Bioinformatician (JDHAN_0123_003)

Department

Laboratory

Location

Base in OUCRU Hanoi.

ACORN2 sites in 5 countries in Asia as required

Hours of work

Full time: Monday – Friday, 37.5 hours per week, extra hours may be required.

Tenure

Initially for 01 years, including a 02 month probation period, with possibility of extension based on annual performance appraisal and Research approval

Reporting to

Head of OUCRU Hanoi laboratory

ACORN project PI

Vacancy reference

JDHAN_0123_003

Background

The Oxford University Clinical Research Unit (OUCRU) is a large-scale clinical and public health research unit, with sites offices in Ho Chi Minh City and Hanoi in Vietnam, Jakarta in Indonesia and Kathmandu in Nepal. In Vietnam, we are hosted by the Hospital of Tropical Diseases (HTD) in Ho Chi Minh City, and the National Hospital for Tropical Diseases (NHTD) in Hanoi. OUCRU Nepal has partnerships with the Patan Academy of Health Sciences and Patan Hospital, and OUCRU Indonesia exists in partnership with the University of Indonesia. As a Wellcome Trust Africa Asia Programme, we have received considerable support from the Wellcome Trust since our establishment in 1991.

OUCRU’s vision is to have local, regional and global impact on health by leading a locally driven research programme on infectious diseases in Southeast Asia. Priority is given to health issues important to the hospitals where we work, and to the countries as a whole where we operate: Vietnam, Indonesia and Nepal. All work is intended not only to benefit the patients seen daily at our host hospitals, but also to help improve patient care.

OUCRU employs approximately 320 people across Viet Nam and has an average annual budget of USD 12mil.

Please see more information on OUCRU Website: www.oucru.org

Bacterial Whole Genome Sequencing (WGS) technologies have evolved from specialised reference / academic laboratory activity to something accessible to routine diagnostic and public health microbiology laboratories in high-income countries and, to a lesser extent, in low- and middle-income countries. The COVID-19 pandemic has highlighted how pathogen genomic data can be harnessed globally in near real time to inform outbreak responses (and ultimately to develop tools for treatment and prevention).

Bioinformatics skills and the need for high-performance computing are frequently cited as major barriers to decentralised WGS data analysis. However, plug and play pipeline tools which can run on laptops (e.g. FlowCraft) and online services such as Pathogenwatch, GPAS and CGE-DTU provide solutions for low-volume standard sequence-based analyses, e.g. species determination, multilocus sequencing typing (MLST), virulence gene detection, and antimicrobial resistance (AMR) gene detection.

ACORN is a clinical surveillance project that links clinical and laboratory data to determine burden and impacts of AMR in a range of hospital settings across Africa and Asia. A pilot of ACORN was conducted in three hospitals in Laos, Cambodia and Vietnam, and currently ACORN2 is being implemented in 18 sites in 9 countries. Over two years, the project expects to collect linked clinical - microbiology data on approximately 37,500 clinical infection episodes and characterise ~1,500 target bloodstream infection isolates. ACORN data will also be used to determine the attributable mortality for bloodstream infections caused by 3rd generation cephalosporin resistant E. coli and methicillin resistant S. aureus. A whole genome sequencing component has been added to the larger ACORN2 project. The focus is on bloodstream isolates of E. coli, K. pneumoniae, S. aureus, given their dominance as global AMR pathogens causing both community- and hospital-acquired infections and Acinetobacter spp., given its emergence as a multi-drug resistant pathogen in hospitals and its capacity to rapidly accumulate resistance mechanisms.

As ACORN is patient centred, pragmatic, and focused on local feedback and utility, ACORN sites will be able to use sequencing capacity to respond to outbreaks as they occur, regardless of the pathogen. ACORN therefore supports on-site capacity building and real-time sequencing of highly resistant isolates to inform infection prevention and control measures, not limited to ACORN wards, and with central support from bioinformaticians.

Job summary

· Work within the ACORN (A Clinically Oriented antimicrobial Resistance surveillance Network) project in the substudy on whole genome sequencing of bacterial isolates from surveillance in hospitals in 9 countries in Africa and Asia

· Be part of a small project team consisting of 1 project manager and 2 bioinformaticians. The team will coordinate sample collection, storage, sequencing and analysis within the project

· Work with high-throughput genomic datasets generated by short-read Illumina and long-read Nanopore MinION sequencers

· Develop, maintain and perform bioinformatics analysis using available hardware and online platforms

Key responsibilities and tasks

·         Implement and maintain bioinformatics pipelines for Illumina and Nanopore WGS datasets from pathogenic bacteria to identify AMR and virulence genes, species-specific typing (e,g, MLST, serotype,…), to measure the genetic relatedness with other sequences from national and international datasets, and to analyze the genetic epidemiology of isolates and AMR genes 

·         Set up and configure computer system, network for bioinformatics analysis

·         Communicate and assist bench-top biologists on bioinformatics related sequencing tasks

·         Conduct data processing, statistical analysis, comparative genomics analysis, genomic epidemiology, presentation and interpretation of bioinformatic data, and contribute to the preparation of manuscripts.

·         Provide technical advice/support, design training curricula, and conduct training on bioinformatics analysis for other researchers, collaborators, and PhD/M.Sc. students on site and remotely

Selection criteria

Essential

·         Strong background (MSc or PhD) in Bioinformatics, Computer Science, Biostatistics, Mathematical Biology, Statistics, or a related computational subject, proficiency in Linux and at least one programming language.

·         Excellent communication and interpersonal skills, as engagement with scientists in related projects throughout the unit and collaborators will be key to success in the role.

·         Strong experience in Linux, Cloud (Open Stack) and HPC (SLURM)

·         Fluent in an advanced programming language (preferably Python or R)

·         Experience of handling data and managing an RDBMS (PostgreSQL, MySQL)

·         Ability to supervise junior staff

·         Ability to work independently and as part of a team

Desirable

·         Experience of utilizing open source bioinformatics software and a workflow manager (Snakemake, Nextflow, Galaxy)

·         Knowledge of packaging bioinformatics software (Bioconda, Brew) and containerisation solution (Docker, Singularity)

·         Experience of comparative genomic analysis and genomic epidemiology for prokaryotic genomes

·         Experience with the presentation of complex datasets

·         Experience with the writing of scientific manuscripts

·         Knowledge of infectious disease epidemiology

·         Knowledge of bacteria, viruses, antimicrobial resistance

Benefits

-          Contracted salary:  Negotiable (depending on actual experience and education).

-          Optional insurance: In-patient and out-patient medical coverage; Personal accident insurance coverage

-          Two months’ salary for annual bonus and clothes 

-          Annual leave 18 days each year for the first year

-          Other responsibilities and benefits are based on Viet Nam Labour Law.

How to apply

Interested qualified candidates are invited to send their detailed resume and cover letter in English, including copies of relevant degrees, certificates by email to Ms. Pham Thi Thanh Hoa - Operations Manager.

* The cover letter should detail:

- What part of your education, training or employment history has best equipped you for this position and why you would be a good candidate?

- Contacts of two referees who are your latest HR/ line manager and can provide details of relevant work experience and attitude

* We thank all applicants for their interest but only short-listed candidates will be contacted for interview.

Contact person

Ms. Pham Thi Thanh Hoa

Deadline for submission

25th February 2023

Cập nhật gần nhất lúc: 2023-02-04 16:54:03