Employer: Australian Institute of Tropical Health and Medicine (AITHM)
Closing date: 30 September
Brief position description: Calling for Systems Biology PhD applications to join the new “Health and Disease” theme of the Centre for Tropical Bioinformatics and Molecular Biology (CTBMB) and Australian Institute of Tropical Health and Medicine (AITHM), at James Cook University (Cairns, Australia).
Bioinformatics and Systems Biology projects opportunities exist in a range of infectious and chronic diseases that affect the tropics, such as tuberculosis, malaria, dengue, and diabetes as well as ongoing national and international collaborations in neuroscience and malaria. Systems Biology aims to better understand human disease using a combination of high-throughput technology (such as DNA/RNA sequencing, proteomics etc.) and bioinformatics. Projects are available in pure bioinformatics/systems biology, utilising and developing bioinformatics/systems biology/statistics/machine learning methods as well as joint wet-lab/dry-lab projects through excellent cross-cutting co-supervision.
Specific project opportunities exist for:
1) Development of bioinformatics methods for untangling disruptive signalling in neurological disease (collaboration with Dr Mark Graham; Children's Medical Research Institute)
2) Establishment of host-pathogen interaction bioinformatics platforms and methods for simultaneous analysis of host and pathogen transcriptomics (collaboration with Dr Firth)
3) Multi-omics bioinformatics of BCG vaccinated and Mtb-infected children (collaboration with Dr Kuptz, TB Immunology Group)
4) Systems immunology and multi-omics approaches to understand protective immunity to human malaria (collaboration with Prof Doolan and Dr Wise). This is supported by an AITHM Scholarship and details about this project are available here (closes, 13th September): https://www.aithm.jcu.edu.au/phd-stipend-scholarship/
Supervisor contacts:
Dr Ashley Waardenberg – Research Fellow (Bioinformatics), Theme Leader, JCU Centre for Tropical Bioinformatics and Molecular Biology https://research.jcu.edu.au/portfolio/ashley.waardenberg/
Ashley.Waardenberg@jcu.edu.au; (61-7) 4232 2046
Professor Denise Doolan – Professorial Research Fellow (Molecular Immunology), AITHM Deputy Director; Director of JCU Centre for Molecular Therapeutics https://research.jcu.edu.au/portfolio/denise.doolan/
denise.doolan@jcu.edu.au; (61-7) 4232 1492
Dr Ingrid Wise – Research Fellow (Molecular Immunology) https://research.jcu.edu.au/portfolio/ingrid.wise/
ingrid.wise@jcu.edu.au
Dr Andreas Kupz – Senior Research Fellow, Group Leader - Tuberculosis Immunology, Centre for Molecular Therapeutics
https://research.jcu.edu.au/portfolio/andreas.kupz/
andreas.kupz@jcu.edu.au; (61-7) 4232 2048
Dr Cadhla Firth – Hot North Career Development Fellow (pathogen genomics)
cadhla.firth@jcu.edu.au
Job website: http://www.jcu.edu.au/graduate-research-school/candidates/postgraduate-research-scholarships
Contact name: Ashley Waardenberg
Contact email: ashley.waardenberg@jcu.edu.au
PhD Scholarship - Genomic Data Analytics @ Monash
Employer: Monash University
Closing date: Saturday 30 November 2019, 11:55 pm AEST
Brief position description: Job No: 589959
Location: The Alfred Centre, 99 Commercial Road, Melbourne
Employment Type: Full-time
Duration: 3 year fixed-term appointment
Remuneration: Monash University Research Training Program (RTP) stipend: $27,872 per annum
The Opportunity
This is a unique opportunity to undertake a PhD in the Public Health Genomics program at Monash University, with direct access to one of the highest quality cohorts in Australia, the ASPirin in Reducing Events in the Elderly (ASPREE) study.
ASPREE have generated genomic data on over 15,000 Australians, now amongst the most comprehensive genomic data ever produced for an Australian cohort (13,500 exomes, 3,000 whole genomes, 15,000 SNP genotyping). The genomic data is accompanied by an unprecedented level of longitudinal phenotype, clinical and lifestyle information collected over 5+ years, to the highest standards of a clinical trial.
We seek talented PhD students to undertake data-driven studies with ASPREE, to begin to build their research careers around this important cohort study. Various projects are available making use of genomic + phenotypic data.
We seek candidates with backgrounds in human genetics, computational biology, statistical genetics, genetic epidemiology and/or clinical DNA sequencing analysis, with a desire for innovative analysis of large datasets. Candidates need to have a baseline knowledge of human genetics and be proficient with command line and R.
