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

Staff Bioinformatician (Genome Medicine) @ Melbourne

Employer:University of Melbourne Centre for Cancer Research

Closing date:28/8/2019

Brief position description:We have a new opening for a Bioinformatician (PSC 8 - $103,409 -$111,927 p.a.).

## What would I be doing?

We are looking for a bioinformatician who will provide vital support to the [UoM Clinical Genomics Platform][1]: assisting with the flow of data through our systems, providing quality control assessments of sequencing data and helping to troubleshoot bottlenecks. You would help drive our ongoing WGS/WTS accreditation effort and be responsible for managing, analyzing and interpreting genomic data for accreditation, with corresponding documentation, and assess the DRAGEN environment using both HPC and cloud computing to improve our clinical reports. If you are interested in exploring large scale genomic data sets in a clinical setting (see [this paper][2] or [this poster][3] for typical examples) this might be the role for you. You will also have the opportunity to work with commercial partners at Illumina, AWS and Google as well as National Sequencing Initiatives to explore genomics data sharing technologies.

The team is inclusive and diverse, spans the whole range from biologists over bioinformaticians to software engineers, with junior and senior members. We collaborate with a number of international groups, e.g., the Broad Institute, Genomics England and global initiatives such as the Global Alliance for Genomics Health. This particular role will work in close collaboration with Illumina.

The role comes with 17% superannuation. We offer flexible working arrangements including working from home. Applications for part-time work are welcome!

[1]: https://research.unimelb.edu.au/centre-for-cancer-research/engage/services#clinical-genomics-platform
[2]: https://www.biorxiv.org/content/10.1101/623702v1
[3]: https://www.nygenome.org/bioinformatics/wp-content/uploads/2019/05/BOG-poster-20194.pdf

Job website:http://umccr.org/blog/hiring-take2/

Contact name:Oliver Hofmann

Contact email:ohofmann72@gmail.com

Postdoctoral researcher @ UNSW Sydney

Employer: UNSW Sydney

Closing date: 11pm 15th August 2019

Brief position description: UNSW Medicine is a national leader in learning, teaching and research, with close affiliations to a number of Australia’s finest hospitals, research institutes and health care organisations. The UNSW Future Institute on Cellular Genomics has been established to represent a leading institute in single cell genomics in Australia and internationally. The institute is seeking a Postdoctoral Fellow who will be responsible for Analysis and modelling of single cell multi-omics in immuology related to the research in autoimmune disease and CAR T cells. The successful candidate will operate within the UNSW Future Cellular Genomics, and specifically at the Kirby Institute and the School of Medical Science, with active collaborations with close collaborators at the Garvan Institute.

The role involves both experimental and computational research activities, identifying opportunities for collaboration and funding and assisting the broader team with other research related duties. This position will focus on the development and application of single cell technologies including machine learning approaches) for analysing and interpreting muti-omics data of immune cells.

Job website: https://external-careers.jobs.unsw.edu.au/cw/en/job/497438/postdoctoral-fellow

Contact name: Fabio Luciani

Contact email: luciani@unsw.edu.au

Post-doc position in bioinformatics @ ULB

Post-doc position in bioinformatics at ULB: Genes and gene networks analysis related to root morphological response to nitrogen supply in Brassicaceae species

Employer: Universite libre de Bruxelles

Closing date: Applications must be received by August 1st 2019

Brief position description: One post-doc fellowship for non-Belgian resident (3 years) - as early as October 2019

Relevant experience: Arabidopsis - Brassica genomics, QTL mapping (association and linkage), ShoreMap, gene networks

Eligibility: Maximum 6 years after PhD, no more than 24 months residence in Belgium during the three last years

Mineral nitrogen (N) is the quantitatively most important nutrient in cropping systems. However, a considerable N fraction is lost through runoffs with detrimental consequences for the environment and human health. Increasing the plant N uptake by optimizing the degree of root branching for exploring a larger soil volume in search of the mobile nitrate resource may contribute to limit soil leaching. Oilseed rape (Brassica napus L.) is a major oil crop showing whose production highly dependents on N fertilization. The project aims at understanding the genetic control of root system architecture and how it is impacted by N nutrition. A measurable outcome will be to provide genetic markers for selecting new crop genotypes with positive root morphological features.

Enthusiastic researchers meeting these criteria (only those with previous experience in bioinformatics will be considered) are kindly invited to contact Christian HERMANS (chermans@ulb.ac.be). Include your CV, qualifications and the names of two academic referees whom I can approach prior to appointment.

Job website:

Contact name: Christian Hermans

Contact email: chermans@ulb.ac.be

4 funded PhD Positions in Bioinformatics, Machine Learning, Systems and Synthetic Biology @ Melbourne

Closing date:15th July 2019

Brief position description:We are inviting applications for 4 funded PhD positions to develop whole-cell mathematical simulation models for Bacillus subtilis. If you are interested in multidisciplinary research and have relevant undergraduate and masters degrees in the life sciences, engineering, mathematics, statistics, physics, or computer science this is an excellent opportunity to embark on a research career in a world-leading, friendly and supportive computational biology research environment.
Understanding and being able to explain and predict the behaviour of Bacillus subtilis is of fundamental importance. But mathematical models are also essential for synthetic biology and biotechnology. For example, we need mathematical simulation models to design B. subtilis strains that help us tackle the effects of global warming and pollution. These four PhD projects will jointly work towards such a model:

1. Biological text-mining and knowledge representation
2. Statistical bioinformatics and bacterial genomics
3. Modelling of biophysical processes and cell cycle dynamics
4. Modelling of gene regulation and metabolic networks

You will join a thriving and collaborative community at the University of Melbourne. We are particularly keen to have a diverse cohort of researchers, who want to contribute to this environment. This is a perfect opportunity to engage in exciting and multidisciplinary research, and actively shape the future of systems, synthetic and computational cell biology.

Please address your questions and inquires to mstumpf@unimelb.edu.au

To apply please send your application including Cover Letter, CV, final transcripts (where available), and the details of two referees to mstumpf@unimelb.edu.auby the 15th of July.

We can assist international students with their relocation expenses.

Job website:

Contact name:Michael Stumpf

Contact email:mstumpf@unimelb.edu.au