Position title: Australian Biocommons Senior Bioinformatics Technical Officer
Employer: University of Sydney
Closing date: 28/10/2020
Brief position description: A great opportunity to contribute to the BioCommons Bring Your Own Data (BYOD) platform project
Located on the Camperdown/ Darlington Campus
Full-time, 3 year fixed term with a base salary of $95K p.a., plus leave loading and a generous employer’s contribution to superannuation
In this role as an Australian BioCommons Senior Technical Officer, you will contribute to the BioCommons Bring Your Own Data (BYOD) platform project, delivering a suite of software and workflow development and deployment activities that enables highly accessible, available, y scalable analysis and data sharing capabilities for the benefit of life science researchers nationally.
You will focus on developing and delivering a Command Line Interface (CLI)-focussed BYOD platform. The CLI-focussed platform will provide a scalable and flexible set of open programmatic resources to create, access and exchange workflows, tools and training across national, institutional, and commercial compute infrastructures.
Job website: https://sydney.nga.net.au/cp/index.cfm?event=jobs.checkJobDetailsNewApplication&returnToEvent=jobs.listJobs&jobid=A7413C55-64CE-42E2-8576-AC3E00C5BC83&CurATC=EXT&CurBID=949319BC%2D8898%2D4F11%2DAC4B%2D9DB401358504&JobListID=731bade1%2D6333%2Dccb4%2D725f%2D88e75150540a&jobsListKey=3df6a6e0%2D431c%2D49d6%2D976a%2D40697cd99956&persistVariables=CurATC,CurBID,JobListID,jobsListKey,JobID&lid=70307070232
Contact name: Tooba Fida
Contact email: tooba.fida@sydney.edu.au
Bioinformatician - The Garvan Weizmann Centre for Cellular Genomics @ Sydney
Position title: Bioinformatician - The Garvan Weizmann Centre for Cellular Genomics
Employer: Garvan Institute of Medical Research
Closing date: 31/10/2020
Brief position description: The Garvan Institute of Medical Research brings together world-leading clinicians and basic and translational researchers 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 Garvan Research Foundation (GRF) is the marketing and fundraising arm of the Institute raising critical philanthropic investment, and awareness, for Garvan’s medical research.
In 2017, The Garvan Weizmann Centre for Cellular Genomics (GWCCG) was formed, bringing together the Garvan Institute of Medical Research and The Weizmann Institute of Science to build Australia’s first Centre for Cellular Genomics. The Garvan and the Weizmann Institutes have harnessed their synergistic strengths (in Cytometry, Genomics, Informatics, and Data Visualisation) to allow cellular and single cell genomics to become routine tools for clinical and scientific analysis of many disease states. The focus of the GWCCG is both to support and conduct medical research using cellular genomics techniques across four research areas: Stem cells, statistical genetics, cancer and new diagnostics methodology
The Opportunity
The incumbent Bioinformatician will work with members of the GWCCG Research team to support computational research activities across the following areas:
Population genetics meets single cell sequencing
Resolving the genetic mechanisms of complex human disease using stem cells
Clinical translation of single cell sequencing for diagnosis and precision medicine
The role will involve curation, management, and analysis of high-throughput genomic data and patient medical records. In addition to supporting the research activities of other group members, opportunities will be made available to pursue and publish leading research.
A strong background in computational genomics, biology or bioinformatics preferred. Highly motivated individuals with a strong attention to detail, multi-tasking; and a willingness to learn new technologies are encouraged to apply. This is a two-year full-time position.
Key Responsibilities
Analysis of data generated for research within the GWCCG labs, by collaborators or in the public domain, method development and testing and writing computer code data analysis
Supporting role in manuscript preparation and presentation of results in lab meetings and conferences
Record-keeping and administrative aspects that underlie scientific research in discussion with lab heads, development of timelines
Collaboration with other group members, and as part of national and international consortia
Meeting with Associate Professor Joseph Powell and members of the laboratory
Attending, discussing and reviewing current and future techniques within Garvan’s Bioinformatics (BUG) meetings
About You
In order to be successful in this position, you will demonstrate the following key skills and attributes:
A degree in a relevant field e.g. computer science, genetics, physics, statistics, epidemiology, bioinformatics or other relevant areas, or an equivalent combination of relevant experience and/or education/training
Excellent computational background, especially in the management of large data sets in HPC environment and analysis and interpretation of large genomic data sets (WGS, RNA-Seq, scRNA-Seq)
High proficiency in programming and scripting languages (e.g. C/C++, Java, Perl, Python); Advanced user of the R programming language and R-based statistical packages and tools, such as those available from the Bioconductor project for high throughput genomic data analysis
Good knowledge of statistics and presentation of molecular/clinical data.
