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Species diversity and risk factors of gastrointestinal nematodes in smallholder dairy calves in Kenya.Cheptoo, S., Yalcindag, E., Gordon, L G., Rukwaro, B., Kimatu, J S., Wasonga, J., Karani, B E., Ndambuki, G., Kagai, J., Kiprotich, L E., Saya, N., Vasoya, D., Nangekhe, G., Onguso, J., Mungai, G., Bronsvoort, M., Elizabeth A. J. Cook(2025) Frontiers
Unlocking the African bioeconomy and strengthening biodiversity conservation through genomics and bioinformatics.Hayah, I., Ezebuiro, V., Kagame, S P., Kuja, J O., Waruhiu, C., Nesengani, L T., Mdyogolo, S., Molotsi, A H., Abechi, P., Houaga, I., et al.(2025) Nature Portfolio
Accurate determination of breed origin of alleles in a simulated smallholder crossbred dairy cattle population.Welderufael, B., Houaga, I., C. Gaynor, G. Gorjanc, J. Hickey(2025) Springer Nature
A chromosomal level genome assembly of Nguni Sheep, Ovis aries.Nesengani, L T., Tshilate, T., Mdyogolo, S., Smith, Rae, Masebe, T., Raphulu, T., Moila, A., Sharaf, A., Muzemil, S., Houaga, I., Muigai, A., Djikeng, A., Kuja, J., Katee, S. M., et al.(2025) Nature
The genetic structure and diversity of smallholder dairy cattle in Rwanda.Opoola, O., Shumbusho, F., Rwamuhizi, I., Houaga, I., Harvey, D., Hambrook, D., Watson, K., Chagunda, M.G.G, Mrode, R., Djikeng, A., et al.(2025) BMC Genomic Data
The African Animal Breeding Network as a pathway towards genetic improvement of livestock.Djikeng, A., Olori, V.E., Houaga, I., Mwai, O., Mrode, R., Chagunda, M.G.G, Tiambo, C.K., Rekaya, R., Nash, O., Opoola, O., Ekine-Dzivenu, C., Okeno, T.O., et al.(2025) Nature Genetics
Integrating Genetic, Environmental, and Phenotypic Information in Within and Between Breed Evaluation of Livestock for Smallholder Farmers in the Tropics.Kebede, F., Dessie, T., Beyts, C., Matika, O., Watson, K.(2024) Animal Science Cases
Multi-environment performance analysis identifies more productive and widely adapted chicken breeds for smallholder farmers.Kebede, Tadelle, D., Hanotte, O., Kemp, S., Alemu, Bastiaansen, J.W.M., Komen, H.(2024) Frontiers in Sustainable Food Systems
Environmental and food security implications of livestock abortions and calf mortality: a case study in Kenya and Tanzania.Gurmu, E.B., Bronsvoort, M., Elizabeth A. J. Cook, Lankester, F., Ozkan, S., Rosenstein, P.K., Semango, G., Wheelhouse, N., Wilkes, A., Arndt, C.(2024) Frontiers in Sustainable Food Systems
Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia.L. Glendinning, Hanotte, O., A. Kebede, S. Oyola(2024) Microbiome
A prospective cohort study of factors associated with the digital cushion thickness in dairy cattle.G. Banos(2024) Journal of Dairy Science
Multiscale 3D genome organization underlies duck fatty liver with no adipose inflammation or serious injury.J. Smith(2024) International Journal of Biological Macromolecules
Breed-specific SNP and genomic regions associated with equine recurrent exertional rhabdomyolysis susceptibility overlapping withup- and down-regulatory histone modification.E. Clark(2024) Conference: 14th International Havemeyer Foundation Equine Genome Workshop
Chicken intestinal organoids: a novel method to measure the mode of action of feed additives.K. Sutton(2024) Frontiers in Immunology
Phenotypic and genomic characterisation of performance of tropically adapted chickens raised in smallholder farm conditions in Ethiopia.Hanotte, O., K. Sutton, Lonneke Vervelde, Banos, G.(2024) Frontiers in Genetics
Comparative transcriptional analysis identifies genes associated with the attenuation of Theileria parva infected cells after long-term in vitro culture.Hassan, M., Connelley, T.(2024) Scientific Reports
Investigative power of Genomic Informational Field Theory (GIFT) relative to GWAS for genotype-phenotype mapping.Matika, O.(2024) bioRxiv
Genetic variance components of the growth curve for Isfahan indigenous chicken.J. Smith(2024) Veterinary Medicine and Sciences
Consistent detection of Trypanosoma brucei but not T. congolense DNA in faeces of experimentally infected cattle.L. Morrison(2024) Nature
A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families.J. Smith(2024) BMC Biology
Whole-genome resource sequences of 57 indigenous Ethiopian goats.Abulgasim. A(2024) Nature
Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress.Dessie, T., J. Smith, Hanotte, O.(2024) Scientific Report
The feeding of heather (Calluna vulgaris) to Teladorsagia circumcincta infected lambs reduces parasitism but can detrimentally impact performance.Jos G. M. Houdijk(2024) The Veterinary Journal
Delineation of chicken immune markers in the era of omics and multicolour flow cytometry.K. Sutton(2024) Frontiers in Veterinary Science
A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes.J. Smith(2023) Communications Biology
