Position title:
Employer: Neuroscience Research Australia
Closing date: 5PM Thursday 12th December 2019
Brief position description: This position will support the molecular genetics laboratory, Mackenzie's Mission and the CRE-NCD by assisting with clinical cloud-based bioinformatics requirements for the analysis of next generation sequencing (NGS) data, implementation and maintenance of bioinformatics pipelines around design, performance, validation and quality control. The clinically targeted NGS panels, exomes or genomes and bioinformatics pipelines require embedded bioinformatic expertise. NGS data analysis using computer programming and Unix-based servers is required. This is also largely a development role, so experience with front-end and back-end development and working with Amazon Web Services is desirable The successful candidate will be working closely with wet lab scientists, clinicians, pathologists, genomic analysts, and other bioinformaticians/software developers.
We are seeking an experienced and motivated development 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 for two years.
Job website: https://www.seek.com.au/job/40482739?searchrequesttoken=879cd838-195d-4389-b29d-6ce0f80c1f5d&type=standout
Contact name: Tony Roscioli
Contact email: Tony.Roscioli@health.nsw.gov.au
Research Officer/Senior Research Officer @ Melbourne
Position title: Research Officer/Senior Research Officer
Employer: The Walter and Eliza Hall Institute
Closing date: December, 20th, 2019
Brief position description: An opportunity exists for two Research Officers / Senior Research Officers (Bioinformatician / Computational Biologist / Statistical Bioinformatician) to join the Colonial Foundation Healthy Ageing Centre (CFHAC) in joint appointments with WEHI's Bioinformatics Division.
The WEHI and the Royal Melbourne Hospital have come together to create the CFHAC to lead the complex change necessary to deliver the next generation diagnostics for ageing related disease within Victoria’s healthcare system. The newly founded Centre headed by Associate Professor Andrew Webb brings together clinicians, pathologists and researchers from hospitals and research centres to apply the latest knowledge and technologies to transform the clinical discovery process and rapidly translate discoveries into clinical utility.
The positions will be part of the CFHAC and will be jointly supervised by Associate Professor Melissa Davis and Professor Gordon Smyth. Please contact them for further information. Position descriptions for the two positions are available on request.
Job website: http://www.wehi.edu.au/research-officersenior-research-officer-bioinformatician
Contact name: Melissa Davis
Contact email: davis.m@wehi.edu.au
Biological Testing Facility Manager @ Sydney
Employer: Garvan Institute of Medical Research
Closing date: 26-12-2019
Brief position description: At Garvan our research is focused upon understanding the role of genes and molecular and cellular processes in health and disease as the basis for developing future preventions, treatments and cures. Our scientists are researchers who work towards making significant breakthroughs in scientific discovery to positively impact human health.
Our support staff are the foundation of our scientific operations and we only recruit the best talent. Our support teams are experts in their fields and are driven by the dynamic culture, innovation and cutting edge research that the Garvan offers.
The Opportunity
We are currently seeking to appoint a Biological Testing Facility (BTF) Manager who will be responsible for the day to day management of the facility. The BTF holds rodents and zebrafish, and is essential for animal based research at Garvan.
Key responsibilities of this position include:
• Manage and recruit BTF staff to develop a cohesive, client-focused team.
• Ensure that staffing levels meet facility requirements.
• Ensure the BTF meets all legislative requirements.
• Liaise with researchers to ensure the BTF meets their experimental requirements.
• Manage the BTF budget and cost recovery.
• Ensure procedures promote the well being of experimental animals, the safety of staff and the efficient running of the facility.
• Manage the BTF laboratories and equipment, including selection, maintenance and quality checks.
• Provide training for staff and researchers in use of the facility and the animal management software.
