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3. The African Human Microbiome Portal: a public web portal of curated metagenomic metadata

Author

Kiran, Anmol, primary, Hanachi, Mariem, additional, Alsayed, Nihad, additional, Fassatoui, Meriem, additional, Oduaran, Ovokeraye H, additional, Allali, Imane, additional, Maslamoney, Suresh, additional, Meintjes, Ayton, additional, Zass, Lyndon, additional, Rocha, Jorge Da, additional, Kefi, Rym, additional, Benkahla, Alia, additional, Ghedira, Kais, additional, Panji, Sumir, additional, Mulder, Nicola, additional, Fadlelmola, Faisal M, additional, and Souiai, Oussema, additional

Published
2024
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4. Proceedings of a Sickle Cell Disease Ontology workshop — Towards the first comprehensive ontology for Sickle Cell Disease

Author

Mulder, Nicola, Nembaware, Victoria, Adekile, Adekunle, Anie, Kofi A, Inusa, Baba, Brown, Biobele, Campbell, Andrew, Chinenere, Furahini, Chunda-Liyoka, Catherine, Derebail, Vimal K, Geard, Amy, Ghedira, Kais, Hamilton, Carol M, Hanchard, Neil A, Haendel, Melissa, Huggins, Wayne, Ibrahim, Muntaser, Jupp, Simon, Kamga, Karen Kengne, Knight-Madden, Jennifer, Lopez-Sall, Philomène, Mbiyavanga, Mamana, Munube, Deogratias, Nirenberg, Damian, Nnodu, Obiageli, Ofori-Acquah, Solomon Fiifi, Ohene-Frempong, Kwaku, Opap, Kenneth Babu, Panji, Sumir, Park, Miriam, Pule, Gift, Royal, Charmaine, Sangeda, Raphael, Tayo, Bamidele, Treadwell, Marsha, Tshilolo, Léon, and Wonkam, Ambroise

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Pediatric, Orphan Drug, Rare Diseases, Pain Research, Sickle Cell Disease, Hematology, Good Health and Well Being
Abstract

Sickle cell disease (SCD) is a debilitating single gene disorder caused by a single point mutation that results in physical deformation (i.e. sickling) of erythrocytes at reduced oxygen tensions. Up to 75% of SCD in newborns world-wide occurs in sub-Saharan Africa, where neonatal and childhood mortality from sickle cell related complications is high. While SCD research across the globe is tackling the disease on multiple fronts, advances have yet to significantly impact on the health and quality of life of SCD patients, due to lack of coordination of these disparate efforts. Ensuring data across studies is directly comparable through standardization is a necessary step towards realizing this goal. Such a standardization requires the development and implementation of a disease-specific ontology for SCD that is applicable globally. Ontology development is best achieved by bringing together experts in the domain to contribute their knowledge. The SCD community and H3ABioNet members joined forces at a recent SCD Ontology workshop to develop an ontology covering aspects of SCD under the classes: phenotype, diagnostics, therapeutics, quality of life, disease modifiers and disease stage. The aim of the workshop was for participants to contribute their expertise to development of the structure and contents of the SCD ontology. Here we describe the proceedings of the Sickle Cell Disease Ontology Workshop held in Cape Town South Africa in February 2016 and its outcomes. The objective of the workshop was to bring together experts in SCD from around the world to contribute their expertise to the development of various aspects of the SCD ontology.

Published
2016

5. Leveraging crowdsourcing to accelerate global health solutions

Author

Davis, Sage, Button-Simons, Katrina, Bensellak, Taoufik, Ahsen, Eren Mehmet, Checkley, Lisa, Foster, Gabriel J., Su, Xinzhuan, Moussa, Ahmed, Mapiye, Darlington, Khoo, Sok Kean, Nosten, Francois, Anderson, Timothy J. C., Vendrely, Katelyn, Bletz, Julie, Yu, Thomas, Panji, Sumir, Ghouila, Amel, Mulder, Nicola, Norman, Thea, Kern, Steven, Meyer, Pablo, Stolovitzky, Gustavo, Ferdig, Michael T., and Siwo, Geoffrey H.

Published
2019
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8. Genome-Wide Analysis of Cancer/Testis Gene Expression

Author

Hofmann, Oliver, Caballero, Otavia L., Stevenson, Brian J., Chen, Yao-Tseng, Cohen, Tzeela, Chua, Ramon, Maher, Christopher A., Panji, Sumir, Schaefer, Ulf, Kruger, Adele, Lehvaslaiho, Minna, Carninci, Piero, Hayashizaki, Yoshihide, Jongeneel, C. Victor, Simpson, Andrew J. G., Old, Lloyd J., and Hide, Winston

Published
2008
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9. African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Author

Othman, Houcemeddine, primary, Zass, Lyndon, additional, da Rocha, Jorge E. B., additional, Radouani, Fouzia, additional, Samtal, Chaimae, additional, Benamri, Ichrak, additional, Kumuthini, Judit, additional, Fakim, Yasmina J., additional, Hamdi, Yosr, additional, Mezzi, Nessrine, additional, Boujemaa, Maroua, additional, Okeke, Chiamaka Jessica, additional, Tendwa, Maureen B., additional, Sanak, Kholoud, additional, Chaouch, Melek, additional, Panji, Sumir, additional, Kefi, Rym, additional, Sallam, Reem M., additional, Ghoorah, Anisah W., additional, Romdhane, Lilia, additional, Kiran, Anmol, additional, Meintjes, Ayton P., additional, Maturure, Perceval, additional, Jmel, Haifa, additional, Ksouri, Ayoub, additional, Azzouzi, Maryame, additional, Farahat, Mohammed A., additional, Ahmed, Samah, additional, Sibira, Rania, additional, Turkson, Michael E. E., additional, Ssekagiri, Alfred, additional, Parker, Ziyaad, additional, Fadlelmola, Faisal M., additional, Ghedira, Kais, additional, Mulder, Nicola, additional, and Kamal Kassim, Samar, additional

