Emmanuel James San

San James is Pursuing a PhD in Medicine, Majoring in Virology and a Bioinformatics Research Associate at the Kwazulu Natal Research and Innovation Sequencing Platform (KRISP). Research interests are in the areas of Bioinformatics Software and Pipelines Development, Next Generation Sequence Data Management and Analysis, and High Performance Computing for Data Intensive Projects

Contact Details:

Email: sanemmanueljames@gmail.com

Telephone: +27 (0) 72 529 0848

Background:

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.



Affiliations:

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).



Education:

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


Videos Videos Descriptions

YouTube Video

Social Worker Workshop with Adolescents on ARVs in South Africa

Author: Pretty Nkosi & Nokuthula Skhosana - Date: 2012-12-30

Anti-retroviral (ARV) therapy workshop organized by social workers with adolescents as part of the Hlabisa HIV and Care Treatment Program and the Southern African Treatment and Resistance Network (SATuRN)


Blogs Blogs Description & Link

bioafrica - Blogs from Bioafrica and SATuRN websites

Social Worker perspective: Adolescents on Antiretroviral (ARV) therapy - a VideoBlog

Author: Pretty Nkosi, Nokuthula Skhosana, Lungani Ndwandwe and Tulio de Oliveira - 2012-02-10

bioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websitesbioafrica - News Section from Bioafrica and SATuRN websites
News News Description and Link

bioafrica - News Section from Bioafrica and SATuRN websites

KRISP Papers

Nature paper: Renewing Felsenstein's phylogenetic bootstrap in the era of big data

KRISP Papers - 2018-04-18

KRISP Nature paper with Pasteur Institute on a new phylogenetic method to analyse large HIV and mammalian DNA sequence datasets!


KRISP News

Science Discovery: Biomarkers for HIV treatment

KRISP News - 2018-01-19

Mercury Reporter, Durban, KwaZulu-Natal, 19 Jan 2018: Scientists led an in ternational research team which discovered new genetic markers that identify why the onset of Aids appears to occur so quickly in some people after they are infected with HIV The study published in the journal Science (Ramsuran et al. Science 2018), sheds new light on how specific human genes can lead to a faster deterioration for people living with HIV who are not on treatment.


KRISP News

SA study reveals important link between genes and Aids

KRISP News - 2018-01-19

HIV/AIDS researchers have never understood why people infected with HIV developed Aids at different times? but now they suspect that it all has to do with their genes. A study by South African and US researchers (Ramsuran et al. Science 2018) has shed new light on how specific genes in people can lead to the faster progression of Aids-related illnesses in people living with HIV who are not on treatment.


KRISP News

Why some HIV-positive people develop AIDS quicker than others is now clearer

KRISP News - 2018-01-19

The study, published in the prestigious journal Science (Ramsuram et al. 2018), was led by South African scientists who, together with an international research team, discovered that a specific-type human leucocyte antigen (HLA) gene helps infected cells to evade the body's first line of defence


KRISP News

Prevention of HIV transmission by antiretroviral therapy

KRISP News - 2017-11-30

Commentary by Jens Lundgren & Andrew Phillips, Lancet HIV, 30 November 2017.


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


KRISP News

KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP) Established

KRISP News - 2017-07-12

The Technology Innovation Agency (TIA) and UKZN have signed an agreement for the establishment of KRISP - the KwaZulu-Natal Research and Innovation Sequencing Platform.


SANTHE

We have been awarded a collaborative grant from SANTHE/Wellcome Trust programme in Africa

SANTHE - 2017-02-28

The Wellcome Trust DELTAS funded SANTHE program awarded seven grants to develop collaborative research projects to address critical challenges to African capacity in HIV and/or TB clinical, social/behavioural, and biomedical science.


The Lancet

Two manuscripts featured in the Lancet website front webpage on AIDS day.

The Lancet - 2016-12-01

Two of our recently published manuscripts (de Oliveira et al. Lancet HIV 2016 & Gregson et al Lancet Infectious Diseases 2016) are highlighed in the Lancet website front webpage...


SASBi & SAGS

4th Joint Congress of the South African Society for Bioinformatics (SASBi) and the South African Genetics Society (SAGS)

SASBi & SAGS - 2016-09-23

The biennial SASBi and SAGS congresses are the premier national scientific meetings on bioinformatics and genetics in South Africa. In total, 187 participats delivered 40 oral presentations and 65 posters in SASBi-SAGS-2016. This congress provided an exciting opportunity to learn about cutting-edge research in both disciplines, and to network with members of the two societies and with leading international scientists.


