TRAIL Research Bioinformatician - Genomics @ NSW

POSITION TITLE: TRAIL Research Bioinformatician - Genomics

EMPLOYER: The Sydney Children's Hospitals Network

CLOSING DATE: 11/08/2023 - 11:59 PM

BRIEF POSITION DESCRIPTION:

Employment Type: Temporary Full Time up to 31/08/2027
Position Classification: Health Mgr Lvl 2
Remuneration: 102640 - 121739 full time equivalent base salary range (excludes super, leave loading and salary packaging)
Hours Per Week: 38
Requisition ID: REQ420864

Sydney Children's Hospitals Network (SCHN) is seeking a Bioinformatician or Computational Biologist to join the Clinical Team fulltime at Sydney Children's Hospitals Network. The ideal candidate has practical experience in bioinformatics as well as statistics and advanced programming abilities. 

This role will join a high-performing team, embedded across NSW Health Pathology (NSWHP) and SCHN. This role will also enable close collaboration with the CSIRO, and Australian Genomics initiatives in Queensland, Victoria, NSW and South Australia.

** Background ** 
In 2022 the Australian Government committed to increase equity of access and consistency and expand the number of conditions screened through existing newborn bloodspot screening (NBS) programs. In Australia, these programs are managed and delivered along jurisdictional lines by State Health Departments under a federated health model.

Equally in 2022, the Genomics Health Futures Mission (GHFM) and the National Health and Medical Research Council (NHMRC) awarded more than AUD$15 million to support 5 research programs, which are exploring the application of first-tier and second-tier genomic NBS as well as health economic, ethics and equity considerations. 

The Newborn GEN SEQ TRAIL (aka the TRAIL study) is one of these 5 studies, looking to implement genomic NBS in NSW, led by Clinical Professor Bruce Bennetts.

** The Role ** 
The successful candidate will play a significant role in delivering new and existing projects in collaboration with NSWHP ICT and local clinical laboratory services. Reporting to the Senior Bioinformatician, this position is responsible for the efficient and effective delivery of defined project outcomes within agreed timeframes, budgets, quality, and resources.

Specific contributions will include the MRFF funded NEWBORN GEN SEQ TRAIL study. This role will support the development of a bioinformatics pipeline associated with the potential of offering genomic Newborn Bloodspot Screening (NBS) to parents of newborn babies across NSW. 

Please visit https://iworkfor.nsw.gov.au/job/trail-research-bioinformatician-genomics-419204 for more details and see https://ocxz.cit.health.nsw.gov.au/excluded-apps/XXRecRequisitionPD-context-root/faces/XXRecRequisitionPDPG?xxJobId=REQ420864 for the position description.

JOB WEBSITE: http://iworkfor.nsw.gov.au/job/trail-research-bioinformatician-genomics-419204

CONTACT NAME: Eva Chan

CONTACT EMAIL: eva.chan@health.nsw.gov.au

Research Fellow in Multiomics, AI and Machine Learning @ VIC

POSITION TITLE: Research Fellow in Multiomics, AI and Machine Learning

EMPLOYER: WEHI

CLOSING DATE: 23 August 2023

BRIEF POSITION DESCRIPTION:

An opportunity exists for a talented and motivated computational scientist to join an exciting new program developing and applying artificial intelligence and machine learning methods to analyze biomedical molecular data at Australia's pre-eminent biomedical research institute.

About the Position
Recognizing the emerging importance of artificial intelligence and machine learning in biomedical research, WEHI is investing strongly in a new research program and is creating multiple new AI Research Fellow positions.

This position will be based in the Papenfuss Laboratory within the Computational Biology Theme. It will involve developing and applying machine learning techniques to integrate large-scale multi-omics data to identify disease subtypes and predictive biomarkers in a variety of health-related settings, including infectious disease and cancer. Projects will involve large-scale single cell or spatial omics, imaging, genome and/or other omics data. There will be opportunity for methods development.