Essential Criteria
- Australian Citizen or Australian permanent resident
- An undergraduate (Honours) or Masters degree in biology, genetics, computer science and/or a related discipline
- Good written and oral communication skills and an ability to work in a team environment
- Proficiency (or high aptitude) for R programming and command line
Enquires and How to Apply
Interested candidates, please contact the Head of Public Health Genomics; Paul Lacaze (Paul.Lacaze@monash.edu) for more detail of the application procedure.
Please specify the project name above when making enquiries.
Closing Date
Saturday 30 November 2019, 11:55 pm AEST
Job website: http://careers.pageuppeople.com/513/cw/en/job/589959/phd-scholarship-genomic-data-analytics
Contact name: Paul Lacaze
Contact email: Paul.Lacaze@monash.edu
Post-doctoral position in Structural Bioinformatics @ CEA
Employer:Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA)
Closing date:30 November 2019
Brief position description:The successful candidate will be a key member of a research project, MODAMDH, funded by the French Research Agency (ANR) and carried out in the Research Unit of Genoscope (CEA, CNRS, Paris-Saclay Univ., UMR8030). From its inception, Genoscope has been at the forefront of large-scale sequence-based science. Today, our institute performs biological and bioengineering research with applications in environment, healthcare and alternative energy. The Genoscope encompasses multidisciplinary team of ~100 staff with postdocs and engineers having expertise in genomics, bioinformatics, microbiology, biochemistry and biocatalysis.
The MODAMDH project aims at finding new amine dehydrogenases among biodiversity. It will be carried out by innovative approaches based on distant homology and 3D modeling of enzymes to mine massive (meta)genomic data. This project involved the biocatalysis (LBMS) and bioinformatics (LABGeM) teams of the Genoscope in collaboration with the York Structural Biology Laboratory (York, UK).
The candidate will be in charge of conducting bioinformatics analysis using cutting-edge methods in structural bioinformatics and sequence analysis. Large amount of candidate enzymes will be experimentally screened and selected hits will be characterized for biocatalysis application by a PhD student involved in this project. In addition, structural determination of the enzymes will be performed with another PhD student of the York laboratory.
Job website:https://bit.ly/2Zs2QEG
Contact name:Carine Vergne Vaxelaire
Contact email:carine.vergne@genoscope.cns.fr
Postdoctoral Scientist - Bioinformatician @ VCCRI Sydney
Employer:Victor Chang Cardiac Research Institute
Closing date:30/09/2019
Brief position description:We are seeking an enthusiastic post-doctoral scientist to join the Computational Genomics Laboratory, led by Dr Eleni Giannoulatou. The successful candidate will be involved in the analysis of whole genome sequencing datasets of patients with dilated cardiomyopathy and congenital heart disease recruited and sequenced by the Cardiovascular Genetic Disorders Flagship of Australian Genomics. The candidate will work closely with the laboratories of Prof Diane Fatkin and Prof Sally Dunwoodie.
Duties and responsibilities include:
• Development and application of quantitative methods on large genomic datasets
• Visualisation and interpretation of genomic data
• Supervision of junior lab members
• Publications in bioinformatics or genetics journals and presentations at conferences
This is a full-time appointment for three years with an annual review, and the possibility of renewal subject to funding.
Job website:https://www.nature.com/naturecareers/job/postdoctoral-scientist-bioinformatician-victor-chang-cardiac-research-institute-vccri-702675
Contact name:Eleni Giannoulatou
Contact email:e.giannoulatou@victorchang.edu.au
Postdoctoral Research Fellow in Bacterial Genomics @ Sydney
Employer:Macquarie University
Closing date:15/09/19
Brief position description:An exciting role has become available in the Department of Molecular Sciences (MolSci) at Macquarie University, Sydney, under the supervision of Dr Amy Cain. We are currently seeking a full-time Postdoctoral Research Fellow in Bacterial Genomics to develop and contribute to multiple bacterial genomics projects across the laboratory. You will be embedded within a small, enthusiastic and focused research team and expected to run your own projects as well as contribute to the ongoing lab work within the team in order to answer large and important biological questions focusing on bacterial responses to antibiotic stress.
This will be a largely bioinformatics-based position, but will likely include laboratory components depending on the research interests and capabilities of the successful candidate. Projects span areas of research using functional genomics to study antimicrobial resistance, antibiotic mode of action, evolutionary biology, pathogen/host infection, antibiotic development, hospital outbreaks and more. Within this team, you will run your own research and work in a team across multiple projects (depending on interests and background) within the core theme of understanding how antibiotics act on various hospital ESKAPE pathogens.