Demonstrated experience using version control for code development and curation.
Excellent problem-solving ability with good communication skills
Ability to work independently and yet amicably in a team environment to meet deadlines
How to Apply
Australian/NZ citizen, permanent resident of other applicants with full working rights can only apply. All applications must include a cover letter along with your resume with at least 2 referees. We are reviewing applications as they are received.
Job website: https://garvan.wd3.myworkdayjobs.com/garvan_institute/job/Sydney/Bioinformatician---The-Garvan-Weizmann-Centre-for-Cellular-Genomics_PRF5615-1
Contact name: Michelle Earle
Contact email: m.earle@garvan.org.au
Computational genomics and statistics @ Melbourne
Position title: Computational genomics and statistics
Employer: The University of Melbourne
Closing date: 22 October 2020
Brief position description: The School of Mathematics and Statistics (https://ms.unimelb.edu.au), and its partner Melbourne Integrative Genomics (MIG, https://research.unimelb.edu.au/integrative-genomics) are seeking a qualified and enthusiastic Research Fellow to lead cutting-edge research in method development, implementation and analysis of biological data.
The position will be based at MIGand will report to A/Prof Kim-Anh Lê Cao, whose lab specialises in the development of computational methods for cutting-edge ‘omics data (https://lecao-lab.science.unimelb.edu.au). The successful incumbent will work closely with our collaborative network across the campus, including the biomedical and computational biology precinct: Walter and Eliza Hall Institute of Medical Research (https://www.wehi.edu.au), the School of Biomedical Sciences (Centre for Stem Cells Systems) as well as external Australian and international institutions (France, Canada). A/Prof. Lê Cao lab’s research combines statistical modelling, computational frameworks and ‘omics data analysis, including but not limited to transcriptomics and epigenomics at the single cell level and metagenomics, to obtain a holistic understanding of a biological system in a healthy or disease state. We are interested in a range of analysis frameworks, such as unsupervised, supervised and longitudinal.
The position offers a rare opportunity to work in a multi-disciplinary environment amongst statisticians, bioinformaticians and biologists. The successful applicant will be highly skilled in R programming, will have an excellent understanding of the context in which biological data arise, and will be an excellent team player with the ability to mentor other team members. The successful applicant will be highly encouraged in developing their own research career path and research directions. An opportunity to teach some postgraduate lectures at the University within the incumbent’s expertise area is also offered.
Job website: http://obs.unimelb.edu.au/caw/en/job/898848/research-fellow-computational-genomics-statistics
Contact name: Kim-Anh Le Cao
Contact email: kimanh.lecao@unimelb.edu.au
Academic Specialist – Bioinformatics @ Melbourne
Position title: Academic Specialist – Bioinformatics
Employer: The University of Melbourne
Closing date: 07 Oct 2020
Brief position description: This is one of two exciting positions, representing an opportunity for a talented bioinformatician to forge a career in this new frontier. Melbourne Bioinformatics creates an environment for bioinformaticians to work on a range of high-impact research projects, share their expertise and develop their teaching and training skills, all in the company of a team of dedicated experts across computer science, data sciences, biology and research infrastructure bioinformatics. We perform a very important function in the precinct; creating a pipeline of talent and building up bioinformatics capacity-building at a time of great skills shortage in this specialised area.
The preferred candidate will enjoy teaching, have strong analytical and programming skills and possess demonstrable personal qualities in the areas of communication, collaboration and organisation. As a member of the Melbourne Bioinformatics expert team it is also expected that the role will involve contributing to our teaching and training program and community skills development activities.
Melbourne Bioinformatics operates at the Parkville Campus of The University of Melbourne and supports researchers who recognise that life science research is fast becoming a data science. Our experts assist with research design and grant applications, advise on computing options, engage in deep research collaborations, develop bioinformatics algorithms and software, create and deliver both online and hands-on bioinformatics training, and deliver the MSc (Bioinformatics) course, as well as supervising PhD and Masters research projects.
Melbourne Bioinformatics collaborates on a range of national and international platform development and digital research infrastructure projects and hosts the Australian BioCommons, a $20m NCRIS-funded digital research infrastructure program for life science research (2019-2023).
