The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism

Trimmomatic: a flexible trimmer for Illumina sequence data

Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607

PLINK: a tool set for whole-genome association and population-based linkage analyses.

Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046

Detecting the number of clusters of individuals using the software structure: a simulation study

Evanno, G., Regnaut, S., & Goudet, J. (2005) · Molecular Ecology · doi:10.1111/j.1365-294x.2005.02553.x · Cited by 21,540

ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE

Weir, B. S., & Cockerham, C. C. (1984) · Evolution · doi:10.1111/j.1558-5646.1984.tb05657.x · Cited by 18,909

ModelFinder: fast model selection for accurate phylogenetic estimates

Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A., & Jermiin, L. S. (2017) · Nature Methods · doi:10.1038/nmeth.4285 · Cited by 18,449

The variant call format and VCFtools

Danecek, P., Auton, A., Abecasis, G. R., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G. A., Marth, G., Sherry, S. T., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr330 · Cited by 16,450

Evolutionary trees from DNA sequences: A maximum likelihood approach.

Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w 1118 ; iso-2; iso-3

Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., Land, S. J., Lu, X., & Ruden, D. M. (2012) · Fly · doi:10.4161/fly.19695 · Cited by 11,816

Fast model-based estimation of ancestry in unrelated individuals

Alexander, D. H., Novembre, J., & Lange, K. (2009) · Genome Research · doi:10.1101/gr.094052.109 · Cited by 9,898

GCTA: a tool for genome-wide complex trait analysis

Yang, J., Lee, S. H., Goddard, M. E., & Visscher, P. M. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.11.011 · Cited by 8,279

The Reactome pathway Knowledgebase

Fabregat, A., Sidiropoulos, K., Garapati, P., Gillespie, M., Hausmann, K., Haw, R., Jassal, B., Jupe, S., Korninger, F., McKay, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1351 · Cited by 5,605

Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering

Browning, S. R., & Browning, B. L. (2007) · The American Journal of Human Genetics · doi:10.1086/521987 · Cited by 3,217

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

Mi, H., Muruganujan, A., Ebert, D., Huang, X., & Thomas, P. D. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1038 · Cited by 3,030

A Map of Recent Positive Selection in the Human Genome

Voight, B. F., Kudaravalli, S., Wen, X., & Pritchard, J. K. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040072 · Cited by 2,925

Ancient Admixture in Human History

Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T., & Reich, D. (2012) · Genetics · doi:10.1534/genetics.112.145037 · Cited by 2,848

STING regulates intracellular DNA-mediated, type I interferon-dependent innate immunity

Ishikawa, H., Ma, Z., & Barber, G. N. (2009) · Nature · doi:10.1038/nature08476 · Cited by 2,759

Ensembl 2018

Zerbino, D. R., Achuthan, P., Akanni, W., Amode, M. R., Barrell, D., Bhai, J., Billis, K., Cummins, C., Gall, A., Girón, C. G., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1098 · Cited by 2,605

GeneCards Version 3: the human gene integrator

Safran, M., Dalah, I., Alexander, J., Rosen, N., Stein, T. I., Shmoish, M., Nativ, N., Bahir, I., Doniger, T., Krug, H., et al. (2010) · Database · doi:10.1093/database/baq020 · Cited by 2,134

ggmap: Spatial Visualization with ggplot2

Kahle, D. J., & Wickham, H. (2013) · The R Journal · doi:10.32614/rj-2013-014 · Cited by 2,126

The Reactome pathway knowledgebase

Croft, D., Mundo, A. F., Haw, R., Milacic, M., Weiser, J., Wu, G., Caudy, M., Garapati, P., Gillespie, M., Kamdar, M. R., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1102 · Cited by 1,889

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z. X. P., Pool, J. E., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T. S., et al. (2010) · Science · doi:10.1126/science.1190371 · Cited by 1,611

The NLRC4 inflammasome receptors for bacterial flagellin and type III secretion apparatus