CAPRISA, UKZN & MRC Flagship

PhD Fellowship II: Genomics, Bioinformatics, Epidemioloy and Phylogenetics

CAPRISA, UKZN & MRC Flagship - 2016-08-23

The Professional Development Programme (PDP) at CAPRISA aims to develop and retain South African scientists and professionals of the highest calibre. The genomics and bioinformatics project in HIV-1 phylogenetics and molecular epidemiology is inter-disciplinary in nature and involves collaboration between the CAPRISA's MRC HIV-TB Pathogenesis and Treatment Research Unit and the Flagship Program of the MRC, which are two of the most prestigious research programs in South Africa.


Science

South Africa's bid to end AIDS

Science - 2016-06-29

Science magazine (Vol. 353, Issue 6294, pp. 18-21, 2016). This issue was published before the AIDS conference in Durban 2016 and highlights some of our research, including our treatment as prevention trial (TasP) as well our phylogenetic analysis (de Oliveira et al. Lancet HIV 2016).


Rega Institute & Korea University College of Medicine

21st International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (VEME)

Rega Institute & Korea University College of Medicine - 2016-03-15

The 21st International Workshop on Virus Evolution and Molecular Epidemiology (VEME2016) will be hosted by the Korea University College of Medicine, 14-19 August, Seoul, Republic of Korea. Abstract deadline: 15 March 2016


Science

MOLECULAR EPIDEMIOLOGY: HIV family trees reveal viral spread.

Science - 2015-06-12

By John Cohen, Science, 12 June 2015. New studies could aid public health efforts. Last week at the New York Academy of Sciences in New York City, researchers, public health specialists, and HIV/AIDS advocates discussed how to exploit the potential of the technique, called phylogenetic analysis - and the thorny ethical and legal issues it raises...


New York Academy of Sciences

HIV 2015: Using Phylogenetics to Enhance the HIV Response, New York, June 4, 2015

New York Academy of Sciences - 2015-06-04

A discussion meeting presented by the Joint United Nations Programme on HIV/AIDS (UNAIDS) and the Microbiology & Infectious Diseases Discussion Group at the New York Academy of Sciences on the use of phylogenetics to enhance HIV response.


KRISP Talks

Seminar: Virus and host genetics: where and how to look in big data for associations with infectious disease

KRISP Talks - 2015-02-13

The Wellcome Trust Africa Centre Genomics & Bioinformatics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Paul Kellam, 13 February 2015, K-RITH building, Nelson R Mandela School of Medicine, Durban, South Africa


UKZN

Inaugural Lecture: Bioinformatics, Genomics and HIV Research in Africa: A Brief Personal History

UKZN - 2014-07-14

The Vice-Chancellor and Principal Professor Malegapuru Makgoba cordially invites you and your spouse/partner to attend an inaugural lecture presented by Professor Tulio de Oliveira, 30 July 2014, K-RITH, Durban


KRISP Talks

Seminar: 30 years of HIV diversity research: a personal perspective

KRISP Talks - 2014-01-31

The Wellcome Trust Africa Centre Genomics Programme & UKZN MRC Flagship project cordially invites you to a seminar presented by Prof. Susan Engelbrecht, 31 January 2014, Durban


Wellcome Trust

New Director named for leading HIV research centre in South Africa

Wellcome Trust - 2013-09-02

Deenan Pillay, Professor of Virology at UCL (University College London), is today named as the new Director of the Africa Centre for Health and Population Studies, one of the Wellcome Trust's major overseas programmes.


FioCruz

Bioinformatics in the tropics I: 1st International Bioinformatics & Molecular Viral Evolution Workshop, Salvador, Bahia, Brazil, 22-26 July 2013

FioCruz - 2013-06-01

This is the first workshop of the bioinformatics in the tropics series, which will be presented at the Oswaldo Moniz Research Center (CPqGM), Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia, Brazil, 22 to 26 July 2013.


Wellcome Trust

Infectious Disease Genomics and Global Health Wellcome Trust Conference

Wellcome Trust - 2013-05-24

We are pleased to announce that we are presenting at the Sixth Infectious Disease Genomics and Global Health conference, Cambridge, U.K, 16-18 October 2013. The focus of this meeting is the application of genomic technologies to the problems of infectious disease in a global health context.