In order to be successful in this positon, you will demonstrate the following key skills and attributes:
• A degree in science, animal science or equivalent
• Previous management experience
• Experience managing a cost recovery facility
• Experience in working with small laboratory animals
• Strong commitment to the health and wellbeing of laboratory animals
• Ability to negotiate with stakeholders
• Strong commitment to quality and service delivery
• Strong analytical, critical thinking, and problem-solving skills
• Excellent organisational, verbal and written communication
How to apply
To apply, please submit your application via the Garvan careers site: https://www.garvan.org.au/careers
Please prepare and submit your application as per the directions below:
• A Cover Letter
• CV including 3 Referees
• Academic Transcripts
Closing date
We are reviewing applications as they are received. This position will remain open until filled.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Biological-Testing-Facility-Manager_PRF5327
Contact name: Shree Chattopadhyay
Contact email: shreec@garvan.org.au
Production Bioinformatics Engineer @ Sydney
Employer: Garvan Institute of Medical Research
Closing date: 21-12-2019
Brief position description: The Garvan Institute of Medical Research (Garvan) is one of Australia’s leading medical research institutes, with over 600 scientists, students and support staff. Its mission is to make significant contributions to medical research that will change the directions of science and medicine and have major impacts on human health. Garvan’s research encompasses immunology, bone biology, neuroscience, diabetes and metabolism, cancer, and genomics and epigenetics. These research activities are organised within four themes: Cancer, Inflammatory Diseases, Healthy Aging, and Genomics, and two Centres: the Kinghorn Centre for Clinical Genomics and the Garvan-Weizmann Centre for Cellular Genomics.
The Kinghorn Centre for Clinical Genomics (KCCG) advances the use of genomic information in patient care by employing world-leading DNA analysis technology and expertise in genetics, pathology and bioinformatics to deliver and interpret genome sequences for research and clinical use. The KCCG is closely affiliated with the Garvan-Weizmann Centre for Cellular Genomics (GWCCG), Australia’s only multidisciplinary facility for cellular genomics.
As part of KCCG’s core strategic aims, the Genomic Technologies Group extends and complements Garvan’s capabilities in genomic, transcriptomic, and epigenomic research by implementing, evaluating, and refining new and existing technologies for both clinical and research applications.
The Opportunity
The Production Bioinformatics Engineer will be responsible for the management of next generation sequencing (NGS) data and the efficient implementation of data analysis pipelines for KCCG. This role will support the objectives of the group by implementing efficient analytic workflows and best practices for the generation and processing of next-generation sequencing data. The role will also involve close collaboration with researchers from different divisions to provide them with custom bioinformatics support.
This is a two year fixed term position with the possibility to extend.
Key Responsibilities
Transform research-grade bioinformatics analysis workflows into products that are robust, transparent and reassuring;
Responsible for researching, planning, implementing, testing, and optimising bioinformatics software tools for NGS data that meet the analysis needs for laboratory research scientists;
Ensure that NGS pipelines are consistently, reliably, efficiently, and correctly processing data;
Perform initial stage analysis on next-generation sequencing data;
Work closely with Garvan’s Data Intensive Computer Engineering (DICE) group regarding the building of software pipelines that will run on DICE’s HPC and OpenStack computing environment, Australia’s supercomputing facility, the National Computational Infrastructure (NCI), as well as on commercial clouds (AWS, Google, and Azure);
Responsible for documenting and communicating pipeline processes and building the team knowledge base;
Provide bioinformatics support and training to end-users (transforming data from sequence to information meaningful for laboratory research scientists);
All staff are required to comply with Garvan’s Work Health & Safety (WHS) Policy and work in accordance with the WHS management system at all times;
About You
The successful candidate should possess the following:
BSc, BE, or higher in software engineering, biomedical engineering, biotechnology, bioinformatics, or a related discipline, or equivalent experience;
Excellent knowledge and experience with Unix and basic system administration (e.g. installing 3rd party software);
Fluency in programming;
Experience with source code management tools
Strong analytical, critical thinking, and problem-solving skills;
Ability to contribute to preparation of written reports and oral presentations;
Excellent interpersonal skills and ability to work cooperatively with other team members;
Excellent organisational and time management skills.
Desirable skills:
Experience with NGS data analysis;
Familiarity with one or more of the following: Python, bash, C/C++, Java, Perl;
How to Apply
To apply for this position, please submit your application with a CV, cover letter and academic transcripts. As we will be reviewing applications as they are received, we encourage you to submit yours as soon as possible.
Only applicants with full working rights in Australia are eligible to apply for this role.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Production-Bioinformatics-Engineer_PRF5285-1
Contact name: Shree Chattopadhyay
Contact email: shreec@garvan.org.au
Research Bioinformatician @ The Australian Wine Research Institute
Position title: Research Bioinformatician
Employer: The Australian Wine Research Institute (AWRI)
Closing date: 29/11/2019
Brief position description: The Australian Wine Research Institute (AWRI) is the Australian grape and wine industry’s own research organisation. It supports a sustainable and successful grape and wine industry through world class research, practical solutions and knowledge transfer. The culture at the AWRI is professional, innovative and sets high standards. As part of these standards the AWRI offers favourable working conditions and an environment conducive to success. The AWRI has strong links with the wine industry and other research organisations both nationally and internationally and provides a stimulating and challenging environment.