Zhao, Y., Yang, J., Shi, J., Gong, Y., Lu, Q., Xu, H., Liu, L., & Shao, F. (2011) · Nature · doi:10.1038/nature10510 · Cited by 1,312

Inference of Population Structure using Dense Haplotype Data

Lawson, D. J., Hellenthal, G., Myers, S., & Falush, D. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002453 · Cited by 1,188

The diversity of the DnaJ/Hsp40 family, the crucial partners for Hsp70 chaperones

Qiu, X., Shao, Y., Miao, S., & Wang, L. (2006) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-006-6192-6 · Cited by 900

Evidence for Two Independent Domestications of Cattle

Loftus, R. T., MacHugh, D. E., Bradley, D. G., Sharp, P. M., & Cunningham, P. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.7.2757 · Cited by 812

A genetic atlas of human admixture history

Hellenthal, G., Busby, G. B. J., Band, G., Wilson, J. F., Capelli, C., Falush, D., & Myers, S. (2014) · Science · doi:10.1126/science.1243518 · Cited by 798

An activating NLRC4 inflammasome mutation causes autoinflammation with recurrent macrophage activation syndrome

Canna, S., de Jesus, A. A., Gouni, S., Brooks, S. R., Marrero, B., Liu, Y., DiMattia, M. A., Zaal, K. J. M., Sanchez, G. A. M., Kim, H., et al. (2014) · Nature Genetics · doi:10.1038/ng.3089 · Cited by 747

Physiological and cellular adaptations of zebu cattle to thermal stress

Hansen, P. J. (2004) · Animal Reproduction Science · doi:10.1016/j.anireprosci.2004.04.011 · Cited by 642

Mitochondrial diversity and the origins of African and European cattle

Bradley, D. G., MacHugh, D. E., Cunningham, P., & Loftus, R. T. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.10.5131 · Cited by 584

African Pastoralism: Genetic Imprints of Origins and Migrations

Hanotte, O., Bradley, D. G., Ochieng, J. W., Verjee, Y., Hill, E. W., & Rege, J. E. O. (2002) · Science · doi:10.1126/science.1069878 · Cited by 567

Microsatellite DNA Variation and the Evolution, Domestication and Phylogeography of Taurine and Zebu Cattle (Bos taurus and Bos indicus)

MacHugh, D. E., Shriver, M. D., Loftus, R. T., Cunningham, P., & Bradley, D. G. (1997) · Genetics · doi:10.1093/genetics/146.3.1071 · Cited by 547

Genes and speciation

Wu, C.-I., & Ting, C.-T. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1269 · Cited by 532

Inferring admixture histories of human populations using linkage disequilibrium

Loh, P.-R., Lipson, M., Patterson, N., Moorjani, P., Pickrell, J. K., Reich, D., & Berger, B. (2013) · Genetics · doi:10.1534/genetics.112.147330 · Cited by 466

Untitled work

(1971) · CGSPace A Repository of Agricultural Research Outputs (Consultative Group for International Agricultural Research) · Cited by 426

The Origins and Development of African Livestock

Blench, R. M., & MacDonald, K. C. (2006) · Routledge eBooks · doi:10.4324/9780203984239 · Cited by 420

Whole-Genome Resequencing Reveals World-Wide Ancestry and Adaptive Introgression Events of Domesticated Cattle in East Asia

Chen, N., Cai, Y., Chen, Q., Li, R., Wang, K., Huang, Y., Hu, S., Huang, S., Zhang, H., Zheng, Z., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04737-0 · Cited by 403

A UAF1-Containing Multisubunit Protein Complex Regulates the Fanconi Anemia Pathway

Cohn, M. A., Kowal, P., Yang, K., Haas, W., Huang, T. T., Gygi, S. P., & D’Andrea, A. D. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.09.031 · Cited by 355

The Origins and Development of African Livestock: Archaeology, Genetics, Linguistics and Ethnography

