​​​​​​​​​​​​​​​Division of Molecular Biology and Huma​​n Gene​​tics​​ ​  

VACANCIES​

EMPLOYMENT OPPORTUNITIES

No opportunities currently available.


POSTDOCTORAL OPPORTUNITIES​

Postdoctoral position: Tuberculosis Diagnostics​​​

​Host/Location: Division of Molecular Biology and Human Genetics, Clinical Mycobacteriology & Epidemiology (CLIME) Group, Faculty of Medicine and Health Sciences, Stellenbosch University Tygerberg Medical Campus 

Value of Award: Competitive tax-free fellowship. Fellowship embedded within the EDCTP2-sponsored project: Automated smartphone-based cough audio classification for rapid tuberculosis triage testing (Cough Audio triaGE for TB, CAGE-TB)​

Duration: 3 years (renewed annually contingent on progress)

The CLIME group and CAGE-TB consortium are seeking to fill at least one exciting post-doctoral scientist position related to the discovery, validation, and design of a smartphone-based cough recording app to triage patients in primary care for confirmatory TB testing. 

The position is part of a three-year internationally funded study (PI Theron) that builds upon proof-of-concept work showing machine learning methods can distinguish cough audio sounds from patients with TB from sick people without TB. The project will expand cough audio collection for signature discovery (Cape Town), independently validate signature performance (Cape Town, Kampala), and develop a user-friendly app for evaluation in clinical trials.

The successful candidate will join an experienced clinical diagnostics evaluation team, gain exposure to digital signal processing engineers developing the audio classifier, and work alongside costing, implementation science, and human-centred design members of the consortium (Amsterdam, Gottingen). The candidate will primarily be responsible for facilitating day-to-day site needs, approvals applications, SOP development, monitoring weekly patient data, diagnostic accuracy analyses, gathering and co-publishing data, participating in regular consortium meetings, and site visits (annual international travel required). The candidate will have the opportunity to co-supervise students and participate in other projects within the group.​

Application Details:

Applicants should have a PhD within the last 5 years and a background in epidemiology, microbiology, mHealth, diagnostics or related disciplines, and be fluent in spoken and written English

Familiarity with TB diagnosis and care in low- middle-income counties and/or project management experience is helpful but not critical.

The candidate will be assisted in applying for additional funding that they are entitled to keep in conjunction with the base bursary. For more information, please contact Dr Marisa Klopper (marisat@sun.ac.za) and Prof Grant Theron (gtheron@sun.ac.za).

To apply, please send a cover letter, a CV containing details of relevant experience, publications, grades, and the email addresses and telephone numbers of three references to the above addresses before 31 January 2022. Please include a one-page motivation letter which includes a brief statement of research interests and experience and a two-page concept fellowship note with a summary of recent literature.

CLIME is in the new BMRI facility at the SU Faculty of Medicine and Health Sciences situated 20 minutes from central Cape Town and 30 minutes from the Stellenbosch campus by car.

Early applications are encouraged. We will stop looking when we find candidates we like. We are seeking to fill the position as soon as possible.

Candidates are encouraged to submit applications as soon as possible even if they have queries that cannot be rapidly responded to, given the year-end break.​


Postdoctoral position: Parkinson's Disease Research

​Host/Location: Division of Molecular Biology and Human Genetics, Parkinson's Disease Research Group, Faculty of Medicine and Health Sciences, Stellenbosch University Tygerberg Medical Campus 

Value of Award: Competitive tax-free fellowship. 

Duration: 2 years (dependent on progress)

 An opportunity exists within the Parkinson’s Disease Research Group​ for a postdoctoral research fellow for 2022. Our research focuses on Parkinson’s disease (PD) and uses different approaches to identify genetic causes and disease mechanisms underlying this neurological disorder. The postdoctoral project will involve investigating new genes and pathways implicated in PD using genomics approaches, in collaboration with the Global Parkinson’s Genetics Program (GP2). We offer a stimulating and friendly work environment, and the opportunity to develop into an independent researcher.​

Skills required: 

  • Applicants must have obtained a PhD in the last five years.
  • Extensive experience in molecular and/ or human molecular genetics
  • Experience in bioinformatics/ computational biology would be an advantage
  • Ability to work independently
  • A publication record
  • Good communication skills

Applications must be submitted by the deadline of 9 February 2022 and must include:

  1. One-page letter of motivation
  2. Detailed CV with publications
  3. Names of two references (one of whom must be the PhD supervisor)​

Please send applications to Prof. Soraya Bardien (sbardien@sun.ac.za)​​


Postdoctoral position: Rare Disease Genomics

​Host/Location: Division of Molecular Biology and Human Genetics, Rare Disease Genomics Group, Faculty of Medicine and Health Sciences, Stellenbosch University Tygerberg Medical Campus 

Value of Award: Competitive tax-free fellowship. 

Duration:  2 years, renewable upon sufficient funding. Please note that postdoctoral fellows are not appointed as employees at SU and are therefore not eligible for employee benefits.