Applications are invited for the position of Research Bioinformatician within the Metabolomics Australia facility at the AWRI. The position will provide bioinformatics support in computational metabolomics and data management, contribute to development and implementation of new methods and workflows, and assist with service delivery to research and industry clients.
The ideal candidate will have a PhD, a BSc or MSc and will be technically proficient in bioinformatics or computational metabolomics, have experience with at least one programming language (e.g. R) and have sound knowledge of statistical tools and methods.
Experience with multi-omics data integration; meta-data capture integration with analytical data; cloud-based computing and database administration; and familiarity with Linux/Unix command line are desirable.
For a position description please visit the link below or for more information please contact Dr Natoiya Lloyd on (08) 8313 6600 or natoiya.lloyd@awri.com.au.
Applications should be completed via the online application form (see link below) by Friday 29 November 2019. Only applications that are completed via the online application form will be accepted.
Job website: https://www.awri.com.au/about_the_awri/people/careers/position-vacant-research-bioinformatician-2/
Contact name: Natoiya Lloyd
Contact email: natoiya.lloyd@awri.com.au
Bioinformatics Research Officer - Epigenetics Research @ Sydney
Employer: Garvan Institute of Medical Research
Closing date: 13-12-2019
Brief position description: The Garvan Institute of Medical Research (Garvan) is one of Australia’s leading medical research institutes, with over 600 scientists, students and support staff. Its mission is to make significant contributions to medical research that will change the directions of science and medicine and have major impacts on human health. Garvan’s research encompasses immunology, bone biology, neuroscience, diabetes and metabolism, cancer, and genomics and epigenetics. These research activities are organised within four themes: Cancer, Inflammatory Diseases, Healthy Aging, and Genomics, and two Centres: the Kinghorn Centre for Clinical Genomics and the Garvan-Weizmann Centre for Cellular Genomics.
The Genomics and Epigenetics Theme is an integrated series of strongly interactive Research Groups undertaking research aimed at understanding genome biology and its impact on disease. The Theme's vision is to interpret the information encoded within the genome and elucidate how the pattern of spatial and temporal epigenetic and resulting transcriptional processes control human development. In addition to this how disruption of these processes contributes to cancer and other diseases, including diabetes and neurological and immunological disorders; and to translate this knowledge to improve health outcomes through development of biomarkers and potential therapeutic targets
The Opportunity
The Genomics and Epigenetics Theme is expanding its bioinformatics team for the development and implementation of statistical and bioinformatics tools and analyses of large genomic and epigenomic and chromatin conformation sequencing data. This includes projects in DNA methylation biomarker discovery and validation. The incumbent will also have close interaction with other post-doctoral scientists, PhD students and Research Assistants in the Epigenetics group, as well as with other members of this group and the wider Cancer Theme.
This is a one year fixed term position with possibility to extend.
Key Responsibilities
Co-lead the computational and statistical analysis of epigenome and genomic sequencing data sets and integration with RNA, chromatin immunoprecipitation sequencing data to define new paradigms of cancer epigenome regulation.
Co-lead the computational and statistical analysis of chromatin conformation sequencing and capture sequencing data to determine three dimensional epigenome regulation.
Enhance DNA methylation biomarker discovery and validation projects, using large scale DNA methylation array based studies and multiplex PCR bisulphite sequencing.
Development of and implementation of existing and new bioinformatics tools and systems available for large scale genome and epigenome analysis.
Aid in the management of data storage and maintain and update computational pipelines to ensure best practice.
Teach bioinformatics skills to other researchers in the Epigenetics Laboratory on a regular basis.
Development of and implementation of existing bioinformatics tools and systems available for large scale genome analysis.
Keeping abreast of emerging tools and statistical methods and develop new tools in the bioinformatics field.
All staff are required to comply with Garvan’s Work Health & Safety (WHS) Policy and work in accordance with the WHS management system at all times.
About You
The successful candidate should possess the following:
A PhD graduate from a quantitative discipline (statistics, bioinformatics, mathematics, physics, software engineering, information technology, computer science or a relate field) who is looking to develop an independent research career.