You will distill biological insights from various datasets of functional genomics sequencing data from cutting-edge sequencing technologies, such as transposon-insertion sequencing, RNAseq, phenotypic arrays, microfluidics, metabolomics and FACS using network analysis, correlation analysis, and/or machine learning techniques will be confirmed and placed back into biological significance in the laboratory. You will have the opportunity to publish new methodologies in Github and work on our servers.
Job website:http://jobs.mq.edu.au/cw/en/job/506471/postdoctorate-research-fellow-in-bacterial-genomics
Contact name:Amy Cain
Contact email:amy.cain@mq.edu.au
AITHM PhD scholarship ($28k) - Systems immunology and multi-omics approaches to understand protective immunity to human malaria @ Cairns
Employer:Australian Institute of Tropical Health and Medicine (AITHM)
Closing date:13th September 2019
Brief position description:The Australian Institute of Tropical Health and Medicine (AITHM) at James Cook University (Cairns) is a cross-disciplinary research institute comprised of bioinformaticians, systems biologists, immunologists, molecular biologists, and chemists. The scope of research encompasses basic science through to clinical translation and impact.
We invite applications for a PhD position focused on identifying human host factors that predict immune control of malaria. The project will utilise systems-based immunology and multi-omics approaches to profile the host immune response in controlled infection models of malaria at molecular, cellular, transcriptome and proteome-wide scale. The overall aim will be to develop and apply computational/biostatistical approaches, including network theory and machine learning, which integrate genomics, proteomics, transcriptomics and molecular immunology to improve our understanding of the host-parasite relationship and predict immune responsiveness and parasite control. Molecular signatures of immunity to malaria will inform the development of vaccines, immunotherapies or diagnostic biomarkers.
This project will provide an opportunity to be involved in cutting-edge advances integrating diverse fields of high dimensional -omic datasets. It will complement ongoing systems-based and therapeutic development efforts at AITHM directed at malaria and other tropical pathogens. The successful candidate will learn from, and be supported by, a team of researchers in bioinformatics, immunology, molecular sciences and biostatistics.
Methodologies:
Bioinformatics, Machine Learning, Immunology, Systems Immunology, Systems Biology, Genomics/Proteomics/Transcriptomics, Molecular and Cell Biology, Statistics
Eligibility:
Entry: BSc Honours Class I (or equivalent via outstanding record of professional or research achievements)
Experience/Background: Experience with programming languages, mathematics, statistics and/or background in immunology and molecular sciences, with an interest in integrating the fields of immunology and bioinformatics.
Excellent computer, communication, and organisational skills are required. Forward thinking, innovation and creativity are encouraged.
Scholarship: $28,000 per annum for three years.
Closing date: 13th Sept 2019
Please send your Curriculum Vitae, a copy of your academic record, and 1-page outline of your goals for a PhD (as per contact details below).
Supervisors:
• Dr Ashley Waardenberg – Research Fellow (Bioinformatics), Theme Leader, JCU Centre for Tropical Bioinformatics and Molecular Biology https://research.jcu.edu.au/portfolio/ashley.waardenberg/
• Professor Denise Doolan – Professorial Research Fellow (Molecular Immunology), AITHM Deputy Director; Director of JCU Centre for Molecular Therapeutics https://research.jcu.edu.au/portfolio/denise.doolan/
• Dr Ingrid Wise – Research Fellow (Molecular Immunology) https://research.jcu.edu.au/portfolio/ingrid.wise/
Contact details:
Dr Ashley Waardenberg: Ashley.Waardenberg@jcu.edu.au; (61-7) 4232 2046
Professor Denise Doolan: Denise.Doolan@jcu.edu.au; (61-7) 4232 1492
Job website:
Contact name:Ashley Waardenberg
Contact email:ashley.waardenberg@jcu.edu.au
Postdoctoral Research Fellow @ Monash University
Employer: Institute of Vector Borne Disease - Monash University
Closing date: 10 Sept
Brief position description: The Vector and Pathogen Genomics group at the Institute of Vector-Borne disease at Monash University is looking for a skilled postdoctoral Research Fellow to investigate genomic rearrangement and mobile element insertion in Aedes aegypti and its effect on gene flow in wild populations. As well as being a fascinating aspect of genome evolution, this is also a subject of prime interest to the success of population replacement interventions and the specific work of the World Mosquito Program.
