UCT has several Tuberculosis researchers tackling the problem of TB and TB-related issues. In order to be more effective in dealing with TB, collobration between groups are crucial. We have summarised the current UCT human resources involved in Mycobacterium (MTB) and MTB host data generation and analysis.


Current MTB Research Data at UCT

Principal investigator Data source and Type
This email address is being protected from spambots. You need JavaScript enabled to view it. MTB: WGS
This email address is being protected from spambots. You need JavaScript enabled to view it. Host: Whole blood RNA-Seq, Plasma proteomic
This email address is being protected from spambots. You need JavaScript enabled to view it. MTB: WGS
This email address is being protected from spambots. You need JavaScript enabled to view it. MDR MTB: WGS
This email address is being protected from spambots. You need JavaScript enabled to view it. MTB: Tn-seq; MTB: Tn-seq
Keertan Dheda Host: BAL RNAseq, lung tissue RNAseq, urine proteomics; MTB: WGS, RNAseq, proteomics; MDR and XDR TB: WGS and RNAseq


Several tools exist for investigating TB drug resistance mutations in sequence data:

TB Profiler: Given raw sequence data as input, TB Profiler infers strain type and identifies known drug resistance markers. This in silico diagnostic uses a library generated from 1,325 mutations predictive of drug resistance for 15 anti-tuberculosis drugs. The library was validated for 11 of these drugs using genomic-phenotypic data from 792 strains (Coll et al).


ReSeqTB: "...catalogs a vast amount of genotypic, phenotypic and related metadata from Mycobacterium tuberculosis (Mtb) strains to enable the development of clinically useful, WHO-endorsed in vitro diagnostic assays for rapid drug susceptibility testing of MTb..."

The Science Faculty at UCT will offer an interdisciplinary degree in Data Science from 2017. Participating departments are Statistical Sciences, Computer Science, Astronomy, Physics, and the Bioinformatics unit (Health Sciences Faculty). Read more...

Prof Mulder is one of  'The world's most influential scientific minds 2014’

Six South Africa-based scientists represent Africa on a list of the world’s currently most influential scientific minds, released on 18 June by the intellectual property and science business of Thomson Reuters. The six are Nicola Mulder and William Bond from the University of Cape Town; Stellenbosch University’s David Richardson; Guy Midgley from the South African National Biodiversity Institute; and Rachel Jewkes and Lyn Wadley from the University of the Witwatersrand.

The researchers on the list wrote the most ‘highly cited papers’—that is, ranking among the top 1 per cent most cited in their subject field and year—between 2002 and 2012. More than 3,000 scientists made it onto the list. Another four highly cited researchers list ‘secondary affiliations’ to South African institutions: Matthias Egger (University of Bern, Switzerland, and UCT), Bruce Walker (Howard Hughes Medical Institute, US, and University of KwaZulu-Natal), Yves Van De Peer (Ghent University, Belgium, and University of Pretoria), and Christopher Henshilwood (University of Bergen, Norway, and Wits University).


However, no researchers on the list are associated with other African countries. “The global nature of the study highlights the countries, institutions and researchers on the cutting edge of science. It’s our mission at Thomson Reuters to support these individuals as they advance innovation globally,” said Basil Moftah, president of Thomson Reuters IP & Science.


The South Africa-based researchers excelled in biology, clinical medicine, environmental sciences and social sciences. “The ‘highly cited’ badge is one result of the research made possible by the centre of excellence programme that has produced a vibrant research hub in South Africa which is enjoying international recognition,” said David Richardson, one of the South Africans on the list.


In its first 10 years, Richardson’s Centre for Invasion Biology has produced over 800 papers in peer-reviewed journals and trained over 200 students. “South Africa is a superb natural laboratory for studying the ecology of invasive species, how they affect humans, and how humans perceive the problems,” he says.


The original article above from researchprofessional can be accessed here.

The full report of the world's most influential scientific minds 2014 can be accessedhere

UCT researchers assist in tsetse fly genetic code breakthrough

An international team, including researchers at the University of Cape Town and Yale University in the USA, has sequenced and annotated the genetic code for a representative species of the tsetse fly (Glossina morsitans), which carries the potentially fatal African trypanosomes to humans and animals in sub-Saharan Africa. Read More...

CBIO Joins the Global Alliance

The Global Alliance was created to enable the sharing of genomic and clinical data to accelerate progress in medicine. Providing widespread access to genomic and clinical data will be achieved by developing a common framework of international technical, operational and ethical standards needed to ensure the interoperability of genomic research platforms in a secure and responsible manner. In order to achieve these goals, The Global Alliance will work to (i) bring together the research, clinical, and disease advocacy communities and the private sector to support and promote the responsible sharing of genomic data and (ii) collaborate with interested parties to create an information platform that is open and accessible, and provides common standards, formats and tools to stakeholders in the genomic research community.


For more information see the factsheet. A number of institutions/consortia, including H3ABioNet have signed us as founding partners.


The Alliance was recently announced in Nature, The New York Times, and The Guardian:




CBIO tools