Site specific insertion of a transgene into the murine α-casein (CSN1S1) gene results in the predictable expression of a recombinant protein in milk.Lillico, S., Whitelaw, B.(2023) Biotechnology Journal
Laying and growth performance of local chicken (Gallus gallus domesticus) ecotype Konde in Burkina Faso.Houaga, I.(2023) International Journal of Environment, Agriculture and Biotechnology
The potential for use of haematological and anti-IgE humoral responses as phenotypic markers for tick resistance in cattle.Matika, O., Djikeng, A., K. Watson(2023) Current Research in Parasitology & Vector-Borne Diseases
1200 High Quality Metagenome-Assembled Genomes from the Rumen of African Cattle and their relevance in the context of sub-optimal feeding.Matika, O., K. Watson, Djikeng, A.(2023) Elsevier
Accounting for nuclear and mito genome in dairy cattle breeding – a simulation study.I. Pocrnic, G. Gorjanc(2023) bioRxiv
Genetic diversity and breed-informative SNPs identification in domestic pig populations using coding SNPs.Houaga, I.(2023) Frontiers in Genetics
Genomic markers associated with antibody response to Newcastle disease virus of Sasso chickens raised in Ethiopia.Banos, G., Lonneke Vervelde, Hanotte, O., K. Sutton(2023) Conference: 39th International Society for Animal Genetics
Anti-parasitic benzoxaboroles are ineffective against Theileria parva in vitro.T. Connelley, Liam J. Morrison(2023) International Journal for Parasitology: Drugs and Drug Resistance
Evolutions in Commercial Meat Poultry Breeding.A. Kranis(2023) Animals
Identification of temporal patterns of environmental heat stress of Holstein dairy heifers raised in Mediterranean climate during their in-utero and post-natal life periods and modelling their effects on age at first calving.Banos, G.(2023) Journal of Thermal Biology
A case of forensic genomics in Uganda reveals animal ownership and low exotic genetic introgression in indigenous cattle.Opoola, O.(2023) Veterinary Sciences
Sensitivity of broiler performance, organ weights and plasma constituents to amino acid supplementation and reused litter exposure using ideal protein-formulated rations.Lonneke Vervelde, Jos G. M. Houdijk(2023) Animal
A review of machine learning models applied to genomic prediction in animal breeding.Houaga, I.(2023) Frontiers in Genetics
Genome-wide diversity and admixture of five indigenous cattle populations from the Tigray region of northern Ethiopia.Vallejo-Trujillo, A.(2023) Frontiers in Genetics
Investigating the benefits and perils of importing genetic material in small cattle breeding programs via simulation.G. Gorjanc, I. Pocrnic(2023) Journal of Dairy Science
Disentangling the Innate Immune Responses of Intestinal Epithelial Cells and Lamina Propria Cells to Salmonella Typhimurium Infection in Chickens.K. Sutton, S. Sives, Lonneke Vervelde(2023) bioRxiv
Developing digital contact tracing tailored to haulage in East Africa to support COVID-19 surveillance: a protocol.Muwonge, A, Bronsvoort, M.(2023) Frontiers in Biology
Meta-analysis of heritability estimates and genome-wide association for tick-borne haemoparasites in African cattle.Riggio, V., Djikeng, A., Prendergast, J.(2023) Frontiers in Genetics
The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species.Djikeng, A., James G. D. Prendergast(2023) Genome Biology
Generation of sheep with defined FecBB and TBXT mutations and porcine blastocysts with KCNJ5G151R/+ mutation using prime editing.Lillico, S.(2023) BMC Genomics
An analysis of the maxillary beak shape variation between two pure layer lines and its relationship to the underlying premaxillary bone, feather cover, and mortality.Oswald Matika(2023) Poultry Science
Livestock phenomics and genetic evaluation approaches in Africa: current state and future perspectives.Houaga, I., Opoola, O., Djikeng, A., Mrode, R., Chagunda, M.G.G, Mwai, O., Nash, O., Banga, C.B., Okeno, T.O.(2023) Frontiers in Genetics
A method for partitioning trends in genetic mean and variance to understand breeding practices.I. Pocrnic, G. Gorjanc(2023) Genetics Selection Evolution
Effect of a co-feed liquid whey-integrated diet on crossbred pigs’ fecal microbiota.Riggio, V.(2023) Animals
Profiling the immune epigenome across global cattle breeds.Jessica Powell, Talenti, A., Fisch, A., Johanneke D. Hemmink, Paxton, E., Toye, P., Santos, I., Ferreira, B.R., Connelley, T., Morrison, L.J., James G. D. Prendergast(2023) Genome Biology
Genomic selection for genotype performance and stability using information on multiple traits and multiple environments.G. Gorjanc, J. Bancic, B. Ovenden(2023) Theoretical Applied Genetics
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing.Salavati, M., Clark, E(2023) bioRxiv