Experience with machine learning methods and multivariate statistics operating at a senior level
Experience with Stata, R and BioConductor
Proficiency in programming skills in Java (preferably experience with Java 8) with the ability to work comfortably in a Linux environment is desirable
Familiarity with the Unix command line
Familiarity with web-based bioinformatics resources such as NCBI, UCSC and NetAffx
Knowledge of the fundamentals of molecular biology: DNA transcription and translation
Skills in analysis of WGS, WGBS data, RNA-seq, ChIP-seq, and HiC-seq data
Strong commitment to data organisation and implementation of quality controls
Excellent communication skills for written reports and oral presentations
Capacity to work co-operatively with other team members
Be well organised and a good time manager
How to Apply
To apply for this position, please submit your application with a CV, cover letter and academic transcripts. As we will be reviewing applications as they are received, we encourage you to submit yours as soon as possible.
Only applicants with full working rights in Australia are eligible to apply for this role.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Bioinformatics-Research-Officer---Epigenetics-Research_PRF5301-1
Contact name: Shree Chattopadhyay
Contact email: shreec@garvan.org.au
Research Assistant - Epigenetics Research @ Sydney
Employer: Garvan Institute of Medical Research
Closing date: 13-12-2019
Brief position description: The Garvan Institute of Medical Research (Garvan) is one of Australia’s leading medical research institutes, with over 600 scientists, students and support staff. Its mission is to make significant contributions to medical research that will change the directions of science and medicine and have major impacts on human health. Garvan’s research encompasses immunology, bone biology, neuroscience, diabetes and metabolism, cancer, and genomics and epigenetics. These research activities are organised within four themes: Cancer, Inflammatory Diseases, Healthy Aging, and Genomics, and two Centres: the Kinghorn Centre for Clinical Genomics and the Garvan-Weizmann Centre for Cellular Genomics.
The Genomics and Epigenetics Theme is an integrated series of strongly interactive Research Groups undertaking research aimed at understanding genome biology and its impact on disease. The Theme's vision is to interpret the information encoded within the genome and elucidate how the pattern of spatial and temporal epigenetic and resulting transcriptional processes control human development. In addition to this how disruption of these processes contributes to cancer and other diseases, including diabetes and neurological and immunological disorders; and to translate this knowledge to improve health outcomes through development of biomarkers and potential therapeutic targets
The Opportunity
We are currently seeking a Research Assistant (RA) who will be responsible for planning and conducting experiments under supervision with the lab. The RA will also assist with the general maintenance and upkeep of the lab supplies, equipment and procedure. The incumbent will also have close interaction with other post-doctoral scientists, PhD students and Research Assistants in the Epigenetics group, as well as with other members of this group and the wider Cancer Theme.
Reporting to the Laboratory Head, Epigenetic Research, this is a one year fixed term position with possibility to extend.
Key Responsibilities
Conducting molecular biology experiments, including cell culture, transfections, gene editing and DNA and RNA analyses under supervision of a senior researcher
Performing epigenome techniques including, chromatin ChIP, chromatin capture and DNA methylation and other sequencing library preparations
Developing and applying new methodologies, as the need arises
Analysing data including bioinformatic analysis in a timely, efficient and diligent manner.
Evaluating and applying alternative methodologies/algorithms to optimise sensitivity and reproducibility; Record experimental procedures and results
Regularly attend meetings with the wider Research Division community as required
Contributing to research projects through to joint authorship of abstracts and publications in journals specific to their scientific field.
About You
The successful candidate should possess the following:
Masters’ Degree in Science or Medicine (preferably with Honours) or a related field with an interest to gain relevant research experience and in PhD studies
Competent computer skills (Excel, Word & PowerPoint)
Highly collaborative with a strong commitment to quality
High degree of flexibility and ability to take direction well
Showing ability to time manage by appropriate prioritisation of workload
Good communication skills, and
Comfortable with basic decision making
The incumbent should have experience in one or more of the following areas:
Chromatin immunoprecipitation and DNA methylation sequencing
Cell culture
RNA and DNA handling
PCR
Quantitative Gene Expression Analysis
Bioinformatic analysis and coding experience
Proficiency in R language
How to Apply
To apply for this position, please submit your application with a CV, cover letter and academic transcripts by 8 November 2019. As we will be reviewing applications as they are received, we encourage you to submit yours as soon as possible.
