KRISP NEWS
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.
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 Talks by Prof Tulio de Oliveira, Power of Diversity. Nature editorial covers a variety of studies that have tracked different types of diversity — ethnic, gender, nationality and scientific discipline — and suggest that particularly diverse groups publish a higher number of papers and receive more citations per paper than average. Thursday, 31 January 2019 (11:00am - 12:00), K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa. All welcome!
From NGS data to real-time tracking of viruses' outbreaks: NextStrain and Genome Detective workshop. KRISP, Nelson Mandela School of Medicine, UKZN, Durban, South Africa, 24-25 January. Training is free to post-graduate students of UKZN and members of the H3AbioNet Bioinformatics Network.
This month, we focused our newsletter on KRISP training the next generation of scientists and positions available for PhDs and Post-Doctoral fellows at a Flagship program of UKZN. We also highlight publications on TB next generation sequencing and diagnostics, ethics and trans-disciplinary perspectives of HIV research and new phylodynamics models to characterize viral outbreaks.
We invite applications from ambitious Post-Docs (x10) and PhD (x10) students, to undertake research in a Flagship programme of UKZN in Durban and Pietermaritzburg, South Africa. In this Flagship, leading investigators from different disciplines come together to develop cutting-edge research ideas on precision medicine, precision public health and translational science.
We invite applications from ambitious Post-Docs and PhD students, to undertake research in a Flagship programme of the UKZN in Pietermaritzburg, South Africa. This project aims to establish Zebrafish Models for Human Disease and Toxicology, including the development of genetic models for non-communicable diseases (NCD) such as Type 2 Diabetes and for pollutants and contaminants of emerging concern (CEC).
We invite applications from ambitious post doctoral scientists, to undertake research in a Flagship programme of the UKZN and the MRC in Durban, South Africa. This Fellowship aims to generate large geographically indexed HIV, TB and cancer datasets in South Africa. The fellow will apply advanced geospatial analysis techniques and molecular epidemiology and geographical analysis techniques to identify “hotspots” in space-time and describe the characteristics of HIV, TB and HPV transmission networks and its impact on the development of cancer.
We invite applications from ambitious post doctoral scientists, to undertake research in a Flagship programme of the UKZN and the MRC in Durban, South Africa. This project aims to identify factors associated with the acquisition and progression of HIV and the development of HIV drug resistance. The postdoctoral fellow will use human and viral genetic data combined with high quality clinical and epidemiological data to characterize genetic and epigenetic factors that are associated with health outcomes.
We invite applications from ambitious post students, to undertake a PhD in a Flagship programme of the UKZN and the MRC in Durban, South Africa. This project exemplifies how analysis of genomic, clinical, social and epidemiological data could directly impact human health in Africa. PhD fellows will receive outstanding training and be mentored by leading scientists, who commonly publish in some of of the top biomedical journals
KRISP PAPERS
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:.
Community engagement with HIV drug adherence in rural South Africa: a transdisciplinary approach.
Treffry-Goatley A, Lessells RJ, Moletsane R, de Oliveira T, Gaede B, BMJ Med Humanit (2018), 44:239–246.
HIV drug resistance in sub-Saharan Africa: public health questions and the potential role of real-world data and mathematical modelling.
de waal R, Lessells R, Hauser A, Kouyos R, Davies M-A, Egger M, Wandeler G, for ieDeA-Southern Africa, Journal of Virus Eradication (2018), 4(Supplement 2): :55–58.
Predicted antiviral activity of tenofovir versus abacavir in combination with a cytosine analogue and the integrase inhibitor dolutegravir in HIV-1-infected South African patients initiating or failing first-line ART.
Derache A, Iwuji CC, Danaviah S, Giandhari J, Marcelin AG, Calvez V, de Oliveira T, Dabis F, Pillay D, Gupta RK, J Antimicrob Chemother. (2018), doi: 10.1093/jac/dky428:doi:10.1093/jac/dky428.
Genomic and epidemiological monitoring of yellow fever virus transmission potential.
Faria NR, Kraemer MUG, S C Hill, J Goes de Jesus, R S Aguiar, F C M Iani, J Xavier, J Quick, L du Plessis, S Dellicour, J Thézé, R D O Carvalho, G Baele, C-H Wu, P P Silveira, M B Arruda, M A Pereira, G C Pereira, J Lourenço1, U Obolski, L Abade, T I Vasylyeva, M Giovanetti, D Yi, D J Weiss, G R W Wint, F M Shearer, S Funk, B Nikolay, Fonseca V, T E R Adelino, M A A Oliveira, M V F Silva, L Sacchetto, P O Figueiredo, I M Rezende, E M Mello, R F C Said, D A Santos, M L Ferraz, M G Brito, L F Santana, M T Menezes, R M Brindeiro, A Tanuri, F C P dos Santos, M S Cunha, J S Nogueira, I M Rocco, A C da Costa, S C V Komninakis, V Azevedo, A O Chieppe, E S M Araujo, M C L Mendonça, C C dos Santos, C D dos Santos, A M Mares-Guia, R M R Nogueira, P C Sequeira, R G Abreu, M H O Garcia, A L Abreu, O Okumoto, E G Kroon, C F C de Albuquerque, K Lewandowski, S T Pullan, M Carroll, de Oliveira T, E C Sabino, R P Souza, M A Suchard, P Lemey, G S Trindade, B P Drumond, A M B Filippis, N J Loman, S Cauchemez, Alcantara LCJ, Pybus OG , Science (2018), DOI: 10.1126/science.aat7115:.
Genome Detective: An Automated System for Virus Identification from High-throughput sequencing data..
Vilsker M, Moosa Y, Nooij S, Fonseca V, Ghysens Y, Dumon K, Pauwels R, Alcantara LC, Vanden Eynden E, Vandamme AM, Deforche K, de Oliveira T, Bioinformatics (2018), doi: 10.1093/bioinformatics/bty695:.
Patterns of genomic site inheritance in HIV-1M inter-subtype recombinants delineate the most likely genomic sites of subtype-specific adaptation.
Tongo M, de Oliveira T, Martin DP, Virus Evolution (2018), Volume 4, Issue 1, 1 January 2018, vey015:.
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
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.
2016-08-20
Yellow Fever Virus Typing Tool
This is the first version of the Yellow Fever typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.