CpG dinucleotide enrichment in the influenza A virus genome as a live attenuated vaccine development strategy.Colin Sharp, Tessa Nash, Ola Diebold, Rute Pinto, Luke Thorley, Oliver Lin, Samantha Sives, Helen Wise, Sara Hendry, Finn Grey, Lonneke Vervelde, Peter Simmonds, Paul Digard, Eleanor Gaunt(2023) PLOS Pathogens
KOunt – A reproducible KEGG orthologue abundance workflow.Watson, M.(2023) bioRxiv
Yolk Fatty Acid Content, Lipid Health Indices, and Oxidative Stability in Eggs of Slow-Growing Sasso Chickens Fed on Flaxseed Supplemented with Plant Polyphenol Extracts.Dessie, T., Hanotte, O.(2023) Foods
Recent Advances in the Genomic Resources for Sheep.Salavati, M., Clark, E(2023) Frontiers in Genetics
Seroepidemiology of Leptospira serovar Hardjo and associated risk factors in smallholder dairy cattle in Tanzania.Motto, S. K., Shirima, G. M., B. Mark deC. Bronsvoort, Elizabeth A. J. Cook, Komwihangilo, D.M.(2023) PLOS Neglected Tropical Diseases
Growth performance, caecal microbiome profile, short-chain fatty acids, and litter characteristics in response to placement on reused litter and combined threonine, arginine and glutamine supplementation to juvenile male broiler chickens.Marwa A. Hussein, Farina Khattak, Lonneke Vervelde, Spiridoula Athanasiadou, Jos G. M. Houdijk(2023) Animal Microbiome
Quantifying morphometric and adaptive characteristics of indigenous cattle genetic resources in northwest Ethiopia.Tadelle, D.(2023) Quantifying morphometric and adaptive characteristics of indigenous cattle genetic resources in northwest Ethiopia
nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.J. Smith(2023) Bioinformatics
Genomic selection strategies for clonally propagated crops.C. Werner, R. Gaynor, D. Sargent, A. Lillo, G. Gorjanc, J. Hickey(2023) Theoretical and Applied Genetics
RNA-Seq profiling between commercial and indigenous Iranian chickens highlights differences in innate immune gene expression.Ayeh Sadat Sadr, Mohammad Reza Nassiri, Mostafa Ghaderi-Zefrehei, Maryam Heidari, Smith, J., Mustafa Mohaghegh Dolatabady(2023) MDPI Poultry Genetics and Genomics
Genomics of dwarfism in Italian local chicken breeds.F. Perini, F. Cendron, Z. Wu, N. Servane, Z. Li, C. Huang, J. Smith, E. Lasagna, M. Cassandro, M. Penasa(2023) MDPI Animal Genetics and Genomics
Identification of alternative splicing events related to fatty liver formation in duck using full-length transcripts.Y. Wang, L. Song, M. Ning, J. Hu, H. Cai, W. Song, D. Gong, L. Liu, J. Smith, H. Li, Y. Huang(2023) BMC Genomics
Assessment of long-term trends in genetic mean and variance after the introduction of genomic selection in layers: a simulation study.I. Pocrnic, G. Gorjanc, C. Gaynor(2023) bioRxiv, at Cold Spring Harbor Laboratory
Assessment of long-term trends in genetic mean and variance after the introduction of genomic selection in layers: a simulation study.I. Pocrnic, J. Obsteter, C. Gaynor, A. Wolc, G. Gorjanc(2023) bioRxiv, at Cold Spring Harbor Laboratory
The Status and Risk Factors of Brucellosis in Smallholder Dairy Cattle in Selected Regions of Tanzania.Isaac Joseph Mengele, Shirima, G. M., B. Mark deC. Bronsvoort, Motto, S. K., Komwihangilo, D.M., E. Lyatuu, Elizabeth A. J. Cook, Luis E. Hernandez-Castro(2023) Veterinary Sciences
Fourth Report on Chicken Genes and Chromosomes 2022.J. Smith(2023) Cytogenetic and Genome Research
Gene drive: past, present and future roads to vertebrate biocontrol.McFarlane, G., Lillico, S., Whitelaw, B.(2022) Applied Biosciences
A locus conferring tolerance to Theileria infection in African cattle.James G. D. Prendergast, et al.(2022) PLOS Genetics
Jersey cattle in Africa – From the Breed’s Documented Past to a Profit Index-Linked Future.Opoola, O.(2021) https://africanjerseyforum.com/wp-content/uploads/2021/11/Jersey-Cattle-in-Africa-Review-2021.pdf
Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci.Lv, F-H., et al.(2021) Molecular Biology and Evolution
Detection of Novel Variations Related to Litter Size in BMP15 Gene of Luzhong Mutton Sheep (Ovis aries).Di, R., Wang, F., Yu, P., Wang, X., He, X., Mwacharo, J.M., Pan, L., Chu, M.(2021) animals
Discussing the drawbacks of the implementation of Access and Benefit Sharing of the Nagoya Protocol following the COVID-19 Pandemic.Tiambo, C.K., Katee, S. M.(2021) Frontiers in Public Health
A genetic approach to tackling East Coast Fever.Pye-Smith, C., Toye, P., Prendergast, J.(2021) CGIAR Research Program on Livestock Innovation Brief
Epidemiology of leptospirosis in Tanzania: A review of the current status, serogroup diversity and reservoirs.Motto, S. K., Shirima, G. M., Bronsvoort, M., Cook, E.(2021) PLOS neglected tropical diseases
VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity.Denoyelle, L., Talouarn, E, Bardou, P., Colli, L., Alberti, A, Danchin, C., Del Corvo, M., Engelen, S., Orvain, C., Palhiere, I., Rupp, R., Sarry, J., Salavati, M., Amills, M., Clark, E, Crepaldi, P., Faraut, T., Masiga, C.W., Pomanon, F., Rosen, B.D., Stella, A., Van Tassell, C.P., Tosser-Klopp, G.(2021) Genetics Selection Evolution