The successful candidate will join an interactive team of computational scientists in a supportive and flexible working environment. They will work alongside other AI and machine learning experts as part of a broader AI research community developing at WEHI. The research is well-supported by state-of-the-art computing facilities and engineering expertise.

The successful candidate will have a PhD in a quantitative discipline such as Computer Science, Bioinformatics, Computational Biology, Mathematics, Statistics or Physics, together with expertise in machine learning techniques applied to multi-omics data.

Selection Criteria
Personal Qualities:
A PhD in Bioinformatics, Computational Biology, Computer Science, Mathematics, Statistics or Physics demonstrated through publications or a thesis
A collegiate approach and interest in collaboration
Good time management skills
Excellent skills engaging with and managing collaborators and stakeholders
Essential Knowledge and Skills:
Expertise in machine learning, artificial intelligence and multiomics
Experience with genomic, transcriptomic or other high-throughput data
Experience applying machine learning techniques to biological data
High-level data management skills
Highly developed written and verbal communication skills
Terms of Appointment
This full-time position is for a period of 3 years in the first instance, with possible extension dependent on performance. Salary Scale will be from Research Officer (RO) A6 to Senior Research Officer (SRO) B1 between $97,152 - $109,778. Salary will be dependent on the candidate’s experience.

Up to 17% superannuation and very attractive salary packaging options are available. Salary will be dependent on the candidate’s experience.

JOB WEBSITE: https://wehi.wd3.myworkdayjobs.com/WEHI/job/Parkville-Victoria-Australia/Research-Officer-Senior-Research-Officer-in-Multi-omics-Integration---Biomarker-Discovery_JR2084-1

CONTACT NAME: Tony Papenfuss

CONTACT EMAIL: papenfuss@wehi.edu.au

Research Officer/Research Assistant @ QLD

POSITION TITLE: Research Officer/Research Assistant

EMPLOYER: QIMR Berghofer Medical Research Institute

CLOSING DATE: 21 August 2023

BRIEF POSITION DESCRIPTION:

Applications are invited for an enthusiastic and highly-motivated bioinformatician to join the Cancer Genetic Susceptibility Laboratory. This position is to work on the study of gynaecological cancer genetics, using functional genomic datasets.

We are seeking someone with strong statistical and computational skills who is interested in working with GWAS and large scale functional genomic datasets to perform integrative analyses and identify target genes. We are looking for someone with experience in analysis of functional genomics assays, such as CRISPR screens, RNA-seq, ATAC-seq and global chromatin conformation capture data (e.g. HiChIP). The successful applicant would be provided opportunity for dissemination of research findings (e.g. meetings and conferences) and for publication of research articles.

JOB WEBSITE: http://www.seek.com.au/job/68857920?type=standout#sol=28b665e8495a65ad3bdb216e849190d1fe4d342f

CONTACT NAME: Tracy O'Mara

CONTACT EMAIL: tracy.omara@qimrberghofer.edu.au

CSIRO Postdoctoral Fellowship in Anti-viral Immuno-engineering Bioinformatics

Position title: CSIRO Postdoctoral Fellowship in Anti-viral Immuno-engineering Bioinformatics