Only applicants with full working rights in Australia are eligible to apply for this role.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Research-Assistant---Epigenetics-Research_PRF5260-2
Contact name: Shree Chattopadhyay
Contact email: shreec@garvan.org.au
Research Assistant - Connie Johnson Breast Cancer Research Laboratory @ Sydney
Employer: Garvan Institute of Medical Research
Closing date: 13-12-2019
Brief position description: The Garvan Institute is a leading multi-disciplinary biomedical research institute in Darlinghurst, Sydney. With some of the brightest scientific minds and best technologies on the planet, we see the big picture of health and disease. Our researchers harness all the information of the genome to better predict, diagnose, prevent and treat disease — to realise our vision of a future where everyone lives longer, healthier lives.
Garvan’s mission is to make significant contributions to medical research that will change the directions of science and medicine and have major impacts on human health. Its research encompasses bone biology, cancer, diabetes and metabolism, genomics and epigenetics, immunology, and neuroscience. These research activities are organised within four encompassing research themes: Cancer, Genomics, Aging Diseases, Immunity & Inflammatory Diseases, and two major Centres: the Kinghorn Centre for Clinical Genomics and the Garvan-Weizmann Centre for Cellular Genomics.
The Connie Johnson Breast Cancer Research Laboratory led by A/Prof Elgene Lim performs clinically focussed laboratory research with an emphasis on hormone receptor-driven breast cancer.
The Opportunity
The Research Assistant is accountable - under supervision - for conducting experiments within his/her Research Division. They will also be responsible for managing the breast cancer biobank. This involves consenting patients for tissue collection, banking tissue from St Vincent’s Hospital and performing experiments in the laboratory. The position will be full time for one year in the first instance.
Key Responsibilities
The key responsibilities of this position include:
Manage the breast cancer biobank database
Liaise with internal and external stakeholders, including clinical staff and patients, to facilitate the collection of tissues and other patient samples for the biobank project
Conduct experimental procedures in the lab as part of the overall scientific programme of the research group
Record experimental procedures and results
Regularly attend meetings with the research group and wider Research Division community as required
Be involved in junior lab responsibilities such as:
Store duties, wash-up and cleaning of shared rooms;
Stock control, monitoring and ordering consumables under supervision
Responsible for imparting knowledge in relation to skills or experimental expertise
Other duties as assigned.
About You
In order to be successful in this position, you will demonstrate the following key skills and attributes:
Either a PhD or level 5 RA wet-lab research experience
Bachelors’ Degree (preferably with honours) or equivalent in Science, Medicine or Allied Health
Familiarity with medical and scientific terminology
Experience planning and implementing experimental procedures in a biomedical research context
High level interpersonal skills
High degree of accuracy and attention to detail
Competent computer skills (Excel, Word & PowerPoint)
Highly desirable:
Previous biobanking experience
Experience with using database software
Familiarity with cell and molecular biology techniques
Experience in a molecular biology laboratory
Experience working with laboratory animal models
How to Apply
To apply for this position, please submit your application with a CV, a cover letter and copies of relevant qualifications / academic transcripts. The position will remain open until filled. As we will be reviewing applications as they are received, we encourage you to submit yours as soon as possible.
Only applicants with full working rights in Australia are eligible to apply for this role.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Research-Assistant-3_PRF5283-1
Contact name: Shree Chattopadhyay
Contact email: shreec@garvan.org.au
Senior Bioinformatician @ Newcastle
Employer: HMRI (Newcastle)
Closing date: 24/11/2019
Brief position description: The Hunter Medical Research Institute (HMRI), has earned a reputation for translating its world-class medical research into real and immediate benefits for patients and their families. It’s an exciting time at HMRI, with new leadership and building capabilities for growth. We are broadening our research scope and funding opportunities and are now looking for a Senior Bioinformatician to support the Bioinformatics and integrated data services.
About the Role
The Senior Bioinformatician will consult with researchers and clinicians in the design, implementation, analysis and seamless delivery of bioinformatics services to support cutting-edge medical research activities at HMRI. Working closely with the Senior Bioinformatics and Integrated Data Analyst, this role is responsible for integrating high throughput sequencing data with clinical, imaging and multi-omics. Specifically, this role will:
Perform quality control, assembly, annotation, and analysis of high throughput next generation multi-omics data;
Apply and develop computational biology techniques to the analysis of these and other large medical datasets;
Develop bioinformatics data analysis pipelines in standalone machines and high-performance computing clusters, including cloud computing;
Collaborate with researchers in the design, testing and quality control of analytical approaches.