Inherited tolerance in cattle to the apicomplexan protozoan Theileria parva is associated with decreased proliferation of parasite-infected lymphocytes.Latre de Late, P., Cook, E., Wragg, D., Poole, J., Ndambuki, G., Makau, M.C, Mwaura, S., Ndiwa, N., Prettejohn, G., Sitt, T., van Aardt, R., Morrison, W.I., Prendergast, J., Toye, P.(2021) Frontiers in Cellular & Infection Microbiology
Morpho-Biometric Evaluation of the Genetic Diversity of Local Chicken Ecotypes in Four Regions (Centre-East, Sahel, Centre-North and South-West) of Burkina Faso.Zare, Y., Gnanda, B.I., Houaga, I., Kere, M., Traore, B., Zongo, M., Bamouni, S., Traore, A. P., Zangre, M., Rekaya, R., Nianogo, A. J.(2021) International Journal of Poultry Science
Biobanking African Poultry Breeds Livestock for the Future.Tiambo, C.K., McGrew, M.J.(2021) CGIAR Livestock Innovation Brief
Typology, management and smallholder farmer-preferred traits for selection of indigenous goats (Capra hisrcus) in three agro-ecological zones in the Democratic Republic of Congo.Baenyi Simon, P., Owino Joseph, J., Wungo Ochieng, J., Tiambo, C.K., Mekuriaw Tarekegn, G., Machuka, E.M., Kabange, D., Musale, K., Mushalusa Ciza, A., Yumilia Kizungu, R., Pelle, R.(2021) Journal of Applied Animal Research
Clinical evaluation of Corridor disease in Bos indicus (Boran) cattle naturally infected with buffalo-derived Theileria parva.Cook, E., Sitt, T., Poole, J., Ndambuki, G., Mwaura, S., Chepkwony, M., Latre de Late, P., Miyunga, A., van Aardt, R., Prettejohn, G., Wragg, D., Prendergast, J., Morrison, W.I., Toye, P.(2021) Frontiers in Veterinary Science
Avian Primordial Germ Cells Are Bipotent for Male or Female Gametogenesis.Ballantyne, M., Taylor, L., Hu, T., Meunier, D., Nandi, S., Sherman, A., Flack, B., Henshall, J.M., Hawken, R.J., McGrew, M.J.(2021) Frontiers in Cell & Developmental Biology
Demographic expansion and high level of matrilineal diversity in two populations of East African Baggara cattle.Kambal. S., Abdelrahim, A., Hanotte, O., Nakao, R., Alkhaibari, A. M., Salim, B.(2021) Journal of Animal Breeding Genetics
Evaluation of Bayesian Alphabet and GBLUP Based on Different Marker Density for Genomic Prediction in Alpine Merino Sheep.Zhu, S., Guo, T., Yuan, C., Liu, J., Li, J., Han, M., Zhao, H., Wu, Y., Sun, W., Wang, T., Tiambo, C.K., Yue, Y., Yang, B.(2021) G3 Genes
Breeding strategies for improving smallholder dairy cattle productivity in Sub-Saharan Africa.Chawala, A.R., Sanchez-Molano, E., Dewhurst, R.J., Peters, A., Chagunda, M.G.G, Banos, G.(2021) Animal Breeding and Genetics
Multiple country and breed genomic prediction of tick resistance in beef cattle.Cardoso, F.F., Matika, O., Djikeng, A., Mapholi, N., Burrow, H.M., Yokoo, M.J.I., Campos, G.S., Gomes, C.C.G., Riggio, V., Pong-Wong, R., Porto-Neto, L.R., Maiwashe, A., Hayes, B.(2021) Frontiers in Immunology
High throughput analysis of MHC-I and MHC-DR diversity of Brazilian cattle populations.Vasoya, D., Oliveira, P.S., Agundez Muriel, L., Tzelos, T., Vrettou, C., Morrison, W.I., Santos, I.K.F.D.M., Connelley, T.(2021) HLA
Domestic chicken diversity: Origin, distribution and adaptation: Review Paper.Lawai, R.A., Hanotte, O.(2021) Animal Genetics
Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens.Gheyas, A., Vallejo-Trujillo, A., Kebede, A., Lozano-Jaramillo, M., Dessie, T., Smith, J., Hanotte, O.(2021) Molecular Biology and Evolution
Integral use of immunopeptidomics and immunoinformatics for the characterization of antigen presentation and rational identification of BoLA-DR presented peptides and epitopes.Fisch, A., Reynisson, B., Benedictus, L., Nicastri, A., Vasoya, D., Morrison, I., Buss, S., Ferreira, B.R., Santos, I., Terrentte, N., Connelley, T., Nielson, M.(2021) Journal of Immunology
Socio-economic, technical characteristics and challenges in indigenous (taurine-type cattle) beef production in Cameroon.Ojong, E.T., Oben, P.M., Hako, T.B.A., Ectu, K.A., Motsa, J.S., Wozerou, N.N., Keambou, C.T.(2021) Applied Animal Husbandry & Rural Development
Genome-wide insights on gastrointestinal nematode resistance in autochthonous Tunisian sheep.Ahbara, A., Rouatbi, M., Gharbi, M., Rekik, M., Haile, A., Rischkowsky, B., Mwacharo, J.M.(2021) Nature Scientific Reports
Inference of ancestries and heterozygosity proportion and genotype imputation in West African cattle populations.Gebrehiwot, N.Z., Aliloo, H., Strucken, E.M., Marshall, K., Gibson, J.P.(2021) Frontiers in Genetics
SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle.Gebrehiwot, N.Z., Strucken, E.M., Marshall, K., Aliloo, H., Gibson, J.P.(2021) Genetics Selection and Evolution