Blench, R. M., & MacDonald, K. C. (2006) · Medical Entomology and Zoology · Cited by 348

The MAGUK Family Protein CARD11 Is Essential for Lymphocyte Activation

Hara, H., Wada, T., Bakal, C., Kozieradzki, I., Suzuki, S., Suzuki, N., Nghiem, M. P., Griffiths, E. K., Krawczyk, C. M., Bauer, B., et al. (2003) · Immunity · doi:10.1016/s1074-7613(03)00148-1 · Cited by 336

Identification of FAAP24, a Fanconi Anemia Core Complex Protein that Interacts with FANCM

Ciccia, A., Ling, C., Coulthard-Graf, R., Yan, Z., Xue, Y., Meetei, A. R., Laghmani, E. H., Joenje, H., McDonald, N. Q., de Winter, J. P., et al. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.01.003 · Cited by 335

Population admixture, biological invasions and the balance between local adaptation and inbreeding depression

Verhoeven, K. J. F., Macel, M., Wolfe, L. M., & Biere, A. (2010) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2010.1272 · Cited by 321

Physiology and pathophysiology of the vasopressin-regulated renal water reabsorption

Boone, M., & Deen, P. M. T. (2008) · Pflügers Archiv - European Journal of Physiology · doi:10.1007/s00424-008-0498-1 · Cited by 303

Ancient west Eurasian ancestry in southern and eastern Africa

Pickrell, J. K., Patterson, N., Loh, P.-R., Lipson, M., Berger, B., Stoneking, M., Pakendorf, B., & Reich, D. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1313787111 · Cited by 300

- Invited Review - African Indigenous Cattle: Unique Genetic Resources in a Rapidly Changing World

Mwai, O., Hanotte, O., Kwon, Y.-J., & Cho, S. (2015) · Asian-Australasian Journal of Animal Sciences · doi:10.5713/ajas.15.0002r · Cited by 300

Mitochondrial Genomes of Extinct Aurochs Survive in Domestic Cattle

Achilli, A., Olivieri, A., Pellecchia, M., Uboldi, C., Colli, L., Al-Zahery, N., Accetturo, M., Pala, M., Kashani, B. H., Perego, U. A., et al. (2008) · Current Biology · doi:10.1016/j.cub.2008.01.019 · Cited by 290

An inherited mutation in NLRC4 causes autoinflammation in human and mice

Kitamura, A., Sasaki, Y., Abe, T., Kano, H., & Yasutomo, K. (2014) · The Journal of Experimental Medicine · doi:10.1084/jem.20141091 · Cited by 288

On the Origin of Cattle: How Aurochs Became Cattle and Colonized the World

Ajmone‐Marsan, P., Garcia, J. F., & Lenstra, J. A. (2010) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.20267 · Cited by 287

Domesticating animals in Africa: implications of genetic and archaeological findings

Gifford-Gonzalez, D., & Hanotte, O. (2011) · Journal of World Prehistory · doi:10.1007/s10963-010-9042-2 · Cited by 274

The Genome Landscape of Indigenous African Cattle

Kim, J., Hanotte, O., Mwai, O. A., Dessie, T., Bashir, S., Diallo, B., Agaba, M., Kim, K., Kwak, W., Sung, S., et al. (2017) · Genome biology · doi:10.1186/s13059-017-1153-y · Cited by 271

A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics

Bibi, F. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-166 · Cited by 267

"Dark" Purkinje cells of the cerebellar cortex.

