Bioinformatician – Vivax Malaria

Up to 3 year full time contract based in Darwin About Menzies:Menzies School of Health Research is one of Australia’s leading medical research institutes dedicated to improving Indigenous, global and tropical health. Menzies has a history of over 30 years of scientific discovery and public health achievement. Menzies works at the frontline, joining with partners across the Asia-Pacific as well as Indigenous communities across Northern and Central Australia.Menzies is renowned for its translational and global health research programs. The malaria program at Menzies spans a diverse range of research activities aimed at both prevention and treatment. We collaborate with partners from more than 20 malaria-endemic countries, with a focus on tackling the burden of disease in the Asia-Pacific region.Since 2010, Menzies has established a world-leading Plasmodium vivax genomics program through ongoing collaboration with international partners at the Wellcome Sanger Institute and over 20 endemic country partners. To date, our global collaborative network (the vivax Genomic Epidemiology Network) has generated a biobank of over 6,000 infections, including over 1,000 high-quality P. vivax genomes derived from bespoke cross-sectional and longitudinal surveys, with detailed clinical metadata  .The P. vivax genomics program also aligns with the WorldWide Antimalarial Resistance Network (WWARN), and the Australian Centre for Research Excellence in Malaria Elimination (ACREME). In addition to our research partnerships, Menzies currently coordinates the Vivax Working Group of the Asia Pacific Malaria Elimination Network (APMEN), connecting our research activities with the real-world needs of National Malaria Control Programs and other key stakeholders. The Menzies P. vivax genomics program focuses on developing novel molecular surveillance tools that provide clinically relevant information on emerging parasite adaptations, transmission dynamics, the major routes of parasite spread within and across borders, and the impact of local treatment policies on the dormant liver stage. Our research program incorporates molecular biology, population genetics and genomics, and software development to inform on the biology and epidemiology of P. vivax. We are working closely with partners in malaria-endemic sites to support in-country implementation of the molecular surveillance tools and ensure their effective translation to generate locally informative data in a timely manner. Ultimately, the objective is to support the rapid containment and elimination of P. vivax.About the position:The successful applicant will work on the P. vivax genomics program within the Menzies malaria team, with additional support from local collaborators in the ACREME network, and international collaborators at the Wellcome Sanger Institute and the Big Data Institute, Oxford.  The position will entail exploration of P. vivax genomic data from our unique repository to identify important adaptations in the parasite genome such as novel drug resistance candidates. These new markers will be incorporated into our P. vivax genotyping barcodes with the aim of building in-country capacity to genotype isolates at our partner sites. Bioinformatic methods will also be applied to characterize the complexity of individual P. vivax infections to inform on local patterns of transmission, and to assess the connectivity between parasite populations to assess the spatial and temporal dynamics of parasite spread.The position will also support the development of new, open-access software for analyzing amplicon deep sequencing data generated at our P. vivax genotyping barcodes, and the expansion of these tools to include host genotyping at the gene encoding the G6PD enzyme and other relevant loci. The aim of the G6PD genotyping is to define vivax endemic populations with genetic variants associated with G6PD deficiency that confer risk of drug induced haemolysis.In addition to the bioinformatic analyses, the successful applicant will be responsible for assisting in the ongoing oversight, reporting and quality assurance of the research activities, and engagement with relevant project scientists, post-graduate students, and key stakeholders.The successful applicant will be encouraged to pursue independent research interests/projects and supported in their career development with opportunities to extend their publication record in high-impact journals, facilitate workshops, supervise post-graduate students and establish their own funded program of work.The position is based in Darwin, with opportunities to spend time at the Wellcome Sanger Institute and the Big Data Institute, UK. Overseas travel of up to 2 weeks, annually may be required. Opportunities for mentoring and networking with others outside the Northern Territory working in relevant genomics programs will be fostered by the supervisor and Menzies-based colleagues to support the successful applicant, including through relevant formal post-doctoral support and mentoring programs at Menzies.The Bioinformatician will:Lead the bioinformatic analysis and manuscript preparation for assigned tasks and contribute to these activities for broader projects within the team.Provide guidance to post-graduate students and external collaborators with respect to data analysis and manuscript preparation tasks.Support the bioinformatics system administration for the malaria team on the Menzies computer cluster.Support database management in accordance with ethical guidelines.Prepare and manage ethics applications relevant to the research program.Maintain regular communication and engagement with team members at Menzies and relevant external collaborators.Contribute to the preparation of program grant applicationsContribute to the academic program and broader Menzies objectives including participation in the seminar series and attendance at divisional or institutional meetings and events. The successful applicant will have:PhD and post-doctoral experience in a relevant bioinformatics / pathogen genomics field.Ability to install and utilise bioinformatic software on relevant computational platforms.Demonstrated competence with coding in python, perl, R or related programming languages.Proven experience with the software, tools and databases for analyzing massively parallel sequencing data.Excellent publication record related to pathogen genomics, as demonstrated by a record of publications in Q1 journals (Scimago) as first or corresponding author.Proven ability to work with others, including from diverse cultures, as an integral member of a team or collaborator.Ability to be solutions focused and troubleshoot technical and process challenges.Excellent communication and organizational skills.Contact: Dr Sarah Auburn via email sarah.auburn@menzies.edu.auWhat we offer:6 weeks annual leaveOption to increase super to 14%Attractive salary package and benefits $119,812 - $139,394 pa salary package (comprising gross salary $94,935 - $111,277 pa, superannuation and salary packaging benefits.Closing date: Sunday, 27 September 2020Aboriginal and/or Torres Strait Islander people are strongly encouraged to apply.For information on how to apply for this position and to obtain the Position Description and Selection Criteria please visit www.menzies.edu.au/careers or phone 08 8946 8626. PD_Bioinformatician – Vivax Malaria 94935 AUD Darwin