Direct allele introgression into pure chicken breeds using Sire Dam Surrogate (SDS) mating.Ballantyne, M., Woodcock, M., Doddamani, D., Hu, T., Taylor, L., Hawken, R., McGrew, M.J.(2021) Nature Communications
Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations.Weiner, P., Robert, C., Ahbara, A., Salavati, M., Abebe, A., Kebede, A., Wragg, D., Friedrich, J., Vasoya, D., Hume, D.A., Djikeng, A., Watson, M., Prendergast, J., Hanotte, O., Mwacharo, J.M., Clark, E(2021) Genome Biology and Evolution
The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data.Gebrehiwot, N.Z., Strucken, E.M., Aliloo, H., Marshall, K., Al Kaladeh, M., Gibson, J.P.(2020) BMC Genetics
Single-cell RNA-seq reveals CD16- monocytes as key regulators of human monocyte transcriptional response to Toxoplasma.Patir, A., Gossner, A., Ramachandran, P., Alves, J., Freeman, T., Henderson, N., Watson, M., Hassan, M.(2020) Nature Scientific Reports
Determinants of vitamin D status in Kenyan calves.Callaby, R., Hurst, E., Handel, I., Toye, P., Bronsvoort, M., Mellanby, R.J.(2020) Nature Scientific Reports
Genetic Parameter estimates for Milkability Traits and their Relationship with Somatic Cell Score in South African Holstein Cattle.Tshilate, T.S., Bhebhe, E., Dude, C., Rhode, C., Mapholi, N.O., Matika, O., Banga, C.B.(2020) Tropical Animal Health and Production
Genetic diversity of Cameroon cattle and a putative genomic map for resistance to bovine tuberculosis.Callaby, R., Kelly, R., Mazeri, S., Egbe, F., Benedictus, L., Clark, E, Doeschl-Wilson, A, Bronsvoort, M., Salavati, M., Muwonge, A(2020) Frontiers in Genetics
Global analysis of transcription start sites in the new ovine reference genome (Oar rambouillet v1.0).Salavati, M., Caulton, A., Clark, R., Gazova, I., Smith, T.P.L., Worley, K.C., Cockett, N.E., Archibald, A.L., Clarke, S.M., Murdoch, B.M., Clark, E(2020) Frontiers in Genetics
Inverted CD4+/CD8+ T cell ratio in Boran (Bos indicus) cattle.Makau, M.C, Powell, J., Prendergast, J., de Late, P.L., Morrison, L.J., Fisch, A., Gathura, P., Kitala, P., Connelley, T., Toye, P.(2020) Veterinary Immunology & Immunopathology
A genome-wide loss-of-function screen identifies Toxoplasma gondii genes that determine fitness in interferon gamma-activated murine macrophages.Wang, Y., Sangare, L.O., Paredes-Santos, T.C., Krishnamurthy, S., Hussan, M., Furuta, A.M., Markus, B.M., Lourido, S., Saeij, J.P.J.(2020) Nature Communications
Integrating genetic and genomic analyses of combined health data across ecotypes to improve disease resistance in indigenous African chickens.Banos, G., Lindsay, V., Desta, T.T., Bettridge, J., Sanchez-Molano, E., Vallejo-Trujillo, A., Matika, O., Dessie, T., Wigley, P., Christley, R., Kaiser, P., Hanotte, O., Psifidi, A.(2020) Frontiers in Genetics
The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism.Kim, K., Kwon, T., Dessie, T., Yoo, D., Mwai, O., Jang, J., Sung, S., Lee, S., Salim, B., Jung, J., Jeong, H., Tarekegn, G.M., Tijjani, A., Lim, D., Cho, S., Oh, S.J., Lee, H-K., Kim. J., Jeong, C., Kemp, S., Hanotte, O., Kim, H.(2020) Nature Genetics
Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of recent selection across domesticated species.Dutta, P., Talenti, A., Young, A., Jayaraman, S., Callaby, R., Jadhav, S.K., Dhanikachalam, V., Manikandan, M., Biswa, B.B., Low, W.Y., Williams, J.L., Cook, E., Toye, P., Wall, E., Djikeng, A., Marshall, K., Archibald, A.L., Gokhale, S., Kumar, S., Hume, D.A., Prendergast, J.(2020) Nature Comms
Comprehensive transcriptome of the maize stalk borer, Busseola fusca, from multiple tissue types, developmental stages, and parasitoid wasp exposures.Hardwick, K.M., Bichang'a, G., Abtew, A.B., Awori, R.M., Cepko, L., Chebon-Bore, L.J., Darby, A., deVries, J.D., Filee, J., Fuad, M., Gachara, G., Githae, D., Gunga, P., Held, M., Kariuki, H., Sioma Kataka, E., Kerfua, S.D., Kimenyi, K.M., Le Ru, B., Lutomia, E.M., Luvai, E.A., Luvanda, M.K., Lyimo, B.M., Machuka, E.M., Maeda, D.G., Maini, S., Mathenge, P.G., Matoke-Muhia, D., Miller, C., Miruka, S.A., Mitema, A., Miyunga, A.A., Mukolwe, S.A., Muge, E.K., Mule, S.N., Murithi, M.K., Musabyimana, J.P., Muzoora, S., Mwangi, E.W., Mwangi, H.N., Mwangi, N., Mwaura, A.N., Ndungu, N., Ngalah, B.S., Ng'ang'a, P.N., Nyandika, B.N., Nyasani, J.O., Obange, F.A., Ochieng, S.J., Obhiambo, W.O., Ogat, H.A., Ojwang, A.M.E., Osowo, F.O., Ratemo, B.O., Sonta, T., Ssamula, A., Towett-Kirui, S., Twizerimana, A.P., Wachuin, K.M., Wacoo, A.P., Wamae, K., Webale, M.K., Yaa, R.M., Gunderson-Rindal, D.E., Stomeo, F., Djikeng, A., Calatayud, P-A., Schaack, S.(2020) Genome Biology and Evolution
Donor-derived spermatogenesis following stem call transplantation in sterile NANOS2 knockout males.Ciccarelli, C., Giasetti, M.I., Miao, D., Oatley, M.J., Robbins, C., Lopez-Biladeau, B., Waqas, M.S., Tibary, A., Whitelaw, B., Lillico, S., Park, C-H., Park, K-E., Telugu, B., Fan, Z., Liu, Y., Regouski, M., Polejaeva, I.A., Oatley, J.(2020) PNAS
