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MalariaGEN-PAMCA Anopheles genomic surveillance training

MalariaGEN-PAMCA training course in data analysis for genomic surveillance of African malaria vectors

This training course deals with data analysis for genomic surveillance of African malaria vectors, and was developed jointly by MalariaGEN and PAMCA (the Pan-African Mosquito Control Association).

More information is available on the course webpage here.


Progess towards malaria elimination has stalled since 2015. Neither malaria incidence nor mortality have reduced substantially since then. Part of the reason for this may be mosquitoes developing resistance to the insecticides being used in long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS). Vector genomic surveillance could enable early detection of new insecticide resistance variants emerging in mosquito populations. This intelligence could be beneficial in designing and adapting insecticide resistance management plans.

But the data comes from multiple sources, and can be messy, complex, and confusing. This course will introduce participants to the basics of data analysis for genome surveillance, with particular reference to African malaria vectors.

Who is this training for?

Scientists and data analysts in African research groups and disease control programmes.


At the end of this course, participants will be able to:

  1. Perform a range of analyses of Anopheles genomic data that are relevant to malaria vector surveillance.
  2. Generate plots, tables and statistics that can be used in a surveillance report.
  3. Interpret results and explain to others what they mean.


The training program consists of eight virtual workshops spread over 12 weeks. Workshops combine hands-on coding with discussions and lectures.

The first cohort completed the program in early 2023. A second intake was held from June and July 2023. The third iteration is to be held from March to May 2024.

Contact for more information.

Course leads

Alistair Miles, Vector Surveillance Lead, Wellcome Sanger Institute, UK – Course Lead


Paballo Chauke, Training Coordinator, MalariaGEN, Wellcome Sanger Institute, UK – Course Coordinator



Instructors and Teaching Assistants

Find out more about the participants, instructors, and teaching assistants by downloading the Delegate Pack.


Marilou Boddé, PhD Candidate, University of Cambridge/Wellcome Sanger Institute, UK – Teaching Assistant/Instructor

Kelly Bennett, Wellcome Sanger Institute, UK – Teaching Assistant

Jon Brenas, Post-doctoral Fellow, Wellcome Sanger Institute, UK – Teaching Assistant/Instructor

Louise Cerdeira, Post-doctoral Research Associate, Liverpool School of Tropical Medicine, UK – Teaching Asssistant

Chris Clarkson, Principal Data Scientist, Wellcome Sanger Institute, UK – Teaching Asssistant/Instructor

Nsa Dada, Research Fellow, Centers for Disease Control (CDC), USA – Teaching Assistant

Luc Salako Djogbenou, Director, Institut Régional de Santé Public; Deputy Director, Tropical Infectious Diseases Research Centre, University of Abomey-Calavi, Benin

Penny Hancock, Lecturer, Imperial College London, UK

Elijah Juma, Program Manager, Pan-African Mosquito Control Association (PAMCA), Kenya – Teaching Assistant

Nace Kranjc, Post-doctoral Researcher, Imperial College London, UK – Teaching Assistant

Eric Lucas, Senior Research Associate, Liverpool School of Tropical Medicine, UK – Teaching Assistant/Instructor

Carlo de Marco, PhD Candidate, Sapienza University of Rome, italy – Teaching Assistant

Joachim Nwezeobi, Postdoctoral Fellow, Wellcome Sanger Institute, UK – Teaching Assistant/Instructor

Sanjay Nagi, PhD Candidate, Liverpool School of Tropical Medicine, UK – Teaching Assistant

Eric Ochomo, Senior Research Officer/Head of Entomology, Kenya Medical Research Institute (KEMRI), Kenya – Teaching Assistant

Josh Reynolds, PhD Candidate, Imperial College London, UK – Teaching Assistant

Helga Saïzonou, PhD Candidate, University of Abomey-Calavi (UAC)/Tropical Infectious Diseases Research Center (TIDRC), Benin

Brandy St. Laurent, Staff Scientist, Wellcome Sanger Institute, UK – Instructor


First Cohort (2022-2023) Participants

You can read more about the participants’ research interests by downloading the Delegate Pack.

