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Omooja, Jonah; Bbosa, Nicholas; Lule, Dan Bugembe; Nannyonjo, Maria; Lunkuse, Sandra; Nassolo, Faridah; Nabirye, Stella Esther; Suubi, Hamidah Namagembe; Kaleebu, Pontiano; Ssemwanga, Deogratius; (2022) HIV-1 drug resistance genotyping success rates and correlates of Dried-blood spots and plasma specimen genotyping failure in a resource-limited setting. BMC Infectious Diseases, 22 (1). 474-. ISSN 1471-2334 DOI: https://doi.org/10.1186/s12879-022-07453-9

Ssekagiri, Alfred; Jjingo, Daudi; Lujumba, Ibra; Bbosa, Nicholas; Bugembe, Daniel L; Kateete, David P; Jordan, I King; Kaleebu, Pontiano; Ssemwanga, Deogratius; (2022) QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data. Bioinformatics advances, 2 (1). vbac089-. ISSN 2635-0041 DOI: https://doi.org/10.1093/bioadv/vbac089

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Amoako, Daniel G; Diagne, Moussa M; Sisay, Abay; Zekri, Abdel-Rahman N; Gueye, Abdou Salam; Sangare, Abdoul K; Ouedraogo, Abdoul-Salam; Sow, Abdourahmane; Musa, Abdualmoniem O; Sesay, Abdul K; Abias, Abe G; Elzagheid, Adam I; Lagare, Adamou; Kemi, Adedotun-Sulaiman; Abar, Aden Elmi; Johnson, Adeniji A; Fowotade, Adeola; Oluwapelumi, Adeyemi O; Amuri, Adrienne A; Juru, Agnes; Kandeil, Ahmed; Mostafa, Ahmed; Rebai, Ahmed; Sayed, Ahmed; Kazeem, Akano; Balde, Aladje; Christoffels, Alan; Trotter, Alexander J; Campbell, Allan; Keita, Alpha K; Kone, Amadou; Bouzid, Amal; Souissi, Amal; Agweyu, Ambrose; Naguib, Amel; Gutierrez, Ana V; Nkeshimana, Anatole; Page, Andrew J; Yadouleton, Anges; Vinze, Anika; Happi, Anise N; Chouikha, Anissa; Iranzadeh, Arash; Maharaj, Arisha; Batchi-Bouyou, Armel L; Ismail, Arshad; Sylverken, Augustina A; Goba, Augustine; Femi, Ayoade; Sijuwola, Ayotunde E; Marycelin, Baba; Salako, Babatunde L; Oderinde, Bamidele S; Bolajoko, Bankole; Diarra, Bassirou; Herring, Belinda L; 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Doumbia, Seydou; Makiala-Mandanda, Sheila; Aryeetey, Sherihane; Ahmed, Shymaa S; Ahmed, Side Mohamed; Elhamoumi, Siham; Moyo, Sikhulile; Lutucuta, Silvia; Gaseitsiwe, Simani; Jalloh, Simbirie; Andriamandimby, Soa Fy; Oguntope, Sobajo; Grayo, Solène; Lekana-Douki, Sonia; Prosolek, Sophie; Ouangraoua, Soumeya; van Wyk, Stephanie; Schaffner, Stephen F; Kanyerezi, Stephen; Ahuka-Mundeke, Steve; Rudder, Steven; Pillay, Sureshnee; Nabadda, Susan; Behillil, Sylvie; Budiaki, Sylvie L; van der Werf, Sylvie; Mashe, Tapfumanei; Mohale, Thabo; Le-Viet, Thanh; Velavan, Thirumalaisamy P; Schindler, Tobias; Maponga, Tongai G; Bedford, Trevor; Anyaneji, Ugochukwu J; Chinedu, Ugwu; Ramphal, Upasana; George, Uwem E; Enouf, Vincent; Nene, Vishvanath; Gorova, Vivianne; Roshdy, Wael H; Karim, Wasim Abdul; Ampofo, William K; Preiser, Wolfgang; Choga, Wonderful T; Ahmed, Yahaya Ali; Ramphal, Yajna; Bediako, Yaw; Naidoo, Yeshnee; Butera, Yvan; de Laurent, Zaydah R; Africa Pathogen Genomics Initiative (Africa PGI)‡; Ouma, Ahmed EO; von Gottberg, Anne; Githinji, George; Moeti, Matshidiso; Tomori, Oyewale; Sabeti, Pardis C; Sall, Amadou A; Oyola, Samuel O; Tebeje, Yenew K; Tessema, Sofonias K; de Oliveira, Tulio; Happi, Christian; Lessells, Richard; Nkengasong, John; Wilkinson, Eduan; (2022) The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. 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Bbosa, Nicholas; Ssemwanga, Deogratius; Nsubuga, Rebecca N; Kiwanuka, Noah; Bagaya, Bernard S; Kitayimbwa, John M; Ssekagiri, Alfred; Yebra, Gonzalo; Kaleebu, Pontiano; Leigh-Brown, Andrew; (2021) Phylogenetic Networks and Parameters Inferred from HIV Nucleotide Sequences of High-Risk and General Population Groups in Uganda: Implications for Epidemic Control. Viruses, 13 (6). p. 970. ISSN 1999-4915 DOI: https://doi.org/10.3390/v13060970

