Clinical Bioinformatician, NSW

Position title: Clinical Bioinformatician

Employer: NSW Health Pathology/Mackenzie’s Mission and CRE in Neurocognitive Disorders (CRE-NCD)

Closing date: 1st March, 2019

Brief position description: The NSW Health Pathology Randwick Genetics Laboratory is one of the major Australian centres for genetic diagnostics, providing a comprehensive genome diagnostic service in a consultative pathology context. The laboratory is recognised as a training site by both the HGSA and RCPA for advanced training in laboratory genetics for both scientific and medical personnel. NSW Health Pathology Randwick Genetics Laboratory has held continuous accreditation from NATA/RCPA since 1988, providing testing compliant with the ISO 15189 and ISO 9001 Standards and NPAAC Requirements. 
Mackenzie's Mission is a large-scale reproductive carrier screening pilot study which will screen 10,000 couples across Australia for ~500 rare and debilitating genetic disorders including spinal muscular atrophy (SMA), fragile X syndrome and cystic fibrosis (CF).
The CRE-NCD, based at Neuroscience Research Australia, is a five year-funded NHMRC centre that aims to transform the diagnosis and management of intellectual disability (also known as neurocognitive disorders) through whole exome sequencing (WES) and whole genome sequencing (WGS). 
This position will support the molecular genetics laboratory, Mackenzie's Mission and the CRE-NCD by assisting with clinical bioinformatics requirements for the analysis of next generation sequencing (NGS) data, implementation and maintenance of pipelines around design, performance, validation and quality control. The clinically targeted NGS panels, exomes or genomes and bioinformatics pipelines require embedded bioinformatic expertise. The ability to perform NGS data analysis using computer programming and Unix-based servers is required. The successful candidate will be working closely with wet lab scientists, clinicians and pathologists, genomic analysts, and other bioinformaticians/software developers.
We are seeking an experienced and motivated Bioinformatician interested in applying their skills in a clinical setting and able to work both independently and as part of a team. This is a full time position, fixed term three years.
For further information about this opportunity, please review the position description or contact us for a confidential discussion.

Job website: https://www.seek.com.au/job/38062803?searchrequesttoken=a3f93400-9a4f-45dc-a1f8-ed211d898bb5&type=standard

Contact name: Tony Roscioli

Contact email: Tony.Roscioli@health.nsw.gov.au

Contact name: Edwin Kirk

Contact email: Edwin.kirk@health.nsw.gov.au

Bioinformatician (Research Officer), Melbourne

Position title: Bioinformatician (Research Officer)

Employer: Murdoch Children's Research Institute

Closing date: 08/02/19

Brief position description: We are seeking a Full Time Research Officer/Postdoc (on a 2.5 Year contract) with strong experience in bioinformatics and a passion for understanding the genetics of rare disease. The role will be focused on the generation, analysis and interpretation of genomic and transcriptomic data from cohorts of individuals with rare genetic disorders. The successful applicant will join the join the Translational Bioinformatics group led by Dr Cas Simons, and work in collaboration with clinicians from the Victorian Clinical Genetics Service, the Royal Children’s Hospital, and national and international collaborators.

The position will be responsible for the analysis of whole genome, exome and transcriptomic data with the aim to establish the molecular basis of rare genetic disorders. 

To be successful in this role you will have:

- PhD in genomics, computational biology, bioinformatics, molecular biology, or a related discipline, with significant computational components
- Substantial experience in the analysis and interpretation of next-generation sequence data
- Evidence of advanced programming skills in Python and BASH
- Experience with version control (e.g. Git, Mercurial) and high-performance computing environments (e.g. PBS, SLURM)
- Evidence of well-developed written and verbal communication skills, for example in academic publications and conference presentations
- Proven ability to work effectively as part of a team to develop and complete research tasks, as well as the motivation and discipline to carry out autonomous research

Salary Range: $90,912 - $97,585 per annum plus super
Position Reference: 15380

Job website: http://career10.successfactors.com/career?company=C0007531036P&career_job_req_id=15380&career_ns=job_listing&navBarLevel=JOB_SEARCH

Contact name: Cas Simons

Contact email: cas.simons@mcri.edu.au

Bioinformatician (Research Officer), Melbourne

Position title: Bioinformatician (Research Officer)