Employer: CSIRO

Closing date: 11 August

Brief position description: CERC Fellows are appointed for three years or full time equivalent. 
The CERC Fellow will play a critical role in an overarching project which involves a multi-disciplinary, multi-CERC Fellow team to develop and validate a novel solution to address viral outbreaks in livestock and aquaculture species, leveraging new developments in the field of gene editing. The overarching project brings together a multi-disciplinary team to address this challenge which cost the agricultural industry millions of dollars every year. Harnessing the collective expertise across the fields of immunology, genome engineering and bioinformatics, the multi-CERC Fellow team will draw on the SynBio principle of “Design-Build-Test-Learn” to adapt and optimize a key antiviral mechanism from bacteria. The adapted antiviral platform can then be transplanted into agricultural species to enhance resilience to viral pathogens.
The CERC Fellow will develop models of viral evolution and use this to inform the design of CRISPR/Cas13 based antivirals for applications in livestock and aquaculture industries. Specifically, they will use machine learning to approaches to understand how viruses evolve in response to selection pressure to better understanding escape pathways and use this to design CRISPR/Cas13 anti-viral that are robust to escape mutations. The Fellow will work closely with multidisciplinary experts in aquaculture, livestock, virology and genome engineering to achieve project outcomes. The project also aligns to the Immune Resilience Future Science Platform (FSP) which aims to harness the fundamental understanding of the immune system to develop novel strategies and platforms that will build resilience in animals to combat disease and parasite challenges.
This role is part of a “Team Sport” CERC Fellowship where three CERC Fellows work with multiple teams collaborating on an overarching, multi-disciplinary research project. Each CERC Fellow will lead an individual sub-project, contributing their expertise, and work closely with the other team members with the aim of delivering significant scientific and translational impact on a broad research topic.

Job website: http://jobs.csiro.au/job-invite/93532/

Contact name: Laurence Wilson

Contact email: laurence.wilson@csiro.au

Research Officer, Bioinformation @ VIC

Position title: Research Officer, Bioinformation

Employer: University of Melbourne

Closing date: 04 Aug 2023

Brief position description: This is an exciting opportunity for a highly motivated Research Officer to join the research group of Professor Lachlan Coin at The Peter Doherty Institute for Immunity and Infection. As part of the NHMRC-funded project NITRIC, you will have the unique opportunity to contribute to the largest pediatric cardiac surgical intervention trial worldwide. By implementing cutting-edge genomic analyses and machine learning approaches, you will play a crucial role in identifying gene expression patterns associated with patient outcomes in congenital heart disease. Join our collaborative team and make a significant impact in the field of computational biology and bioinformatics, while developing your own independent program of research and contributing to leading specialist journals.

Job website: http://jobs.unimelb.edu.au/en/job/913455/research-officer-bioinformation

Contact name: Lachlan Coin

Contact email: lachlan.coin@unimelb.edu.au

Domain Bioinformatician (Research Officer) @ VIC

Position title: Domain Bioinformatician (Research Officer)

Employer: Baker Heart and Diabetes Institute

Closing date: 15/07/2023

Brief position description: This is a position for a Research Officer eager to provide their biostatistics expertise for experimental and study design, data analyses and interpretation at the Institute, and perform high quality research in bioinformatics, genomics or computational biology. Half of the effort will be supporting other labs in Baker, and the other half will be independent research. Since many collaborations involve biobank data analysis, a basic understanding of epidemiology is desirable. We are particularly interested in candidates with experience and a strong interest in single-cell analysis.

Job website: http://www.seek.com.au/job/68128798

Contact name: Fumihiko Takeuchi

Contact email: Fumihiko.Takeuchi@baker.edu.au

Bioinformatics Research Officer / Senior Research Officer @ VIC

Position title: Bioinformatics Research Officer / Senior Research Officer

Employer: WEHI

Closing date: 07/07/2023

Brief position description: An excellent opportunity is available for a Bioinformatics Research Officer / Senior Research Officer to work on spatial omics as part of the Advanced Technology and Biology Division and Bioinformatics Division (Phipson Lab) at Australia’s pre-eminent biomedical research institute. 

WEHI is building on its reputation for excellence in advanced technologies with the development of a nationally leading centre for spatial omics and the acquisition of multiple new technologies in a highly collaborative and open framework. 
In conjunction with the Bioinformatics Division and many scientific collaborators, the Advanced Genomics Facility at WEHI comes to grips with data from many cutting-edge technologies, and ground-breaking projects, every day. 
In this role, you will share in the analysis of data from experiments in single-cell and spatial omics, applying rigorous principles and using the latest computational and statistical approaches. 
You will combine contributions to many diverse projects, taking on experimental design, trouble-shooting and data evaluation in a close partnership with our laboratory team, with a more prominent role in developing methodologies or the detailed analysis of selected key projects. 
The role is pivotal in building closer links between technology and analytical streams at WEHI and designed to suit someone keen to work in one of the most dynamic areas of bioscience, looking either to build on a recent PhD by gaining a lot of experience quickly (RO) or who has substantial existing experience in computational data analysis but may wish to enter a new and dynamic field (SRO). 
This post could lead to either fully research-driven or staff-scientist career pathways. 

