About Emmanuel James San

sanemmanueljames@gmail.com +27 (0) 72 529 0848


San James is Pursuing a PhD in Medicine, Majoring in Virology at the Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, South Africa and is a Bioinformatics Research Associate at the Kwazulu Natal Research and Innovation Sequencing Platform. Owing to his experience working as a Systems Analyst and Programmer with the Infectious Diseases Research Collaboration where he participated in exciting projects such the development of a clinical data visualization platform and Data Management Specialist at Global Health Uganda, he developed a keen interest bioinformatics research especially in the areas of Bioinformatics Software and Pipelines Development, Next Generation Sequence Data Management and Analysis (Phylogenetics, Recombinants and Drug Resistance), and High Performance Computing for Data Intensive Projects. His PhD research focus is in Microbial Classification and Detection, Development of SOPs for Sequence Analysis Projects, Validation of Existing Pipelines and setting up a standardized and structured bioinformatics environment.


KRISP - KwaZulu-Natal Research and Innovation Sequencing Platform, UKZN, Durban, South Africa.

Department of Virology, National Health Laboratory Service (NHLS), Durban, South Africa (PhD Fellow).


Master of Science in Data Communications and Software Engineering, Makerere University, 2016. Funded by the Forgarty International Center Scholarship.

Bachelor of Science in Computer Science, Makerere University, 2009


Sixteen novel lineages of SARS-CoV-2 in South Africa.
Tegally H, Wilkinson E, Lessells R, Giandhari J, Pillay S, Msomi N, Mlisana K, Bhiman J, Gottberg A, Walaza S, Fonseca V, Allam M, Ismail A, Engelbrecht S, Van Zyl G, Preiser W, Williamson C, Pettruccione F, Sigal A, Gazy I, Hardie D, Hsiao M, Martin D, York D, Goedhals D, San EJ, Giovanetti M, Lourenco J, Alcantara LCJ, de Oliveira T, Nature Medicine (2021), https://doi.org/10.1038/s41591-021-01255-3:.

Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression.
Morais-Rodrigues F, Silv Erio-Machado R, Kato RB, Rodrigues DLN, Valdez-Baez J, Fonseca V, San EJ, Gomes LGR, Dos Santos RG, Vinicius Canário Viana M, da Cruz Ferraz Dutra J, Teixeira Dornelles Parise M, Parise D, Campos FF, de Souza SJ, Ortega JM, Barh D, Ghosh P, Azevedo VAC, Dos Santos MA, Gene (2020), 144168. doi: 10.1016/j.gene.2019.144168.:.

Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls.
San EJ, Baichoo S, Kanzi A, Moosa Y, Lessells R, Fonseca V, Mogaka J, Power R, de Oliveira T, Front. Microbiol. (2020), https://doi.org/10.3389/fmicb.2019.03119:.

A computational method for the identification of Dengue, Zika and Chikungunya virus species and genotypes.
Fonseca V, Libin PJK, Theys K, Faria NR, Nunes MRT, Restovic MI, Freire M, Giovanetti M, Cuypers L, Nowé A, Abecasis A, Deforche K, Santiago GA, Siqueira IC, San EJ, Machado KCB, Azevedo V, Filippis AMB, Cunha RVD, Pybus OG, Vandamme AM, Alcantara LCJ, de Oliveira T, PLoS Negl Trop Dis (2019), 13(5):e0007231: doi: 10.1371/journal.pntd.0007231.

Mosquito-Borne Viral Diseases: Control and Prevention in the Genomics Era.
Fonseca V, Xavier J, San EJ, de Oliveira T, de Filippis AMB, Alcantara LCJ, Giovanetti M, Current Topics in the Epidemiology of Vector-Borne (2019), DOI: 10.5772/intechopen.88769:.

News Section from Bioafrica and SATuRN websites


A Virus Variant by Any Other Name - Please - The New York Times - 2021-03-03

South African scientists on pandemic’s frontline - Financial Times - 2021-02-15

The New Covid-19 Strain in South Africa: What We Know - The Wall Street Journal - 2021-01-11

KRISP produces over 1000 HIV-1 genomes in record time - SAMRC Press Release - 2020-12-03

The Pros and Cons of high-speed science - Daily Maverick - 2020-04-24

SA scientists on breaking the Covid-19 code - Saturday Independent - 2020-04-21

Odd drop in how Covid-19 numbers grow - Mail & Guadian - 2020-04-02

Social media helped scientists with coronavirus - Independent on Saturday - 2020-02-15

KRISP 2020 - Strategy Meeting - KRISP News - 2019-11-29

KRISP Preparing Next Generation Scientists - UKZN Ndaba News - 2018-10-18

South Africa's bid to end AIDS - Science - 2016-06-29

21st International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME) - Rega Institute & Korea University College of Medicine - 2016-03-15

Case book tackles HIV and TB drug resistance - Zululand Observer - 2013-04-15

Searching for Virus Phylotypes - Pirate Science - 2013-01-22

The Machine That Will Help End TB - MIT Technology review - 2012-12-11


Blogs from Bioafrica and SATuRN websites


Social Worker perspective: Adolescents on Antiretroviral (ARV) therapy - a VideoBlog - by Pretty Nkosi, Nokuthula Skhosana, Lungani Ndwandwe and Tulio de Oliveira - 2012-02-10

KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).

Location: K-RITH Tower Building
Nelson R Mandela School of Medicine, UKZN
719 Umbilo Road, Durban, South Africa.
Director: Prof. Tulio de Oliveira