Job website: http://jobs.unimelb.edu.au/caw/en/job/903263/academic-specialist-bioinformatics-2-positions
Contact name: Fiona Kerr
Contact email: fiona.kerr@unimelb.edu.au
Research Officer- Systems Stem Cell Biology @ NSW
Position title: Research Officer- Systems Stem Cell Biology
Employer: Children’s Medical Research Institute (CMRI), USyd
Closing date: 30 Sep 2020
Brief position description: The opportunity
The Computational Systems Biology (CSB) Group and Embryology Research Unit at CMRI is welcoming applications for a Research Officer to conduct bench (“wet-lab”) research in the areas of single cell analytics and systems stem cell biology, with an overarching goal of functionally characterising the stem cell models and apply them for regenerative medicine.
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 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) with potential extension to 5 years. Salary: $88,499 – $94,998 + Superannuation + Annual Leave Loading + Salary Packaging benefits.
About you
The ideal candidate should have the follow research experience.
• A PhD in biological sciences. A strong background in molecular biology, cell biology, systems biology, biochemistry, developmental biology is desired.
• Good knowledge of stem cell biology and development.
• Experience in cell culture, experimental design, and high-through omics data generation.
• Experience in omics analysis, single cell biology, chromatin immunoprecipitation (ChIP) is highly desirable.
• Proven ability in the formulation of research strategy and the preparation of research reports and publications.
• Proven track record of high-quality research output
• Proven excellence in written and oral communications, interacting with a variety of researchers and stakeholders
• Evidence of self-motivation and potential for undertaking original research endeavour
About the role
This position will help you building a collaboration network across multiple teams 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 stem cells biology, developmental biology and systems biology.
Prepare and publish work and present scientific results in national/international conferences.
Develop and co-supervise research projects for honours and graduate research students.
Assist in the recruitment of research students and working towards attracting new funding.
Build collaboration with CMRI teams and multiple institutes at USYD (e.g. CPC and School of Mathematics and Statistics) and beyond.
Computational Systems Biology lab and Embryology lab
This position will be jointly mentored by CSB head Dr Pengyi Yang and Head of Embryology Research Unit Prof. Patrick Tam. The CSB lab (https://pyanglab.github.io) specializes in computational methods for omics analysis and the Embryology lab specializes in development biology and stem cell science. The two labs combine computational and experimental expertise to understand stem cell systems, providing close collaboration among computational and systems biologists; and molecular and developmental biologists.
The key research directions include:
CSB: 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).
Embryology: Transcriptional and functional properties of mouse epiblast stem cells (Kojima…Tam, Cell Stem Cell, 2014); Lineage specification and tissue organization in mouse embryo (Peng et al. Nature, 2019); Signalling in epiblast stem cells (Osteil…Tam, Development, 2019).
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 PV2026), curriculum vitae and contact details (phone/email) of three professional referees and be forwarded to recruitment@cmri.org.au
Closing date for applications is 30th September 2020.
Please direct enquiries regarding the position to Dr Pengyi Yang (pengyi.yang@sydney.edu.au) or Prof. Patrick Tam (PTam@cmri.org.au).
Job website: http://www.seek.com.au/job/50568775?type=standout
Contact name: Pengyi Yang
Contact email: recruitment@cmri.org.au
PhD student @ New South Wales
Position title: PhD student
Employer: Victor Chang Cardiac Research Institute
Closing date: Open until filled
Brief position description: We are looking for a new team member to join our dynamic regulatory systems group led by Emily Wong at Victor Chang Cardiac Research Institute. We have a PhD stipend available for a local student which includes a generous top-up.
Our main goal is to understand gene regulatory control in aging and regeneration, using comparative genomics and novel technologies such as single-cell sequencing. We are largely computational, but we also go beyond the dry lab to generate molecular data to address fundamental questions. As a student in our lab, you will have the opportunity to study the genetic and molecular mechanisms underpinning aging and regeneration using high-throughput sequencing. The successful candidate may also develop new methods to understand genetic systems. You will be enrolled through the School of Biotechnology and Biomolecular Sciences, UNSW.
About you:
• Enthusiasm and drive for science and research (essential!)