1200 High Quality Metagenome-Assembled Genomes from the Rumen of African Cattle and their relevance in the context of sub-optimal feeding.Wilkinson, T., Korir, D., Ogugo, M., Stewart, R.D., Watson, M., Paxton, E., Goopy, J., Robert, C.(2020) Genome Biology
First detection of African swine fever (ASF) virus genotype X and serogroup 7 in symptomatic pigs in the Democratic Republic of Congo.Bisimwa, P.N., Ongus, J.R., Tiambo, C.K., Machuka, E.M., Bisimwa, E.B., Steinaa, L., Pelle, R.(2020) Virology Journal
Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-saharan African goats.Tarekegn, G.M., Khayatzadeh, N., Liu, B., Osama, S., Haile, A., Rischkowsky, B., Zhang, W., Tesfaye, K., Dessie, T., Mwai, O., Djikeng, A., Mwacharo, J.M.(2020) Evolutionary Application
Paternal Origins and Migratory Episodes of Domestic Sheep.Deng, J., Xie, X-L., Wang, D-F., Zhao, C., Lv, F-H., Li, X., Yang, J., Yu, J-L., Shen, M., Gao, L., Yang, J-Q., Liu, M-J., Li, W-R., Wang, Y-T., Wang, F., Li, J-Q., Hehua, E., Liu, Y-G., Shen, Z.Q., Ren, Y-L., Liu, G-J., Chen, Z-H., Gorkhali, N.A., Rushdi, H.E., Salehian-Dehkordi, H., Esmailizadeh, A., Nosrati, M., Paivi, S.R., Caetano, A.R., Stepanek, O., Olsaker, I., Weimann, C., Erhardt, G., Curik, I., Kantanen, J., Mwacharo, J.M., Hanotte, O., Bruford, M.W., Ciani, E., Periasamy, K., Amills, M., Lenstra, J.A., Han, J-L., Zhang, H-P., Li, L., Li, M-H.(2020) Current Biology
Transcriptional Analyses Identify Genes That Modulate Bovine Macrophage Response to Toxoplasma Infection and Immune Stimulation.Gossner, A., Hussan, M.(2020) Frontiers in Cellular and Infection Microbiology
Joint genetic analysis for dairy cattle performance across countries in sub-Saharan Africa.Opoola, O., Banos, G., Ojango, J.M.K, Mrode, R., Simm, G., Banga, C.B., Beffa, L.M., Chagunda, M.G.G(2020) South African Journal of Animal Science
Genetic Diversity and Population Structure of Brachiaria (syn. Urochloa) Ecotypes from Uganda.Namazzi, C., Sserumaga, J.P., Mugerwa, S., Kyalo, M., Mutai, C., Mwesigwa, R., Djikeng, A., Ghimire, S.(2020) Agronomy
Reflections on IDEAL.Callaby, R., Jennings, A., Mwangi, S.T., Mbole-Kariuki, M., Van Wyk, I., Kiara, H., Coetzer, J.A.W., Woolhouse, M.E.J., Hanotte, O., Toye, P., Bronsvoort, M.(2020) Preventative Veterinary Medicine
IDEAL, the Infectious Diseases of East African Livestock project open access database and biobank.Callaby, R., Pendarovski, C., Jennings, A., Mwangi, S.T., Van Wyk, I., Mbole-Kariuki, M., Kiara, H., Toye, P., Kemp, S., Hanotte, O., Coetzer, J.A.W., Handel, I., Woolhouse, M.E.J., Bronsvoort, M.(2020) Nature Scientific Data
Comparative Transcriptomics of the Bovine Apicomplexan Parasite Theileria parva Developmental Stages Reveals Massive Gene Expression Variation and Potential Vaccine Antigens.Atchou, K., Ongus, J.R., Machuka, E.M., Juma, J., Tiambo, C.K., Djikeng, A., Silva, J.C., Pelle, R.(2020) Frontiers in Veterinary Science
Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits.Li, X., Yang, J., Shen, M., Xia, X-L., Liu, G-J., Xu, Y-X., Lv, H-H., Yang, H., Yang, Y-L., Liu, C-B, Zhou, P., Wan, P-C., Zhang, Y-S., Gao, L., Yang, J-Q., Pi, W-H., Ren, Y-L., Shen, Z.Q., Wang, F., Deng, J., Xu, S-S, Salehian-Dehkordi, H., Hehua, E., Esmailizadeh, A., Dehghani-Qanatqestani, M., Stepanek, O., Weimann, C., Erhardt, G., Amane, A., Mwacharo, J.M., Han, J-L., Hanotte, O., Lenstra, J.A., Kantanen, J., Coltman, D.W., Kijas, J.W., Bruford, M.W., Periasamy, K., Wang, X-H., Li, M-H.(2020) Nature Communications
Diversity of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in indigenous chickens.Mason, A., Miedzinska-Bielecka, K., Kebede, A., Bamidele, O., Al-Jumaili, A.S., Dessie, T., Hanotte, O., Smith, J.(2020) Genetic Selection Evolution
Bioengineering horizon scan 2020.Kemp, L., Adam, L., Boehm, C.R., Breitling, R., Casagrande, R., Dando, M., Djikeng, A., Evans, N.G., Hammond, R., Hills, R., Holt, L.A., Kuiken, T., Markotic, A., Millett, P., Napier, J.A., Nelson, C., OhEigeartaigh, S.S., Osbourn, A., Palmer, M., Patron, N.J., Perello, E., Piyawattanametha, W., Restrepo-Schild, V., Rios-Rojas, C., Rhodes, C., Roessing, A., Scott, D., Shapira, P., Simuntala, C., Smith, R.D., Sundaram, L.S., Takano, E., Uttmark, G., Wintle, B., Zahra, N.B., Sutherland, W.J.(2020) eLife
Analysis of the Role of TpUB05 Antigen from Theileria parva in Immune Responses to Malaria in Humans Compared to Its Homologue in Plasmodium falciparum the UB05 Antigen.Dinga, J.N., Perimbie, S.N., Gamau, S.D., Chuma, F.N.G., Njimoh, D.L., Djikeng, A., Pelle, R., Titanji, V.P.K.(2020) Pathogens
Association of LEI0258 Marker Alleles and Susceptibility to Virulent Newcastle Diseases Infection in Kuroiler, sasso and Local Tanzanian chicken embryos.Mpenda, F.N., Keambou, C.T., Kyallo, M., Juma, J., Pelle, R., Lyantagaye, S.L., Buza, J.(2020) Journal of Pathogens
