostatistics, genomics or genetics, and an interest in cancer biology are encouraged to apply. Experience with programming skills such as R statistical language and working in a UNIX environment is required. Bash scripting, additional programming skills such as perl, python, C++ would be a plus. Next generation sequencing related knowledge such as file formats, alignment tools/methods, or basic bioinformatics algorithm knowledge would also be advantageous. Applicants must remain enrolled as a full-time PhD student of Faculty of Science Medicine and Health, University of Wollongong for the duration of this scholarship.
Applicants will be enrolled in the Faculty of Science Medicine and Health, University of Wollongong and are expected to commit to full-time study based at the Illawarra Health and Medical Research Institute located on the UOW campus.
Scholarship open to domestic and international applicants but must be available to start in early 2022 at UOW.
Supervisors/collaborators
Prof Marie Ranson, Cancer Cell and Molecular Biology Group leader,
Theme Leader Diagnostics and Therapeutics, Illawarra Health and Medical Research Institute (IHMRI)
School of Chemistry and Molecular Bioscience, Molecular Horizons, UOW, and IHMRI,
A/Prof Bruce Ashford,
Head and Neck Surgeon, IHMRI Clinical Director, School of Medicine/IHMRI/ISLHD
Dr Amarinder Thind; Bioinformatician, cSCC Group
School of Medicine/IHMRI
Prof Jonathan Clark; Head and Neck Surgeon, Director of Head and Neck Research
TPG lead, Chris O'Brien Lifehouse Centre, Camperdown, Sydney
HOW TO APPLY
Applicants are encouraged to contact Prof Marie Ranson (mranson@uow.edu.au) or A/Prof. Bruce Ashford (bgashford@gmail.com) with an Expression of Interest (EOI). The EOI should include: (1) CV clearly outlining education qualifications with GPA, research and work experiences, (2) copies of academic transcripts, and (3) list of publications
(if any).
Proposal background
The non-melanoma skin cancer cutaneous squamous cell carcinoma
(cSCC) is one of the most common malignancies in Australia and is a
major health resource burden (Ashford et al 2017). Excessive exposure to
ultraviolet (UV) radiation, which causes cumulative DNA damage, is the
primary risk factor (Ashford et al 2017). Metastases to regional lymph
nodes occur in 2-5% of cases and impart a significant risk of morbidity and
mortality. Standard treatment for these metastases involves a
combination of radical surgery and radiation treatment which profoundly
reduces patient’s quality of life. There are no standardised
chemotherapeutic regimens and radiotherapy can stimulate aggressive
recurrence. Our group is attempting to decipher the driver mutations and
molecular pathways that promote metastasis in cSCC. This will facilitate
the stratification of potential clinically important genes (biomarkers) as
predictors of metastatic potential in primary cSCC and identify potential
new therapeutic targets. We have already completed the largest cohort of
metastatic cSCC whole genome sequencing (WGS). WGS has allowed us to
describe UV-induced mutation patterns that persist in metastases of cSCC
and excessively affect insulator binding sites. Recurrent patterns of
variation in key regulatory elements, and recurrent copy number and short variation in cancer-associated genes were also found (Mueller et al
2019; Ashford et al submitted).
We are currently extending our WGS and completing RNA sequencing and
methylome analysis across the clinicopathologic spectrum of cSCC
including metastasising and non-metastasising primary tumours and their
coincident metastases. This PhD project will provide the student the
opportunity to work with our team of clinicians and molecular and
bioinformatics scientists to explore cSCC disease by integrating the cSCC
related data obtained from our multi-Omics (whole
genome/transcriptome/methylome) approach. We hope to use these
sophisticated methods to better understand the biology of cSCC and to
identify candidate genes as discriminating biomarkers of metastasis in
cSCC; ie a potential prognostic “gene signature” that distinguishes
primary tumours with potential to metastasize from those with
clinicopatholigical “high risk” features but without metastatic potential.
Findings from these analyses can then also be employed in functional
genomic analyses and drug response profiling in cSCC patient-derived
cultures established in the Ranson lab (Perry et al 2020).
REFERENCES
Ashford, BG, Clark, J, Gupta, R, Iyer, NG, Yu, B, Ranson, M (2017)
Reviewing the genetic alterations in high-risk cutaneous squamous cell
carcinoma: A search for prognostic markers and therapeutic targets. Head
and Neck 39, 1462-1469. doi: 10.1002/hed.24765
Mueller SA, et al (2019) Mutational Patterns in Metastatic Cutaneous
Squamous Cell Carcinoma. Journal of Investigative Dermatology (2019)
139, 1449e1458; doi:10.1016/j.jid.2019.01.008.