• Undergraduate degree in genetics/genomics, molecular biology, computational biology, biostatistics or a relevant field
• Some experience in R, and a scripting language such as Python
• Interest in using statistical methods
• Good written communication skills
• Australian citizenship or permanent residency
Please directly contact Emily (e.wong@victorchang.edu.au) for more details
Job website:
Contact name: Emily Wong
Contact email: E.Wong@victorchang.edu.au
Bioinformatician - vivax malaria @ Northern Territory
Position title: Bioinformatician - vivax malaria
Employer: Menzies School of Health Research
Closing date: Sep 27, 2020
Brief position description: The successful applicant will work on the P. vivax genomics program within the Menzies malaria team, with additional support from local collaborators in the Australian Center for Research Excellence in Malaria Elimination (ACREME), and international collaborators at the Wellcome Sanger Institute, Cambridge, and the Big Data Institute, Oxford. The position will entail exploration of P. vivax genomic data from our unique repository to identify important adaptations in the parasite genome such as novel drug resistance candidates. These new markers will be incorporated into our P. vivax genotyping barcodes with the aim of building in-country capacity to genotype isolates at our partner sites. Bioinformatic methods will also be applied to characterize the complexity of individual P. vivax infections to inform on local patterns of transmission, and to assess the connectivity between parasite populations to assess the spatial and temporal dynamics of parasite spread.
The position will also support the development of new, open-access software for analyzing amplicon deep sequencing data generated at our P. vivax genotyping barcodes, and the expansion of these tools to include host genotyping at the gene encoding the G6PD enzyme and other relevant loci. The aim of the G6PD genotyping is to define vivax endemic populations with genetic variants associated with G6PD deficiency that confer risk of drug induced haemolysis.
In addition to the bioinformatic analyses, the successful applicant will be responsible for assisting in the ongoing oversight, reporting and quality assurance of the research activities, and engagement with relevant project scientists, post-graduate students, and key stakeholders.
The successful applicant will be encouraged to pursue independent research interests/projects and supported in their career development with opportunities to extend their publication record in high-impact journals, facilitate workshops, supervise post-graduate students and establish their own funded program of work.
The position is based in Darwin, with opportunities to spend time at the Wellcome Sanger Institute and the Big Data Institute, UK. Overseas travel of up to 2 weeks, annually may be required. Opportunities for mentoring and networking with others outside the Northern Territory working in relevant genomics programs will be fostered by the supervisor and Menzies-based colleagues to support the successful applicant, including through relevant formal post-doctoral support and mentoring programs at Menzies.
Job website: http://careers.menzies.edu.au/job-details/query/Bioinformatician+-+Vivax+Malaria/in/Northern+Territory/7951036/
Contact name: Sarah Auburn
Contact email: sarah.auburn@menzies.edu.au
Bioinformatician – Zoonotic Malaria @ Northern Territory
Position title: Bioinformatician – Zoonotic Malaria
Employer: Menzies School of Health Research
Closing date: Sept 27, 2020
Brief position description: The Bioinformatician position will collaboratively work with and be supervised through the recently expanded Menzies GTH genomics/bioinformatics group, in addition to an international team of co-investigators at James Cook University (JCU) and the Wellcome Sanger Institute to examine zoonotic malaria transmission in Indonesia and Malaysia. This role will be part of a successful NHMRC funded project entitled ‘Parasite and human genetic risk factors for emerging Plasmodium knowlesi malaria’. The project will develop and modify appropriate genomic tools to use cutting-edge approaches to simultaneously explore parasite, host and host-parasite interactions, aiming to identify novel P. knowlesi and human loci underlying the risk of infection and disease. In addition, regional P. knowlesi population genetic analyses will explore the factors contributing to the complex and evolving dynamics of zoonotic malaria transmission. The proposed research activities are the culmination of years of fieldwork and an unprecedented number of samples, including detailed clinical phenotypes and a broad array of potentially integrative datasets involving geospatial land-types, ecological, and mosquito vector co-variates.
The successful applicant will be responsible for assisting in the design, implementation and data analysis of the above study, including engagement with relevant project scientists, post-graduate students, and key stakeholders. They will also be encouraged to pursue independent research interests/projects, including opportunities through the following current projects: (a) ‘Evaluating zoonotic malaria transmission between agricultural activities and agricultural and forestry land use in Indonesia (ZOOMAL)’ (b) State-wide human surveillance of P. knowlesi malaria in Sabah, Malaysian Borneo, and, (c) the Malaysian Armed Forces cohort study (ZOMAC) also conducted in Sabah.
