Position title: Bioinformatics research assistant
Employer: Hogan Laboratory, Peter MacCallum Cancer Centre
Closing date: 25/03/2021
Brief position description: An opportunity exists for a talented and motivated Research Assistant to work with Professor Ben Hogan and Dr Lizzie Mason in the Program for Organogenesis and Cancer, at the Peter MacCallum Cancer Centre.
The Hogan Laboratory is a cross-disciplinary team that aims to understand the development of lymphatic vasculature (lymphangiogenesis), which plays an important role in the metastatic spread of cancer. The computational team applies bioinformatic and statistical methodologies to provide new insights into the molecular mechanisms that underpin developmental and pathological lymphangiogenesis. They are developing a comprehensive, single cell transcriptomic atlas of lymphangiogenesis, and using systems biology to derive the regulatory networks governing cell fate transitions in developmental, and pathological settings. The computational team have collaborative relationships with statistical and bioinformatic research groups throughout the Parkville precinct.
The successful candidate will have an Honour’s or Master’s degree in Bioinformatics, Computational Biology, Systems Biology or Computer Science. The candidate will have strong computational skills and experience applying them in the analysis of bulk and or single cell transcriptomic data.
Job website: http://petermac.mercury.com.au/ViewPosition.aspx?id=UnxDgndmz9w=&jbc=ere
Contact name: Elizabeth Mason
Contact email: Elizabeth.Mason@petermac.org
Genome Informatician @ SA
Position title: Genome Informatician
Employer: SA Pathology - Statewide Clinical Support Services
Closing date: 9th March 2021
Brief position description: - Contributes to the development of analysis pipelines for application to infectious diseases
- Contributes to the delivery of high-throughput microbial genomic testing technologies as part of the public health response to outbreaks and surveillance due to infectious diseases.
- Maintaining microbial genomic analysis pipelines for diagnostic and public health applications.
- Understanding and experience in phylogenomic analysis
Contributes to the delivery of NGS testing by:
- Identifying, evaluating and implementing software solutions for data analysis
- Automating NGS data analysis pipelines
- Maintaining currency of annotation resources
- Maintaining database of sequence variants
- Applying specialist knowledge of genome analysis to perform analysis of next-generation sequencing data
- Education and training of other staff within the MID directorate in the use of software tools and data analysis pipelines
Job website: http://careers.pageuppeople.com/532/caw/en/job/748898/genome-informatician
Contact name: Lex Leong
Contact email: lex.leong@sa.gov.au
Production Bioinformatician @ NSW
Position title: Production Bioinformatician
Employer: Garvan Institute of Medical Research
Closing date: 15/3/2021
Brief position description: The Garvan Institute of Medical Research brings together world-leading basic and translational researchers with expert clinicians to break down barriers between traditional scientific disciplines and find solutions to disease. Founded in 1963, Garvan’s mission is to harness all the information encoded in our genome to better diagnose, treat, predict and prevent disease.
Our scientists work across four intersecting research themes: medical genomics, epigenetics, and cellular genomics; diseases of immunity and inflammation; cancer; and diseases of ageing affecting bone, brain and metabolism. And three major Centres: the Kinghorn Centre for Clinical Genomics, the Garvan-Weizmann Centre for Cellular Genomics, and the Centre for Population Genomics.
This position will be collaborating with both the Kinghorn Centre for Clinical Genomics (KCCG) and the Garvan-Weizmann Centre for Cellular Genomics (GWCCG)
The Opportunity
The Production Bioinformatician will oversee the development, implementation and support of software and computational pipelines to translate raw single cell sequence data through to researchers. In addition, the production bioinformatician will deploy and support tools to assist researchers and clinicians with their genomic research.
The role will focus on supporting robust and production scale pipelines that run on either local or national HPC systems, as well as cloud services.
This is a unique opportunity for a bioinformatician to get exposure to research in single cell transcriptomics, genomics and epigenetics. This is a one-year full-time, fixed term role with a high possibility to extend, reporting to Joseph Copty - Bioinformatics Lead (KCCG Sequencing lab) and working closely with the GWCCG team. There is remote working flexibility with an option to choose your own days of work on site.
Key Responsibilities
Develop, implement and maintain the computational infrastructures required to support the analysis of high-throughput genome and single cell sequencing data.