Akena Stephen Abwoye, Biostatistician/Field Epidemiology Graduate, Msc. Clinical Epidemiology & Biostatistics; Ministry of Health, Uganda

Jewelna Akorli, Senior Research Fellow & Principal Investigator, Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana

Lucas Amenga-Etego, Senior Research Fellow, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Ghana

Nathalie Amvongo-Adjia, Post-doctoral Research Assistant, Centre for Research in Infectious Diseases (CRID); Research Officer, Institute of Medical Research and Medicinal Plant Studies (IMPM), Cameroon

Antonio Nkondjio Christophe, Senior research staff, OCEAC Yaoundé, Cameroon

Moussa Diallo, Scientific Officer, Medical Research Council Unit the Gambia at London School of Hygiene and Tropical Medicine (MRCG at LSHTM), The Gambia

Albert Gangbadja, MSc Candidate, University of Abomey-Calvi/Tropical Infectious Diseases Research Center, Benin

Lemu Golassa, Associate Professor of Medical Parasitology/Head of Medical parasitology Research, Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Ethiophia

Westone Hamwata, Scientific Officer, Entomology, Tropical Diseases Research Centre, Ndola, Zambia

Kondwani Kachali, Research Assistant, Malaria Alert Centre-Communicable Diseases Action Centre (MAC-CDAC), Kamuzu University of Health Sciences, Malawi

Luna Kamau, Principal Research Scientist & Deputy Director, Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Kenya

Ruth Kouamé, PhD Candidate, Centre Suisse de Recherches Scientifiques, Côte d’Ivoire

Mahamadi Kientega, PhD Candidate (Applied Biology and Modelling of Biological Systems/Medical Entomology), Nazi Boni University (ACE ITECH-MTV), Burkina Faso

Zandile Langa, MSc. Candidate, Wits University; Research Assistant, Vector Control Reference Laboratory, National Insitute of Communicable Diseases, South Africa

Ibra Lujumba, Bioinformatics Trainer Fellow, PAMCA, Uganda

Mbanga Muleba, Scientific Officer, Tropical Diseases Research Centre, Ndola, Zambia

Givemore Munhenga, Principal Medical Scientist, National Institute for Communicable Diseases; Senior Researcher, University of the Witwatersrand, South Africa

Sophia Hussein Mwinyi, Research and Data Scientist, Ifakara Health Institute, Tanzania

Faridah Nansamba, Data Manager, Division of Health Information, Ministry of Health, Uganda

El Hadji Amadou Niang, Deputy director, Laboratoire d’Ecologie Vectorielle et Parasitaire, Université Cheikh Anta Diop, Senegal

Jane Njeri Mwangi,  Bioinformatics Fellow, Pan-African Mosquito Control Association, Kenya

Joel Odero, PhD Candidate, University of Glasgow, UK and Ifakara Health Institute, Tanzania

Fatoumata Seck, PhD Candidate (Applied Biology and Modelling of Biological Systems/Medical Entomology), African Centre of Excellence in Biotechnological Innovations for the Elimination of Vector-borne Diseases (ACE ITECH-MTV), Burkina Faso


Additional Participants

Deriba Abera

Faraji Abilahi

Enock Kofi Amoako

Kala Chouakeu

Nelly Armanda

Benoit Sessinou Assogba

Mayi Marie Paul Audrey

Alex Auyang

Catherine Bakari

Lemonde Bouafou

Soromane Camara

Joseph Chabi

Edi Constant

Joseph Gichuhi

Alexandria Harrot

Mahamadi Kientega

Pilate Kwi

Ruth Lekundayo

Edward Lukyamuzi

Surina Maharaj

Mara Maquina

Sylvia Milanoi

Leon Mugenzi

Emmanuel Mwanga

Dyane Nanmede

Edwin Ogola

Diana Omoke

Brian Polo

Nsango Sandrine

Jacqueline Waweru

Rosine Z. Wolie

Ayebi Hermann

Florent Yapo

Josue Zanga

Go to the course webpage to rewatch lectures, download example code, and find additional readings.

Meet the course trainers and participants by reading through the Delegate Pack.