The maternal origin of indigenous domestic chicken from the Middle East, the north and the horn of Africa.Al-Jumaili, A.S., Boudali, S.F., Kebede, A., Al-Bayatti, S.A., Essa, A.A., Ahbara, A., Alijumaah, R.S., Alatiyat, R.M., Mwacharo, J.M., Bjornstad, G., Naqvi, A.N., Gaouar, S.B.S., Hanotte, O.(2020) BMC Genetics
The wild species genome ancestry of domestic chickens.Lawal, R.A., Martin, S.H., Vanmechelen, K., Vereijken, A., Silva, P., Al-Atiyat, R.M., Alijumaah, R.S., Mwacharo, J.M., Wu, D.D., Zhang, Y.P., Hocking, P.M., Smith, J., Wragg, D., Hanotte, O.(2020) BMC Biology
Genetic and antigenic variation of the bovine tick-borne pathogen Theileria parva in the Great Lakes region of Central Africa.Amzati, G.S., Djikeng, A., Odongo, D., Nimpaye, H., Sibeko, K.P., Muhigwa, J.B.B., Madder, M., Kirschvink, N., Marcotty, T.(2019) Parasites and Vectors
Leveraging genomic diversity to promote human and animal health.Ramsay, M., Brunner, H.G., Djikeng, A.(2019) Nature Communications Biology
Evidence for the Presence of African Swine Fever Virus in Apparently Healthy Pigs in South-Kivu Province of the Democratic Republic of Congo.Patrick, B.N., Machuka, E.M., Githae, D., Banswe, G., Amimo, J.O., Ongus, J.R., Masembe, C., Bishop, R.P., Steinaa, L., Djikeng, A., Pelle, R.(2019) Veterinary Microbiology
A mini-atlas of gene expression for the domestic goat (Capra hircus).Muriuki, C., Bush, S.J., Salavati, M., McCulloch, M.E.B., Lisowski, Z.M., Agaba, M., Djikeng, A., Hume, D.A., Clark, E(2019) Frontiers in Genetics
A comprehensive survey of the prevalence and spatial distribution of ticks infesting cattle in different agro-ecological zones of Cameroon.Silatsa, B.A., Simo, G., Githaka, N., Mwaura, S., Kamga, R.M., Oumarou, F., Keambou, C.T., Bishop, R.P., Djikeng, A., Kuiate, J.R., Njiokou, F., Pelle, R.(2019) Parasites and Vectors
Genome-wide identification of splicing quantitative trait loci (sQTL) in diverse ecotypes of Arabidopsis thaliana.Khokhar, W., Hassan, M., Reddy, A.S.N., Chaudhary, S., Jabre, I., Byrne, L.J., Syed, N.H.(2019) Frontiers in Plant Science
Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome.Song, B., Song, Y., Fu, Y., Kizito, E.B., Kamenya, S.N., Kabod, P.N., Liu, H., Muthemba, S., Kariba, R., Njuguna, J., Maina, S., Stomeo, F., Djikeng, A., Hendre, P.S., Chen, X., Chen, W., Li, X., Sun, W., Wang, S., Cheng, S., Muchugi, A., Jamnadass, R., Shapiro, H.Y., Van Deynze, A., Yang, H., Wang, J., Xu, X., Odeny, D.A., Liu, X.(2019) GigaScience
Breeding and Productivity in Ending Hunger and Achieving Food Security and Nutrition.Avana-Tientcheu, M.L., Keambou, C.T.(2019) Chapter in 'Zero Hunger' Book
Functional evolution of the Colony Stimulating Factor 1 Receptor (CSF1R) and its ligands in birds.Hume, D.A., Gutowska-Ding, W., Garcia-Morales, C., Kabade, A., Bamidele, A., Vallejo-Trujillo, A., Gheyas, A., Smith, J.(2019) Journal of Leukocyte Biology
Draft genome of Busseola fusca, the maize stalk borer, a major crop pest in Sub-Saharan Africa.Hardwick, K.M., Ojwang, A.M.E., Stomeo, F., Maina, S., Bichang'a, G., Calatayud, P-A., Filee, J., Djikeng, A., Miller, C., Cepko, L., Darby, A., Le Ru, B., Schaack, S.(2019) Genome Biology and Evolution
Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu.Bahbahani, H., Tijjani, A., Mukasa, C., Wragg, D., Almathen, F., Nash, O., Akpa, G.N., Mbole-Kariuki, M., Malla, S., Woolhouse, M., Sonstegard, T., Van Tassell, C., Blythe, M., Huson, H., Hanotte, O.(2019) Frontiers in Genetics
Towards a new phenotype for tick resistance in beef and dairy cattle: a review.Burrow, H.M., Mans, B.J., Cardoso, F.F., Birkett, M.A., Kotze, A.C., Hayes, B.J., Mapholi, N., Dzama, K., Marufu, M.C., Githaka, N.W., Djikeng, A.(2019) Animal Production Science
Livestock genomics for developing countries – African examples in practice.Marshall, K., Gibson, J.P., Mwai, O., Mwacharo, J.M., Haile, A., Tesfaye, G., Mrode, R., Kemp, S.(2019) Frontiers in Genetics
Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3.Bassano, I., Ong, S.H., Sanz-Hernandez, M., Vinkler, M., Kebede, A., Hanotte, O., Onuigbo, E., Fife, M., Kellam, P.(2019) BMC Genetics
Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics.Tarekegn, G.M., Wouobeng, P., Jaures, K.S., Mrode, R., Edea, Z., Liu, B., Zhang, W., Mwai, O., Dessie, T., Tesfaye, G., Strandberg, E., Berglund, B., Mutai, C., Osama, S., Wolde, A.T., Birungi, J., Djikeng, A., Meutchieye, F.(2019) PLoS ONE
A countrywide molecular survey leads to a seminal identification of the invasive cattle tick Rhipicephalus (Boophilus) microplus in Cameroon, a decade after it was reported in Cote d’Ivoire.Silatsa, B.A., Kuiate, J.R., Nijiokou, F., Simo, G., Kameni, J-M.F., Alabi, T., Amzati, G.S., Bett, B., Bishop, R., Githaka, N.W., Opiyo, S.O., Djikeng, A., Pelle, R.(2019) Ticks and Tick-borne Diseases