A rare disease (RD) is defined as one that affects fewer than 1 in 2000 people. Although individually “rare”, collectively there are over 7000 different RDs, which affect a significant proportion of the population and impact the lives of millions of South Africans. Over 80% of RDs are genetic in origin and most have their onset in childhood. However, to date, people with RDs have been disproportionately underrepresented in terms of research, diagnosis and treatment, especially in Africa. Using conventional testing, patients remain on their “diagnostic odysseys” indefinitely. Next-generation sequencing (NGS) technology has revolutionized diagnosis in RDs. The Rare Disease Genomics group has recently established an undiagnosed disease programme (UDP) at Stellenbosch University, to use state of-the-art Next Generation Sequencing technologies to end the diagnostic odyssey for South African patients with RDs. 

We are seeking an enthusiastic postdoctoral fellow to join our multidisciplinary team, to oversee and develop the bioinformatics arm of the UDP. The successful candidate will benefit from working in a young, dynamic and diverse research group with national and international collaborations and numerous opportunities for further training.​


Duties:

Research 

  • Analysis of NGS datasets (whole exome and genome)
  • Analytical method development specifically suited to NGS technologies
  • Data mining, analysis and interpretation
  • Construction and curation of databases and specific computational tools
  • Hypothesis generation for new scientific questions and research studies
  • Manuscript and grant writing​

Management 

  • Oversee the bioinformatics arm of the Rare Disease Genomics in South Africa: UDP project
  • Contribute to study design and implementation – including student projects
  • Development of key documents such as protocols, SOPs, etc​

Teaching 

  • Training of students and other scientists
  • Oversee reporting and interpretation of data​

Job requirements

  • PhD in Human Genetics, Bioinformatics or a related field, obtained within last 5 years
  • Experience with analysis of NGS datasets (advantage if exome and genome sequencing)
  • Experience in working in Linux environments, Docker, Cloud-based computing
  • Proficiency in common scripting languages (Python, R, other)
  • Sequencing analysis and pipeline design
  • Experience in computational and statistical analysis of high-dimensional and multivariate data
  • Comprehensive use of computational clusters and cloud-based computing
  • Excellent organisational, planning and interpersonal skills
  • High level of accountability, integrity and a good understanding of confidentiality

Commencement of duties: 01 March 2022 - or as soon as possible 

Application Details

To apply, please send the following to Professor Shahida Moosa at shahidamoosa@sun.ac.za 

  • Motivation for applying for this position
  • Updated CV including publication list
  • Proof of PhD qualification and copy of academic transcript
  • Names and email addresses of two referees, who can be contacted immediately upon shortlisting

Closing date: 28 February 2022. Early applications are encouraged. We will stop looking when we find a suitable candidate. Candidates without the necessary skills will not be contacted.​


​STUDENT OPPORTUNITIES

Two funded PhD positions: Tuberculosis Diagnostics​​​ implementation research (Costing and/or mHealth focus)

​Host/Location: Division of Molecular Biology and Human Genetics, Clinical Mycobacteriology & Epidemiology (CLIME) Group, Faculty of Medicine and Health Sciences, Stellenbosch University Tygerberg Medical Campus 

Value of Award: A competitive tax-free bursary is provided. The candidate will be assisted in applying for additional funding that they are entitled to keep in conjunction with the base bursary​. Fellowship embedded within the EDCTP2-sponsored project: Automated smartphone-based cough audio classification for rapid tuberculosis triage testing (Cough Audio triaGE for TB, CAGE-TB)​

Duration: 3 years ​

We are recruiting two PhD students to join the The Cough Audio triaGE for TB (CAGE-TB) CAGE-TB programme, a multisiciplinary consortium supported by a grant from the European Commission and coordinated by Stellenbosch University. CAGE-TB brings together African and European scientists to develop a mobile phone-based cough audio triage test for tuberculosis (TB).

CAGE-TB aims to promote the adoption of mobile health-based cough audio triage testing for active pulmonary tuberculosis in health facilities in high-burden settings. It will generate and separately validate a cough audio classifier that meets World Health Organization (WHO) triage test target product profile sensitivity and specificity criteria, produce data on potential cost savings, and package the underlying technology into an easy-to-use smartphone app built using human-centered design ready-for-use in largescale clinical evaluations. It will do so through:

    1. Collecting cough audio data in a discovery cohort of patients with a prolonged cough who present to primary care clinics in Cape Town, South Africa; and optimizing a classifier scheme;
    2. Validating the audio classifier algorithm in separate clinical validation cohorts in Cape Town, South Africa and Kampala, Uganda and calculate potential cost savings;
    3. Using a human-centered design process to integrate the classifier into a smartphone application and identifying potential barriers and facilitators to its successful deployment.