Employer: Murdoch Children's Research Institute

Closing date: 08/02/19

Brief position description: We are seeking a Full Time Research Officer/Postdoc (on a 2.5 year contract) with strong experience in bioinformatics and a passion for understanding the genetics of rare disease. The role will be focused on the generation, analysis and interpretation of genomic and transcriptomic data from cohorts of children with neurodevelopmental disorders, including epilepsy, brain malformations and leukodystrophies. The position will be responsible for developing NGS analysis pipelines, as well as analysis of sequencing data and biological interpretation of results. The successful applicant will join the Translational Bioinformatics group led by Dr Cas Simons, and work as part of the new neurodevelopmental flagship at the MCRI in collaboration with paediatric neurologists A/Prof Richard Leventer and Dr Katherine Howell from the Royal Children’s Hospital and MCRI Neurosciences Research Group, and A/Prof Paul Lockhart from the MCRI Neurogenetic Research Group. In addition to research activities, the successful applicant will have opportunities to interface with clinicians, and patients and gain exposure to clinical tools such as magnetic resonance imaging, by being based within a research group composed of members from all sectors of the Melbourne Children’s Campus.

To be successful in this role you will have:
- PhD in genomics, computational biology, bioinformatics, molecular biology, or a related discipline
- Substantial experience in the analysis and interpretation of next-generation sequence data and an interest in neurodevelopmental disorders
- Demonstrated understanding of Mendelian disorders and a deep understanding of the underlying genetic and biological concepts
- Evidence of advanced programming skills in Python and BASH
- Evidence of well-developed written and verbal communication skills, for example in academic publications and conference presentations
- Proven ability to work effectively as part of a team to develop and complete research tasks, as well as the motivation and discipline to carry out autonomous research

Salary Range: $90,912 - $97,585 per annum plus super
Closing Date: 5pm Friday 8 February 2019
Position Reference: 15892

Job website: http://career10.successfactors.com/career?career%5fns=job%5flisting&company=C0007531036P&navBarLevel=JOB%5fSEARCH&rcm%5fsite%5flocale=en%5fGB&career_job_req_id=15892&selected_lang=en_GB&jobAlertController_jobAlertId=&jobAlertController_jobAlertName=&_s.crb=NaoaVbSHCpDmpuu7pKm%2fZ3gmaM0%3d

Contact name: Cas Simons

Contact email: cas.simons@mcri.edu.au

Research Associate - Bioinformatics Officer, Perth

Employer: University of Western Australia

Closing date: 31st January 2019

Brief position description: The Cancer Research Trust (http://cancerresearchtrust.org.au) has recently funded a 9 year program to enable single cell approaches to study tumour biology. The program led by Professor Alistair Forrest at the Harry Perkins Institute of Medical research is based in Perth Western Australia and is a collaboration involving all of the major hospitals, medical research institutes and Universities in the region.

Seeking to employ a postdoctoral researcher with a PhD at the time of appointment (or equivalent experience) in bioinformatics, computer science, biostatistics, molecular biology or a related discipline with an emphasis in the specific fields of bioinformatics, genomics and systems biology. The candidate will be working directly with Prof Forrest and his team on analysis of single cell datasets.

Essential selection criteria:
• Demonstrated capacity to analyse NGS data, form hypotheses, test them and follow through to publications.
• Experience in documenting, testing and reusing code.
• Proficiency with R or other languages.
• Experience in cancer biology and analysis of single cell data is a bonus.

Job website: http://external.jobs.uwa.edu.au/cw/en/job/502428/research-associate-bioinformatics-officer

Contact name: Alistair Forrest

Contact email: alistair.forrest@perkins.uwa.edu.au

Research Assistant - Bioinformatics & Cellular Genomics, Melbourne

Employer: St Vincent's Institute (SVI)

Closing date: 3 Feb 2019

Brief position description: 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 (University of Melbourne School of Mathematics and Statistics) and under the direction of NHMRC Fellow and Oxford graduate Dr Davis McCarthy, the Bioinformatics & Cellular Genomics Laboratory will be capable of using large-scale studies of DNA and single-cell genetics to drive future medical discoveries. 