Published
2022
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11. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

Author

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

Published
2021
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16. The Extent and Impact of Variation in ADME Genes in Sub-Saharan African Populations

Author

da Rocha, Jorge E. B., primary, Othman, Houcemeddine, additional, Botha, Gerrit, additional, Cottino, Laura, additional, Twesigomwe, David, additional, Ahmed, Samah, additional, Drögemöller, Britt I., additional, Fadlelmola, Faisal M., additional, Machanick, Philip, additional, Mbiyavanga, Mamana, additional, Panji, Sumir, additional, Wright, Galen E. B., additional, Adebamowo, Clement, additional, Matshaba, Mogomotsi, additional, Ramsay, Michéle, additional, Simo, Gustave, additional, Simuunza, Martin C., additional, Tiemessen, Caroline T., additional, Baldwin, Sandra, additional, Chiano, Mathias, additional, Cox, Charles, additional, Gross, Annette S., additional, Thomas, Pamela, additional, Gamo, Francisco-Javier, additional, and Hazelhurst, Scott, additional

Published
2021
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17. Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa

Author

Ras, Verena, primary, Botha, Gerrit, additional, Aron, Shaun, additional, Lennard, Katie, additional, Allali, Imane, additional, Claassen-Weitz, Shantelle, additional, Mwaikono, Kilaza Samson, additional, Kennedy, Dane, additional, Holmes, Jessica R., additional, Rendon, Gloria, additional, Panji, Sumir, additional, Fields, Christopher J, additional, and Mulder, Nicola, additional

Published
2021
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18. H3ABioNet genomic medicine and microbiome data portals hackathon proceedings

Author

Fadlelmola, Faisal M, primary, Ghedira, Kais, additional, Hamdi, Yosr, additional, Hanachi, Mariem, additional, Radouani, Fouzia, additional, Allali, Imane, additional, Kiran, Anmol, additional, Zass, Lyndon, additional, Alsayed, Nihad, additional, Fassatoui, Meriem, additional, Samtal, Chaimae, additional, Ahmed, Samah, additional, Da Rocha, Jorge, additional, Chaqsare, Souad, additional, Sallam, Reem M, additional, Chaouch, Melek, additional, Farahat, Mohammed, additional, Ssekagiri, Alfred, additional, Parker, Ziyaad, additional, Adil, Mai, additional, Turkson, Michael, additional, Benchaalia, Aymen, additional, Benkahla, Alia, additional, Panji, Sumir, additional, Kassim, Samar, additional, Souiai, Oussema, additional, and Mulder, Nicola, additional

Published
2021
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19. The African coelacanth genome provides insights into tetrapod evolution

Author

Amemiya, Chris T., Alföldi, Jessica J, Lee, Alison P., Fan, Shaohua S, Philippe, Hervé H, MacCallum, Iain I, Braasch, Ingo I, Manousaki, Tereza T, Schneider, Igor I, Rohner, Nicolas N, Organ, Chris C, Chalopin, Domitille D, Smith, Jeramiah J., Robinson, Mark M, Dorrington, Rosemary A., Gerdol, Marco M, Aken, Bronwen B, Biscotti, Maria Assunta, Barucca, Marco M, Baurain, Denis D, Berlin, Aaron M., Blatch, Gregory L., Buonocore, Francesco F, Burmester, Thorsten T, Campbell, Michael S., Canapa, Adriana A, Cannon, John P., Christoffels, Alan A, De Moro, Gianluca G, Edkins, Adrienne L., Fan, Lin L, Fausto, Anna Maria, Feiner, Nathalie N, Forconi, Mariko M, Gamieldien, Junaid J, Gnerre, Sante S, Gnirke, Andreas A, Goldstone, Jared V., Haerty, Wilfried W, Hahn, Mark E., Hesse, Uljana U, Hoffmann, Steve S, Johnson, Jeremy J, Karchner, Sibel I., Kuraku, Shigehiro S, Lara, Marcia M, Levin, Joshua Z., Litman, Gary W., Mauceli, Evan E, Miyake, Tsutomu T, Mueller, Gail M., Nelson, David R., Nitsche, Anne A, Olmo, Ettore E, Ota, Tatsuya T, Pallavicini, Alberto A, Panji, Sumir S, Picone, Barbara B, Ponting, Chris P., Prohaska, Sonja J., Przybylski, Dariusz D, Saha, Nil Ratan, Ravi, Vydianathan V, Ribeiro, Filipe J., Sauka-Spengler, Tatjana T, Scapigliati, Giuseppe G, Searle, Stephen M. J., Sharpe, Ted T, Simakov, Oleg O, Stadler, Peter F., Stegeman, John J., Sumiyama, Kenta K, Tabbaa, Diana D, Tafer, Hakim H, Turner-Maier, Jason J, van Heusden, Peter P, White, Simon S, Williams, Louise L, Yandell, Mark M, Brinkmann, Henner H, Volff, Jean-Nicolas J, Tabin, Clifford J., Shubin, Neil N, Schartl, Manfred M, Jaffe, David B., Postlethwait, John H., Venkatesh, Byrappa B, Di Palma, Federica F, Lander, Eric S., Meyer, Axel A, and Lindblad-Toh, Kerstin K