Leranth, C., & Hámori, J. (1970) · PubMed · Cited by 264

Geographic distribution and frequency of a taurine Bos taurus and an indicine Bos indicus Y specific allele amongst sub‐Saharan African cattle breeds

Hanotte, O., Tawah, C. L., Bradley, D. G., Okomo, M., Verjee, Y., Ochieng, J., & Rege, J. E. O. (2000) · Molecular Ecology · doi:10.1046/j.1365-294x.2000.00858.x · Cited by 257

Pervasive introgression facilitated domestication and adaptation in the Bos species complex

Wu, D., Ding, X., Wang, S., Wójcik, J. M., Zhang, Y., Tokarska, M., Li, Y., Wang, M.-S., Faruque, O., Nielsen, R., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0562-y · Cited by 249

HEXIM1 and NEAT1 Long Non-coding RNA Form a Multi-subunit Complex that Regulates DNA-Mediated Innate Immune Response

Morchikh, M., Cribier, A., Raffel, R., Amraoui, S., Cau, J., Séverac, D., Dubois, E., Schwartz, O., Bennasser, Y., & Benkirane, M. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.06.020 · Cited by 239

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Park, S. D. E., Magee, D. A., McGettigan, P., Teasdale, M. D., Edwards, C. J., Lohan, A. J., Murphy, A., Braud, M., Donoghue, M. T. A., Liu, Y., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0790-2 · Cited by 234

Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis

Ma, L., O’Connell, J. R., VanRaden, P. M., Shen, B., Padhi, A., Sun, C., Bickhart, D. M., Cole, J. B., Null, D. J., Liu, G. E., et al. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005387 · Cited by 232

Genetics of adaptation in domestic farm animals: A review

Mirkena, T., Duguma, G., Haile, A., Tibbo, M., Okeyo, A. M., Wurzinger, M., & Sölkner, J. (2010) · Livestock Science · doi:10.1016/j.livsci.2010.05.003 · Cited by 214

CARD11 mediates factor‐specific activation of NF‐κB by the T cell receptor complex

Pomerantz, J. L., Denny, E. M., & Baltimore, D. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf505 · Cited by 211

A whole genome Bayesian scan for adaptive genetic divergence in West African cattle

Gautier, M., Flori, L., Riebler, A., Jaffrézic, F., Laloë, D., Gut, I. G., Moazami‐Goudarzi, K., & Foulley, J. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-550 · Cited by 200

Mapping of quantitative trait loci controlling trypanotolerance in a cross of tolerant West African N'Dama and susceptible East African Boran cattle

Hanotte, O., Ronin, Y. I., Agaba, M. K., Nilsson, P. R., Gelhaus, A., Horstmann, R., Sugimoto, Y., Kemp, S. J., Gibson, J. P., Korol, A. B., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1232392100 · Cited by 196

Hybridisation is associated with increased fecundity and size in invasive taxa: meta‐analytic support for the hybridisation‐invasion hypothesis

Hovick, S. M., & Whitney, K. D. (2014) · Ecology Letters · doi:10.1111/ele.12355 · Cited by 193

Animal Disease Challenges to the Emergence of Pastoralism in Sub-Saharan Africa

Gifford-Gonzalez, D. P. (2000) · African Archaeological Review · doi:10.1023/a:1006601020217 · Cited by 183

The Peopling of Africa: A Geographic Interpretation.

McCall, D. F., & Newman, J. L. (1996) · The American Historical Review · doi:10.2307/2170286 · Cited by 150

Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

Porto-Neto, L. R., Sonstegard, T. S., Liu, G. E., Bickhart, D. M., Silva, M. V. D., Machado, M. A., Utsunomiya, Y. T., Garcia, J. F., Gondro, C., & Tassell, C. P. V. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-876 · Cited by 147

TMEM173 variants and potential importance to human biology and disease

Patel, S., & Jin, L. (2018) · Genes and Immunity · doi:10.1038/s41435-018-0029-9 · Cited by 146

Inside the “African Cattle Complex”: Animal Burials in the Holocene Central Sahara

di Lernia, S., Tafuri, M. A., Gallinaro, M., Alhaique, F., Balasse, M., Cavorsi, L., Fullagar, P. D., Mercuri, A. M., Monaco, A. L., Perego, A., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0056879 · Cited by 136

Mason's world encyclopedia of livestock breeds and breeding. Volume 1 and Volume 2

