Position title: Clinical Genomics Scientist Australia
Employer: Invitae
Closing date: 31-03-2022
Brief position description: Location: Australia
Language requirements: English. Additional languages are a plus!
Start date: ASAP
Invitae is on a mission to drive genetic information into mainstream medicine to improve healthcare for billions of people.
To bolster our shared mission and help Invitae expand, we are looking for a Clinical Genomic Scientist. In this position, you will be curating, analyzing, interpreting, and reporting clinical genetic data derived from a variety of core technologies such as NGS panels, MPS exome sequencing, and chromosomal microarray among others.
A day in the life
Your typical day might include the following:
- Focusing up to 75% of your time on variant interpretation (aka variant curation), applying validated in-house genetic evidence systems, using these interpretations to build clear and concise clinical reports;
- Collaborating with our genetic pathologists, medical geneticists, genetic counselors, genomics scientists, bioinformaticians, quality managers, etc;
- Performing analyses of clinical and genetic information, including published literature, public and private databases, functional studies and modeling, as well as patient clinical records;
- Crafting, curating, and detailing genetic content for a broad range of genetic disorders to support our operations and clinical offerings.
This job might be for you if:
- You hold a FFSc, FHGSA/MHGSA, MD/MBBS, PhD or MSc in genetics, genetic counseling, or a related field. We encourage candidates with undergraduate degrees and relevant work experience to apply!
- You have developed skills in interpreting, synthesizing, and evaluating complex genetic information; Knowledge in variant interpretation (variant curation) is a plus;
- You possess excellent written and verbal communication skills;
- You are familiar with next-generation/massively-parallel sequencing or acquainted with sophisticated methods of copy number detection and have experience at a NATA-accredited diagnostic laboratory. This is valued, but not essential.
Job website: https://www.invitae.com/en
Contact name: Rosa Markus
Contact email: rosa.markus@invitae.com
Associate Director, Translational Bioinformatics @ VIC
Position title: Associate Director, Translational Bioinformatics
Employer: CSL Limited
Closing date: 13 February 2022
Brief position description: The Opportunity:
We have an exciting opportunity available for an Associate Director, Translational Bioinformatics to join our Research team, based at Bio 21 Institute, in the heart of Melbourne's Biomed Precinct.
In this newly created position, you will deliver a translational bioinformatics strategy for selected therapeutic areas and set priorities to support the execution and evolution of CSL R&D strategy. You will lead and collaborate with a lean global team of bioinformaticians with expertise in various -omics and high throughput screening technologies to develop and apply advanced bioinformatics methods and analyses to support translational activities across CSL R&D portfolio.
You will work with Therapeutic Area Leads, Translational Science and Clinical Development functions to deliver product strategies, data science plans and project goals focused on, but not limited to, MoA studies, predictive biomarker development, patient stratification and target discovery and validation. You will ensure robust experimental design of -omics and high throughput assays based on sound research and/or clinical questions.
You will report to the Head of Bioinformatics & AI and work with Data Science peer functions across R&D and I&T organizations, to provide bioinformatics and AI platforms and partnerships to advance translational research and allow the utility of -omics and high throughput technologies in R&D studies. Furthermore, you will support reviewing new product opportunities and partnerships from external collaborators to bring new projects into the pipeline and support the progression of existing research and clinical programs across multiple therapeutic areas.
You will collaborate with peer functions to establish and manage an integrative outsourcing strategy working with external collaborators from academia and industry and work with CSL’s academic partners to develop new bioinformatics & AI talent through undergraduate internships and postgraduate research co-supervision/placements.
You will require:
• PhD in computational biology, bioinformatics, statistical genomics, computer science, or a related discipline with computational and biomedical components
• 4+ years post-doctoral experience in bioinformatic data analytics in a collaborative, interdisciplinary environment in academia and/or industry with a focus on translational research.
• 4+ years’ experience as a group lead in the biotechnology or pharmaceutical industry (or where relevant a biomedical research organisation)
• Experience applying advanced statistical, bioinformatic and AI methods to analyse multi-omic datasets (including phenotypic, non-genomic assay, bulk tissue, and single cell data) and working with life scientists to draw statistically sound biological insights from experimental data.
• Experience building and using bioinformatic methods and databases to answer key research questions related to experimental design, biomarker discovery, patient stratification and target discovery and validation (e.g., gene expression databases, clinical variants,).
• Experience working in a Unix-like and high-performance computing (HPC) environment on-premises and/or in the cloud using Python, R and other scientific computing languages.
• Track record of publications and presentations at national and international conferences and industry events.
Apply now to join an ASX Top 5 organisation that directly helps patients and public health in Australia and overseas!
Applications close 13 February 2022
Please include a covering letter addressing the selection criteria.
CSL is an Equal Opportunity Employer
Job website: https://csl.wd1.myworkdayjobs.com/CSL_External/job/APAC-AU-Victoria-Parkville-CSL-Limited-Australia/Associate-Director--Translational-Bioinformatics_R-157835-1
Contact name: Sophie Saba
Contact email: Sophie.Saba@csl.com.au
Bioinformatics Research Officer @ QLD
Position title: Bioinformatics Research Officer
Employer: QIMR Berghofer Medical Research Institute
Closing date: 25th January 2022
Brief position description: Applications are invited for an experienced bioinformatician to join the Medical Genomics Group headed by Dr Nic Waddell. The exciting position involves working on large cancer datasets including whole genome sequencing, transcriptomics, immunohistochemistry and long read sequencing from a variety of tumour types. The position involves developing and using analytical workflows to analyse cancer genomes. Working independently and with collaborators, a number of scientific questions will be explored including: unravelling tumour heterogeneity, finding new treatment opportunities, and studying the tumour microenvironment.
You are expected to have a strong track record in bioinformatics. This position will work alongside other bioinformaticians in the Medical Genomics Group, and will work closely with a PhD student who is focused on using long read sequencing to explore genomic heterogeneity.
Job website: http://qimrberghofer.turborecruit.com.au/job/job_details.cfm?id=498584&from=
Contact name: Nic Waddell
Contact email: nic.waddell@qimrberghofer.edu.au
ioinformatician - Statewide Genomics @ NSW
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.
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Job website:
Contact name: Marie Ranson
Contact email: mranson@uow.edu.au