Published
2013
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20. A review of clinical pharmacogenetics Studies in African populations

Author

Radouani, Fouzia, primary, Zass, Lyndon, additional, Hamdi, Yosr, additional, Rocha, Jorge da, additional, Sallam, Reem, additional, Abdelhak, Sonia, additional, Ahmed, Samah, additional, Azzouzi, Maryame, additional, Benamri, Ichrak, additional, Benkahla, Alia, additional, Bouhaouala-Zahar, Balkiss, additional, Chaouch, Melek, additional, Jmel, Haifa, additional, Kefi, Rym, additional, Ksouri, Ayoub, additional, Kumuthini, Judit, additional, Masilela, Phumlani, additional, Masimirembwa, Collen, additional, Othman, Houcemeddine, additional, Panji, Sumir, additional, Romdhane, Lilia, additional, Samtal, Chaimae, additional, Sibira, Rania, additional, Ghedira, Kais, additional, Fadlelmola, Faisal, additional, Kassim, Samar Kamal, additional, and Mulder, Nicola, additional

Published
2020
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21. Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience

Author

Ahmed, Azza E., primary, Mpangase, Phelelani T., additional, Panji, Sumir, additional, Baichoo, Shakuntala, additional, Souilmi, Yassine, additional, Fadlelmola, Faisal M., additional, Alghali, Mustafa, additional, Aron, Shaun, additional, Bendou, Hocine, additional, De Beste, Eugene, additional, Mbiyavanga, Mamana, additional, Souiai, Oussema, additional, Yi, Long, additional, Zermeno, Jennie, additional, Armstrong, Don, additional, O'Connor, Brian D., additional, Mainzer, Liudmila Sergeevna, additional, Crusoe, Michael R., additional, Meintjes, Ayton, additional, Van Heusden, Peter, additional, Botha, Gerrit, additional, Joubert, Fourie, additional, Jongeneel, C. Victor, additional, Hazelhurst, Scott, additional, and Mulder, Nicola, additional

Published
2019
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23. Rapid evolution of cancer/testis genes on the X chromosome

Author

Simpson Andrew J, Old Lloyd J, Hide Winston, Zahn-Zabal Monique, Panji Sumir, Iseli Christian, Stevenson Brian J, and Jongeneel C Victor

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Cancer/testis (CT) genes are normally expressed only in germ cells, but can be activated in the cancer state. This unusual property, together with the finding that many CT proteins elicit an antigenic response in cancer patients, has established a role for this class of genes as targets in immunotherapy regimes. Many families of CT genes have been identified in the human genome, but their biological function for the most part remains unclear. While it has been shown that some CT genes are under diversifying selection, this question has not been addressed before for the class as a whole. Results To shed more light on this interesting group of genes, we exploited the generation of a draft chimpanzee (Pan troglodytes) genomic sequence to examine CT genes in an organism that is closely related to human, and generated a high-quality, manually curated set of human:chimpanzee CT gene alignments. We find that the chimpanzee genome contains homologues to most of the human CT families, and that the genes are located on the same chromosome and at a similar copy number to those in human. Comparison of putative human:chimpanzee orthologues indicates that CT genes located on chromosome X are diverging faster and are undergoing stronger diversifying selection than those on the autosomes or than a set of control genes on either chromosome X or autosomes. Conclusion Given their high level of diversifying selection, we suggest that CT genes are primarily responsible for the observed rapid evolution of protein-coding genes on the X chromosome.

Published
2007
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24. Development of Bioinformatics Infrastructure for Genomics Research in H3Africa

Author

Mulder, Nicola J, Adebiyi, Ezekiel, Adebiyi, Marion, Adeyemi, Seun, Ahmed, Azza, Ahmed, Rehab, Akanle, Bola, Alibi, Mohamed, Armstrong, Don L, Aron, Shaun, Ashano, Efejiro, Baichoo, Shakuntala, Benkahla, Alia, Brown, David K, Chimusa, Emile R., Fadlelmola, Faisal M., Falola, Dare, Fatumo, Segun, Ghedira, Kais, Ghouila, Amel, Hazelhurst, Scott, Isewon, Iunu, Jung, Segun, Kassim, Samar Kamal, Kayondo, Jonathan K, Mbiyavanga, Mamana, Meintjes, Ayton, Mohammed, Somia, Mosaku, Abayomi, Moussa, Ahmed, Muhammd, Mustafa, Mungloo-Dilmohamud, Zahra, Nashiru, Oyekanmi, Odia, Trust, Okafor, Adaobi, Oladipo, Olaleye, Osamor, Victor, Oyelade, Jellili, Sadki, Khalid, Salifu, Samson Pandam, Soyemi, Jumoke, Panji, Sumir, Radouani, Fouzia, Souiai, Oussama, and Tastan Bishop, Özlem

Subjects
Biomedical Research, Africa, Computational Biology, Humans, Genomics, Article
Abstract