In our group we apply omics tools to vectors, viruses and parasites in order to better understand disease transmission and develop tools for disease surveillance and control. Specific interests of the group include population structure and speciation in mosquito vectors, pathogen diversity and relatedness, pathogen-vector interactions and genomic epidemiology. This is all performed within the context of the World Mosquito Program and their global network of Wolbachia-based interventions into dengue and Zika transmission.
The role would suit either a computational biologist looking to work in an important field of infectious disease research, or an experienced entomologist who would like to pursue a postdoc in a computational field. Researchers with previous experience in statistical / population genetics or genomic evolution in insect species are encouraged to apply.
Job website: http://jobs.sciencecareers.org/job/501505/research-fellow/
Contact name: Seth Redmond
Contact email: seth.redmond@monash.edu
PhD candidate @ ANU
Employer: The John Curtin School of Medical Research, Australian National University
Closing date: 24/08/2019
Brief position description: We are looking for motivated bioinformaticians to work with long-read technologies and challenging genomic problems relevant for cancer and evolution. We are seeking a skilled and motivated candidate for a PhD position to work in an interdisciplinary project to characterise ribosomal DNA repeats, their variability and transcriptional properties, using nanopore long-read sequencing technologies. The successful candidate will work under the supervision of Prof. Ross Hannan and Prof. Eduardo Eyras, at the John Curtin School of Medical Research (Australian National University), and Dr. Austen Ganley (University of Auckland). Additionally, there will be the opportunity to develop the work both in Auckland, New Zealand, and Canberra, Australia.
We look for candidates with outstanding qualifications in biology, biochemistry, computer science, biostatistics, or similar. Good working knowledge of statistics and programming is required. Experience in the area of genomics and transcriptomics will be a plus. The successful candidate will work in close collaboration with the experimental groups generating the datasets, and will contribute with new analyses and tools to process long and short read sequencing data.
Applicants should send their CV, motivation letter, plus transcription of their graduate and postgraduate marks to eduardo.eyras@anu.edu.au
Job website:
Contact name: Eduardo Eyras
Contact email: eduardo.eyras@anu.edu.au
Bioinformatician @ AGRF
Employer: Australian Genome Research Facility
Closing date: Sunday 25 August 2019
Brief position description: About us:
Australian Genome Research Facility (AGRF) is a not-for-profit organisation committed to quality and innovation. AGRF provides the gateway to a national network of essential genomic technology, expertise and innovation through our main laboratory operations located at the Victorian Comprehensive Cancer Centre in Melbourne, and laboratories located in Adelaide, Brisbane, Perth and Sydney,
We seek to empower Australia to be recognised for world-class genomics and innovation. By collaborating and sharing our knowledge and expertise, and providing local access to innovative and state-of-the-art genomic technologies, we enable Australian academia and industry to advance leading-edge genomic research internationally. We are a team of dependable, collaborative and innovative thinkers who are empowered to generate and deliver solutions to the scientific community.
About the role:
In this full-time, 12 month contract role of Bioinformatician you will report directly to the Bioinformatics Manager and support AGRF's national bioinformatics capability through delivering innovative and tailored solutions for clients' research hypotheses and acting as Primary Analyst responsible for specific analysis. You will also provide support for internal and external training workshops, promote the service via liaison with external Bioinformatics groups and the life science community. As a team player you will support the optimisation of team operations and contribute to improving work efficiencies within the team.
•PhD or Masters in Bioinformatics, Computational Biology or an equivalent combination of experience and/or training
•Experience with common bioinformatics software for Next Generation Sequencing
•In-depth knowledge of and experience in high throughput sequencing data analysis
•Familiarity with basic concepts in biology
•Familiarity with research design and scientific methods
•Computer programming skills Linux/UNIX plus at least one of Python, Perl, R, shell scripting and/or other relevant languages
•Strong written and verbal communication skills
•Demonstrated ability to work effectively in a service role emphasising client satisfaction
•Demonstrated ability to handle tight deadlines and maintain high standards of work
Any of the following is desirable but not essential:
•Experience in working with job scheduling systems, such as SLURM, in HPC clusters
•Experience in teaching bioinformatics to life scientists
•Knowledge of working with version control systems such as Git, SVN
•Experience with analysing RNA-seq, GBS, exome/WGS, metagenomics
Benefits:
Attractive remuneration package on offer including 9.5% superannuation, salary packaging benefits and employee benefits discount program.
