GENOMICS LABORATORY

The Genomics Facility at Nelson R Mandela School of Medicine, University of KwaZulu-Natal, UKZN, Durban, South Africa has one of the world’s most advanced genetic sequencing systems in order to enable and support world-class genomics research in Africa. Our objective is to use NextGen sequencing and bioinformatics to answer scientific questions that are of local, national and international importance.


Genomics Facility:
Information:

Nelson R Mandela School of Medicine Campus in Durban, South Africa, is where our Genomics Facility is based.


Open access pdf Publications (latest 5)

Sexual partnership age pairings and risk of HIV acquisition in rural South Africa.
Akulliana A, Bershteyna A, Kleina D, Vandormael A, Barnighausen T, Tanser F, AIDS (2017), :DOI:10.1097/QAD.0000000000001553.

Incidence rate estimation, periodic testing and the limitations of the mid-point imputation approach.
Vandormael A, Dobra A, Barnighausen T, de Oliveira T, Tanser F, International Journal of Epidemiology (2017), :doi.org/10.1093/ije/dyx134.

Mutational Correlates of Virological Failure in Individuals Receiving a WHO-Recommended Tenofovir-Containing First-Line Regimen: An International Collaboration.
Rhee SY, Varghese V, Holmes SP, Van Zyl GU, Steegen K, Boyd MA, Cooper DA, Nsanzimana S, Saravanan S, Charpentier C, de Oliveira T, Etiebet MA, Garcia F, Goedhals D, Gomes P, Gunthard HF, Hamers RL, Hoffmann CJ, Hunt G, Jiamsakul A, Kaleebu P, Kanki P, Kantor R, Kerschberger B, Marconi VC, D'amour Ndahimana J, Ndembi N, Ngo-Giang-Huong N, Rokx C, Santoro MM, Schapiro JM, Schmidt D, Seu L, Sigaloff KCE, Sirivichayakul S, Skhosana L, Sunpath H, Tang M, Yang C, Carmona S, Gupta RK, Shafer RW., EBioMedicine (2017), :doi: 10.1016/j.ebiom.2017.03.024.

High Rates of Transmission of Drug-resistant HIV in Aruba Resulting in Reduced Susceptibility to the WHO Recommended First-line Regimen in Nearly Half of Newly Diagnosed HIV-infected Patients.
Hofstra LM, Rivas ES, Nijhuis M, Bank LEA, Wilkinson E, Kelly K, Mudrikova T, Schuurman R, de Oliveira T, de Kort J, Wensing AMJ, Clinical Infectious Diseases (2017), :doi: 10.1093/cid/cix056.

Virological Outcomes of Second-line Protease Inhibitor-Based Treatment for Human Immunodeficiency Virus Type 1 in a High-Prevalence Rural South African Setting: A Competing-Risks Prospective Cohort Analysis.
Collier D, Iwuji C, Derache A, de Oliveira T, Okesola N, Calmy A, Dabis F, Pillay D, Gupta RK, for ANRS 12249 TasP Study Group, Clinical Infectious Diseases (2017), :doi: 10.1093/cid/cix015.

All publications - Bioinformatics, genomics and drug resistance peer-reviewed papers on HIV, TB and other pathogens
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Videos Videos Descriptions

YouTube Video

Krisp - a next generation DNA sequencing research centre opens in Durban, South Africa - eTV news

Author: Tulio de Oliveira, Veron Ramsuran, Nicolette Crozier, Zandile Sibisi, Marcel Tongo, Benjamin Chimukangara, Thabiso Dlamini - Date: 2017-07-24

Krisp at South African eTV channel evenning news


YouTube Video

Transmission networks and risk of HIV infection in KwaZulu-Natal, South Africa: a community-wide phylogenetic study - Keynote presentation at AIDS 2016.

Author: Anthony Fauci, Quarraisha Abdool Karim, David Khanyile, Tulio de Oliveira, Salim Abdool Karim - Date: 2016-06-20

This is a short video of our keynote presentation at the AIDS 2016 conference in Durban.


YouTube Video

Completion of a world-class genomics lab at KRISP/UKZN, Durban, South Africa - Part III

Author: Prevashinee Padayachee and Tulio de Oliveira - Date: 2014-08-06

This short video diary is the third in a series that traced the creation of a world class DNA genomic facility in the African continent that focuses on research on diseases that affect human health. This video shows the completion of genomics centre. It shows Illumina Miseq and Life Technologies Next Generation (NextGen) sequencing Facilities used in HIV & TB research.