Support the translation of new computational techniques from a research setting to production scale tools.
Design and implement pipelines to run on the internal and external high performance compute infrastructure and commercial clouds (AWS, GCP, Azure).
Deploy and support research tools for genomic variant filtration and interpretation.
Contribute code and features to open source bioinformatics tools.
Assist collaborators in data analysis and to check the validity of experimental results.
Create computational solutions to generate automated reports from raw high-throughput sequence data
Establish and maintain excellent records of the computational analysis and techniques for all projects in KCCG and GWCCG
About You
In order to be successful in this position, you will demonstrate the following key skills and attributes:
Bachelor degree (or higher) in Bioinformatics, Computer Science or related fields
Expertise in computational bioinformatics techniques, with a special focus on single cell transcriptomics, genomics and epigenetics
Demonstrated experience in the development and implementation of new and cutting-edge bioinformatics tools and pipelines using workflow languages
Strong skills in Linux command line and scripting languages (Python, Bash, R or other)
Experience with source code management tools (git preferred)
Experience in cloud infrastructure
Experience in using high performance computers (HPC) and job schedulers (e.g. PBS pro, SGE).
Demonstrated experience in containerisation using Docker and/or Singularity
Demonstrated experience in the development and implementation of new and cutting-edge bioinformatics tools and pipelines using workflow languages
Demonstrate experience in SQL and NoSQL based Databases
Desirable
Demonstrated experience in containerisation using Docker and/or Singularity
Knowledge of web frameworks: Django, Flask etc. is a plus
Experience with laboratory information management systems (LIMS)
Excellent written and oral communication, representation and interpersonal skills essential for interaction with internal and external stakeholders, including KCCG and GWCCG leaders
Excellent problem solving abilities and strong attention to detail
Ability to work independently
How to Apply
Only applicants with full work rights can apply. We are actively looking to hire for this role preferably by this month, so candidates are encouraged to submit their application along with a cover letter attached with the CV as one document, as soon as possible. If you think you’re the right person for this role, don’t delay as we’re assessing applications as they are received. We’d love to hear how your capabilities, achievements and experience set you apart.
Job website: https://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Production-Bioinformaticiann_PRF5816
Contact name: Michelle Earle
Contact email: m.earle@garvan.org.au
Computational Biologist/Bioinformatician @ South Australia
Position title: Computational Biologist/Bioinformatician
Employer: South Australian Genomics Centre (SAGC)
Closing date: 5th March, 2021
Brief position description: Key responsibilities include:
- Provide collaborative analysis support to SAGC clients with bioinformatics components of their projects.
- Develop efficient analysis and data integration strategies for projects involving multiple omics approaches and techniques, including genomics, transcriptomics, epigenomics, metagenomics, metabolomics and proteomics.
- Lead or assist with drafting publications and scientific reports relating to the projects across academic, industry and government areas.
- Contribute to development of competitive funding applications.
Job website: http://www.seek.com.au/job/51434189
Contact name: Jimmy Breen
Contact email: jimmy.breen@sahmri.com
Bioinformatician (Proteomics) in Computational Functional Genomics @ NSW
Position title: Bioinformatician (Proteomics) in Computational Functional Genomics
Employer: Children's Medical Research Institute
Closing date: 1st March 2021
Brief position description: We are seeking a qualified Bioinformatician / Data Scientist to join the Functional Genomics program with a focus on proteomics. This role will involve supporting researchers from the CMRI and collaborating institutions in the analysis of proteomics data of rare genetic diseases, cancers and disease modelling. The successful applicant will have opportunities to explore and interrogate a diverse range of data, including transcriptomics and proteomics data. Additionally, the successful applicant will work alongside highly experienced research data scientists/bioinformaticians.
Job website: https://www.cmrijeansforgenes.org.au/about/careers
Contact name: Patrick Tam
Contact email: ptam@cmri.org.au
Computational Biologist @ NSW
Position title: Computational Biologist
Employer: Garvan Institute of Medical Research
Closing date: 28/02/2021
Brief position description: The Garvan Institute of Medical Research brings together world-leading basic and translational researchers with expert clinicians to break down barriers between traditional scientific disciplines and find solutions to disease. Founded in 1963, Garvan’s mission is to harness all the information encoded in our genome to better diagnose, treat, predict and prevent disease.