Responsibilities include, but are not limited to: 

- Data analysis on a variety of fast-developing spatial omics technologies available at WEHI including 10x Visium, 10x Xenium, BGI STOmics, and Vizgen MERSCOPE. 
- Leveraging and integrating the analysis of spatial omics data from different platforms and with other omics data types (e.g., single-cell RNA-sequencing). 
- Collaborative analyses with wet-lab and clinical researchers. 
- Communicating analysis results and methodologies to technical and non-technical researchers. 
- Developing statistical and computational methods to enable these analyses. 
- Benchmarking of technologies and analysis methods to develop technology recommendations and best-practice data analysis workflows. 

Selection Criteria 
- PhD or equivalent in statistics/bioinformatics (or other relevant disciplines) with a strong interest in biological research. Research experience is advantageous. 
- Demonstratable knowledge and experience in a data analysis programming language (e.g., R, Python). 
- Ability to work independently and in a multi-disciplinary team. 
- Effective time management skills and ability to work on several projects in parallel. 
- Strong communication skills, written and oral, and an ability to communicate technical concepts to non-technical researchers. 
- A basic understanding of molecular biology and sequencing is highly desirable. 

This position is available for an initial period of 2 years in a full-time or near-full-time capacity. Salary is RO/SRO ($105,555-$125,339).

Job website: http://wehi.wd3.myworkdayjobs.com/en-US/WEHI/details/Bioinformatics-Research-Officer---Senior-Research-Officer_JR1916-3

Contact name: Peter Hickey

Contact email: hickey@wehi.edu.au

Bioinformatician @ QLD

Position title: Bioinformatician

Employer: QIMR Berghofer Medical Research Institute

Closing date: 12 June 2023

Brief position description: The Molecular Oncology team uses bioinformatic and machine learning approaches to analyse cancer molecular profiling data, including genomic, transcriptomic and DNA methylation data, to link it with treatment responses and patient outcomes. The research spans multiple solid cancer types, including ovarian, endometrial and lung cancers.

Role Purpose / Responsibilities
Applications are invited for a bioinformatician to join the Molecular Oncology team led by Olga Kondrashova. The exciting position involves analysis of a variety of next-generation sequencing data using existing and newly developed pipelines in lung, endometrial and ovarian cancers. The research is centred around linking tumour molecular profiles with patient treatment responses, improving understanding of drug resistance and identification of novel treatment strategies through analysis of pre-clinical models. The role involves utilising and developing bioinformatic approaches to analyse data, such as whole-exome and whole-genome sequencing, RNA-sequencing and CRISPR screen sequencing. This position will involve working independently and alongside other bioinformaticians in the Molecular Oncology and collaborators. 

The following duties will apply:
•Bioinformatic analysis of next-generation sequencing data
•Research and implementation of appropriate analysis methodology
•Development of custom analysis pipelines
•Presentation of results in internal and external meetings
•Contribution to scientific publications
•Ensure work practices comply with the requirements of the Work Health and Safety Act, related legislative requirements and the Institute's WH&S policies and procedures. 

About you
The role calls for an experienced and enthusiastic bioinformatician with the following skills:
•Masters or PhD in computational biology/bioinformatics with demonstrated experience
•Experience in genomics and next-generation sequencing data analysis
•Strong experience using the Linux/Unix Operating System
•Proficiency in R and/or Python
•Willingness and ability to learn new technical skills
•Ability to work independently
•Interest in cancer research and a desire to further a career in science
•Experience in machine learning is beneficial

Remuneration: Salary range is $82,369 to $95,329 p.a. depending on experience, plus super and salary packaging. This is a two-year, full-time appointment with possible extension.

