KRISP NEWS
24th International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME), The University of Hong Kong, Hong Kong, China, 4-9 August, 2019. The VEME workshop is recognised as one of the best international virus bioinformatics courses.
UKZN African Health Flagship Talks by Prof. Michael Pepper (University of Pretoria & SAMRC Unit for Stem Cell Research & Therapy) - the Academy of Science of South Africa (ASSAf) Consensus Study on the Ethical, Legal and Social Implications of Genetics & Genomics in South Africa. Tuesday, 7 May 2019 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!
KRISP at UKZN challenges the status quo to create a scientific environment in (South) Africa that delivers high level science, creates innovations and reverses the brain drain. This vision is starting to pay off, and we are happy to say that in just two years, we published twelve manuscripts in Nature, Science and Lancet journals!
UKZN African Health Flagship Postgraduate Training Program present the Research Ethics and Conflicts of Interest Workshop. Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 1 April 2019. Training is open to University Post-Graduate Students & Post-Doctoral Fellows.
This month, we focused our newsletter on KRISP partnership with the Department of Global Health at University of Washington in Seattle. We also focus on our new post-graduate training workshops. This month, we also have many publications on African Health, including on HIV and TB phylogenetic and drug resistance analysis.
UKZN African Health Flagship, KRISP, DIPLOMICS & Thermo Education Program on DNA Sequencing Fragment Analysis Workshop . Thermo-KRISP Lab, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 28-29 March 2019. Training is open to University Post-Graduate Students & Technical Staff of Commercial and Academic laboratories. Scholarships available to previously disadvantaged South African learners.
UKZN African Health Flagship, KRISP, DIPLOMICS & Thermo Education Program on Capillary Electrophoresis (i.e. Sanger Sequencing) . Thermo-KRISP Lab, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 25-26 March 2019. Training is open to University Post-Graduate Students & Technical Staff of Commercial and Academic laboratories. Scholarships available to previously disadvantaged South African learners.
KRISP is presenting at the UCL/UKZN workshop on translational research, Health Innovation and Commercialisation. The workshop starts 19th March, Tuesday, at 12pm, finishes 20th March, Wednesday, at 2pm in Durban, South Africa.
UKZN African Health Flagship Talk by Dr. Maryam Fish - Cancer Genomics at KRISP will cover some of the genomics tests and bioinformatics pipelines for the analysis of whole exome sequencing (WES) and cancer panels from Thermo Fisher Scientific, Illumina and other sequencing methods. Friday, 15 March 2019 (8:30am - 9:30am), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!
KRISP challenges the status quo to create a scientific environment in (South) Africa that delivers the highest level of science, creates innovations and reverses the brain drain. This vision is starting to pay off, and we are happy to say that in just two years, we have been awarded over twenty grants to produce and analyze omics data in the African continent. Please contact us to discuss collaborative grants applications.
KRISP PAPERS
The effect of interventions on the transmission and spread of HIV in South Africa: a phylodynamic analysis.
Wilkinson E, Junqueira DM, Lessells R, Engelbrecht S, van Zyl G, de Oliveira T, Salemi M, Scientific Reports (2019), 9:2640:https://doi.org/10.1038/s41598-018-37749-3.
Sociobehavioral and community predictors of unsuppressed HIV viral load: multilevel results from a hyperendemic rural South African population.
Tomita A, Vandormael A, Bärnighausen T, Phillips A, Pillay D, De Oliveira T, Tanser F, AIDS (2019), 33(3):559–569.
Spatial structure of depression in South Africa: A longitudinal panel survey of a nationally representative sample of households.
Cuadros DF, Tomita A, Vandormael A, Slotow R, Burns JK, Tanser F, Scientific Reports (2019), 9(1):979:doi.org/10.1038/s41598-018-37791-1.
Early detection of emergent extensively drug resistant tuberculosis (XDR-TB) by flow cytometry-based phenotyping and whole genome sequencing.
O'Donnell MR, Larsen MH, Brown TS, Jain P, Munsamy V, Wolf A, Uccellini L, Karim F, de Oliveira T, Mathema B, Jacobs WR, Pym A, Antimicrob Agents Chemother. (2019), pii: AAC.01834-18.:doi: 10.1128/AAC.01834-18.
Moderate to high levels of pre-treatment HIV drug resistance in KwaZulu-Natal Province, South Africa.
Chimukangara B, Kharsany AB, Lessells RJ, Naidoo K, Rhee SY, Manasa J, Gräf T, Lewis L, Cawood C, Khanyile D, Diallo K, Ayalew KA, Shafer R, Hunt G, Pillay D, Abdool SK, de Oliveira T, AIDS Research and Human Retroviruses (2019), https://doi.org/10.1089/AID.2018.0202:.
Experts' Perspectives on Key Ethical Issues Associated With HIV Phylogenetics as Applied in HIV Transmission Dynamics Research.
Mutenherwa F, Wassenaar DR, de Oliveira T, J Empir Res Hum Res Ethics (2018), 1556264618809608. doi: 10.1177/1556264618809608:.
Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa.
Rasmussen DA, Wilkinson E, Vandormael A, Tanser F, Pillay D, Stadler T, de Oliveira T, Virus Evolution (2018), 4(2): vey037:.
KRISP VIDEOS
STEM Education in Africa: KRISP & Thermo Fisher Scientific PCR Workshops
By: Deseree Rajpal, Sahil Tulsi, Veron Ramsuran, Jennifer Giandhari, Nicolette Crozier and Tulio de Oliveira
KRISP TEAM
KRISP BLOGS
KRISP TOOLS
2019-02-12
REGA HIV Subtyping Tool V3 - Belgium Mirror
Phylogenetic tool to identify the HIV-1 subtypes and recombinants. Query sequences are analysed for recombination using bootscanning methods. The version 3 contains new CRFs (CRF01_AE to CRF47_BF).
2018-12-05
Booster: a new bootstrap method for construction of large trees
A new version of the phylogenetic bootstrap in which the presence of inferred branches in replications is measured using a gradual 'transfer' distance rather than the binary presence or absence index used in Felsenstein's original version. The resulting supports are higher and do not induce falsely supported branches.
2016-08-21
REGA HIV Subtyping Tool V3 - South African mirror
This tool is designed to use phylogenetic methods in order to identify the HIV-1 subtype of a specific sequence. The sequence is analysed for recombination using bootscanning methods. The version 3 contains new CRFs (CRF01_AE to CRF47_BF).
2016-08-20
This is the first version of the Zika typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.
2016-08-20
This is the first version of our Arbovirus typing tool for Chikungunya, Dengue, Yellow Fever and Zika
2016-08-20
This is the first version of the Chikungunya typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.