What you’ll need to succeed
Post-graduate/doctoral qualifications in computer science, statistics, mathematics or engineering with a background in applied bioinformatics and extensive relevant experience.
Demonstrated experience in the application of state-of-the-art tools and techniques for bioinformatics analysis.
Advanced knowledge of biological cellular processes at the molecular level and current measurement techniques capabilities and limitations.
Demonstrated ability in working collaboratively in a multidisciplinary environment to answer complex research questions.
Project management skills, including ability to prioritise multiple deadlines and managing client expectations.
Strong written and verbal communication skills, including high quality reporting and presentation skills.
Demonstrated experience in consulting within the biomedical industry or government.
This position is offered on a full-time, fixed-term three-year contract (with the possibility of renewal subject to availability of funding).
How to Apply
A position description can be obtained at www.hmri.org.au/careers.
All applications should be forwarded to recruitment@hmri.org.au and must include a cover letter, current resume including at least two (2) work-related referees, and responses to all of the selection criteria outlined above.
Please note that applications that do not address the selection criteria will not be considered.
Only candidates with the right to work in Australia may apply for this position.
For further questions contact Michelle Gillam on 02 4042 0500.
Applications close: Sunday 24 November 2019
Job website: https://www.seek.com.au/job/40326966?searchrequesttoken=40034123-ff30-4348-bce8-8af530ce5511&type=standout
Contact name: Michelle Gillam
Contact email: recruitment@hmri.org.au
KCCG Genomics Summer Scholarship @ Sydney
Employer: Garvan Institute of Medical Research
Closing date: 07-12-2019
Brief position description: The Garvan Institute of Medical Research (Garvan) is one of Australia’s leading medical research institutes, with over 600 scientists, students and support staff. Its mission is to make significant contributions to medical research that will change the directions of science and medicine and have major impacts on human health. Garvan’s research encompasses immunology, bone biology, neuroscience, diabetes and metabolism, cancer, and genomics and epigenetics. These research activities are organised within four themes: Cancer, Inflammatory Diseases, Healthy Aging, and Genomics, and two Centres: the Kinghorn Centre for Clinical Genomics and the Garvan-Weizmann Centre for Cellular Genomics.
The Kinghorn Centre for Clinical Genomics (KCCG), established by the Garvan Institute is an Australian research and sequencing centre delivering genomic information for clinical use. The KCCG facilitates genome-based research, particularly in cancer and monogenic diseases, but also in complex disease such as diabetes, osteoporosis and immunological disease. Our vision is to translate medical research into clinical care in Australia and beyond by integrating sequencing, bioinformatics and data management in a cutting-edge Genomics research environment.
The Opportunities
The KCCG is offering currently enrolled undergraduate students opportunities to carry out projects during summer 2019/2020. These projects provide hands-on research experience in the following topics:
1. Integration of “real” real-time nanopore analysis
State of the art nanopore sequencers produce terabytes of data over a sequencing run of 48 hours. To improve turnaround times, we have designed a proof-of-concept system that processes the data from the sequencer on the fly. In this project, you will go one step further by interfacing the computing system with the sequencer at the software level, and also add failure handling so the system can be used in a production workflow.
2. Signal analysis algorithm and parameter optimisation
Nanopore sequencing offers the possibility of portable genome sequencing, but analysing the terabytes of data generated is both compute and memory intensive. We have heavily optimised gold-standard "nanopore event alignment" software to efficiently leverage the power of embedded CPU-GPU heterogeneous computing systems. You will work on improvements such as optimising runtime parameters (data chunk size, number of threads, etc.) and accelerating algorithm performance using SIMD (Single Instruction Multiple Data).
3. Developing a National Genomics Resource Research Centre at KCCG
KCCG is developing a National Genomics Resource Centre (NGRC) to assist researchers develop sound research proposals with ethically defensible plans, as well as partnering with researchers to notify study participants of clinically actionable findings, and providing comprehensive follow-up support for such participants. In this project, you will help set up various aspects of the NGRC, which will comprise a web-based platform, a tailored messaging system and 1800 telephone line staffed by appropriately trained, dedicated genetic counsellors accessible to both researchers and research participants.