Although pockets of bioinformatics excellence have developed in Africa, generally, large-scale genomic data analysis has been limited by the availability of expertise and infrastructure. H3ABioNet, a pan-African bioinformatics network, was established to build capacity specifically to enable H3Africa (Human Heredity and Health in Africa) researchers to analyze their data in Africa. Since the inception of the H3Africa initiative, H3ABioNet's role has evolved in response to changing needs from the consortium and the African bioinformatics community.H3ABioNet set out to develop core bioinformatics infrastructure and capacity for genomics research in various aspects of data collection, transfer, storage, and analysis.Various resources have been developed to address genomic data management and analysis needs of H3Africa researchers and other scientific communities on the continent. NetMap was developed and used to build an accurate picture of network performance within Africa and between Africa and the rest of the world, and Globus Online has been rolled out to facilitate data transfer. A participant recruitment database was developed to monitor participant enrollment, and data is being harmonized through the use of ontologies and controlled vocabularies. The standardized metadata will be integrated to provide a search facility for H3Africa data and biospecimens. Because H3Africa projects are generating large-scale genomic data, facilities for analysis and interpretation are critical. H3ABioNet is implementing several data analysis platforms that provide a large range of bioinformatics tools or workflows, such as Galaxy, the Job Management System, and eBiokits. A set of reproducible, portable, and cloud-scalable pipelines to support the multiple H3Africa data types are also being developed and dockerized to enable execution on multiple computing infrastructures. In addition, new tools have been developed for analysis of the uniquely divergent African data and for downstream interpretation of prioritized variants. To provide support for these and other bioinformatics queries, an online bioinformatics helpdesk backed by broad consortium expertise has been established. Further support is provided by means of various modes of bioinformatics training.For the past 4 years, the development of infrastructure support and human capacity through H3ABioNet, have significantly contributed to the establishment of African scientific networks, data analysis facilities, and training programs. Here, we describe the infrastructure and how it has affected genomics and bioinformatics research in Africa.

Published
2017

25. The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa's capacity for genomics research.

Author

Kumuthini, Judit, Zass, Lyndon, Panji, Sumir, Salifu, Samson P., Kayondo, Jonathan K., Nembaware, Victoria, Mbiyavanga, Mamana, Olabode, Ajayi, Kishk, Ali, Wells, Gordon, and Mulder, Nicola J.

Subjects
BIOINFORMATICS, TICKETS
Abstract

Background: Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic bioinformatics support to researchers through an online ticketing platform. The following article reports on the H3ABioNet HD (H3A-HD)'s development, outlining its design, management, usage and evaluation framework, as well as the lessons learned through implementation. Results: The H3A-HD evaluated using automatically generated usage logs, user feedback and qualitative ticket evaluation. Evaluation revealed that communication methods, ticketing strategies and the technical platforms used are some of the primary factors which may influence the effectivity of HD. Conclusion: To continuously improve the H3A-HD services, the resource should be regularly monitored and evaluated. The H3A-HD design, implementation and evaluation framework could be easily adapted for use by interested stakeholders within the Bioinformatics community and beyond. [ABSTRACT FROM AUTHOR]

Published
2019
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26. Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics

Author

Baichoo, Shakuntala, primary, Souilmi, Yassine, additional, Panji, Sumir, additional, Botha, Gerrit, additional, Meintjes, Ayton, additional, Hazelhurst, Scott, additional, Bendou, Hocine, additional, Beste, Eugene de, additional, Mpangase, Phelelani T., additional, Souiai, Oussema, additional, Alghali, Mustafa, additional, Yi, Long, additional, O’Connor, Brian D., additional, Crusoe, Michael, additional, Armstrong, Don, additional, Aron, Shaun, additional, Joubert, Fourie, additional, Ahmed, Azza E., additional, Mbiyavanga, Mamana, additional, Heusden, Peter van, additional, Magosi, Lerato E., additional, Zermeno, Jennie, additional, Mainzer, Liudmila Sergeevna, additional, Fadlelmola, Faisal M., additional, Jongeneel, C. Victor, additional, and Mulder, Nicola, additional

Published
2018
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27. Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience

Author

Ahmed, Azza E., primary, Mpangase, Phelelani T., additional, Panji, Sumir, additional, Baichoo, Shakuntala, additional, Souilmi, Yassine, additional, Fadlelmola, Faisal M., additional, Alghali, Mustafa, additional, Aron, Shaun, additional, Bendou, Hocine, additional, De Beste, Eugene, additional, Mbiyavanga, Mamana, additional, Souiai, Oussema, additional, Yi, Long, additional, Zermeno, Jennie, additional, Armstrong, Don, additional, O'Connor, Brian D., additional, Mainzer, Liudmila Sergeevna, additional, Crusoe, Michael R., additional, Meintjes, Ayton, additional, Van Heusden, Peter, additional, Botha, Gerrit, additional, Joubert, Fourie, additional, Jongeneel, C. Victor, additional, Hazelhurst, Scott, additional, and Mulder, Nicola, additional

Published
2018
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28. H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