Zululand Observer

Case book tackles HIV and TB drug resistance

Zululand Observer - 2013-04-15

By Jonathan Davis, 15 April 2013 - Researchers from the Africa Centre for Health and Population Research near Mtubatuba have published a important book to help rural doctors, nurses and pharmacists working on the frontline of the country's interlinked HIV and tuberculosis (TB) pandemics manage increasing levels of resistance to the drugs needed to fight the diseases.


Africa Centre

PRESS RELEASE: Book Launch: HIV and TB Drug Resistance & Clinical Management Case Book

Africa Centre - 2013-03-06

Prof Eric Buch, Dean of the Faculty of Health Sciences at the University of Pretoria, in partnership with European Delegation to South Africa, MRC Inflammation and Immunity Unit and the Africa Centre for Health and Population Studies, UKZN, invite members of the media to attend the launch of the 'HIV and TB Resistance & Clinical Management Case Book' that is authored by Dr Theresa Rossouw of UP and Drs Richard Lessells and Tulio de Oliveira of the Africa Centre for Health and Population Studies. The details are as follows:


University of Pretoria

Invitation to the launch of the HIV and TB drug resistance & clinical management case book

University of Pretoria - 2013-03-05

University of Pretoria invites you to attend the launch of the publication HIV and TB resistance & clinical management case book. The invitation is writen in three official South African languages: Afrikaans, English and Sepedi.


Pirate Science

Searching for Virus Phylotypes

Pirate Science - 2013-01-22

Viral phylogenies have wide use: studying evolution, tracing the origin of epidemics, establishing dominant mode of transmission, identifying the apparition of drug resistance, even tracking individual body compartments.


MIT Technology review

The Machine That Will Help End TB

MIT Technology review - 2012-12-11

By Jon Cohen on December 11, 2012 - Nearly 1.5 million people die from tuberculosis every year, even though most cases can be cured with routine antibiotic treatments. One country's fight to get the ancient scourge under control has an unlikely hero: a simple diagnostic test.


TB Union

SATuRN at the 43rd Union World Conference on Lung Health

TB Union - 2012-11-20

KUALA LUMPUR, MALAYSIA, 14-17 Nov 2012, SATuRN researchers Dr. Richard Lessells and Dr. Tulio de Oliveira had a very successful TB conference. In this post we cover their presentations, workshops participation and tweeter coverage.


LabMedica

Collaboration to Undertake HIV Resistance Testing in Africa

LabMedica - 2012-08-06

Sequencing-based diagnostics for human immunodeficiency virus (HIV)-infected individuals will be carried out in Africa in order to determine resistance to antiretroviral drugs.


GenomeWeb

Life Tech, SATuRN Collaborate on Dx for Antiretroviral Resistance in HIV in Africa

GenomeWeb - 2012-07-26

NEW YORK (GenomeWeb News) - Life Technologies today announced a collaboration with the Southern African Treatment and Resistance Network (SATuRN) covering sequencing-based diagnostics for HIV patients in Africa.


Reuters

Life Technologies Corporation And Southern African Treatment and Resistance Network Collaborate To Increase Access To HIV Testing In Africa

Reuters - 2012-07-24

Life Technologies Corporation announced a collaboration with the Southern African Treatment and Resistance Network (SATuRN) on sequencing-based diagnostics for HIV-infected individuals in Africa.


The Wall Street Journal

Life Technologies and SATuRN Collaborate to Increase Access to HIV Testing in Africa

The Wall Street Journal - 2012-07-24

Life and Southern African Treatment and Resistance Network (SATuRN) Partner in Sequencing-Based Surveillance of Drug Resistance


Los Angeles Times

HIV drug resistance is spreading in Africa, experts say

Los Angeles Times - 2012-07-23

WASHINGTON (By Erin Loury, LA Times) - Scaling up the distribution of HIV medication over the last decade has vastly increased the number of people receiving treatment around the world. An estimated 8 million infected people received the antiretroviral drugs in 2011, compared to just 400,000 in 2003.


SATuRN

SATuRN meeting, presentations & tweet coverage at the XIX International AIDS 2012 Conference, Washington

SATuRN - 2012-07-14

WASHINGTON, 22-27 July 2012 - We are hosting a meeting, presenting many talks and posters and tweeting on the XIX International AIDS 2012 Conference.



Page design updated by Prof. Tulio de Oliveira, 2015