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Journals


  • Kiyuka, Patience K, Agoti, Charles N, Munywoki, Patrick K, Njeru, Regina, Bett, Anne, Otieno, James R, Otieno, Grieven P, Kamau, Everlyn, Clark, Taane G, van der Hoek, Lia, Kellam, Paul, Nokes, D. James, Cotten, Matthew. 2018. Human coronavirus NL63 molecular epidemiology and evolutionary patterns in rural coastal Kenya. The Journal of Infectious Diseases, 217 (11), pp. 1728-1739, View
  • Morpeth, Susan C., Munywoki, Patrick, Hammitt, Laura L., Bett, Anne, Bottomley, Christian, Onyango, Clayton O., Murdoch, David R., Nokes, D. James, Scott, J. Anthony G.. 2018. Impact of viral upper respiratory tract infection on the concentration of nasopharyngeal pneumococcal carriage among Kenyan children. Scientific Reports, 8 (1), View
  • Nyiro, Joyce Uchi, Munywoki, Patrick, Kamau, Everlyn, Agoti, Charles, Gichuki, Alex, Etyang, Timothy, Otieno, Grieven, Nokes, D. James. 2018. Surveillance of respiratory viruses in the outpatient setting in rural coastal Kenya : baseline epidemiological observations. Wellcome Open Research, 3, View
  • Munywoki, Patrick K., Koech, Dorothy C, Agoti, Charles N., Cane, Patricia A., Medley, Graham, Nokes, D. James. 2018. Continuous invasion by respiratory viruses observed in rural households during a respiratory syncytial virus seasonal outbreak in coastal Kenya. Clinical Infectious Diseases, View
  • Sande, Charles J., Mutunga, Martin, Muteti, Jacqueline, Berkley, James A., Nokes, D. James, Njunge, James. 2018. Untargeted analysis of the airway proteomes of children with respiratory infections using mass spectrometry based proteomics. Scientific Reports, 8 (1), View
  • Otieno, J. R., Kamau, E. M., Oketch, J. W., Ngoi, J. M., Gichuki, A. M., Binter, Å ., Otieno, G. P., Ngama, M., Agoti, C. N., Cane, P. A., Kellam, P., Cotten, M., Lemey, P., Nokes, D. James. 2018. Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains. Virus Evolution, 4 (2), View
  • Mohammed, Khadija Said, Kibinge, Nelson, Prins, Pjotr, Agoti, Charles N., Cotten, Matthew, Nokes, D. James, Brand, Samuel, Githinji, George. 2018. Evaluating the performance of tools used to call minority variants from whole genome short-read data. Wellcome Open Research, 3, View
  • Pan-Ngum, Wirichada, Kinyanjui, Timothy M., Kiti, Moses C., Taylor, Sylvia, Toussaint, Jean-François, Saralamba, Sompob, Van Effelterre, Thierry, Nokes, D. James, White, Lisa J.. 2017. Predicting the relative impacts of maternal and neonatal respiratory syncytial virus (RSV) vaccine target product profiles : a consensus modelling approach. Vaccine, 35 (2), pp. 403-409, View
  • Kamau, Everlyn, Agoti, Charles N., Lewa, Clement S., Oketch, John, Owor, Betty E., Otieno, Grieven P., Bett, Anne, Cane, Patricia A., Nokes, D. James. 2017. Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR. Journal of clinical virology, View
  • Otieno, James R., Kamau, Everlyn M., Agoti, Charles N., Lewa, Clement, Otieno, Grieven, Bett, Ann, Ngama, Mwanajuma, Cane, Patricia A., Nokes, D. James. 2017. Spread and evolution of respiratory syncytial virus A genotype ON1, coastal Kenya, 2010-2015. Emerging Infectious Diseases, 23 (2), pp. 264-271, View