Author

Mulder, Nicola J, Adebiyi, Ezekiel, Alami, Raouf, Benkahla, Alia, Brandful, James, Doumbia, Seydou, Everett, Dean, Fadlelmola, Faisal M, Gaboun, Fatima, Gaseitsiwe, Simani, Ghazal, Hassan, Hazelhurst, Scott, Hide, Winston, Ibrahimi, Azeddine, Jaufeerally Fakim, Yasmina, Jongeneel, C Victor, Joubert, Fourie, Kassim, Samar, Kayondo, Jonathan, Kumuthini, Judit, Lyantagaye, Sylvester, Makani, Julie, Mansour Alzohairy, Ahmed, Masiga, Daniel, Moussa, Ahmed, Nash, Oyekanmi, Ouwe Missi Oukem-Boyer, Odile, Owusu-Dabo, Ellis, Panji, Sumir, Patterton, Hugh, Radouani, Fouzia, Sadki, Khalid, Department of Integrative Biomedical Sciences (IBMS), and Faculty of Health Sciences

Subjects
Computer Systems, Genetics, Medical, Africa, Computational Biology, Genetic Variation, Humans, Genomics, Health Promotion, African Continental Ancestry Group
Abstract

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet.

Published
2016
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29. Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network

Author

Jongeneel, C. Victor, primary, Achinike-Oduaran, Ovokeraye, additional, Adebiyi, Ezekiel, additional, Adebiyi, Marion, additional, Adeyemi, Seun, additional, Akanle, Bola, additional, Aron, Shaun, additional, Ashano, Efejiro, additional, Bendou, Hocine, additional, Botha, Gerrit, additional, Chimusa, Emile, additional, Choudhury, Ananyo, additional, Donthu, Ravikiran, additional, Drnevich, Jenny, additional, Falola, Oluwadamila, additional, Fields, Christopher J., additional, Hazelhurst, Scott, additional, Hendry, Liesl, additional, Isewon, Itunuoluwa, additional, Khetani, Radhika S., additional, Kumuthini, Judit, additional, Kimuda, Magambo Phillip, additional, Magosi, Lerato, additional, Mainzer, Liudmila Sergeevna, additional, Maslamoney, Suresh, additional, Mbiyavanga, Mamana, additional, Meintjes, Ayton, additional, Mugutso, Danny, additional, Mpangase, Phelelani, additional, Munthali, Richard, additional, Nembaware, Victoria, additional, Ndhlovu, Andrew, additional, Odia, Trust, additional, Okafor, Adaobi, additional, Oladipo, Olaleye, additional, Panji, Sumir, additional, Pillay, Venesa, additional, Rendon, Gloria, additional, Sengupta, Dhriti, additional, and Mulder, Nicola, additional

Published
2017
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30. Development of Bioinformatics Infrastructure for Genomics Research

Author

Mulder, Nicola J., primary, Adebiyi, Ezekiel, additional, Adebiyi, Marion, additional, Adeyemi, Seun, additional, Ahmed, Azza, additional, Ahmed, Rehab, additional, Akanle, Bola, additional, Alibi, Mohamed, additional, Armstrong, Don L., additional, Aron, Shaun, additional, Ashano, Efejiro, additional, Baichoo, Shakuntala, additional, Benkahla, Alia, additional, Brown, David K., additional, Chimusa, Emile R., additional, Fadlelmola, Faisal M., additional, Falola, Dare, additional, Fatumo, Segun, additional, Ghedira, Kais, additional, Ghouila, Amel, additional, Hazelhurst, Scott, additional, Isewon, Itunuoluwa, additional, Jung, Segun, additional, Kassim, Samar Kamal, additional, Kayondo, Jonathan K., additional, Mbiyavanga, Mamana, additional, Meintjes, Ayton, additional, Mohammed, Somia, additional, Mosaku, Abayomi, additional, Moussa, Ahmed, additional, Muhammd, Mustafa, additional, Mungloo-Dilmohamud, Zahra, additional, Nashiru, Oyekanmi, additional, Odia, Trust, additional, Okafor, Adaobi, additional, Oladipo, Olaleye, additional, Osamor, Victor, additional, Oyelade, Jellili, additional, Sadki, Khalid, additional, Salifu, Samson Pandam, additional, Soyemi, Jumoke, additional, Panji, Sumir, additional, Radouani, Fouzia, additional, Souiai, Oussama, additional, Tastan Bishop, Özlem, additional, and Members of the HAfrica Consortium, The HABioNet Consortium, as, additional

Published
2017
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32. Ten simple rules for organizing a webinar series.

Author

Fadlelmola, Faisal M., Panji, Sumir, Ahmed, Azza E., Ghouila, Amel, Akurugu, Wisdom A., Entfellner, Jean-Baka Domelevo, Souiai, Oussema, Mulder, Nicola, and null, null

Subjects
*WEBINARS, *COMMUNITIES, *AUDIENCES, *EMAIL, *SOCIAL media
Abstract

The article presents ten simple rules for hosting a regular webinar series with particular emphasis on resource-constrained communities like many in Africa. Topics include aligning a webinar theme to the expectations of the audience; settling on a convenient and user friendly webinar platform; and announcing webinars through mailing lists and social media platform.