Our scientists work across four intersecting research themes: medical genomics, epigenetics, and cellular genomics; diseases of immunity and inflammation; cancer; and diseases of ageing affecting bone, brain and metabolism. And three major Centres: the Kinghorn Centre for Clinical Genomics, the Garvan-Weizmann Centre for Cellular Genomics, and the Centre for Population Genomics.
The Kinghorn Centre for Clinical Genomics (KCCG) advances the use of genomic information in patient care. KCCG acts as a mechanism to translate genomic research information into patient care. To do this KCCG employs experts in genomics including researchers, bioinformaticians, clinicians, educators and software engineers. We use and develop multi-omics based technology to enhance diagnosis and treatment for patients.
The Opportunity
KCCG's Computational Biology Group is a newly established group focusing on genomics and biomedical data analysis, combining computational skills with biological domain expertise. The group applies and develops computational methods to better understand human disease. We take a collaborative approach, working closely with experimental researchers to tackle problems that address critical unmet medical needs.
We have multiple positions for computational scientists at different levels who are looking for an opportunity to establish themselves in a new team. Successful candidates will work on genomics studies with experimental researchers across research themes at Garvan and KCCG. Example projects from Cancer Genomics include liquid biopsy analyses to monitor cancer patients, single-cell analyses of clinical trial samples, genomics study of patients with an unusual response to therapy to understand underlying molecular mechanisms. Successful candidates will contribute to the different phases of genomics studies, including design and planning, data analysis, interpretation and manuscript writing.
Key Responsibilities
This position will be responsible for helping to provide direction and support in genomics studies. This will include:
Analysis of high-throughput datasets, including quality control, unsupervised and supervised analyses, with an emphasis on biological interpretation
Preparing figures for publication, contributing to manuscript writing
Experimental design and planning
Creating and maintaining modular, reusable and reproducible workflows through use of container and workflow management technologies
Developing best practices for computational workflows through evaluation/benchmarking of existing methods and/or original method development
Import and analysis of external datasets as resource or for validation purposes
Staying abreast on advances in genomics, computational methods, as well as building and maintaining biological domain expertise
Contribute to internal education programs through mentoring, technical supervision, code reviews
Occasionally represent KCCG at events, or talks with external stakeholders
About You
The following key skills and attributes are essential to undertaking the role:
PhD degree in a related area of science or engineering
Good knowledge of biology
Good statistical knowledge and programming skills
Previous experience working with next-generation sequencing data, e.g. RNA-seq, targeted or whole genome sequencing, ChIP-seq, ATAC-seq, single-cell sequencing
Publication record commensurate with experience
Comfortable working with Unix and in an HPC environment
Proficient in at least one scripting language (R, Python, Perl)
Familiar with version control systems
Highly developed written and verbal communications skills
Project management skills
Able to work independently
Desired
Postdoctoral research experience
Interest in biomedical data science, including statistical, machine learning, and visualisation methods
Interest in personalised medicine and clinical genomics
Experience with R/Bioconductor
Experience working with single-cell sequencing data
Experience with software containers, workflow management systems, databases, cloud computing
How to Apply
Australian/NZ citizen, permanent resident or other applicants with full working rights can only apply. To apply for this position, please submit your application including CV and cover letter addressing the above criteria. As we will be reviewing applications as they are received, we encourage you to submit yours as soon as possible.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Computational-Biologist_PRF5804-1
Contact name: Michelle Earle
Contact email: m.earle@garvan.org.au
Research Officer, Computational Cancer Biology and Bioinformatics @ Melbourne
Position title: Research Officer, Computational Cancer Biology and Bioinformatics
Employer: Walter and Eliza Hall Institute of Medical Research
Closing date: Feb 1, 2021, 5:00pm
Brief position description:
An exciting new opportunity exists for a talented bioinformatics researcher to join the Davis Laboratory in the Bioinformatics Division at WEHI.
The position will involve the development of new research methods in computational cancer biology involving the analysis of data from newly emerging technologies such as spatial transcriptomics and spatial proteomics. This position will present ample opportunities to participate in active collaborative research projects across Australia. The successful candidate will also have the opportunity to supervise post-graduate students and participate in the development of new research directions and projects.