The Position 

We are seeking a talented Research Assistant to support the single-cell genetics research of the laboratory. Playing a key role alongside the senior scientists, you will carry out a range of supervised work activities across a variety of projects using computational methods, approaches, and software to enable single-cell genetics research. 

The successful incumbent will have an Honours Degree in a computational discipline relevant to bioinformatics and cellular genomics (bioinformatics, statistics, machine learning, computer science, applied mathematics, physics or similar) and have proficiency in one or more of R, Python, C++, Go, Nim, Rust, Java, Perl and/or SQL computer programming and scripting languages. You will have a demonstrated ability in the use of Unix-based systems, computing clusters and related queueing systems and experience in data analysis and management. 

Ideally you will have prior experience working in a high-performance computing environment where you have developed expertise in statistics and/or machine learning. Prior exposure to research in genomics (ideally single-cell genomics), genetics, computational biology or bioinformatics will enhance your success in the role. Exposure to the statistical analysis of large-scale human and/or mouse genomic datasets will be highly regarded. 

Salary: $70,000 - $80,000 per annum, commensurate with qualifications and experience, plus: 

- 9.5% superannuation 

- generous $15,900 FBT exempt salary packaging Position Description - see job website link below

Applications: via Seek please. Please include current CV, covering letter addressing key selection criteria based on the Position Description

Position Enquiries: Dr Davis McCarthy dmccarthy@svi.edu.au

Job website: https://www.svi.edu.au/careers_students/careers/current_vacancies/

Contact name: Helen Ritchie

Contact email: hritchie@svi.edu.au

Post Doctoral Research Officer - Bioinformatics & Cellular Genomics (Melbourne)

Employer: St Vincent's Institute (SVI)

Closing date: 3 Feb 2019

Brief position description: 

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. 

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, $83,000 - $90,000 pa plus:

• 9.5% superannuation
• generous $15,900 FBT exempt salary packaging

Position Description - see job website listing below

Applications - via Seek please. Include current CV, covering letter addressing selection criteria, based on Position Description

Enquiries - Dr Davis McCarthy dmccarthy@svi.edu.au

Job website: https://www.svi.edu.au/careers_students/careers/current_vacancies/

Contact name: Helen Ritchie

Contact email: hritchie@svi.edu.au

PhD Position (with Stipend), NSW

Opportunity: PhD Position (with Stipend)

Research Topic: The Epigenomics of Multiple Sclerosis

Closing date: 22/02/2019

Brief Outline:This project will involve analysis of genome-wide methylation data sets in relation to Multiple Sclerosis (MS) outcomes. Given the large amount of data involved and the complex computational and statistical models to be applied, this project will be heavily focused on data analysis including the use of novel approaches.

Detailed Description:MS is a common autoimmune disorder that can lead to severe neurological symptoms like such as reduced cognitive function, psychiatric problems and physical disabilities. The disease is complex, arising from the complex interplay of genetic factors and environmental exposures. A major goal in MS research is to understand these gene-environment interactions and to use this information to personalise treatments to improve patient outcomes. Epigenetics is the study of DNA-based factors that can influence gene expression independently of underlying DNA sequence and can be modified by environmental exposures (eg, medicines). As such, epigenetics provides a natural interface for the environment to interact with the genome to influence disease onset, severity and progression. DNA methylation is an one epigenetic mechanism that can now be measured on a genome-wide scale (ie. epigenomics) and has given rise to the epigenome-wide association study (EWAS) design. The MS group at the Hunter Medical Research Institute have been performing MS EWASs for a number of years and have identified a number of exciting findings. Thanks to some newly awarded funding we are now continuing this line of investigation in an effort to identify epigenetic factors that influence MS onset, severity and progression This project will involve analysis of MS EWAS data sets currently being generated using the Illumina Epic Arrays. Given the large amount of data involved and the complex computational and statistical models to be applied, this project will be heavily focused on data analysis. Specifically, the project will involve using a number of different bioinformatics approaches to address the specific research questions. These include identifying differentially methylated regions with programs like MINFI, cellular deconvolution of methylation signal using custom algorithms, estimation of epigenetic aging using DNAage, and application of machine learning to build predictive models (eg. GLMNet).