Published
2019
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33. Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis : International Glossina Genome Initiative

Author

Watanabe, Junichi, Hattori, Masahira, Berriman, Matthew, Lehane, Michael, Hall, Neil, Solano, Philippe, Aksoy, Serap, Hide, Winston, Touré, Yeya, Attardo, Geoffrey, Darby, Alistair, Toyoda, Atsushi, Hertz-Fowler, Christiane, Larkin, Denis, Cotton, James, Sanders, Mandy, Swain, Martin, Quail, Michael, Inoue, Noboru, Ravel, Sophie, Taylor, Todd, Srivastava, Tulika, Sharma, Vineet, Warren, Wesley, Wilson, Richard, Suzuki, Yutaka, Lawson, Daniel, Hughes, Daniel, Megy, Karyn, Masiga, Daniel, Mireji, Paul, Hansen, Immo, Van Den Abbeele, Jan, Benoit, Joshua, Bourtzis, Kostas, Obiero, George, Robertson, Hugh, Jones, Jeffery, Zhou, Jing-Jiang, Field, Linda, Friedrich, Markus, Nyanjom, Steven, Telleria, Erich, Caljon, Guy, Ribeiro, José, Acosta-Serrano, Alvaro, Ooi, Cher-Pheng, Rose, Clair, Price, David, Haines, Lee, Christoffels, Alan, Sim, Cheolho, Pham, Daphne, Denlinger, David, Geiser, Dawn, Omedo, Irene, Winzerling, Joy, Peyton, Justin, Marucha, Kevin, Jonas, Mario, Meuti, Megan, Rawlings, Neil, Zhang, Qirui, Macharia, Rosaline, Michalkova, Veronika, Dashti, Zahra, Baumann, Aaron, Gäde, Gerd, Marco, Heather, Caers, Jelle, Schoofs, Liliane, Riehle, Michael, Hu, Wanqi, Tu, Zhijian, Tarone, Aaron, Malacrida, Anna, Kibet, Caleb, Scolari, Francesca, Koekemoer, Jacobus, Willis, Judith, Gomulski, Ludvik, Falchetto, Marco, Scott, Maxwell, Fu, Shuhua, Sze, Sing-Hoi, Luiz, Thiago, Weiss, Brian, Walshe, Deirdre, Wang, Jingwen, Wamalwa, Mark, Mwangi, Sarah, Ramphul, Urvashi, Snyder, Anna, Brelsfoard, Corey, Thomas, Gavin, Tsiamis, George, Arensburger, Peter, Rio, Rita, Macdonald, Sandy, Panji, Sumir, Kruger, Adele, Benkahla, Alia, Balyeidhusa, Apollo, Msangi, Atway, Okoro, Chinyere, Stephens, Dawn, Stanley, Eleanor, Mpondo, Feziwe, Wamwiri, Florence, Mramba, Furaha, Siwo, Geoffrey, Githinji, George, Harkins, Gordon, Murilla, Grace, Lehväslaiho, Heikki, Malele, Imna, Auma, Joanna, Kinyua, Johnson, Ouma, Johnson, Okedi, Loyce, Manga, Lucien, Aslett, Martin, Koffi, Mathurin, Gaunt, Michael, Makgamathe, Mmule, Mulder, Nicola, Manangwa, Oliver, Abila, Patrick, Wincker, Patrick, Gregory, Richard, Bateta, Rosemary, Sakate, Ryuichi, Ommeh, Sheila, Lehane, Stella, Imanishi, Tadashi, Osamor, Victor, and Kawahara, Yoshihiro

Abstract

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology. ispartof: Science vol:344 issue:6182 pages:380-386 ispartof: location:United States status: published

Published
2014

34. Proceedings of a Sickle Cell Disease Ontology workshop — Towards the first comprehensive ontology for Sickle Cell Disease

Author

Mulder, Nicola, primary, Nembaware, Victoria, additional, Adekile, Adekunle, additional, Anie, Kofi A., additional, Inusa, Baba, additional, Brown, Biobele, additional, Campbell, Andrew, additional, Chinenere, Furahini, additional, Chunda-Liyoka, Catherine, additional, Derebail, Vimal K., additional, Geard, Amy, additional, Ghedira, Kais, additional, Hamilton, Carol M., additional, Hanchard, Neil A., additional, Haendel, Melissa, additional, Huggins, Wayne, additional, Ibrahim, Muntaser, additional, Jupp, Simon, additional, Kamga, Karen Kengne, additional, Knight-Madden, Jennifer, additional, Lopez-Sall, Philomène, additional, Mbiyavanga, Mamana, additional, Munube, Deogratias, additional, Nirenberg, Damian, additional, Nnodu, Obiageli, additional, Ofori-Acquah, Solomon Fiifi, additional, Ohene-Frempong, Kwaku, additional, Opap, Kenneth Babu, additional, Panji, Sumir, additional, Park, Miriam, additional, Pule, Gift, additional, Royal, Charmaine, additional, Sangeda, Raphael, additional, Tayo, Bamidele, additional, Treadwell, Marsha, additional, Tshilolo, Léon, additional, and Wonkam, Ambroise, additional

Published
2016
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35. A common molecular signature of patients with sickle cell disease revealed by microarray meta-analysis and a genome-wide association study.