The position is based in Darwin, with extended time in Cairns at JCU, and the potential for time at the Wellcome Sanger Institute, UK. Opportunities for mentoring and networking with others outside the Northern Territory working in relevant genomics programs will be fostered by relevant supervisors, including through formal post-doctoral support and mentoring programs at Menzies. Interstate and international travel may be required.
Job website: http://careers.menzies.edu.au/job-details/query/Bioinformatician+-+Zoonotic+Malaria/in/Northern+Territory/7950310/
Contact name: Matt Field
Contact email: matt.field@jcu.edu.au
KCCG Genomics Summer Scholarship @ Sydney
Position title: KCCG Genomics Summer Scholarship
Employer: Garvan Institute of Medical Research
Closing date: 30/11/2020
Brief position description: The Garvan Institute of Medical Research brings together world-leading clinicians and basic and translational researchers 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. In addition, 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), established by the Garvan Institute is an Australian research and sequencing centre delivering genomic information for clinical use. 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 20120/2021. These projects provide hands-on research experience in the following topics:
1. Deep Learning Superstardom
This position is for assisting various projects of the Deep Learning Initiative. Activities involve contributing to development, testing, deployment and documentation of Deep Neural Networks that focus on analysing real time signals from Oxford Nanopore Sequencers, and SkyMapper project, which aims to make sense of complex-multi-dimensional data using imagification and analysis using Convolutional Neural Networks.
2. Community screening program – Laboratory and Bioinformatics consideration
The project will involve reviewing and optimising specific aspects of the laboratory and downstream bioinformatics challenges as part of TKCC’s community screening program. The program currently utilises whole genome sequencing (WGS) to provide valuable genetic and clinical insights of each participant. Evaluations of new software or programming packages for specific diseases could be expected e.g. analysis of tri-nucleotide repeats and structural rearrangements.
3. Community screening program - community consultation interface
Community consultation is of increasing interest and value to KCCG as part of its clinical translation research. This project will require a student to review existing solutions for gathering community input using online interfaces, consult with build a proof of concept in line with stakeholders’ expectations. This may include subscriptions to new polls and questions, incorporating media to engage community members, templates for short surveys and open questions with navigable interfaces, and secure storage and analysis of community responses.
The project is expected to involve development of a user-friendly web interface to either SurveyMonkey or RedCap to engage, gather data and provide immediate feedback to communities on topics related to the use and reuse of genomic information for research and screening.
4. Community screening program – Dynamic Consent and the GeneTrustee™
A key part of Australia’s first genomic Community Genomics screening project is linking the participant’s consent, with their future lifetime access to their sequenced genome. This involves developing a series of APIs and Apps to connect the participant’s identity with their consent, their DNA sample, and the results of its analysis. Many components of this ecosystem have now been developed but are yet to be linked and integrated into a working whole. The project will involve developing proof-of-concept linkages between these ecosystem components, leading to the outcome of a working prototype of an end-to-end Dynamic Consent and GeneTrustee™ workflow.
5. COVID-19 Detection via Chest Sounds Prototype
COVID-19 leaves telltale marks on the lung tissue and it even influences speech. In this project we hypothesize that chest sounds as can be detected by stethoscopes could be a better indicator of lung injury and COVID-19 signature and develop a proof of concept for the hypothesis on iOs or Android and and AI server.
6. Interactive genomes visualization
Project would require strong technical front-end skills and a passion for interactive visualization of complex scientific data. Current generation of web-based UIs for genomes visualization is limited by a number of factors, including performance of REST APIs, overall performance of back end systems and the volume of data and associated network bottlenecks. The goal of the project is to develop a web-based interactive visualization of complex genomics data, using gRPC streams to communicate with back end system.
7. Mapping the locations of the control circuits of the human genome
The human genome has been sequenced. To everyone’s surprise, only ~1% of the genome codes for proteins and enzymes, and it is assumed that ‘control circuits’ must occupy a significant part of the remainder. We have recently developed bioinformatic tools that can locate a large proportion of these control circuits. In this summer project, we will commence making these tools accessible to the broader scientific community as a proposed new and valuable scientific resource. We will be approaching the problem from its two extreme ends:
1. Starting at the level of individual genes, we will be performing high-resolution mapping of the control circuits of individual genes, to increase our understanding of how these control circuits operate in detail
2. Starting at the level of the whole genome, we wish to generate a map that locates where in the genome the control circuits are situated.