  • Nyiro, Joyce U., Kombe, Ivy K., Sande, Charles J., Kipkoech, James, Kiyuka, Patience K., Onyango, Clayton O., Munywoki, Patrick K., Kinyanjui, Timothy M., Nokes, D. James. 2017. Defining the vaccination window for respiratory syncytial virus (RSV) using age-seroprevalence data for children in Kilifi, Kenya. PLoS One, 12 (5), View
  • Ngari, Moses M., Fegan, Greg, Mwangome, Martha K., Ngama, Mwanajuma J., Mturi, Neema, Scott, John Anthony Gerard, Bauni, Evasius, Nokes, D. James, Berkley, James A.. 2017. Mortality after inpatient treatment for severe pneumonia in children : a cohort study.. Paediatric and Perinatal Epidemiology, 31 (3), pp. 233-242, View
  • Agoti, Charles N., Munywoki, Patrick K., Phan, My V. T., Otieno, James R., Kamau, Everlyn, Bett, Anne, Kombe, Ivy, Githinji, George, Medley, Graham, Cane, Patricia A., Kellam, Paul, Cotten, Matthew, Nokes, D. James. 2017. Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis.. Virus Evolution, 3 (1), View
  • Flasche, Stefan, Ojal, John, Le Polain de Waroux, Olivier, Otiende, Mark, O'Brien, Katherine L., Kiti, Moses, Nokes, D. James, Edmunds, W John, Scott, J. Anthony G.. 2017. Assessing the efficiency of catch-up campaigns for the introduction of pneumococcal conjugate vaccine : a modelling study based on data from PCV10 introduction in Kilifi, Kenya. BMC Medicine, 15 (1), View
  • Shi, Ting, McAllister, David A., O'Brien, Katherine L., Simoes, Eric A. F., Madhi, Shabir A., Gessner, Bradford D., Polack, Fernando P., Balsells, Evelyn, Acacio, Sozinho, Aguayo, Claudia, Alassani, Issifou, Ali, Asad, Antonio, Martin, Awasthi, Shally, Awori, Juliet O., Azziz-Baumgartner, Eduardo, Baggett, Henry C., Baillie, Vicky L., Balmaseda, Angel, Barahona, Alfredo, Basnet, Sudha, Bassat, Quique, Basualdo, Wilma, Bigogo, Godfrey, Bont, Louis, Breiman, Robert F., Brooks, W Abdullah, Broor, Shobha, Bruce, Nigel, Bruden, Dana, Buchy, Philippe, Campbell, Stuart, Carosone-Link, Phyllis, Chadha, Mandeep, Chipeta, James, Chou, Monidarin, Clara, Wilfrido, Cohen, Cheryl, de Cuellar, Elizabeth, Dang, Duc-Anh, Dash-yandag, Budragchaagiin, Deloria-Knoll, Maria, Dherani, Mukesh, Eap, Tekchheng, Ebruke, Bernard E., Echavarria, Marcela, de Freitas Lázaro Emediato, Carla Cecà­lia, Fasce, Rodrigo A., Feikin, Daniel R., Feng, Luzhao, Gentile, Angela, Gordon, Aubree, Goswami, Doli, Goyet, Sophie, Groome, Michelle, Halasa, Natasha, Hirve, Siddhivinayak, Homaira, Nusrat, Howie, Stephen R. C., Jara, Jorge, Jroundi, Imane, Kartasasmita, Cissy B., Khuri-Bulos, Najwa, Kotloff, Karen L., Krishnan, Anand, Libster, Romina, Lopez, Olga, Lucero, Marilla G., Lucion, Florencia, Lupisan, Socorro P., Marcone, Debora N., McCracken, John P., Mejia, Mario, Moisi, Jennifer C., Montgomery, Joel M., Moore, David P., Moraleda, Cinta, Moyes, Jocelyn, Munywoki, Patrick, Mutyara, Kuswandewi, Nicol, Mark P., Nokes, D. James, Nymadawa, Pagbajabyn, da Costa Oliveira, Maria Tereza, Oshitani, Histoshi, Pandey, Nitin, Paranhos-Baccalà , Gláucia, Phillips, Lia N., Picot, Valentina