(2016) · CABI eBooks · doi:10.1079/9781845934668.0000 · Cited by 136

Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks

Međugorac, I., Graf, A., Grohs, C., Rothammer, S., Zagdsuren, Y., Александровна, Г. Е., Zinovieva, N. A., Barbieri, J., Seichter, D., Ruß, I., et al. (2017) · Nature Genetics · doi:10.1038/ng.3775 · Cited by 135

Genomic clues of the evolutionary history of Bos indicus cattle

Utsunomiya, Y. T., Milanesi, M., Fortes, M. R. S., Porto‐Neto, L. R., Utsunomiya, A. T. H., Silva, M. V. G. B., Garcia, J. F., & Ajmone‐Marsan, P. (2019) · Animal Genetics · doi:10.1111/age.12836 · Cited by 128

Loter: A Software Package to Infer Local Ancestry for a Wide Range of Species

Alves, T. D., Mairal, J., & Blum, M. G. B. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy126 · Cited by 126

Genome-Wide Scan for Selection Signatures in Six Cattle Breeds in South Africa

Makina, S. O., Muchadeyi, F. C., van Marle-Köster, E., Taylor, J. F., Makgahlela, M. L., & Maiwashe, A. (2015) · Genetics Selection Evolution · doi:10.1186/s12711-015-0173-x · Cited by 125

Genome Sequence and Assembly of Bos indicus

Canavez, F., Luche, D. D., Stothard, P., Leite, K. R. M., de Sousa-Canavez, J. M., Plastow, G. S., Meidânis, J., Souza, M. A., Feijão, P., Moore, S. S., et al. (2012) · Journal of Heredity · doi:10.1093/jhered/esr153 · Cited by 120

Leucine-rich repeat containing 8A (LRRC8A) is essential for T lymphocyte development and function

Kumar, L., Chou, J. S., Yee, C. S. K., Borzutzky, A., Vollmann, E. H., von Andrian, U. H., Park, S., Holländer, G. A., Manis, J. P., Poliani, P. L., et al. (2014) · The Journal of Experimental Medicine · doi:10.1084/jem.20131379 · Cited by 120

Mzb1 Protein Regulates Calcium Homeostasis, Antibody Secretion, and Integrin Activation in Innate-like B Cells

Flach, H., Rosenbaum, M., Duchniewicz, M., Kim, S., Zhang, S. L., Cahalan, M. D., Mittler, G., & Grosschedl, R. (2010) · Immunity · doi:10.1016/j.immuni.2010.11.013 · Cited by 118

Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis

Bahbahani, H. M., Clifford, H., Wragg, D., Mbole-Kariuki, M. N., Tassell, C. P. V., Sonstegard, T. S., Woolhouse, M. E. J., & Hanotte, O. (2015) · Scientific Reports · doi:10.1038/srep11729 · Cited by 111

Admixture and diversity in West African cattle populations

Freeman, A., Meghen, C., MacHugh, D., Loftus, R., Achukwi, M. D., Bado, A., Sauveroche, B., & Bradley, D. (2004) · Molecular Ecology · doi:10.1111/j.1365-294x.2004.02311.x · Cited by 108

The advent of herding in the Horn of Africa: New data from Ethiopia, Djibouti and Somaliland

Lesur, J., Hildebrand, E., Abawa, G., & Gutherz, X. (2013) · Quaternary International · doi:10.1016/j.quaint.2013.11.024 · Cited by 107

Origin and Spread of Bos taurus: New Clues from Mitochondrial Genomes Belonging to Haplogroup T1

Bonfiglio, S., Ginja, C., De Gaetano, A., Achilli, A., Olivieri, A., Colli, L., Tesfaye, K., Agha, S. H., Gama, L. T., Cattonaro, F., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0038601 · Cited by 106

An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle

MacEachern, S., Hayes, B. J., McEwan, J. C., & Goddard, M. E. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-181 · Cited by 103