Job website: https://www.seek.com.au/job/67631404

Contact name: Olga Kondrashova

Contact email: olga.kondrashova@qimrberghofer.edu.au

Statistical geneticist / Bioinformatician

Position title: Statistical geneticist / Bioinformatician

Employer: Seonix Bio

Closing date: 30/6/2023

Brief position description: Seonix Bio is a fast growing clinical genetics company developing polygenic risk score products and services, initially for eye health. Our first offering is a polygenic risk score for glaucoma that helps clinicians save sight by enabling earlier diagnosis and treatment of those at risk. This will be launched as a clinical service in 2023. Our technology is based on world leading research, published in Nature Genetics, and the company is at the cutting edge of polygenic risk score development. 

We are seeking a talented statistical geneticist / bioinformatician to:
• Develop and implement polygenic risk scores and other algorithms for a variety of clinical applications, including methodological development
• Develop statistical models and methods that incorporate both genetic and non-genetic data to improve risk prediction
• Analyse and interpret complex clinical study data, including interfacing with our research partners

The role will be tailored according to experience of the candidate.

The successful candidate will report to the CEO and will work with our Scientific Advisory and software teams. Our leadership team has a track record of building genetics businesses that change clinical care globally, and our Scientific Advisory team is composed of leading academics and clinicians in the area. 

We are involved in a number of research projects with collaborators, and there will be opportunities to participate in publications.

The role is full-time, though part-time could be possible for the right candidate. A minimum of 3 days per week is required. 

We will offer a competitive package, depending on experience. Remote work is possible for the right candidate.

The successful candidate will play a key role in a small team of committed, talented and friendly people. This is a rare opportunity to join an exciting startup company and make a real impact. 

REQUIREMENTS
• Ph.D. in a relevant discipline (including a Ph.D. student shortly to submit)
• Strong statistical genetics / bioinformatics skillset
• Strong programming skills, typically with experience of R at a minimum
• Experience in/knowledge of polygenic risk scores, ideally including development and use of associated scores and pipelines, and statistical analysis of data
• Strong written and verbal communication skills
• Ability to work independently and in a multi-disciplinary team
• Ideally, experience of Nextflow workflow and/or SLURM scheduling
• Ideally, experience with containers and working in the cloud
• Ideally, experience of machine learning/AI algorithms

Job website: https://www.seonixbio.com/careers/

Contact name: Nick Haan

Contact email: careers@seonixbio.com

Research Officer/Post-doctoral Scientist – Bioinformatics Stem Cell Biology @ NSW

Position title: Research Officer/Post-doctoral Scientist – Bioinformatics Stem Cell Biology

Employer: Children's Medical Research Institute, University of Sydney

Closing date: 09 June 2023

Brief position description: About the job
Children’s Medical Research Institute (CMRI) was Australia’s first dedicated paediatric research facility and is now one of the nation’s most highly regarded independent medical research centres. Our research focuses on embryonic development, cancer, neuroscience and gene therapy and we have a strong international reputation based on our research outcomes. CMRI’s research programs are supported by state of the art facilities and committed research and support staff. Our achievements are made possible by a loyal network of community supporters, highly engaged donors and the very successful Jeans for Genes® fundraising campaign.

A two-year Research Officer/Post-doctoral position funded by a Medical Research Future Fund (MRFF) Stem Cell Therapies Mission grant is now available at the Computational Systems Biology lab at CMRI. We are looking for a highly motivated researcher to employ computational and data analytics approaches to investigate cell identity and cell fate decisions using bulk and single-cell multi-omics and spatial transcriptomics data generated from stem cells and organoids systems. The successful applicant will have a PhD (or be in the final stages of completion) with a strong background in data analytics and computational systems biology, and a working knowledge in molecular cell and stem cell biology.

