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
Computational Biologist: Cancer Genomics–The Kinghorn Centre for Clinical Genomics @ Sydney
Position title: Computational Biologist: Cancer Genomics–The Kinghorn Centre for Clinical Genomics
Employer: Garvan Institute of Medical Research
Closing date: 31/08/2020
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 Kinghorn Centre for Clinical Genomics (KCCG's) Translational Genome Informatics Group (TIG) is a multidisciplinary team of bioinformaticians, statisticians, software engineers and clinical researchers. The team develops and applies computational methods to better understand human disease. We take a collaborative approach, working closely with experimental researchers across Garvan to tackle biological problems that address critical unmet medical needs.
The Opportunity
This position will drive somatic analysis capabilities within KCCG. The role includes both an engineering component and computational analysis. The researcher will work with existing in-house pipelines to streamline workflows for analysis of patient cohorts and allow consolidation with large public datasets. On the analysis side, the initial focus is on structural variation in childhood cancer using long-read sequence data.
This is a one-year full-time role. We are happy to provide remote on-boarding (for intra/ interstate) employees keeping the current pandemic in mind and considering health and safety of our employees as our top priority.
Key Responsibilities
This position will be responsible for helping to provide direction and support in clinical genomics, genome informatics and translational research. This will include:
Consolidating in-house somatic analysis pipelines
Bringing in-house high value oncology related datasets and integrating with internal cohorts
Analysing structural variation in childhood cancer using long-read sequence data
Constantly collaborating with cancer researchers
Undertaking and directing translational research with an emphasis on developing biological insights that are relevant to patient outcomes
Staying abreast on advances in genomics and next generation sequencing technology in general as well as maintaining knowledge about clinical genomic testing and personalised medicine.
Occasionally represent KCCG at events, or talks with external stakeholders
About You
In order to be successful in this position, you will demonstrate the following key skills and attributes:
PhD in a related area of science or equivalent and at least 3 years of experience
Highly developed skills in bioinformatics and genomics
Demonstrated a keen interest in Biology and/or Clinical Genomes
Expertise in working with next-generation sequencing data
Project management skills with the ability to work independently and yet amicably in a team environment to meet deadlines
Good communication skills both verbal and written
Desirable
Expertise in working with somatic data
Strong track record of peer review publication
How to Apply
Australian/NZ citizen, permanent resident or other applicants with full working rights can only apply. All applications must include a cover letter along with your resume with at least two referees. We are reviewing applications as they are received. This position will remain open until end of August 2020. You can visit external career page on Garvan website to refer to other similar roles.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Computational-Biologist--Cancer-Genomics-The-Kinghorn-Centre-for-Clinical-Genomics_PRF5629-1
Contact name: Michelle Earle
Contact email: m.earle@garvan.org.au
Bioinformatician – The Kinghorn Centre for Clinical Genomics @ Sydney
Position title: Bioinformatician – The Kinghorn Centre for Clinical Genomics
Employer: Garvan Institute of Medical Research
Closing date: 31/08/2020
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 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 Opportunity
The role will be responsible for consolidating data from across cohorts and incorporate these into the databases/repositories that are accessible to researchers. There is scope within this position to perform genomics and bioinformatics research, publish scientific papers, and to pursue independent funding.
This is a one-year full-time role. We are happy to provide remote on-boarding (inter or intra state) keeping the current pandemic in mind and considering health and safety of our employees as our top priority.
Key Responsibilities
This position will be responsible for helping to provide direction and support in clinical genomics, genome informatics and translational research. This will include:
Seek out genomics datasets from across Garvan and establish a catalogue with clinical information as well as links to genomic data
Develop databases for storage of cohort metadata and interfaces to provide access to researchers
Undertaking and directing translational research with an emphasis on developing biological insights that are relevant to patient outcomes
Occasionally represent KCCG at events, or talks with external stakeholders
And, staying abreast on advances in genomics and next generation sequencing technology in general as well as maintaining knowledge about clinical genomic testing and personalised medicine
About You
In order to be successful in this position, you will demonstrate the following key skills and attributes:
A Bachelor degree in a related area of science or engineering preferably with a couple of years of experience
Demonstrated interest in Biology and/or Clinical Genomes
Excellent problem-solving ability with good communication skills both verbal and written
Project management skills with the ability to work independently and yet amicably in a team environment to meet deadlines
Desirable
A PhD in Bioinformatics/Computational Biology or a related field
Skills in bioinformatics and/or genomics
Experience working with next-generation sequencing data
Software engineering skills: source control management, unit and regression testing, continuous integration
Experience in developing diagnostic assays, and assessing their analytical performance
How to Apply
Australian/NZ citizen, permanent resident or other applicants with full working rights can only apply. All applications must include a cover letter along with your resume with at least two referees. We are reviewing applications as they are received. This position will remain open until end of August 2020. You can visit external career page on Garvan website to refer to other similar roles.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Bioinformatician---The-Kinghorn-Centre-for-Clinical-Genomics_PRF5630-1
Contact name: Michelle Earle
Contact email: m.earle@garvan.org.au
Computational Biologist – The Kinghorn Centre for Clinical Genomics @ Sydney
Position title: Computational Biologist – The Kinghorn Centre for Clinical Genomics
Employer: Garvan Institute of Medical Research
Closing date: 31/08/2020
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 Kinghorn Centre for Clinical Genomics (KCCG's) Translational Genome Informatics Group (TIG) is a multidisciplinary team of bioinformaticians, statisticians, software engineers and clinical researchers. The team develops and applies computational methods to better understand human disease. We take a collaborative approach, working closely with experimental researchers across Garvan to tackle biological problems that address critical unmet medical needs.
