About Emmanuel James San

sanemmanueljames@gmail.com +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


PUBLICATIONS


A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa .
Wilkinson E, Giovanetti M, Tegally H, San EJ, Lessells R, Abdoul K. Sangare, Abdoul-Salam Ouedraogo, Abdul K. Sesay, Abechi Priscilla, Adedotun-Sulaiman Kemi, Adewunmi M. Olubusuyi, Adeyemi O.O. Oluwapelumi, Adnène Hammami, Adrienne A. Amuri, Ahmad Sayed, Ahmed E.O. Ouma, Aida Elargoubi, Ajayi N. Anthony, Ajogbasile F. Victoria, Akano Kazeem, Akpede George, Alexander J. Trotter, Ali A. Yahaya, Alpha K. Keita, Amadou Diallo, Amadou Kone, Amal Souissi, Amel Chtourou, Ana V. Gutierrez, Andrew J. Page, Anika Vinze, Arash Iranzadeh, Arnold Lambisia, Arshad Ismail, Audu Rosemary, Augustina Sylverken, Ayoade Femi, Azeddine Ibrahimi, Baba Marycelin, Bamidele S. Oderinde, Bankole Bolajoko, Beatrice Dhaala, Belinda L. Herring, Berthe-Marie Njanpop-Lafourcade, Bronwyn Kleinhans, Bronwyn McInnis, Bryan Tegomoh, Cara Brook, Catherine B. Pratt, Cathrine Scheepers, Chantal G. Akoua-Koffi, Charles N. Agoti, Christophe Peyrefitte, Claudia Daubenberger, Collins M. Morang’a, D. James Nokes, Daniel G. Amoako, Daniel L. Bugembe, Danny Park, David Baker, Deelan Doolabh, Deogratius Ssemwanga, Derek Tshiabuila, Diarra Bassirou, Dominic S.Y. Amuzu, Dominique Goedhals, Donwilliams O. Omuoyo, Dorcas Maruapula, Ebenezer Foster-Nyarko, Eddy K. Lusamaki, Edgar Simulundu, Edidah M. Ong'era, Edith N. Ngabana, Edwin Shumba, Elmostafa El Fahime, Emmanuel Lokilo, Enatha Mukantwari, Eromon Philomena, Essia Belarbi, Etienne Simon-Loriere, Etilé A. Anoh, Fabian Leendertz, Faida Ajili, Fakayode O. Enoch, Fares Wasfi, Fatma Abdelmoula, Fausta S. Mosha, Faustinos T. Takawira, Fawzi Derrar, Feriel Bouzid, Folarin Onikepe, Fowotade Adeola, Francisca M. Muyembe, Frank Tanser, Fred A. Dratibi, Gabriel K. Mbunsu, Gaetan Thilliez, Gemma L. Kay, George Githinji, Gert van Zyl, Gordon A. Awandare, Grit Schubert, Gugu P. Maphalala, Hafaliana C. Ranaivoson, Hajar Lemriss, Happi Anise, Haruka Abe, Hela H. Karray, Hellen Nansumba, Hesham A. Elgahzaly, Hlanai Gumbo, Ibtihel Smeti, Ikhlas B. Ayed, Ikponmwosa Odia, Ilhem Boutiba-Ben Boubaker, Imed Gaaloul, Inbal Gazy, Innocent Mudau, Isaac Ssewanyana, Iyaloo Konstantinus, Jean B. Lekana-Douk, Jean-Claude C. Makangara, Jean-Jacques M. Tamfum, Jean-Michel Heraud, Jeffrey G. Shaffer, Giandhari J, Jingjing Li, Jiro Yasuda, Joana Q. Mends, Jocelyn Kiconco, John M. Morobe, John O. Gyapong, Johnson C. Okolie, John T. Kayiwa, Johnathan A. Edwards, Jones Gyamfi, Jouali Farah, Joweria Nakaseegu, Joyce M. Ngoi, Joyce Namulondo, Julia C. Andeko, Julius J. Lutwama, Justin O’Grady, Katherine Siddle, Kayode T. Adeyemi, Kefentse A. Tumedi, Khadija M. Said, Kim Hae-Young, Kwabena O. Duedu, Lahcen Belyamani, Lamia Fki-Berrajah, Lavanya Singh, Leonardo de O. Martins, Lynn Tyers, Magalutcheemee Ramuth, Maha Mastouri, Mahjoub Aouni, Mahmoud el Hefnawi, Maitshwarelo I. Matsheka, Malebogo Kebabonye, Mamadou Diop, Manel Turki, Marietou Paye, Martin M. Nyaga, Mathabo Mareka, Matoke-Muhia Damaris, Maureen W. Mburu, Maximillian Mpina, Mba Nwando, Michael Owusu, Michael R. Wiley, Mirabeau T. Youtchou, Mitoha O. Ayekaba, Mohamed Abouelhoda, Mohamed G. Seadawy, Mohamed K. Khalifa, Mooko Sekhele, Mouna Ouadghiri, Moussa M. Diagne, Mulenga Mwenda, Mushal Allam, My V.T. Phan, Nabil Abid, Nadia Touil, Nadine Rujeni, Najla Kharrat, Nalia