On the Breeds of Cattle—Historic and Current Classifications

Felius, M., Koolmees, P. A., Theunissen, B., & Lenstra, J. A. (2011) · Diversity · doi:10.3390/d3040660 · Cited by 102

Indian Ocean Food Globalisation and Africa

Boivin, N. L., Crowther, A., Prendergast, M. E., & Fuller, D. Q. (2014) · African Archaeological Review · doi:10.1007/s10437-014-9173-4 · Cited by 102

Genetic Resistance to African Trypanosomiasis

Murray, M., Trail, J. C. M., Davis, C. E. L. B., & Black, S. J. (1984) · The Journal of Infectious Diseases · doi:10.1093/infdis/149.3.311 · Cited by 99

ATG4B (Autophagin-1) Phosphorylation Modulates Autophagy

Yang, Z., Wilkie-Grantham, R. P., Yanagi, T., Shu, C., Matsuzawa, S., & Reed, J. C. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.658088 · Cited by 96

Spatial complexity of ‘Little Ice Age’ climate in East Africa: sedimentary records from two crater lake basins in western Uganda

Russell, J. M., Verschuren, D., & Eggermont, H. (2007) · The Holocene · doi:10.1177/0959683607075832 · Cited by 90

Studies on Trypanosome-resistant cattle. II. The effect of Trypanosomiasis on N'dama, Muturu and Zebu cattle

Roberts, C. J., & Gray, A. R. (1973) · Tropical Animal Health and Production · doi:10.1007/bf02240423 · Cited by 88

Developing a continental atlas of the distribution and trypanosomal infection of tsetse flies (Glossina species)

Cecchi, G., Paone, M., Argilés-Herrero, R., Vreysen, M. J. B., & Mattioli, R. C. (2015) · Parasites & Vectors · doi:10.1186/s13071-015-0898-y · Cited by 88

Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection

Noyes, H., Brass, A., Obara, I., Anderson, S., Archibald, A. L., Bradley, D. G., Fisher, P., Freeman, A., Gibson, J., Gicheru, M., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1013486108 · Cited by 88

Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu

Bahbahani, H. M., Tijjani, A., Mukasa, C., Wragg, D., Almathen, F. S., Nash, O., Akpa, G. N., Mbole-Kariuki, M. N., Malla, S., Woolhouse, M. E. J., et al. (2017) · Frontiers in Genetics · doi:10.3389/fgene.2017.00068 · Cited by 88

Adaptive admixture in the W est A frican bovine hybrid zone: insight from the B orgou population

Flori, L., Thévenon, S., Dayo, G., Sènou, M., Sylla, S., Berthier, D., Moazami‐Goudarzi, K., & Gautier, M. (2014) · Molecular Ecology · doi:10.1111/mec.12816 · Cited by 87

“Animal disease challenges” fifteen years later: The hypothesis in light of new data

Gifford-Gonzalez, D. P. (2016) · Quaternary International · doi:10.1016/j.quaint.2015.10.054 · Cited by 87

Zebu cattle of Kenya: Uses, performance, farmer preferences, measures of genetic diversity and options for improved use

Rege, J. E. O., Kahi, A. K., Okomo‐Adhiambo, M., Mwacharo, J. M., & Hanotte, O. (2001) · CGSPace A Repository of Agricultural Research Outputs (Consultative Group for International Agricultural Research) · Cited by 86

Rift Valley fever virus inhibits a pro-inflammatory response in experimentally infected human monocyte derived macrophages and a pro-inflammatory cytokine response may be associated with patient survival during natural infection

McElroy, A. K., & Nichol, S. T. (2011) · Virology · doi:10.1016/j.virol.2011.09.023 · Cited by 85

hapbin: An Efficient Program for Performing Haplotype-Based Scans for Positive Selection in Large Genomic Datasets: Fig. 1.