Kayondo, Hassan W; Ssekagiri, Alfred; Nabakooza, Grace; Bbosa, Nicholas; Ssemwanga, Deogratius; Kaleebu, Pontiano; Mwalili, Samuel; Mango, John M; Leigh Brown, Andrew J; Saenz, Roberto A; +2 more... Galiwango, Ronald; Kitayimbwa, John M; (2021) Employing phylogenetic tree shape statistics to resolve the underlying host population structure. BMC bioinformatics, 22 (1). 546-. ISSN 1471-2105 DOI: https://doi.org/10.1186/s12859-021-04465-1

Bbosa, Nicholas; Ssemwanga, Deogratius; Kaleebu, Pontiano; (2020) Short Communication: Choosing the Right Program for the Identification of HIV-1 Transmission Networks from Nucleotide Sequences Sampled from Different Populations. AIDS research and human retroviruses, 36 (11). pp. 948-951. ISSN 0889-2229 DOI: https://doi.org/10.1089/AID.2020.0033

Bbosa, Nicholas; Ssemwanga, Deogratius; Ssekagiri, Alfred; Xi, Xiaoyue; Mayanja, Yunia; Bahemuka, Ubaldo; Seeley, Janet; Pillay, Deenan; Abeler-Dörner, Lucie; Golubchik, Tanya; +3 more... Fraser, Christophe; Kaleebu, Pontiano; Ratmann, Oliver; (2020) Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda. Viruses, 12 (3). p. 331. DOI: https://doi.org/10.3390/v12030331

Grant, Heather E; Hodcroft, Emma B; Ssemwanga, Deogratius; Kitayimbwa, John M; Yebra, Gonzalo; Esquivel Gomez, Luis Roger; Frampton, Dan; Gall, Astrid; Kellam, Paul; de Oliveira, Tulio; +12 more... Bbosa, Nicholas; Nsubuga, Rebecca N; Kibengo, Freddie; Kwan, Tsz Ho; Lycett, Samantha; Kao, Rowland; Robertson, David L; Ratmann, Oliver; Fraser, Christophe; Pillay, Deenan; Kaleebu, Pontiano; Leigh Brown, Andrew J; (2020) Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus evolution, 6 (1). veaa004-. ISSN 2057-1577 DOI: https://doi.org/10.1093/ve/veaa004

Segujja, Farouk; Omooja, Jonah; Lunkuse, Sandra; Nanyonjo, Maria; Nabirye, Stella E; Nassolo, Faridah; Bugembe, Daniel L; Bbosa, Nicholas; Kateete, David P; Ssenyonga, William; +5 more... Mayanja, Yunia; Nsubuga, Rebecca N; Seeley, Janet; Kaleebu, Pontiano; Ssemwanga, Deogratius; (2020) High Levels of Acquired HIV Drug Resistance Following Virological Nonsuppression in HIV-Infected Women from a High-Risk Cohort in Uganda. AIDS research and human retroviruses, 36 (9). pp. 782-791. ISSN 0889-2229 DOI: https://doi.org/10.1089/AID.2019.0279

Ssemwanga, Deogratius; Bbosa, Nicholas; Nsubuga, Rebecca N; Ssekagiri, Alfred; Kapaata, Anne; Nannyonjo, Maria; Nassolo, Faridah; Karabarinde, Alex; Mugisha, Joseph; Seeley, Janet; +3 more... Yebra, Gonzalo; Leigh Brown, Andrew; Kaleebu, Pontiano; (2020) The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda. Viruses, 12 (11). p. 1283. DOI: https://doi.org/10.3390/v12111283

Bbosa, Nicholas; Kaleebu, Pontiano; Ssemwanga, Deogratius; (2019) HIV subtype diversity worldwide. Current opinion in HIV and AIDS, 14 (3). pp. 153-160. ISSN 1746-630X DOI: https://doi.org/10.1097/COH.0000000000000534

Bbosa, Nicholas; Ssemwanga, Deogratius; Nsubuga, Rebecca N; Salazar-Gonzalez, Jesus F; Salazar, Maria G; Nanyonjo, Maria; Kuteesa, Monica; Seeley, Janet; Kiwanuka, Noah; Bagaya, Bernard S; +3 more... Yebra, Gonzalo; Leigh-Brown, Andrew; Kaleebu, Pontiano; (2019) Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations. Scientific reports, 9 (1). 1051-. ISSN 2045-2322 DOI: https://doi.org/10.1038/s41598-018-37458-x

Omooja, Jonah; Nannyonjo, Maria; Sanyu, Grace; Nabirye, Stella E; Nassolo, Faridah; Lunkuse, Sandra; Kapaata, Anne; Segujja, Farouk; Kateete, David Patrick; Ssebaggala, Eric; +5 more... Bbosa, Nicholas; Aling, Emmanuel; Nsubuga, Rebecca N; Kaleebu, Pontiano; Ssemwanga, Deogratius; (2019) Rates of HIV-1 virological suppression and patterns of acquired drug resistance among fisherfolk on first-line antiretroviral therapy in Uganda. The Journal of antimicrobial chemotherapy, 74 (10). pp. 3021-3029. ISSN 0305-7453 DOI: https://doi.org/10.1093/jac/dkz261