The Opportunity
This position will drive the development and validation of approaches for interpreting multi-omic data with a focus on translation. Examples of the projects ongoing include: developing prognostic and predictive biomarkers for Parkinson's Disease, studying the genetics of sleep in individuals with Autism, using liquid biopsy to monitor cancer patients following surgery and identifying molecular mechanisms of tumour metastisis using single cell expression data.
This is a one-year full-time role. We are happy to provide remote on-boarding (for intra/ interstate) employees keeping the current pandemic in mind and considering health and safety of our employees as our top priority.
Key Responsibilities
This position will be responsible for helping to provide direction and support in clinical genomics, genome informatics and translational research. This will include:
Analysing multi-omic data for disease cohorts to understand disease heterogeneity and developing prognostic and predictive biomarkers
Integrating genomic, transcriptomic and single-cell in-house and external datasets to understand disease molecular mechanisms
Undertaking and directing translational research with an emphasis on developing biological insights that are relevant to patient outcomes.
Occasionally represent KCCG at events, or talks with external stakeholders.
Staying abreast on advances in genomics and next generation sequencing technology in general as well as maintaining knowledge about clinical genomic testing and personalised medicine
About You
In order to be successful in this position, you will demonstrate the following key skills and attributes:
PhD in a related area of science or equivalent and at least 3 years of experience
Highly developed skills in bioinformatics and genomics
Expertise in working with next-generation sequencing data
Excellent problem-solving ability with good communication skills both verbal and written
Project management skills with the ability to work independently and yet amicably in a team environment to meet deadlines
Ability to develop, manage and maintain internal and external relationships
Strong track record of peer review publication
Desirable
Software engineering skills: source control management, unit and regression testing, continuous integration
Experience in developing diagnostic assays, and assessing their analytical performance
Experience supervising students and/or junior staff
How to Apply
Australian/NZ citizen, permanent resident or other applicants with full working rights can only apply. All applications must include a cover letter along with your resume with at least two referees. We are reviewing applications as they are received. This position will remain open until end of August 2020. You can visit external career page on Garvan website to refer to other similar roles.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Computational-Biologist---The-Kinghorn-Centre-for-Clinical-Genomics_PRF5627-1
Contact name: Michelle Earle
Contact email: m.earle@garvan.org.au
Computational Biologist/Bioinformatician - Exceptional Responders Study @ Sydney
Position title: Computational Biologist/Bioinformatician - Exceptional Responders Study
Employer: Garvan Institute of Medical Research
Closing date: 31/08/2020
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 Kinghorn Centre for Clinical Genomics (KCCG's) Translational Genome Informatics Group (TIG) is a multidisciplinary team of bioinformaticians, statisticians, software engineers and clinical researchers. The team develops and applies computational methods to better understand human disease. We take a collaborative approach, working closely with experimental researchers across Garvan to tackle biological problems that address critical unmet medical needs.
The Opportunity
The Exceptional Responders Program (ExcRes) is a Nationally-recruiting initiative to progress precision cancer medicine through genomic analysis of treatment-outliers. ExcRes collaborates with cancer clinicians nationally to recruit patients who have had an unusual or unexpected response to anti-cancer treatment. This position will analyse multi-omic data from exceptional responders to tease out the molecular mechanisms driving their unusual response to therapy.
This is a one-year full-time role. We are happy to provide remote on-boarding (for intra/ interstate) employees keeping the current pandemic in mind and considering health and safety of our employees as our top priority.
Key Responsibilities
This position will be responsible for helping to provide direction and support in clinical genomics, genome informatics and translational research. This will include:
Analysing multi-omic data collected from exceptional responders
Identifying appropriate matched controls from in-house and public datasets
Working closely with the ExcRes team to interpret sequence data and design follow on studies
Developing databases for storage of cohort metadata and interfaces to provide access to researchers.
