Publications

Publications

Epidemiology and Demography

Journal of Open Source Software (JOSS): design and first-year review.Smith, A. M. Niemeyer, K. E. Katz, D. S. Barba, L. A. Githinji, G. Gymrek, M. Huff, K. D. Madan, C. R. Mayes, A. C. Moerman, K. M. Prins, P. Ram, K. Rokem, A. Teal, T. K. Guimera, R. V. Vanderplas, J. T.
PeerJ Prepr, (2018). 4:e147

Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013.Owor, B. E. Mwanga, M. J. Njeru, R. Mugo, R. Ngama, M. Otieno, G. P. Nokes, D. J. Agoti, C. N.
Wellcome Open Res, (2018). 3:150

Evaluation of the diagnostic accuracy and cost of different methods for the assessment of severe anaemia in hospitalised children in Eastern Uganda.Olupot-Olupot, P. Prevatt, N. Engoru, C. Nteziyaremye, J. Amorut, D. Chebet, M. Senyondo, T. Ongodia, P. Ndila, C. M. Williams, T. N. Maitland, K.
Wellcome Open Res, (2018). 3:130

Sickle Cell and alpha+-Thalassemia Traits Influence the Association between Ferritin and Hepcidin in Rural Kenyan Children Aged 14-26 Months.Byrd, K. A. Williams, T. N. Lin, A. Pickering, A. J. Arnold, B. F. Arnold, C. D. Kiprotich, M. Dentz, H. N. Njenga, S. M. Rao, G. Colford, J. M, Jr. Null, C. Stewart, C. P.
J Nutr, (2018). 148:1903-1910

Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance.Morobe, J. M. Nyiro, J. U. Brand, S. Kamau, E. Gicheru, E. Eyase, F. Otieno, G. P. Munywoki, P. K. Agoti, C. N. Nokes, D. J.
Wellcome Open Res, (2018). 3:128

Evaluating the performance of tools used to call minority variants from whole genome short-read data.Said Mohammed, K. Kibinge, N. Prins, P. Agoti, C. N. Cotten, M. Nokes, D. J. Brand, S. Githinji, G.
Wellcome Open Res, (2018). 3:21

Erratum: Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains.Otieno, J. R. Kamau, E. M. Oketch, J. W. Ngoi, J. M. Gichuki, A. M. Binter, S. Otieno, G. P. Ngama, M. Agoti, C. N. Cane, P. A. Kellam, P. Cotten, M. Lemey, P. Nokes, D. J.
Virus Evol, (2018). 4:vey036

Coverage and timeliness of vaccination and the validity of routine estimates: Insights from a vaccine registry in Kenya.Adetifa, I. M. O. Karia, B. Mutuku, A. Bwanaali, T. Makumi, A. Wafula, J. Chome, M. Mwatsuma, P. Bauni, E. Hammitt, L. L. Mataza, C. Tabu, C. Kamau, T. Williams, T. N. Scott, J. A. G.
Vaccine, (2018). 36:7965-7974

Modifying Intestinal Integrity and Micro Biome in Severe Malnutrition with Legume-Based Feeds (MIMBLE 2.0): protocol for a phase II refined feed and intervention trial.Walsh, K. Calder, N. Olupot-Olupot, P. Ssenyondo, T. Okiror, W. Okalebo, C. B. Muhindo, R. Mpoya, A. Holmes, E. Marchesi, J. Delamare de la Villenaise de Chenevarin, G. Frost, G. Maitland, K.
Wellcome Open Res, (2018). 3:95

Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains.Otieno, J. R. Kamau, E. M. Oketch, J. W. Ngoi, J. M. Gichuki, A. M. Binter, S. Otieno, G. P. Ngama, M. Agoti, C. N. Cane, P. A. Kellam, P. Cotten, M. Lemey, P. Nokes, D. J.
Virus Evol, (2018). 4:vey027

Untargeted analysis of the airway proteomes of children with respiratory infections using mass spectrometry based proteomics.Sande, C. J. Mutunga, M. Muteti, J. Berkley, J. A. Nokes, D. J. Njunge, J.
Sci Rep, (2018). 8:13814

Surveillance of respiratory viruses in the outpatient setting in rural coastal Kenya: baseline epidemiological observations.Nyiro, J. U. Munywoki, P. Kamau, E. Agoti, C. Gichuki, A. Etyang, T. Otieno, G. Nokes, D. J.
Wellcome Open Res, (2018). 3:89

Impact of viral upper respiratory tract infection on the concentration of nasopharyngeal pneumococcal carriage among Kenyan children.Morpeth, S. C. Munywoki, P. Hammitt, L. L. Bett, A. Bottomley, C. Onyango, C. O. Murdoch, D. R. Nokes, D. J. Scott, J. A. G.
Sci Rep, (2018). 8:11030

Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study.Ndila, C. M. Uyoga, S. Macharia, A. W. Nyutu, G. Peshu, N. Ojal, J. Shebe, M. Awuondo, K. O. Mturi, N. Tsofa, B. Sepulveda, N. Clark, T. G. Band, G. Clarke, G. Rowlands, K. Hubbart, C. Jeffreys, A. Kariuki, S. Marsh, K. Mackinnon, M. Maitland, K. Kwiatkowski, D. P. Rockett, K. A. Williams, T. N. Malaria, G. E. N. Consortium
Lancet Haematol, (2018). 5:e333-e345

Risk factors for mortality and effect of correct fluid prescription in children with diarrhoea and dehydration without severe acute malnutrition admitted to Kenyan hospitals: an observational, association study.Akech, S. Ayieko, P. Gathara, D. Agweyu, A. Irimu, G. Stepniewska, K. English, M. Clinical Information Network, authors
Lancet Child Adolesc Health, (2018). 2:516-524

Caregiver oral rehydration solution fluid monitoring charts versus standard care for the management of some dehydration among Kenyan children: a randomized controlled trial.Kailemia, M. Kariuki, N. Laving, A. Agweyu, A. Wamalwa, D.
Int Health, (2018). 10:442-450

Prevalence, outcome and quality of care among children hospitalized with severe acute malnutrition in Kenyan hospitals: A multi-site observational study.Gachau, S. Irimu, G. Ayieko, P. Akech, S. Agweyu, A. English, M. Clinical Information Network Author, Group
PLoS One, (2018). 13:e0197607

Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya.Kiyuka, P. K. Agoti, C. N. Munywoki, P. K. Njeru, R. Bett, A. Otieno, J. R. Otieno, G. P. Kamau, E. Clark, T. G. van der Hoek, L. Kellam, P. Nokes, D. J. Cotten, M.
J Infect Dis, (2018). 217:1728-1739

Two complement receptor one alleles have opposing associations with cerebral malaria and interact with alpha(+)thalassaemia.Opi, D. H. Swann, O. Macharia, A. Uyoga, S. Band, G. Ndila, C. M. Harrison, E. M. Thera, M. A. Kone, A. K. Diallo, D. A. Doumbo, O. K. Lyke, K. E. Plowe, C. V. Moulds, J. M. Shebbe, M. Mturi, N. Peshu, N. Maitland, K. Raza, A. Kwiatkowski, D. P. Rockett, K. A. Williams, T. N. Rowe, J. A.
Elife, (2018). 7:

Continuous Invasion by Respiratory Viruses Observed in Rural Households During a Respiratory Syncytial Virus Seasonal Outbreak in Coastal Kenya.Munywoki, P. K. Koech, D. C. Agoti, C. N. Cane, P. A. Medley, G. F. Nokes, D. J.
Clin Infect Dis, (2018). 67:1559-1567