Author

Ben Hamda, Cherif, Sangeda, Raphael, Mwita, Liberata, Meintjes, Ayton, Nkya, Siana, Panji, Sumir, Mulder, Nicola, Guizani-Tabbane, Lamia, Benkahla, Alia, Makani, Julie, Ghedira, Kais, and null, null

Subjects
SICKLE cell anemia diagnosis, SICKLE cell anemia, MICROARRAY technology, CHRONIC diseases, PATHOLOGICAL physiology, GENE expression, GENETICS
Abstract

A chronic inflammatory state to a large extent explains sickle cell disease (SCD) pathophysiology. Nonetheless, the principal dysregulated factors affecting this major pathway and their mechanisms of action still have to be fully identified and elucidated. Integrating gene expression and genome-wide association study (GWAS) data analysis represents a novel approach to refining the identification of key mediators and functions in complex diseases. Here, we performed gene expression meta-analysis of five independent publicly available microarray datasets related to homozygous SS patients with SCD to identify a consensus SCD transcriptomic profile. The meta-analysis conducted using the MetaDE R package based on combining p values (maxP approach) identified 335 differentially expressed genes (DEGs; 224 upregulated and 111 downregulated). Functional gene set enrichment revealed the importance of several metabolic pathways, of innate immune responses, erythrocyte development, and hemostasis pathways. Advanced analyses of GWAS data generated within the framework of this study by means of the atSNP R package and SIFT tool identified 60 regulatory single-nucleotide polymorphisms (rSNPs) occurring in the promoter of 20 DEGs and a deleterious SNP, affecting CAMKK2 protein function. This novel database of candidate genes, transcription factors, and rSNPs associated with SCD provides new markers that may help to identify new therapeutic targets. [ABSTRACT FROM AUTHOR]

Published
2018
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36. Hackathons as a means of accelerating scientific discoveries and knowledge transfer

Author

Ghouila, Amel, Siwo, Geoffrey Henry, Entfellner, Jean-Baka Domelevo, Panji, Sumir, Button-Simons, Katrina A., Davis, Sage Zenon, Fadlelmola, Faisal M., Ferdig, Michael T., and Mulder, Nicola

Abstract

Scientific research plays a key role in the advancement of human knowledge and pursuit of solutions to important societal challenges. Typically, research occurs within specific institutions where data are generated and subsequently analyzed. Although collaborative science bringing together multiple institutions is now common, in such collaborations the analytical processing of the data is often performed by individual researchers within the team, with only limited internal oversight and critical analysis of the workflow prior to publication. Here, we show how hackathons can be a means of enhancing collaborative science by enabling peer review before results of analyses are published by cross-validating the design of studies or underlying data sets and by driving reproducibility of scientific analyses. Traditionally, in data analysis processes, data generators and bioinformaticians are divided and do not collaborate on analyzing the data. Hackathons are a good strategy to build bridges over the traditional divide and are potentially a great agile extension to the more structured collaborations between multiple investigators and institutions.

Published
2018
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39. Bioinformatics Education-- Perspectives and Challenges out of Africa.

Author

Bishop, Özlem Tastan, Abediyi, Ezekiel F., Alzohairy, Ahmed M., Everett, Dean, Ghedira, Kais, Ghouila, Amel, Kumuthini, Judit, Mulder, Nicola J., Panji, Sumir, and Patterton, Hugh-G.

Subjects
BIOINFORMATICS, HIGHER education, GRADUATE education, GENOMICS, EDUCATION
Abstract

The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s. The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of virtually every field in the life sciences. This has placed a scientific premium on the availability of skilled bioinformaticians, a qualification that is extremely scarce on the African continent. The reasons for this are numerous, although the absence of a skilled bioinformatician at academic institutions to initiate a training process and build sustained capacity seems to be a common African shortcoming. This dearth of bioinformatics expertise has had a knock-on effect on the establishment of many modern high-throughput projects at African institutes, including the comprehensive and systematic analysis of genomes from African populations, which are among the most genetically diverse anywhere on the planet. Recent funding initiatives from the National Institutes of Health and the Wellcome rust are aimed at ameliorating this shortcoming. In this paper, we discuss the problems that have limited the establishment of the bioinformatics field in Africa, as well as propose specific actions that will help with the education and training of bioinformaticians on the continent. This is an absolute requirement in anticipation of a boom in high-throughput approaches to human health issues unique to data from African populations. [ABSTRACT FROM AUTHOR]

Published
2015
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40. H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

Author

Mulder, Nicola J., Adebiyi, Ezekiel, Alami, Raouf, Benkahla, Alia, Brandful, James, Doumbia, Seydou, Everett, Dean, Fadlelmola, Faisal M., Gaboun, Fatima, Gaseitsiwe, Simani, Ghazal, Hassan, Hazelhurst, Scott, Hide, Winston, Ibrahimi, Azeddine, Jaufeerally Fakim, Yasmina, Jongeneel, C. Victor, Joubert, Fourie, Kassim, Samar, Kayondo, Jonathan, Kumuthini, Judit, Lyantagaye, Sylvester, Makani, Julie, Mansour Alzohairy, Ahmed, Masiga, Daniel, Moussa, Ahmed, Nash, Oyekanmi, Ouwe Missi Oukem-Boyer, Odile, Owusu-Dabo, Ellis, Panji, Sumir, Patterton, Hugh, Radouani, Fouzia, Sadki, Khalid, Seghrouchni, Fouad, Tastan Bishop, Ozlem, Tiffin, Nicki, Ulenga, Nzovu, Adebiyi, Marion, Ahmed, Azza E., Ahmed, Rehab I., Alearts, Maaike, Alibi, Mohamed, Aron, Shaun, Baichoo, Shakuntala, Bendou, Hocine, Botha, Gerrit, Brown, David, Chimusa, Emile, Christoffels, Alan, Cornick, Jennifer, Entfellner, Jean-Baka Domelevo, Fields, Chris, Fischer, Anne, Gamieldien, Junaid, Ghedira, Kais, Ghouila, Amel, Sui, Shannan Ho, Isewon, Itunuoluwa, Isokpehi, Raphael, Dashti, Mahjoubeh Jalali Sefid, Kamng'ona, Arox, Khetani, Radhika S., Kiran, Anmol, Kulohoma, Benard, Kumwenda, Benjamin, Lapine, Dan, Mainzer, Liudmila Sergeevna, Maslamoney, Suresh, Mbiyavanga, Mamana, Meintjes, Ayton, Mlyango, Flora Elias, Mmbando, Bruno, Mohammed, Somia A., Mpangase, Phelelani, Msefula, Chisomo, Mtatiro, Siana Nkya, Mugutso, Dunfunk, Mungloo-Dilmohammud, Zahra, Musicha, Patrick, Nembaware, Victoria, Osamor, Victor Chukwudi, Oyelade, Jelili, Rendon, Gloria, Salazar, Gustavo A., Salifu, Samson Pandam, Sangeda, Raphael, Souiai, Oussema, Van Heusden, Peter, and Wele, Mamadou