Three Toxoplasma gondii dense granule proteins are required for induction of Lewis rat macrophage pyroptosis.Wang, Y., Cirelli, K.M., Barros, P.D.C., Sangare, L.O., Butty, V., Hassan, M., Pasavento, P., Mete, A., Saeij, P.J.(2019) mBio
Clonal and atypical Toxoplasma strain differences in virulence varies with mouse sub-species.Hassan, M., Olijnik, A-A., Frickel, E-M., Saeij, J.P.(2019) International Journal For Parasitology
Transcriptomics reveal potential vaccine antigens and a drastic increase of upregulated genes during Theileria parva development from arthropod to bovine infective stages.Tonui, T., Corredor-Moreno, P., Kanduma, E.G., Njuguna, J., Njahira, M.N., Nyanjom, S.G., Silva, J.C., Djikeng, A., Pelle, R.(2018) PLoS ONE
Genetic diversity and population structure of Urochloa grass accessions from Tanzania using simple sequence repeat (SSR) markers.Kuwi, S.O., Kyalo, M., Mutai, C., Mwilawa, A., Hanson, J., Djikeng, A., Ghimire, S.(2018) Brazilian Journal of Botany
Invited review: Genomic selection for small ruminants in developed countries: how applicable for the rest of the world?.Mrode, R., Tarekegn, G.M., Mwacharo, J.M., Djikeng, A.(2018) Animal
Mitochondrial phylogeography and population structure of the cattle tick Rhipicephalus appendiculatus in the African Great Lakes region.Amzati, G.S., Pelle, R., Muhigwa, J.B.B., Kanduma, E.G., Djikeng, A., Madder, M., Kirschvink, N., Marcotty, T.(2018) Parasites and Vectors
Metagenomic analysis of viruses associated with maize lethal necrosis in Kenya.Wamaitha, M.J., Nigam, D., Maina, S., Stomeo, F., Wangai, A., Njuguna, J.N., Holton, T.A., Wanjala, B.W., Wamalwa, M., Lucas, T., Djikeng, A., Garcia-Ruiz, H.(2018) Virology Journal
Variations in mitochondrial cytochrome b region among Ethiopian indigenous cattle populations assert Bos taurus maternal origin and historical dynamics.Tarekegn, G.M., Ji, X-Y., Bai, X., Liu, B., Zhang, W., Birungi, J., Djikeng, A., Tesfaye, K.(2018) Asian-Australasian Journal of Animal Sciences
Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats.Tarekegn, G.M., Tesfaye, K., Mwai, O., Djikeng, A., Dessie, T., Birungi, J., Osama, S., Zergaw, N., Alemu, A., Achieng, G., Tutah, J., Mutai, C., Njuguna, J., Mwacharo, J.M.(2018) Ecology and Evolution
Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii.Hassan, M., Vasquez, J., Guo-Liang, C., Meissner, M., Siegal, T.N.(2017) BMC Genetics
Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus.Wamonje, F., Michuki, G., Braidwood, L., Njuguna, J.N., Musembi Mutuku, J., Djikeng, A., Harvey, J., Carr, J.(2017) Virology Journal
Whole genome detection of signature of positive selection in African cattle reveals selection for thermotolerance.Taye, M., Lee, W., Caetano-Anolles, K., Dessie, T., Hanotte, O., Mwai, O., Kemp, S., Cho, S., Oh, S.J., Lee, H-K., Kim, H.(2017) Animal Science Journal
Exploring evidence of positive selection signatures in cattle breeds selected for different traits.Taye, M., Lee, W., Jeon, S.M., Yoon, J., Dessie, T., Hanotte, O., Mwai, O., Kemp, S., Cho, S., Jong, S., Lee, H-K., Kim, H.(2017) Mammalian Genome
Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N’Dama.Kim, S-J., Ka, S., Ha, J-W., Kim. J., Yoo, D., Kim, K., Lee, H-K., Lim, D., Cho, S., Hanotte, O., Mwai, O., Dessie, T., Kemp, S., Oh, S.J., Kim, H.(2017) BMC Genetics
Phenotypic and genetic parameters for selected production and reproduction traits of Mpwapwa cattle in low-input production systems.Chawala, A.R., Banos, G., Komwihangilo, D.M., Peters, A., Chagunda, M.G.G(2017) South African Journal of Animal Science
The genome landscape of indigenous African cattle.Kim. J., Hanotte, O., Mwai, O., Dessie, T., Salim, B., Boubacar, D., Morris, A., Kim, K., Woori, K., Sung, S., Minseok, S., Hyeonsoo, J., Taehyung, K., Mengistie, T., Ki-Duk, S., Dajeong, L., Cho, S., Hyon-Jeong, L., Yoon, D., Oh, S.J., Kemp, S., Lee, H-K., Kim, H.(2017) Genome Biology
Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef.Taye, M., Kim. J., Yoon, S.H., Lee, W., Hanotte, O., Dessie, T., Kemp, S., Mwai, O., Caetano-Anolles, K., Cho, S., Oh, S.J., Lee, H-K., Kim, H.(2017) BMC Genetics
Valuing the project: A knowledge-action response to network governance in collaborative research.Freeman, P.L., Millar, A.J.(2017) Public Money & Management
Rapid identification of bovine MHCI haplotypes in genetically divergent cattle populations Using Next-Generation Sequencing.Vasoya, D., Law, A., Degnan, K., Motta, P., Yu, M., Muwonge, A., Cook, E., Li, X., Bryson, K., MacCallam, A., Toye, P., Bronsvoort, M., Watson, M., Morrison, I., Connelley, T.(2016) Immunogenetics
Cloning of the African indigenous cattle breed Kenyan Boran.Yu, M., Muteti, C., Ogugo, M., Ritchie, W.A., Raper, J., Kemp, S.(2016) Animal Genetics