YouTube Video

KRISP Genomics Laboratory Construction - Video Diary Part II

Author: Prevashinee Padayachee and Tulio de Oliveira - Date: 2014-04-05

This short video diary is the second in a series of movies that will trace the transformation of our existing laboratory into a world class DNA genomic facility. The second video provides an introduction to the robotics system and present our new bioinformatics facility. The genomics facility is based at the College of Health Sciences, University of KwaZulu-Natal and funded by the Wellcome Trust Africa Centre, South Africa MRC, UKZN, NRF and BMGF. This will be one of the first facilities in the African continent that focuses on research on diseases that affect human health.


YouTube Video

KRISP Genomics Laboratory Construction - Video Diary Part I

Author: Prevashinee Padayachee and Tulio de Oliveira - Date: 2014-03-13

This short video diary is the first in a series of four weekly movies that will trace the transformation of our existing laboratory into a world class DNA genomic facility. This will be one of the first facilities in the African continent that focuses on research on diseases that affect human health. The first video provides an introduction to the series, a pictorial tour of the current facilities and outlines the exciting renovation plans that are under way. The genomics facility is based at the College of Health Sciences, University of KwaZulu-Natal and funded by the Wellcome Trust Africa Centre, South Africa MRC, UKZN, NRF and BMGF


15 minutes, All videos...
News News Section, printed & online media on our work on genomics and bioinformatics (latest 5)

KRISP Training

11th Annual Workshop on Advanced Clinical Care - AIDS (AWACC), Durban, South Africa, 6-7 Sep 2017

KRISP Training - 2017-10-06

The workshop is targeted at 400 clinicians, clinical virologists and nurses working in the public sector who are currently involved in the treatment of patients with HIV and TB in KwaZulu-Natal, South Africa.


KRISP Training

X-meeting - 13th International Conference of the AB3C, Sao Pedro, Brazil, Oct 4-6, 2017

KRISP Training - 2017-09-04

Bioinformatics is now a strategic area for Brazil and all Latin America and, therefore, it is also strategic to the development of Science, Technology and Economy. The X-Meeting is a Brazilian event with international reach which has an average of 400 participants.


KRISP Training

22nd International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME), Lisbon, Portugal

KRISP Training - 2017-08-27

The workshop provides both theoretical and practical training in phylogenetic inference and evolutionary hypothesis testing. It is recognized as one of the best international virus bioinformatics courses. It covers sequence analysis, phylogenetics, phylodynamics methods and large scale methods for next-generation sequencing (NGS) analytics


KRISP Talks

A multi-centre analysis of internal migration and AIDS/TB and NCD-related mortality in Kenya and South Africa

KRISP Talks - 2017-08-23

KRISP Talks by Dr Carren Ginsburg, SAMRC/Wits Rural Public Health & Health Transitions Research Unit (Agincourt), 23 August 2017 (11am - midday), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!


KRISP Newsletter

KRISP Newsletter - July 2017: news, videos, blogs, publications and training events

KRISP Newsletter - 2017-08-01

The concept behind this newsletter is that anyone with 15 minutes to spare can learn about KRISP work. In this July 2017 issue of our newsletter, we have included interesting news, videos, blogs, reports, tweets, publications and training events of KRISP


All news...
Blogs on genomics annd bioinformatics Twitter

Bioinformaticians are pioneering the future of science

Author: Yumna Moosa - 2017-07-28


Meeting of the Swiss, Swedes and South Africans minds

Author: Nicolette Crozier, Benjamin Chimukangara, Veron Ramsuran - 2017-07-25


Megan Druce: from Cum Laude MSc to a Scholarship for a PhD in Germany...

Author: Megan Druce - 2016-04-18


Sthembiso Msweli: from Hlabisa to MSc and Further Promoted to Laboratory Manager...

Author: Sthembiso Msweli - 2016-04-17


Experience of 3 UKZN/Africa Centre students at the 7-week national bioinformatics workshop 2015

Author: Megan Druce, Zandile Sibisi & Sthembiso Msweli - 2015-04-23


15 minutes, All blogs...


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