There are (up to) three student positions available for this project: one student in each of the two sub-projects, and a third position that will ‘float’ between the two projects and build web- and user-interfaces to connect the projects as they each generate data that needs to be fed into the other.
8. Optimisation of popular bioinformatics software for RISC-V architecture
RISC-V is an open-source hardware architecture that is rapidly becoming popular. In the future, such opensource hardware architectures have the potential to be competitive with today’s popular RISC architectures such as ARM. We have recently demonstrated how ARM architecture can be exploited to design and develop prototypical embedded systems for portable genomic data processing. In this project, you will explore how the emerging RISC-V architecture can be exploited for such a use-case.
In this project, you will first port existing popular bioinformatics software that currently supports ARM processors (e.g. Minimap2, Samtools, Nanopolish/f5c) to work on RISC-V architecture. Then, you will optimise those ported tools to work efficiently on the RISC-V architecture. Optionally, based on the candidate’s performance and skillset, there are possibilities to extend the RISC-V architecture with application-specific instructions customised for specific genomic computations.
9. Automated identification of mode of inheritance for inherited disease
The pattern of inheritance of a disease can give us information about the type(s) of genetic mutations carried by patients and their relatives and the risk of further disease. Currently the interpretation of inheritance information is carried out as a manual step by genetic pathologists. This takes experience and time and can miss obscure or unusual inheritance patterns. This project will develop a bioinformatic framework to automate the identification of all possible modes of inheritance from a given family pedigree and highlight additional risk beyond the presenting patient.
The software developed will be part of command line pipelines, and have a separate web interface. This will form a base for integration into future clinical genetic diagnostic applications under development. Training will include bioinformatics software development and biological aspects of inheritance. Depending on the students aptitude and rate of progression, the project will expand further into clinical or research bioinformatics.
10. SquiggleKit update and web application extension
The management of raw nanopore sequencing data poses a challenge that must be overcome to facilitate the creation of new bioinformatics algorithms predicated on signal analysis. SquiggleKit is a toolkit for manipulating and interrogating raw nanopore sequencing data that simplifies file handling, data extraction, visualization and signal processing. Since its publication in 2019, many things have changed within the data and processing areas. Two updates to the software are needed to maintain its usability, and a further extension to the visualisation methods will enable future developments and data exploration.
You will first port some of the scripts from python2 to python3. Second, you will add some functions to extend the tools usability. And third, you will create a web application allowing for interactive navigation and plotting of data.
11. Excel to Database
Many lab groups are primarily managing data via spreadsheets and file names, with all the problems that this approach implies. This project would involve create database-driven apps with a web front end and migrating existing data onto the new platform.
12. Dataset registry and fetch/migration tool
There are many datasets throughout Garvan. These are managed by many different people on many different platforms (gagri, pandora, BaseSpace, Cloudstor, DNANexus, etc). Not only is it difficult to get an overview of what datasets exist, sometimes individual teams lose track of what data they have, particularly as a result of staff and student turnover. Moreover, different platforms use different tools to upload and download data, making it difficult to share data with collaborators or migrate to a more cost-effective platform.
This project involves building a dataset registry to capture key properties of each dataset, such as ownership, accessibility, storage location and a high level description of the kind of data that the dataset contains. The registry can be used for existing datasets as well as new datasets that are created. As an incentive for taking the time to register datasets with the new system, an extension of the project is to build a tool for transferring data between platforms, based on the metadata stored in the registry. This should greatly simplify collaboration, as well as migration, backups, etc.
13. Natural Language Processing to Extract Clinical Phenotypes from Biomedical Literature
Clinical Genomics tries to understand how changes in our genome (the 'genotype') lead to clinical abnormalities in a patient (the 'phenotype'). This requires analysing large amounts of genomic and phenotypic data. Unfortunately, phenotype data in the biomedical literature consists mainly of free text and is not standardised: ‘large head’, ‘big head’ and ‘macrocephaly’ all mean the same thing. This makes computational processing of phenotype data very difficult.
In this project we will explore Natural Language Processing (NLP) techniques to extract phenotypic descriptions from the biomedical literature and map them to the Human Phenotype Ontology (HPO), a standard vocabulary of over 10’000 terms used to describe the clinical features of patients with rare diseases. Once encoded in HPO terms, the phenotypic information can be computationally processed and enables sophisticated applications such as automated diagnosis.