Ismael, Ndongo Dia, Nedio Mabunda, Nei-yuan Hsiao, Nelson B. Silochi, Ngoy Nsenga, Nicksy Gumede, Nicola Mulder, Nnaemeka Ndodo, Norosoa H Razanajatovo, Nosamiefan Iguosadolo, Oguzie Judith, Ojide C. Kingsley, Okogbenin Sylvanus, Okokhere Peter, Oladiji Femi, Olawoye Idowu, Olumade Testimony, Omoruyi E. Chukwuma, Onwe E. Ogah, Onwuamah Chika, Oshomah Cyril, Ousmane Faye, Oyewale Tomori, Pascale Ondoa, Patrice Combe, Patrick Semanda, Paul E. Oluniyi, Paulo Arnaldo, Peter K. Quashie, Philippe Dussart, Phillip A. Bester, Placide K. Mbala, Reuben Ayivor-Djanie, Richard Njouom, Richard O. Phillips, Richmond Gorman, Robert A. Kingsley, Rosina A.A. Carr, Saâd El Kabbaj, Saba Gargouri, Saber Masmoudi, Safietou Sankhe, Salako B. Lawal, Samar Kassim, Sameh Trabelsi, Samar Metha, Sami Kammoun, Sanaâ Lemriss, Sara H.A. Agwa, Sébastien Calvignac-Spencer, Stephen F. Schaffner, Seydou Doumbia, Sheila M. Mandanda, Sherihane Aryeetey, Shymaa S. Ahmed, Siham Elhamoumi, Soafy Andriamandimby, Sobajo Tope, Sonia Lekana-Douki, Sophie Prosolek, Soumeya Ouangraoua, Steve A. Mundeke, Steven Rudder, Sumir Panji, Sureshnee Pillay, Susan Engelbrecht, Susan Nabadda, Sylvie Behillil, Sylvie L. Budiaki, Sylvie van der Werf, Tapfumanei Mashe, Tarik Aanniz, Thabo Mohale, Thanh Le-Viet, Tobias Schindler, Ugochukwu J. Anyaneji, Ugwu Chinedu, Ramphal U, Uwanibe Jessica, Uwem George, Fonseca V, Vincent Enouf, Vivianne Gorova, Wael H. Roshdy, William K. Ampofo, Wolfgang Preiser, Wonderful T. Choga, Yaw Bediako, Yeshnee Naidoo, Yvan Butera, Zaydah R. de Laurent, Amadou A. Sall, Ahmed Rebai, Anne von Gottberg, Bourema Kouriba, Carolyn Williamson, Daniel J. Bridges, Ihekweazu Chikwe, Jinal Bhiman, Madisa Mine, Matthew Cotten, Sikhulile Moyo, Simani Gaseitsiwe, Ngonda Saasa, Pardis C. Sabeti, Pontiano Kaleebu, Yenew K. Tebeje, Sofonias K. Tessema, Happi Christian, John Nkengasong, de Oliveira T, Science (2021), DOI: 10.1126/science.abj4336:.


The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages .
Martin DP, Weaver S, Tegally H, San EJ, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ; NGS-SA; COVID-19 Genomics UK (COG-UK), Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. , Cell (2021), https://doi.org/10.1016/j.cell.2021.09.003:.


Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing. .
Singh L, Anyaneji UJ, Ndifon W, Turok N, Mattison SA, Lessells R, Sinayskiy I, San EJ, Tegally H, Barnett S, Lorimer T, Petruccione F, de Oliveira T. , Scientific Reports (2021), 11(1):17793. doi: 10.1038/s41598-021-96934-z:.


HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens..
Fischer W, Giorgi EE, Chakraborty S, Nguyen K, Bhattacharya T, Theiler J, Goloboff PA, Yoon H, Abfalterer W, Foley BT, Tegally H, San EJ, de Oliveira T, Network for Genomic Surveillance in South Africa (NGS-SA), Gnanakaran S, Korber B, Cell Host Microbe (2021), 29(7):1093-1110. doi: 10.1016/j.chom.2021.05.012:.


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:.


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:.


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.:.


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:.


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.


News Section from Bioafrica and SATuRN websites

NEWS


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



VIDEOS


Blogs from Bioafrica and SATuRN websites

BLOGS


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