Perry J, Ashford B, Thind AS, Gauthier ME, Minaei E, Major G, Iyer NG,
Gupta R, Clark J, Ranson M. (2020) Comprehensive Mutational and
Phenotypic Characterization of New Metastatic Cutaneous Squamous Cell
Carcinoma Cell Lines Reveal Novel Drug Susceptibilities. Int J Mol Sci.
21(24):9536. doi: 10.3390/ijms21249536.
Page
Job website:
Contact name: Marie Ranson
Contact email: mranson@uow.edu.au
PhD Project: Whole genome sequencing of circulating tumour DNA as a diagnostic method to help resolve challenging cancer diagnoses @ VIC
Position title: PhD Project: Whole genome sequencing of circulating tumour DNA as a diagnostic method to help resolve challenging cancer diagnoses
Employer: University of Melbourne
Closing date: 15th January 2022
Brief position description: Defined by the absence of a confirmed cancer type diagnosis, cancer of unknown primary (CUP) is a devastating disease with an exceptionally poor outcome. The Rare Disease Oncogenomics Laboratory at the University of Melbourne Centre for Cancer Research is seeking a PhD student to undertake an exciting project involving development and application of bioinformatic methods for whole genome sequencing analysis of circulating tumour DNA (ctDNA) from the blood of cancer patients. This project will involve expert supervision both within and outside our laboratory as well as leveraging significant resources of the SUPER-NEXT study that is currently deploying clinical whole genome sequencing to CUP patients recruited from 16 sites across Australia. The PhD project will have a strong computational focus involving methods for mutation signature detection and ctDNA fragment analysis. The project is highly translational with the goal to develop a ctDNA diagnostic method ready for deployment to CUP patients in the short to medium term. The candidate will require prior experience with unix-like operating systems, R and/or python programming languages
and working in a high-performance computing environment. A strong background in mathematics or statistics is also highly desirable. The candidate will also require a strong academic record and be competitive for internal or external PhD scholarships.
Job website:
Contact name: Richard Tothill
Contact email: rtothill@unimelb.edu.au
Bioinformatics Application Specialist - ABLeS Program, Australian BioCommons @ VIC
Position title: Bioinformatics Application Specialist - ABLeS Program, Australian BioCommons
Employer: The University of Melbourne
Closing date: 05 December 2021
Brief position description: The Australian BioCommons Leadership Share (ABLeS) at The University of Melbourne is an Australian BioCommons program aiming to grow and accelerate the ability to construct, maintain and gain insights from community developed life sciences data assets.
To achieve this outcome, ABLeS is providing communities with access to cloud and high-performance computing infrastructure (HPC), as well as the necessary expertise to use that infrastructure effectively.
The communities engaged will be diverse and represent life scientists researching native flora and fauna, threatened species, microbiomes, agriculture, and others. The infrastructures engaged will be similarly diverse, including Australia’s national supercomputing centres at NCI (Canberra) and Pawsey (Perth), as well as commercial cloud computing platforms.
Fundamental to the success of ABLeS are the software tools and methods various researchers and communities will use to generate and analyse data assets.
This new position will be directly involved in coordinating and supporting high profile research collaborations across Australia that will need to utilise various bioinformatics analyses and infrastructures to produce valuable data assets.
This role will report to the Associate Director of Cyberinfrastructure within the Australian BioCommons at the University of Melbourne. It will also work closely with Bioplatforms Australia, and other community leaders.
This is an excellent opportunity for the incumbent to broaden their experience and build new collaborations in this role of national breadth. The incumbent will have the opportunity to work across significant research communities and major national infrastructure facilities in the first-of-its-kind ABLeS initiative.
Job website: http://jobs.unimelb.edu.au/caw/en/job/907049/bioinformatics-application-specialist-ables-program-australian-biocommons
Contact name: Fiona Kerr
Contact email: fiona.kerr@unimelb.edu.au
Postdoctoral bioinformatic researcher in systems immunology of infectious diseases @ QLD
Position title: Postdoctoral bioinformatic researcher in systems immunology of infectious diseases
Employer: James Cook University
Closing date: 12 December 2021
Brief position description: The Australian Institute of Tropical Health and Medicine at James Cook University is seeking an inspired and talented researcher to join the team. This position is based at the JCU Nguma-bada campus in Cairns, the gateway to the Great Barrier Reef and Daintree Rainforest.
With a PhD or equivalent in the field of computational science (such as bioinformatics or computational biology) or biomedical science (such as immunology or cell biology), you will have expertise in bioinformatic analysis using R and other specialist software is required. A background in systems immunology, molecular immunology, single cell analyses, or infectious diseases is advantageous. Excellent computer, communication, and organisational skills are essential. Forward thinking, innovation and creativity are highly encouraged.Vacancy Reference 17691 https://www.aithm.jcu.edu.au/careers/job-opportunities/
Job website: http://www.jcu.edu.au/careers-at-jcu/vacancies
Contact name: Professor Denise Doolan
Contact email: denise.doolan@jcu.edu.au