The positions will be offered full-time for 10 weeks and provide an allowance of $5000 as a tax-free scholarship.
14. Gaucher disease (GD) is an autosomal recessive disorder caused by inherited deficiency of the enzyme beta-glucocerebrosidase (GBA). Individuals who lack working copies of this gene will develop one of several forms of GD: Type I GD (the most common) affects various organs in the body, but does not affect the nervous system. Other GD Types affect the nervous system and are much more serious, some leading to death. A recent development has been the finding that some genetic variants of GBA predispose the individual to develop Parkinson disease later in life. Variants of GBA in those of Ashkenazi Jewish (AJ) ancestry are much more common than in the general population. But paradoxically, although GD is more common in those of AJ ancestry, the incidence of GD is only a fraction of that which should occur based on the prevalence of the GBA variants. In short, something else must be protecting the individual from getting GD, even though they have a faulty GBA gene. We have the whole genome sequence of several thousand non-AJ individuals, and are obtaining the genomic sequence AJ individuals. This project involves collating this data, to understand and identify what might be causing this protective effect. Is it a second gene? Is there some other subtle genetic variant? And might this be of help not only to understanding GD, but also Parkinson disease?
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:
Academic transcripts
Which project(s) you are applying for
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_PRF5656-1
Contact name: Michelle Earle
Contact email: m.earle@garvan.org.au
Bioinformatics Research Officer - Cancer @ Sydney
Position title: Bioinformatics Research Officer - Cancer
Employer: Garvan Institute of Medical Research
Closing date: 30/09/2020
Brief position description: The Garvan Institute of Medical Research brings together world-leading clinicians and basic and translational researchers 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. In addition, three major Centres: The Kinghorn Centre for Clinical Genomics, the Garvan-Weizmann Centre for Cellular Genomics, and the Centre for Population Genomics.
The Opportunity
Reporting to A/Prof Elgene Lim and Dr Liz Caldon as a part of Connie Johnson Breast Cancer Research Group and Replication and Genome Stability Group, Cancer Research Division the Bioinformatics Research Officer is accountable under direction for conducting research that seeks to identify the biological, genetic and molecular processes in breast cancer. Specifically, this position will be responsible for leading the analysis of transcriptomics, genomic and single cell datasets.
A high level of interaction with other bioinformaticians, ROs, RAs and PhD students within the Cancer Research Division is essential.
As the project develops, additional RAs and PhD students may be recruited to the project and the Bioinformatics Research Officer would be expected to assist in their supervision. Assistance in the preparation of research grant proposals, presentations and publications will be expected.
This is a two-year full time opportunity to start.
Key Responsibilities
Recording and assisting with design and interpretation of experimental procedures and results
Conducting leading-edge informatic analysis of genetic and genomic datasets
Working collaboratively and flexibly across multiple projects that may engage different bioinformatic skill sets.
Regular meeting with A/Prof Elgene Lim and Dr Liz Caldon and members of the Cancer Research Division to discuss and review current and future techniques and experiments
Making presentations of research progress to the Cancer Research Division and other collaborative groups as required
Undertaking several research projects in an efficient and timely manner and have the outcomes of these projects published under joint authorship in leading scientific journals.
Providing general research guidance to more junior research staff whose work might have an impact on wider division research goals
About You
Possess a Masters or PhD in Bioinformatics or equivalent experience in a related field
Advanced user of the R programming language and R-based statistical packages and tools, such as those available from the Bioconductor project for high throughput genomic data analysis
The analysis of next generation sequencing data, including single cell RNA-Seq
Running informatic jobs on high performance computing systems
Data visualisation
Good knowledge of statistics and presentation of molecular/clinical data
Experience in the analysis and interpretation of large genomic data sets (WGS, RNAseq)
Excellent computational background, especially in the management of large data sets in unix/linux environment
High proficiency in programming and scripting languages (e.g. C/C++, Java, Perl, Python)
A proven track record, e.g. publications, grants, software/tool development
Familiarity with the ethical issues and guidelines relating to the use of human tissue and clinical data for research
Good background knowledge of cancer genetics/biology is desirable
Excellent problem solving and project management skills is required whilst working independently on projects to meet tight deadlines
How to Apply
All applications must include a cover letter, resume including at least 2 referees and copies of relevant qualifications / academic transcripts and apply in the company website. This 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.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Research-Officer_PRF5464-1
Contact name: Michelle Earle
Contact email: m.earle@garvan.org.au