Staying abreast on advances in genomics and next generation sequencing technology in general as well as maintaining knowledge about clinical genomic testing and personalised medicine
Occasionally represent KCCG at events, or talks with external stakeholders
About You
In order to be successful in this position, you will demonstrate the following key skills and attributes:
PhD in a related area of science or equivalent or Bachelor's degree and at least 3 years of experience
Highly developed skills in bioinformatics and genomics
Ability to develop, manage and maintain internal and external relationships
Excellent problem-solving ability with good communication skills both verbal and written
Project management skills with the ability to work independently and yet amicably in a team environment to meet deadlines
Desirable
Experience working with next-generation sequencing data
Experience analysing cancer genomic data
Strong track record of peer review publication
How to Apply
Australian/NZ citizen, permanent resident or other applicants with full working rights can only apply. All applications must include a cover letter along with your resume with at least two referees. We are reviewing applications as they are received. This position will remain open until end of August 2020. You can visit external career page on Garvan website to refer to other similar roles.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Computational-Biologist-Bioinformatician---Exceptional-Responders-Study_PRF5628-1
Contact name: Michelle Earle
Contact email: m.earle@garvan.org.au
Postdoctoral Research Officer - Bioinformatics & Cellular Genomics @ Melbourne
Position title: Postdoctoral Research Officer - Bioinformatics & Cellular Genomics
Employer: St Vincent's Institute of Medical Research
Closing date: 2020-08-31
Brief position description: We are seeking a motivated and successful postdoctoral Researcher to work on an independent project in machine learning for clinical image data. This role will help develop new deep learning methods and software to transform population screening for breast cancer. You will implement, train, test and deploy machine learning models to detect breast cancer from mammogram images and develop model interpretation strategies that describe why a prediction was made. Working in close collaboration with colleagues at St Vincent’s Hospital Melbourne, the University of Melbourne and the University of Adelaide, you will have the opportunity to provide computational expertise on experimental design and data analysis, and will have project-wide responsibility across the breast cancer screening project. You will have access to a proprietary database of over 200,000 high-quality, annotated clinical images from BreastScreen Victoria that have never before been used to train machine learning models. You will identify opportunities to customise more efficient workflows and methods where warranted and lead prospective studies to test, in a clinical setting, the real-world performance of the models you develop.
Job website: http://www.seek.com.au/job/50287843?
Contact name: Davis McCarthy
Contact email: hr331@svi.edu.au
Bioinformatics Research Officer – Cancer @ Sydney
Position title: Bioinformatics Research Officer – Cancer
Employer: Garvan Institute of Medical Research
Closing date: 30/08/2020
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 Australian Genomic Cancer Medicine Centre (AGCMC) is a not-for-profit, nationwide network of centres and medical research institutes that delivers precision medicine clinical trials and studies for the screening, prevention and treatment of cancers. It has a focus on patients with rare, less common and early onset cancers, and cancers with poor outcomes. The Molecular Screening and Therapeutics (MoST) program is a key component of the AGCMC, running nationally and co-ordinated at the Garvan Institute, and requires a bioinformatics research officer for operations and development.
The Opportunity
The position will work with the Chief of Informatics of the AGCMC to perform research into translational cancer genomics, including developing, streamlining, and validating approaches for analysing and interpreting cancer genomes for clinical research use.
This position will be embedded within the Australian Genomic Cancer Medicine Program at the Garvan Institute, and play a pivotal role in the success of the MoST program. The MoST program is an innovative adaptive signal-seeking framework trial design, aiming to generate evidence to support novel hypotheses behind genotype-guided therapeutic interventions. MoST use fast turn-around, targeted sequencing panels to study patients with rare, and advanced cancers, then use this information to recommend targeted therapies, either within the MoST program, or triaging onto available trials. The MoST program has been running in New South Wales since 2016 but has recently been expanded into a national program, co-ordinated at the Garvan Institute. This role will be jointly responsible for optimising the genomic analysis, and interpretation components of the MoST program, participating in Molecular Tumour Board (MTB) meetings, and have responsibility for preparing Molecular Tumour Board reports for each patient. This exciting opportunity will leverage the outcomes from research projects to change the way cancer patients in Australia and ultimately beyond will be treated in the clinical environment.
The project is also generating substantial cohort data and bioinformatics skills are required in various projects to analyse these data. This is a two year full-time position.
Key Responsibilities
This position will be responsible for helping to provide support in clinical research genomics, genome informatics and translational research in cancer genomics. This will include:
• Undertaking translational research with an emphasis on developing biological insights that are relevant to patient outcomes.
• Improving the breadth, quality and efficiency of existing genomic analysis pipelines, through development of improved bioinformatics approaches.
• Develop approaches to optimise and streamline interpretation of genomic data.
• Staying abreast on advances in genomics and next generation sequencing technology in general as well as maintaining knowledge about genomic testing and personalised medicine.
• Working independently, but importantly being able to work as part of a dynamic team
About You
In order to be successful in this position, you will demonstrate the following key skills and attributes:
• Postgraduate or industry experience (>3 years) in related disciplines
• Highly developed skills in bioinformatics and genomics
• Highly developed Python programming skills
• Project management skills
Desirable
• Knowledge of clinical interpretation of genomic data
• Source control management, unit and regression testing, continuous integration
• Other software engineering skills, e.g. web development
• Database management and SQL skills
• Knowledge developing diagnostic assays, and assessing their analytical performance
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: http://garvan.wd3.myworkdayjobs.com/en-US/garvan_institute/job/Sydney/Bioinformatics-Research-Officer_PRF5622-1
Contact name: Michelle Earle
Contact email: m.earle@garvan.org.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: 16/08/2020
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. This position will remain open until 16, August 2020.
Job website: http://garvan.wd3.myworkdayjobs.com/en-US/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