Job website: http://www.seek.com.au/job/39666898?_ga=2.243061511.445193512.1565824582-1683870033.1565311458
Contact name: Karen Jenkins
Contact email: karen.jenkins@agrf.org.au
Research Associate/Fellow of Bioinformatics @ Perth
Position title: Two positions - Research Associate/Fellow - Bioinformatics
Employer: Curtin University - Centre for Crop & DIsease Management
Closing date: 16/8/2019
Brief position description: Location: Perth
Centre for Crop and Disease Management (CCDM)/School of Molecular and Life Sciences (MLS)
Fixed term, full time until 22 June 2022
$88,135 - $118,115 (ALA /ALB) plus 17% Superannuation
Curtin University is ranked in the top 1% of universities worldwide (ARWU 2018 and QS World University Rankings 2019), and is placed 20th in the world for universities less than 50 years old (QS Top 50 Under 50 2019). Curtin is WA’s most preferred university, with highly engaged industry-facing partners. A major global player, with well-integrated campuses in Singapore, Malaysia, Mauritius and Dubai.
Centre for Crop and Disease Management (CCDM)
The Centre for Crop and Disease Management (CCDM) at Curtin University launched in April 2014 – a bilateral research agreement between the Grains Research and Development Corporation (GRDC) and Curtin University. The CCDM is a major investment in research training, crop disease-focussed research activity and infrastructure. The Centre includes a new high quality research facility at Curtin, used for research and development to sustainably reduce the impact of important grain pathogens and ultimately, to provide solutions to reduce the impact of diseases on farm business resilience. The Centre’s activities integrate molecular sciences with field-based agronomy to generate new avenues to breed disease resistant germplasm and to assist farmers to sustainably utilise a full range of disease control options. The CCDM has three themes of activity with several projects in each theme. There is strong interdisciplinary collaboration within the Centre and active collaboration with leading national and international scientists.
These positions sit within Research Theme B and Research Theme C, respectively.
Research Theme B – Cereal Diseases
Theme B of the CCDM focusses on cereal disease research and targets a range of costly and complex diseases of wheat and barley. Yield and economic losses of both of these crops remain a significant issue for the Australian grains industry. Theme B conducts pre-breeding research using biochemical, genetic and ‘omic’ approaches to help breeders develop disease-resistant varieties as an effective, long-term solution to crop disease control. Our researchers also explore the interaction of pathogens during co-infection and the resulting host responses.
Research Theme C – Canola and Pulse Diseases
Theme C of the CCDM, focuses on research into ascochyta blight of pulses and sclerotinia stem rot of canola and pulses. The successful candidate will work across projects involving the pathogens Ascochyta rabiei and Ascochyta lentis which infect chickpea and lentils, respectively, to identify sources of resistance and will develop links and work closely with breeding entities to ensure successful uptake and deployment of the identified sources of resistance in breeding programs. The successful candidate would also work closely with the broader CCDM bioinformatics team and Theme C colleagues to identify and characterize candidate effector genes of Ascochyta species. The successful candidate will present their research to colleagues in the centre and the field of research, as well as communicate their research to agronomists, growers and breeders.
Your new role
This rare opportunity is to work in a dynamic team of researchers to substantially improve yield stability for Australian grain growers.
These positions will be based at Bentley Campus, Perth Western Australia embedded with the School of Molecular and Life Sciences. The position will involve engaging with collaborators, industry partners both locally and internationally and developing funding proposals. This role may require some teaching activities.
What we offer you
The Faculty of Science and Engineering offers exciting career paths and trajectories including
conducting innovative work that will make real-world difference
interactions with and learnings from industry, government and academic partners
international recognition
Curtin University offers a competitive remuneration and benefits package, a friendly and collaborative work environment, generous leave entitlements, flexible working arrangements, a relocation allowance, generous superannuation, salary-packaging arrangements including childcare, and the potential to support dual-career arrangements.
What we need from you
You are encouraged to respond specifically to the selection criteria:
Essential selection criteria:
Demonstrated ability to conduct innovative research in bioinformatics and/or computational biology
Demonstrated ability to develop experimental plans and pursue novel research approaches.
Ability to work with a broad range of people from varying research backgrounds and evidence of strong oral and written communication skills
Demonstrated commitment to publish the results of research in scientific journals.
Demonstrated ability to work independently under minimal supervision while contributing to overall team performance and proven ability to meet performance deadlines during the course of the project.
Preference will be given to applicants with desirable skills that include:
Experience with plant genetics and the development/utilization of mapping populations
Experience with the analysis of genomic and transcriptomic datasets
Experience with the identification and characterization of candidate fungal effector genes.
Job website: http://staff.curtin.edu.au/job-vacancies/?ja-job=49889
Contact name: Jo Monaghan
Contact email: CCDMAdmin@curtin.edu.au