Sanchez, Rahman, Mustafizur, Rakoto-Andrianarivelo, Mala, Rasmussen, Zeba A., Rath, Barbara A., Robinson, Annick, Romero, Candice, Russomando, Graciela, Salimi, Vahid, Sawatwong, Pongpun, Scheltema, Nienke, Schweiger, Brunhilde, Scott, J Anthony G., Seidenberg, Phil, Shen, Kunling, Singleton, Rosalyn, Sotomayor, Viviana, Strand, Tor A., Sutanto, Agustinus, Sylla, Mariam, Tapia, Milagritos D., Thamthitiwat, Somsak, Thomas, Elizabeth D., Tokarz, Rafal, Turner, Claudia, Venter, Marietjie, Waicharoen, Sunthareeya, Wang, Jianwei, Watthanaworawit, Wanitda, Yoshida, Lay-Myint, Yu, Hongjie, Zar, Heather J., Campbell, Harry, Nair, Harish. 2017. Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015 : a systematic review and modelling study. The Lancet, View
  • Wathuo, Miriam, Medley, Graham, Nokes, D. James, Munywoki, Patrick K.. 2017. Quantification and determinants of the amount of respiratory syncytial virus (RSV) shed using real time PCR data from a longitudinal household study. Wellcome Open Research, 1, View
  • Scheltema, Nienke M., Gentile, Angela, Lucion, Florencia, Nokes, D. James, Munywoki, Patrick K., Madhi, Shabir A., Groome, Michelle J., Cohen, Cheryl, Moyes, Jocelyn, Thorburn, Kentigern, Thamthitiwat, Somsak, Oshitani, Hitoshi, Lupisan, Socorro P., Gordon, Aubree, Sánchez, José F., O'Brien, Katherine L., Gessner, Bradford D., Sutanto, Agustinus, Mejias, Asuncion, Ramilo, Octavio, Khuri-Bulos, Najwa, Halasa, Natasha, de-Paris, Fernanda, Pires, Márcia Rosane, Spaeder, Michael C., Paes, Bosco A., Simàµes, Eric A. F., Leung, Ting F., da Costa Oliveira, Maria Tereza, de Freitas Lázaro Emediato, Carla Cecà­lia, Bassat, Quique, Butt, Warwick, Chi, Hsin, Aamir, Uzma Bashir, Ali, Asad, Lucero, Marilla G., Fasce, Rodrigo A., Lopez, Olga, Rath, Barbara A., Polack, Fernando P., Papenburg, Jesse, Roglic, Srdan, Ito, Hisato, Goka, Edward A., Grobbee, Diederick E., Nair, Harish, Bont, Louis J.. 2017. Global respiratory syncytial virus-associated mortality in young children (RSV GOLD) : a retrospective case series. The Lancet Global Health, 5 (10), pp. e984-e991, View
  • Emukule, Gideon O., Mott, Joshua A., Spreeuwenberg, Peter, Viboud, Cecile, Commanday, Alexander, Muthoka, Philip, Munywoki, Patrick K., Nokes, D. James, Velden, Koos van der, Paget, John W.. 2016. Influenza activity in Kenya, 2007-2013 : timing, association with climatic factors, and implications for vaccination campaigns. Influenza and Other Respiratory Viruses, View
  • Kiti, Moses C., Tizzoni, Michele, Kinyanjui, Timothy M., Koech, Dorothy C., Munywoki, Patrick K., Meriac, Milosch, Cappa, Luca, Panisson, André, Barrat, Alain, Cattuto, Ciro, Nokes, D. James. 2016. Quantifying social contacts in a household setting of rural Kenya using wearable proximity sensors. EPJ Data Science, 5 (1), View
  • Owor, Betty E., Masankwa, Geoffrey N., Mwango, Lilian C., Njeru, Regina W., Agoti, Charles N., Nokes, D. James. 2016. Human metapneumovirus epidemiological and evolutionary patterns in Coastal Kenya, 2007-11. BMC Infectious Diseases, 16 (1), View