The Davis Laboratory applies mathematical, statistical, and computational approaches to drive new cancer discoveries using a combination of large, heterogeneous datasets and targeted experimental data. A major focus of their work is reconstruction of mechanisms of regulation involved in cancer progression and metastasis as well as response to therapy and development of resistance. This is a highly multi-disciplinary research laboratory, and post-doctoral staff and students come from a variety of backgrounds, including statistics, mathematical biology, bioengineering, computer science and genetics.
A position description is available here.
Selection Criteria
Personal qualities
Excellent attention to detail, ensuring that data analysis, new methods and software implementations are of high-quality and accessible to other researchers
Highly collaborative with excellent communication skills and the ability to work constructively in a team environment
Ability to manage time effectively and be reliable and approachable
A passion to work at the intersection of computational research, bioinformatics and biomedical research
Knowledge and skills
A PhD in a relevant discipline such as bioinformatics, computational biology, computer science, statistics, mathematics, physics or biology with strong and demonstrated computational skills
Strong programming and data analysis skills, and a knowledge of the R and/or python programming language(s)
Experience applying analytical and computational skills to large, complex data, including gene expression, proteomics and clinical data
Excellent time management, writing and communication skills.
Knowledge or understanding of cancer biology would be highly regarded
An excellent academic record and achievements
Demonstrated ability and potential for excellence and productivity in research
Research experience that has resulted in publications, conference papers or reports, or an excellent PhD thesis.
Terms of appointment
The position will be for 2 years in a full-time capacity. Salary is Academic Level A6-A8 ($90,053-$96,661). Up to 17% superannuation and very attractive salary packaging options are available.
How to apply
General enquiries can be directed to Melissa Davis; davis.m@wehi.edu.au
Please email your application including cover letter, CV and a letter addressing the key selection criteria in pdf format to jobapplications@wehi.edu.au, quoting the reference WEHIDAMD211220
Job website: www.wehi.edu.au/research-officer-computational-cancer-biology-and-bioinformatics
Contact name: Melissa Davis
Contact email: davis.m@wehi.edu.au
Computational CRISPR Genomics - Bioinformatician @ Melbourne
Position title: Computational CRISPR Genomics - Bioinformatician
Employer: Walter and Eliza Hall Institute of Medical Research
Closing date: Feb 1, 2021
Brief position description: An exciting new opportunity exists for a talented bioinformatics research officer to work on computational CRISPR genomics and develop a key role for computational research in CRISPR activities.
The role will be joint between the laboratories of Prof Tony Papenfuss in the Bioinformatics division and A/Prof Marco Herold in the Blood Cells and Blood Cancers division. The successful candidate will work in close collaborations with bench scientists, contribute to the design of CRISPR experiments, analyse genomic and transcriptomic data, and develop new bioinformatics methods related to CRISPR.
The Papenfuss Laboratory applies mathematical, statistical, and computational approaches to drive new cancer discoveries using large and complex omics datasets. A major focus of their work is cancer evolution, which is critical in understanding how tumours metastasise and develop resistance to therapies. They have particular interests in developing methods for detecting and understanding genomic rearrangements and for applying mathematical modelling and machine learning to make sense of big data.
The Herold Laboratory aims to identify novel genes involved in the development of normal and malignant haematopoiesis. They are using in vivo CRISPR approaches to systematically identify new candidate genes, with the ultimate goal of using these targets as novel anti-cancer therapies. They are also developing new CRISPR models and methodologies (e.g. CRISPR activation or Base Editing) to resemble human disease more accurately and are implementing CRISPR as a diagnostic tool to ultimately use it for detection of infectious disease or malignant cells.
Job website: www.wehi.edu.au/research-officer-computational-crispr-genomics
Contact name: Tony Papenfuss
Contact email: papenfuss@wehi.edu.au
Post doc positions (2) @ Leipzig, Germany
Position title: Post doc positions (2) in Leipzig, Germany
Employer: Ulisses Nunes da Rocha, PhD, Helmholtz Young Investigator, Microbial Data Science and team leader, Department of Environmental Microbiology, Helmholtz Centre for Environmental Research
Closing date: open now from December 2020
Brief position description: Ulisses Nunes da Rocha, PhD, Helmholtz Young Investigator at the Microbial Data Science and team leader in the Department of Environmental Microbiology at the Helmholtz Centre for Environmental Research is seeking two bioinformatics post-docs to work with the them.