MacLean, C., Hong, N. C., & Prendergast, J. G. D. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv172 · Cited by 83

SEPT12 orchestrates the formation of mammalian sperm annulus by organizing SEPT12-7-6-2/-4 core complexes

Kuo, Y., Shen, Y.-R., Chen, H.-I., Lin, Y., Wang, Y., Chen, Y., Wang, C., & Kuo, P. (2015) · Journal of Cell Science · doi:10.1242/jcs.158998 · Cited by 82

EPIDEMICS AND REVOLUTIONS: THE RINDERPEST EPIDEMIC IN LATE NINETEENTH–CENTURY SOUTHERN AFRICA

Phoofolo, P. (1993) · Past & Present · doi:10.1093/past/138.1.112 · Cited by 80

Host genetics in African trypanosomiasis

Courtin, D., Berthier, D., Thévenon, S., Dayo, G., Garcia, A., & Bucheton, B. (2008) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2008.02.007 · Cited by 78

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. O., Dzama, K., Marufu, M. C., Githaka, N., et al. (2019) · Animal Production Science · doi:10.1071/an18487 · Cited by 77

Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle

Tijjani, A., Utsunomiya, Y. T., Ezekwe, A. G., Nashiru, O., & Hanotte, O. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00442 · Cited by 76

Toward the identification of a subset of unexplained infertility: a sperm proteomic approach

McReynolds, S., Dzieciątkowska, M., Stevens, J., Hansen, K. C., Schoolcraft, W. B., & Katz‐Jaffe, M. G. (2014) · Fertility and Sterility · doi:10.1016/j.fertnstert.2014.05.021 · Cited by 71

Identification of mechanisms of natural resistance to African trypanosomiasis in cattle

Naessens, J., Teale, A. J., & Sileghem, M. (2002) · Veterinary Immunology and Immunopathology · doi:10.1016/s0165-2427(02)00070-3 · Cited by 69

Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya

Mbole-Kariuki, M. N., Sonstegard, T., Orth, A., Thumbi, S. M., Bronsvoort, B. M. D. C., Kiara, H., Toye, P., Conradie, I., Jennings, A., Coetzer, K., et al. (2014) · Heredity · doi:10.1038/hdy.2014.31 · Cited by 69

Signatures of positive selection in African Butana and Kenana dairy zebu cattle

Bahbahani, H., Salim, B., Almathen, F., Al Enezi, F., Mwacharo, J. M., & Hanotte, O. (2018) · PLOS ONE · doi:10.1371/journal.pone.0190446 · Cited by 67

Early herders and monumental sites in eastern Africa: dating and interpretation

Hildebrand, E., & Grillo, K. M. (2012) · Antiquity · doi:10.1017/s0003598x00062803 · Cited by 66

Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled

Koufariotis, L. T., Hayes, B. J., Kelly, M., Burns, B. M., Lyons, R. E., Stothard, P., Chamberlain, A. J., & Moore, S. S. (2018) · Scientific Reports · doi:10.1038/s41598-018-35698-5 · Cited by 66

Y‐specific microsatellites reveal an African subfamily in taurine (Bos taurus) cattle

Pérez‐Pardal, L., Royo, L. J., Beja‐Pereira, A., Curik, I., Traoré, A., Fernández, I., Sölkner, J., Alonso, J., Álvarez, I., Bozzi, R., et al. (2010) · Animal Genetics · doi:10.1111/j.1365-2052.2009.01988.x · Cited by 61

Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level

Shin, D., Lee, H. J., Cho, S., Kim, H. J., Hwang, J. Y., Lee, C., Jeong, J., Yoon, D., & Kim, H. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-240 · Cited by 52

Climate, ecology, and the spread of herding in eastern Africa

Chritz, K. L., Cerling, T. E., Freeman, K. H., Hildebrand, E., Janzen, A., & Prendergast, M. E. (2018) · Quaternary Science Reviews · doi:10.1016/j.quascirev.2018.11.029 · Cited by 52