Eligibility Criteria: The applicant will have an aptitude and interest in fields including data science, bioinformatics, computational genomics and statistical genetics. A basic knowledge and skills in using linux operating systems, biostatistical methods and R programming to analyse data sets is required. Good written and oral communication skills and the ability to work independently are desirable. The successful applicant will need to be accepted as a PhD student with either UoN or QUT and will receive a scholarship stipend of $27 082 per annum, tax free, indexed annually for 3.5 years. International students may be required to pay university (tuition) fees.

Contact:  For more information on the project and application process please contact Assoc. Professor Rodney Lea (rodney.a.lea@gmail.com) before Jan 29th, 2019.

Post-doc in Bioinformatics/Computational Biology, Adelaide

Position title: RESEARCH OFFICER/POSTDOCTORAL FELLOW IN BIOINFORMATICS/COMPUTATIONAL BIOLOGY

Employer: South Australian Health & Medical Research Institute

Closing date: Feb 8 2019

Brief position description: The Lynn EMBL Australia Group at the South Australian Health and Medical Research Institute (SAHMRI) in Adelaide, Australia is now seeking applications for a bioinformatics/computational biology researcher to work on a variety of projects in the cancer systems biology and systems immunology areas. Prior experience in at least some of the following areas is essential: analysis of next generation sequencing (NGS) data; network and pathway biology; cancer systems biology; machine learning methods and experience in biomarker discovery and validation. Active collaboration and the ability to manage multiple difference projects simultaneously is essential. An initial 2 year full-time contract is available, potentially renewable. 

Please see https://www.sahmriresearch.org/human-resources/careers/218 for a position description and to apply.

Job website: http://www.sahmriresearch.org/human-resources/careers/218

Contact name: David Lynn

Contact email: david.lynn@sahmri.com

(Sent via Australian Bioinformatics And Computational Biology Society)

Bioinformatician - Pathogen Genomics, NSW

Position title: Bioinformatician - Pathogen Genomics

Employer: NSW Health Pathology

Closing date: 16/12/2018

Brief position description: This position is based at the Public Health Pathogen Genomics Laboratory, Centre for Infectious Disease and Microbiology Laboratory Services, NSWHP-ICPMR at Westmead and plays a key role in the delivery of NSW state-wide pathogen genomics services. The Pathogen genomics bioinformatician is responsible for: 
Lead and manage genome sequencing projects as directed by relevant supervising pathologists and laboratory management from initiation to implementation including the review and evaluation of systems and processes to ensure effectiveness of service delivery. Support reliable and secure collection, storage and archival of genomic data and relevant metadata in accordance with national and international regulations and guidelines. Develop, implement and maintain genomic data QC and analysis pipelines. Organise, coordinate and deliver training in microbial bioinformatics for relevant laboratory staff and other peers.

Refer to the URL for more details.

Job website: http://iworkfor.nsw.gov.au/job/bioinformatician-pathogen-genomics-136518

Contact name: Prof. Vitali Sintchenko

Contact email: Vitali.Sintchenko@health.nsw.gov.au

Two Bioinformatics/Genome analyst positions in South Australia

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

Closing date: 9am Thursday November 29

Brief position description: The Centre for Cancer Biology in Adelaide is advertising two bioinformatics/genome analyst positions within the Molecular Pathology/Lymphatic Development/Bioinformatics groups. The positions will involve analysis and interpretation of RNASeq, ChIPSeq, ATACSeq, HiC, WES and WGS data. Further information is available from Hamish Scott (hamish.scott@sa.gov.au), Natasha Harvey (natasha.harvey@unisa.edu.au)
or Andreas Schreiber (andreas.schreiber@sa.gov.au).

Job website: https://workingatunisa.nga.net.au/cp/index.cfm?event=jobs.checkJobDetailsNewApplication&returnToEvent=jobs.listJobs&jobid=0B2C3592-40A4-BA78-C358-A4A55C37DA9A&CurATC=External&CurBID=62AFB35D-9273-4A11-8DCC-9DB401354197&JobListID=22fc4f47-e994-46a3-b8c9-9bc901269f43&jobsListKey=382f5055-dc54-4de6-ab3d-0677eb4185c5&persistVariables=CurATC,CurBID,JobListID,jobsListKey,JobID&lid=57152020078

Contact name: Andreas Schreiber

Contact email: andreas.schreiber@sa.gov.au