CAGE-TB will provide opportunities for PhD training as part of its research activities. There will be two PhD positions at SU, focussed on items two and three, with topics including aspects of diagnostic implementation and costing research and mHealth and human-centered design. Under the supervision of an international multi-discipinary research team, the PhD candidates will conduct mixed-methods research to:

    1. Explore existing policies and practices of TB triage and diagnosis in primary health facilities;
    2. Conduct cost data collection and analysis of the phone-based cough triage test;
    3. Assess current smartphone and app usage among healthcare staff;
    4. Support participatory app design process.​

The Role:

    1. Design and conduct qualitative (e.g. structured interview guides) and quantitative research (e.g. survey questionnaires);
    2. Develop a research protocol and obtain approval from ethics review committees;
    3. Understand cultural background of participants to evaluate findings and methods in this context;
    4. Analyze qualitative (e.g. coding) and quantitative data (e.g. statistical analyses)
    5. Prepare and hold presentations for an audience with a varied disciplinary background;
    6. Take the lead in authoring articles to be published in international peer-reviewed journals;
    7. Compile a thesis based on the articles (and submitted manuscripts);
    8. Participate in and present findings at CAGE-TB consortium meetings.

Professional Background:

Required

    1. A completed master’s degree in a health-related social science discipline, such as medical anthropology, medical sociolgy, or a masters in global/public health, health services research, epidemiology and biostatistics with significant proportion of qualitative research;
    2. Experience of designing and conducting qualitative and quantitative research;
    3. Demonstrated ability to communicate complex findings to an audience with varied disciplinary background;
    4. Fluency in English;
    5. Willingness and ability to work independently and to collaborate with a multidisciplinary and international team;
    6. Socially engaged, highly motivated to understand social dynamics, autonomous and creative.
    7. Willingness to be part of an international research team.

Desirable

    1. Proficient in qualitative and/or quantitative data analysis software;
    2. Experience of undertaking data collection in primary care settings;
    3. Has taken a leading role in at least one article published in an international peer-reviewed journal(i.e. first author);
    4. Familiarity with TB diagnosis, diagnost and care in a low- middle-income country;
    5. Interest in mobile health and/or digital health interventions to support health services.

We look forward to receiving your application by 28 February 2022. You can apply by sending the following to Dr Marisa Klopper (cagetb2@sun.ac.za) and copy Prof Grant Theron (gtheron@sun.ac.za). Indicate ‘PhD TB-CAGE’ in the subject line. Please combine all documents into a single PDF file.

    1. CV: Please mention the months (not just years) in your CV when referring to your education and work experience;
    2. a transcript of all university courses taken and grades obtained;
    3. a one-page motivation letter which includes a brief statement of research interests and experience;
    4. a concept note: two pages plus one page of relevant literature. Clearly whether you are interested in implementation and costing research, and/or mHealth and human-centered design.
    5. Two reference letters

CLIME is in the new BMRI facility at the SU Faculty of Medicine and Health Sciences situated 20 minutes from central Cape Town and 30 minutes from the Stellenbosch campus by car.

Early applications are encouraged. We will stop looking when we find candidates we like. We are seeking to fill the position as soon as possible.

Candidates are encouraged to submit applications as soon as possible even if they have queries that cannot be rapidly responded to, given the year-end break.​


MSc and PhD positions: TB Genomics Research Group

The TB Genomics Group has applied for project funding and is looking for students to do parts of the work as Masters, or PhD projects. 

Full disclosure: Please note that the project does not have attached bursary funding. As such, any potential students would need to find personal funding.​ The purpose of this call is to find interested students who we can assist with bursary- and Harry Crossley project funding applications.​

For more information related to the project please see below.

Project Title

Identification and characterization of non-tuberculosis mycobacteria (NTM) in South Africa, and their role in modulating the macrophage immune response to other lung pathogens”

Project Abstract

Little is known about nontuberculous mycobacteria (NTM) that cause pulmonary diseases (NTM-PD), which is a rising global health concern. NTM species are naturally resistant to most common antibiotics. Diagnosis of NTM-PD is technically challenging, expensive, and sometimes inaccurate. Despite the frequent isolation of various NTM species from patients with NTM-PD, data on pathogenic NTM species and their genetic characteristics is still incomplete. Several studies have reported the isolation of NTM in patients with pulmonary infection, often concurrently, or after a previous infection with Mycobacterium. tuberculosis(MTB). Interaction between these two mycobacterial species and how they modulate the immune system in the presence of other mycobacterial species is still an unexplored topic. 

NTM-PD samples identified by National Health Laboratory Service, Greenpoint during routine diagnosis, as well as non-pathogenic species from our NTM sample bank will be genetically characterized by whole genome sequencing and compared by phylogenetic analysis of the genomic diversity. To elucidate the immune response to NTM and MTB coinfection, THP-1 macrophages will be infected with both NTM species and MTB H37Rv sequentially and simultaneously. Macrophage cytokine and chemokine secretions in response to coinfection will be measured using qRT-PCR and Luminex, and metabolic pathways will be determined using RNA-sequencing. Mass spectrometry will be used to identify secreted proteins from pathogenic and non-pathogenic NTM strains. 

Characterization of the NTM-PD pathogenic species and identification the immune response to these species may assist in determining the clinical significance of these pathogens and lead to identifying biomarkers of various NTM species' infectivity.  Comparison of the genomic and immune determinants of pathogenic and non-pathogenic species will contribute to knowledge on the fundamental determinants of virulence in mycobacteria. This will have important implications for the diagnosis and the management of this condition.​

If you are interested, please contact marisat@sun.ac.za and shatha@sun.ac.za​​

​​​