IFNAR1 Controls Progression to Cerebral Malaria in Children and CD8+ T Cell Brain Pathology in Plasmodium berghei–Infected Mice

Ball, E. A., Sambo, M. D. R., Martins, M., Trovoada, M. J., Benchimol, C., Costa, J., Gonçalves, L. A., Coutinho, A., & Penha‐Gonçalves, C. (2013) · The Journal of Immunology · doi:10.4049/jimmunol.1300114 · Cited by 51

Inferring Heterozygosity from Ancient and Low Coverage Genomes

Kousathanas, A., Leuenberger, C., Link, V., Sell, C., Bürger, J., & Wegmann, D. (2016) · Genetics · doi:10.1534/genetics.116.189985 · Cited by 50

The Tick Protein Sialostatin L2 Binds to Annexin A2 and Inhibits NLRC4-Mediated Inflammasome Activation

Wang, X., Shaw, D. K., Sakhon, O. S., Snyder, G. A., Sundberg, E. J., Santambrogio, L., Sutterwala, F. S., Dumler, J. S., Shirey, K. A., Perkins, D. J., et al. (2016) · Infection and Immunity · doi:10.1128/iai.01526-15 · Cited by 48

Response of four indigenous cattle breeds to natural tsetse and trypanosomosis challenge in the Ghibe valley of Ethiopia

Lemecha, H., Mulatu, W., Hussein, I., Rege, E., Tekle, T., Abdicho, S., & Ayalew, W. (2006) · Veterinary Parasitology · doi:10.1016/j.vetpar.2006.04.035 · Cited by 47

Deciphering the Genetic Blueprint behind Holstein Milk Proteins and Production

Lee, H. J., Kim, J., Lee, T., Son, J.-K., Yoon, H., Baek, K., Jeong, J. Y., Cho, Y.-M., Lee, K., Yang, B., et al. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu102 · Cited by 46

Trypanosomosis: potential driver of selection in African cattle

Smetko, A., Soudré, A., Silbermayr, K., Müller, S., Brem, G., Hanotte, O., Boettcher, P. J., Stella, A., Mészáros, G., Wurzinger, M., et al. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00137 · Cited by 44

Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with pulmonary hypertension

Heaton, M. P., Smith, T. P. L., Carnahan, J. K., Basnayake, V. R., Qiu, J., Simpson, B., & Kalbfleisch, T. (2016) · F1000Research · doi:10.12688/f1000research.9254.2 · Cited by 38

Genomic signatures of adaptive introgression and environmental adaptation in the Sheko cattle of southwest Ethiopia

Bahbahani, H. M., Afana, A., & Wragg, D. (2018) · PLoS ONE · doi:10.1371/journal.pone.0202479 · Cited by 38

Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations

O’Brien, A. M. P., Holler, D. A., Boison, S. A., Milanesi, M., Bomba, L., Utsunomiya, Y. T., Carvalheiro, R., Neves, H. H. D. R., Silva, M. V. D., Vantassell, C. P., et al. (2015) · Genetics Selection Evolution · doi:10.1186/s12711-015-0109-5 · Cited by 36

A Model of African Indigenous Economy and Society

Schneider, H. K. (1964) · Comparative Studies in Society and History · doi:10.1017/s0010417500003443 · Cited by 33

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

Smedley, D. P., Schofield, P. N., Chen, C.-K., Aidinis, V., Ainali, C., Bard, J., Balling, R., Birney, E., Blake, A., Bongcam‐Rudloff, E., et al. (2010) · Database · doi:10.1093/database/baq014 · Cited by 31

Domesticating Animals in Africa

Gifford-Gonzalez, D. P., & Hanotte, O. (2013) · Oxford University Press eBooks · doi:10.1093/oxfordhb/9780199569885.013.0034 · Cited by 30

Lessons for livestock genomics from genome and transcriptome sequencing in cattle and other mammals

Taylor, J. F., Whitacre, L. K., Hoff, J. L., Tizioto, P. C., Kim, J., