Malawi Liverpool Wellcome Trust
Job Details
Job Title: Senior Research Assistant
Grade: RANC – Step 3
Qualifications: BSc in Biology, Biomedical science, Computer Science, Bioinformatics or similar.
Reports to: Lead Bioinformatician
Accountable to: Lead Bioinformatician
Responsible for: N/A
Liaises with: IT Department, Data Management team, Core Lab team
Job Summary
The person carrying out this role will contribute to the success of MLW’s surveillance of Salmonella in Malawi by ensuring robust, scalable, and reproducible bioinformatics pipelines are in place. They will focus on tracking antimicrobial resistance patterns, virulence factors, and transmission dynamics of both typhoidal and non-typhoidal Salmonella through whole genome sequencing analysis. They will liaise with the MLW Core Lab staff, Salmonella group staff, and external stakeholders, to ensure the smooth running of the Salmonella sequence analysis workflows, as well as communicating with stakeholders to ensure that bioinformatics outputs are understood.
Responsibilities
- Develop and maintain bioinformatics pipelines for processing Salmonella genomes, including quality control, assembly, annotation, and comparative genomics analyses
- Implement and optimize tools for detecting antimicrobial resistance genes, plasmids, and virulence factors in Salmonella genomes
- Perform phylogenetic analyses to track transmission patterns and identify outbreak clusters
- Conduct serotype prediction and multi-locus sequence typing (MLST) analyses
- Monitor the emergence of antimicrobial resistance and novel variants in the Salmonella population
- Integrate genomic data with epidemiological and clinical metadata for comprehensive outbreak investigations
- Provide technical support including management of bioinformatics workstations
- Work collaboratively with colleagues in other departments and institutions
- Manage database of samples received and sequences generated
- Write reports, contribute to manuscripts, interpretation of results
- Develop and maintain standard operating procedures for Salmonella genomics workflows
- Providing analytical support, including benchmarking new methods/protocols or bioinformatics tools
Health & Safety
To take full responsibility for ensuring a safe work environment by following health and safety rules at all times for colleagues, study participants and oneself and maintaining awareness of Health and Safety issues, for example by attending scheduled refresher meeting.
All staff are employed under the MLW Programme and are ultimately responsible to the Programme whether directly employed under the Core Grant, a Research Fellowship or project grant. All staff are expected to be flexible and may be required to contribute to the activities of the Core Programme or another project(s).
Requirements
Essential Criteria
- Must be proficient in Python, R, or an equivalent scripting language.
- Must have significant experience using Linux via the command line.
- BSc degree in Biology, Biomedical science, Computer Science, Bioinformatics or similar.
- Interest in the application of genomics to public health microbiology.
- Works effectively as part of a team and independently.
- Good written and oral communication skills.
- Strong understanding of basic IT infrastructure knowledge, e.g., operating system, networking, data storage
Desirable criteria
- Significant experience with scientific workflow management software e.g. snakemake or nextflow.
- Significant experience with containerization or virtual environments e.g. conda environments or Docker containers.
- Experience using bioinformatics to answer biological questions related to Salmonella in Malawi.
- Experience with SQL databases
- Experience with git or other version control software.
Remuneration and Benefits
MLW offers an attractive remuneration package which includes a competitive salary package commensurate with the position, a medical aid scheme, 24 hours insurance cover, pension scheme, gratuity benefits redeemable once every year, among others.
MLW also offers opportunities such as scholarships, upgrading and training opportunities to employees. These are based on successful job performance and other set criteria.
Applications to be received not later than 18th November 2024.
Method Of Application
Interested applicants should apply by sending, a cover letter, copies of relevant certificates, detailed CV with 3 traceable referees (with at least 2 professional referees) to the address below or email to [email protected] This should be in 1 pdf format.
MLW recognizes its responsibility in safeguarding and protecting communities, research participants and patients with whom MLW is working. Please note that successful candidates will be requested to undergo a safeguarding check prior to appointment and at regular time points during employment.
ONLY SHORT-LISTED CANDIDATES WILL BE ACKNOWLEDGED
To apply for this job email your details to vacancies@mlw.mw