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Georg Teutsch
Administrative Geschäftsführerin/Administrative Managing Director:
Prof. Dr. Heike Graßmann
Job website: http://www.ufz.de/index.php?en=43659
Contact name: Ulisses Nunes da Rocha
Contact email: ulisses.rocha@ufz.de
Research Officer- Computational Systems Biology @ Sydney
Position title: Research Officer- Computational Systems Biology @ Sydney
Employer:
Closing date: 21st December 2020
Brief position description: The Computational Systems Biology (CSB) lab at CMRI is welcoming applications for a Research Officer to conduct research in the broad area of systems stem cell biology and single-cell multi-omics. Our research focuses on the acquisition of stem cell identity and cell fate decisions during differentiation and together the two CMRI labs have established high-throughput experimental techniques such as single-cell omics and computational expertise in multi-omics data analysis.
The CSB lab collaborates closely with other groups and units at CMRI (e.g. Embryology) and also a team of bioinformaticians from the School of Mathematics and Statistics, and systems biologists from Charles Perkins Centre (CPC), at the University of Sydney. The appointee will have ample opportunity to collaborate with bioinformaticians within CMRI and from the School of Mathematics and Statistics, and systems biologists from Charles Perkins Centre (CPC) at the University of Sydney.
Duration: 3-year fixed term (full time).
Salary: $88,499 – $94,998 + Superannuation + Annual Leave Loading + Salary Packaging
About the role
This position will help you building a collaboration network across multiple institutes and a track record that enables you to apply for collaborative research funding and independent research fellowship. Specific roles include (but not limited to) the following:
Lead and carry out research projects in the broad area of systems biology, stem cells biology, and single-cell multi-omics.
Prepare and publish work on scientific journals and present scientific results in national/international conferences.
Develop and co-supervise research projects for undergraduate and graduate research students.
Assist in the recruitment of research students and continuously working towards attracting new funding.
Build collaboration with different labs in CMRI and across multiple institutes/universities at Sydney (e.g. CPC and School of Mathematics and Statistics) and beyond.
About you
We are look for someone with the follow characteristics and research experience.
• A PhD in an appropriate area such as (but not limited to) computational and systems biology, bioinformatics, computer science, statistics or another closely related scientific discipline.
• Proven research ability, and evidence of self-motivation and research potential
• Demonstrated experience with omics, bioinformatics, systems biology and molecular biology
• Demonstrated experience with machine learning, deep learning and data analytics
• Proven excellence in written and oral communications, interacting with a variety of researchers and stakeholders
• Proven commitment to producing high quality work and a demonstrated track record of high-quality publications
• Demonstrated excellence in research within bioinformatics or computational systems biology through published research in refereed journals
• Proven ability to write and contribute to bioinformatic, computational, statistical, or mathematical research papers
• Knowledge of stem cells and development
Computational Systems Biology group
CSB lab (https://pyanglab.github.io) combines computational ('dry') and experimental (‘wet’) expertise to understand stem cell systems. The lab resides in CMRI, Westmead, while also holding office space at both School of Mathematics and Statistics and Charles Perkins Centre, USyd, which enable ample collaboration with statisticians and bioinformaticians; computational and systems biologists; and molecular and developmental biologists.
Current focus of the lab is on transcriptional regulation in stem cells (Yang et al. Molecular Cell, 2017; Kim…Yang, Nucleic Acid Research, 2020); bulk and single-cell multi-omics analysis (Yang et al, Cell Systems, 2019; Kim…Yang, Bioinformatics, 2020); and machine learning application in systems biology (Cao…Yang, Nature Machine Intelligence, 2020). The overarching goal of the lab is to develop computational methods for characterising stem cell systems and harnessing them for tissue regeneration.
You will be provided 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.
Applications should include a cover letter (citing PV2038), curriculum vitae and contact details (phone/email) of three professional referees and be forwarded to recruitment@cmri.org.au
Closing date for applications is 21st December 2020.
Please direct enquiries regarding the position to Dr Pengyi Yang, NHMRC Investigator, pengyi.yang@sydney.edu.au.
Job website:
Contact name: Pengyi Yang
Contact email: pengyi.yang@sydney.edu.au