Abstract

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet.

Published
2016
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41. Analysis of the African coelacanth genome sheds light on tetrapod evolution

Author

Amemiya, Chris T., Alföldi, Jessica, Lee, Alison P., Fan, Shaohua, Philippe, Hervé, MacCallum, Iain, Braasch, Ingo, Manousaki, Tereza, Schneider, Igor, Rohner, Nicolas, Organ, Chris, Chalopin, Domitille, Smith, Jeramiah J., Robinson, Mark, Dorrington, Rosemary A., Gerdol, Marco, Aken, Bronwen, Biscotti, Maria Assunta, Barucca, Marco, Baurain, Denis, Berlin, Aaron M., Blatch, Gregory L., Buonocore, Francesco, Burmester, Thorsten, Campbell, Michael S., Canapa, Adriana, Cannon, John P., Christoffels, Alan, De Moro, Gianluca, Edkins, Adrienne L., Fan, Lin, Fausto, Anna Maria, Feiner, Nathalie, Forconi, Mariko, Gamieldien, Junaid, Gnerre, Sante, Gnirke, Andreas, Goldstone, Jared V., Haerty, Wilfried, Hahn, Mark E., Hesse, Uljana, Hoffmann, Steve, Johnson, Jeremy, Karchner, Sibel I., Kuraku, Shigehiro, Lara, Marcia, Levin, Joshua Z., Litman, Gary W., Mauceli, Evan, Miyake, Tsutomu, Mueller, M. Gail, Nelson, David R., Nitsche, Anne, Olmo, Ettore, Ota, Tatsuya, Pallavicini, Alberto, Panji, Sumir, Picone, Barbara, Ponting, Chris P., Prohaska, Sonja J., Przybylski, Dariusz, Saha, Nil Ratan, Ravi, Vydianathan, Ribeiro, Filipe J., Sauka-Spengler, Tatjana, Scapigliati, Giuseppe, Searle, Stephen M. J., Sharpe, Ted, Simakov, Oleg, Stadler, Peter F., Stegeman, John J., Sumiyama, Kenta, Tabbaa, Diana, Tafer, Hakim, Turner-Maier, Jason, van Heusden, Peter, White, Simon, Williams, Louise, Yandell, Mark, Brinkmann, Henner, Volff, Jean-Nicolas, Tabin, Clifford J., Shubin, Neil, Schartl, Manfred, Jaffe, David, Postlethwait, John H., Venkatesh, Byrappa, Di Palma, Federica, Lander, Eric S., Meyer, Axel, and Lindblad-Toh, Kerstin

Abstract

It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe-finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features . Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues demonstrate the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution.

Published
2013
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42. Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience.

Author

Gurwitz, Kim T., Aron, Shaun, Panji, Sumir, Maslamoney, Suresh, Fernandes, Pedro L., Judge, David P., Ghouila, Amel, Domelevo Entfellner, Jean-Baka, Guerfali, Fatma Z., Saunders, Colleen, Mansour Alzohairy, Ahmed, Salifu, Samson P., Ahmed, Rehab, Cloete, Ruben, Kayondo, Jonathan, Ssemwanga, Deogratius, Mulder, Nicola, and Null, Null

Subjects
BIOINFORMATICS, ONLINE education, DISTANCE education, EDUCATION
Abstract

Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (), the Pan African Bioinformatics Network for H3Africa, has therefore developed an innovative, free-of-charge “Introduction to Bioinformatics” course, taking these challenges into account as part of its educational efforts to provide on-site training and develop local expertise inside its network. A multiple-delivery–mode learning model was selected for this 3-month course in order to increase access to (mostly) African, expert bioinformatics trainers. The content of the course was developed to include a range of fundamental bioinformatics topics at the introductory level. For the first iteration of the course (2016), classrooms with a total of 364 enrolled participants were hosted at 20 institutions across 10 African countries. To ensure that classroom success did not depend on stable internet, trainers pre-recorded their lectures, and classrooms downloaded and watched these locally during biweekly contact sessions. The trainers were available via video conferencing to take questions during contact sessions, as well as via online “question and discussion” forums outside of contact session time. This learning model, developed for a resource-limited setting, could easily be adapted to other settings. [ABSTRACT FROM AUTHOR]

Published
2017
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