Position Summary
The Computational Systems Biology (CSB) lab at CMRI is welcoming applications for a Research Officer/Post-doctoral Scientist to conduct research in the broad area of computational systems biology of stem cells and organoid systems. Our research focuses on the acquisition of particular cell identity and cell fate decisions during cell differentiation, and to translate such knowledge for stem cell engineering and regenerative medicine. In collaboration with the Stem Cell Medicine lab at CMRI, the CSB lab has established experimental techniques including single-cell multi-omics and spatial transcriptomics, and mass spectrometry-based proteomics and phosphoproteomics to profile human and mouse embryonic/adult stem cells and various stem cell-derived organoids (e.g., eye organoids, brain organoids, and heart organoids). This appointment is at CMRI and will be affiliated with the Faculty of Medicine and Health at The University of Sydney. The appointee is expected to lead their own projects, contribute to internal or external collaborations, and when possible guide student research. The ability to work as part of a team is essential.

Position Compensation
Duration: Initially 2-year fixed term with potential for an 1-year extension (full time).
The candidate will be compensated with a competitive remuneration package in accordance with qualifications and experience. Additional benefits include the provision of a Public Benevolent Institution salary packaging scheme and participation in an employer-contributed superannuation fund.

Essential Characteristics
The appointee will be an ambitious post-doctoral scientist with a bold and creative approach to research. They will be capable of independent thought and project design, and will be able to work in a collaborative team setting. Exceptional candidates will be eligible for an internal CMRI post-doctoral fellowship, and the possibilities provided by this unique funding opportunity. The following characteristics and research experience are essential to this position.

• A PhD in computational biology, bioinformatics, applied statistics, computer science, systems biology and molecular biology or another closely related scientific discipline. Candidates in the final stages of PhD submission are welcome to apply.
• High proficiency with at least one programming language (e.g., R, Python).
• Demonstrated experience with data analytics in omics data analysis.
• Proven ability and commitment to produce high quality work, including track record of scientific publication.
• Proven research ability, and evidence of self-motivation and research potential.
• Proven excellence in written and oral communications, interacting with a variety of researchers and stakeholders.

Desirable Characteristics
• Knowledge of stem cells and molecular cell biology.
• Experience with deep learning.

Computational Systems Biology Lab
The CSB lab (https://smex-ctp.trendmicro.com:443/wis/clicktime/v1/query?url=https%3a%2f%2fpyanglab.github.io&umid=4e18582d-3f3e-417b-8f53-15c6fe845f01&auth=2af5473c4b03509246eb08bd803a6cf835f69953-d29bb5b92a435ca262ffa6b231098c9ef9d42797) combines computational (‘dry’) and experimental (‘wet’) expertise to study cell identity and cell fate decisions of stem cells and organoids systems. The lab resides in CMRI, Westmead, while also holding office space both at the School of Mathematics and Statistics, and the Charles Perkins Centre, The University of Sydney. The CSB lab collaborates closely with other lab at CMRI (e.g., Stem Cell Medicine, Embryology) and is part of the Sydney Precision Bioinformatics Alliance and Sydney Precision Data Science Centre, The University of Sydney. The appointee will have ample opportunity to collaborate with bioinformaticians, statisticians, computational and systems biologists, and stem cells and developmental biologists within CMRI and from The University of Sydney.

Current focus of the CSB lab is on using computational approaches and bulk and single-cell multi-omics data to characterise cell identity and predict cell fate decisions for stem cell differentiation and organoid generation. The lab is currently supported by an NHMRC Investigator grant and two MRFF Stem Cell Therapies Mission grants. Most significant publications of the lab in the last five years appears in Cell Press and Nature Portfolio (http://pyanglab.github.io/publications.html) For more information please visit https://pyanglab.github.io/.

Application
Applications should include a cover letter (citing PV2250), curriculum vitae and contact details (phone/email) of three professional referees and be forwarded to recruitment@cmri.org.au

Closing date for applications is (09 June 2023).

Please direct enquiries regarding the position to Associate Professor Pengyi Yang, NHMRC Investigator, pengyi.yang@sydney.edu.au.

Job website: http://pyanglab.github.io/

Contact name: Pengyi Yang

Contact email: pengyi.yang@sydney.edu.au