4. Generating pedigrees from patient information.
Entering pedigree information into computer-readable format is difficult, as mistakes are easily made when entering large numbers of people. The current version of the pedigree-management software uses a graphical interface and can predict some information for adding people to a pedigree. In this project, you will expand this software to include further validation and visualisation, as well as saving additional phenotype information. You will gain experience developing software using Python.
5. Detecting and interpreting genomic structural variants in 4000 Australians
At KCCG we perform genetic testing for disease-causing genomic variants. We also have the largest cohort of healthy individuals with whole genome sequencing data in Australia, which has allowed us to estimate the frequencies of single nucleotide variants in the general population. In this project, you will use our accredited detection pipeline and high-performance compute infrastructure to analyse this cohort for structural variants, summarising the detected variants, determining their frequencies and interpreting biological findings.
6. Identifying tandem repeats from Nanopore sequencing for FSHD diagnostics.
Help develop the code to better identify tandem repeats, then optimise the code for the types of repeats relevant to FSHD diagnostics, including the 3.3Kb macrosatelite and the 68bp b-satelite repeats on chr4q/10q. You will gain experience in programming for a biological application as part of a bioinformatics team. Exact details will vary depending on the state of the project at the time.
7. Characterising detailed methylation patterns across the D4Z4 repeat in FSHD patients.
You will analyse a collection of samples sequenced using nanopore sequencing, including unaffected people and patients with FSHD. You will gain an understanding of the biology of FSHD and experience handling biological data.
8. Clinical diagnosis using Whole Genome Analysis
In clinical practice, Whole Genome Analysis has traditionally been difficult and expensive due to extended manual variant curation. Restricting analysis to panels of curated genes reduces complexity and improves turnaround times but may miss novel pathogenic variants. KCCG has developed Orrery, a variant prioritisation framework that enables rapid analysis of whole genomes, and which has recently been validated and accredited for clinical applications. In this project, you will use Orrery to revisit samples from the cardiogenomics flagship, comparing diagnostic yields and clinical significance with previous panel-based analyses. This work will help determine the optimal diagnostic workflow.
9. Exploring the transcriptional signatures of skeletal dysplasia genes
Skeletal dysplasias are a group of rare genetic disorders characterised by severe deformities of the skeleton. Our group aims to identify the genetic defects responsible for these disorders. In this project, you will help explore the expression patterns of known skeletal dysplasia genes across various tissues and cell types to identify new skeletal dysplasia genes. Identifying these genes is an essential first step in understanding what is causing these disabling diseases and developing a possible cure.
10. Developing an app for “Dynamic Consent” for use of one’s genome and DNA information
We are now able to sequence the entire genome of an individual within hours. This is very valuable data, able to provide information to help not only the individual, but also their relatives, and also to advance medical diagnosis and scientific research. The concept of “Dynamic Consent” allows individuals to specify who can, and who can’t, access their genetic information. And the individual can review and change their consent at any time. This project involves a mock-up (and a basic working prototype) of a website or a mobile app that implements Dynamic Consent for genomic testing.
11. Using text mining to extract knowledge from clinical trial literature for oncology
The literature on oncological clinical trials is expanding so rapidly there is now an urgent need for methods of extracting key knowledge automatically. In this project, you will apply text mining techniques to public repositories to corroboratively extract information such as therapeutic combinations, indications and outcomes. We will then comparatively examine the performance and utility of different text mining methods, including machine learning-based methods in a small case study. The goal is to produce a database of trial results that will help oncology researchers ask more sophisticated questions and thereby design better interventional trials.
12. Using deep learning to extract insights from biological data sets
Skymapper is a new deep learning tool that uses Convolutional Neural Networks to derive insights from large biological data sets, including DNA and RNA sequences, methylation and multi-omics data. You will be involved in testing and documenting Skymapper with the goal of completing the documentation. You can also contribute to projects implemented using Skymapper.
The position will be offered full-time for 10 weeks and provide an allowance of $5000 as a tax-free scholarship.
How to Apply
All applications must be submitted via the Garvan Careers site. Applications from other sites/channels will not be considered.
Your application should include: your CV along with:
Your CV with a cover letter mentioning about which project(s) you are applying for and,
Academic transcripts
Closing Date
The position will remain open until filled. We will be reviewing applications as they are received, and so we encourage you to submit your application as soon as possible.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/KCCG-Genomics-summer-scholarship_PRF5295-1
Contact name: Shree Chattopadhyay
Contact email: shreec@garvan.org.au