  • Agoti, Charles N., Kiyuka, Patience K., Kamau, Everlyn, Munywoki, Patrick K., Bett, Anne, van der Hoek, Lia, Kellam, Paul, Nokes, D. James, Cotten, Matthew. 2016. Human Rhinovirus B and C genomes from rural coastal Kenya. Genome Announcements, 4 (4), pp. 1-2, View
  • Otieno, James R., Agoti, Charles N., Gitahi, Caroline W., Bett, Ann, Ngama, Mwanajuma, Medley, Graham F, Cane, Patricia A., Nokes, D. James. 2016. Molecular evolutionary dynamics of respiratory syncytial virus group A in recurrent epidemics in coastal Kenya. Journal of Virology, 90 (10), pp. 4990-5002, View
  • Adetifa, Ifedayo M.O., Bwanaali, Tahreni, Wafula, Jackline, Mutuku, Alex, Karia, Boniface, Makumi, Anne, Mwatsuma, Pauline, Bauni, Evasius, Hammitt, Laura L., Nokes, D. James, Maree, Ephantus, Tabu, Collins, Kamau, Tatu, Mataza, Christine, Williams, Thomas N., Scott, J. Anthony G.. 2016. Cohort profile : the Kilifi vaccine monitoring study. International Journal of Epidemiology, View
  • Nyiro, Joyce Uchi, Sande, Charles Jumba, Mutunga, Martin, Kiyuka, Patience Kerubo, Munywoki, Patrick Kioo, Scott, John Anthony G., Nokes, D. James. 2016. Absence of association between cord specific antibody levels and severe respiratory syncytial virus (RSV) disease in early infants : a case control study from coastal Kenya. PLoS One, 11 (11), View
  • Poletti, Piero, Merler, Stefano, Ajelli, Marco, Manfredi, Piero, Munywoki, Patrick K., Nokes, D. James, Melegaro, Alessia. 2015. Evaluating vaccination strategies for reducing infant respiratory syncytial virus infection in low-income settings. BMC Medicine, Volume 13 (Number 1), pp. 1-11, View
  • Kinyanjui, Timothy M., House, Thomas A., Kiti, Moses C., Cane, Patricia, Nokes, D. James, Medley, Graham. 2015. Vaccine induced herd immunity for control of respiratory syncytial virus disease in a low-income country setting. PLoS One, 10 (9), pp. 1-16, View
  • Agoti, Charles N., Otieno, James R., Ngama, Mwanajuma, Mwihuri, Alexander G., Medley, Graham, Cane, Patricia A., Nokes, D. James, Kirkegaard, K.. 2015. Successive respiratory syncytial virus epidemics in local populations arise from multiple variant introductions, providing insights into virus persistence. Journal of Virology, 89 (22), pp. 11630-11642, View
  • Munywoki, Patrick K., Koech, Dorothy C., Agoti, Charles N., Bett, Ann, Cane, Patricia A., Medley, Graham F., Nokes, D. James. 2015. Frequent asymptomatic respiratory syncytial virus infections during an epidemic in a rural Kenyan household cohort. Journal of Infectious Diseases, 212 (11), pp. 1711-1718, View
  • Agoti, Charles N., Otieno, James R., Munywoki, Patrick K., Mwihuri, Alexander G., Cane, Patricia, Nokes, D. James, Kellam, Paul, Cotten, Matthew, Perlman, S.. 2015. Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing. Journal of Virology, Volume 89 (Number 7), pp. 3444-3454, View
  • Munywoki, Patrick Kiio, Koech, Dorothy C., Agoti, Charles N., Kibirige, N., Kipkoech, J., Cane, Patricia, Medley, Graham, Nokes, D. James. 2015. Influence of age, severity of infection, and co-infection on the duration of respiratory syncytial virus (RSV) shedding. Epidemiology and Infection, 143 (4), pp. 804-812, View


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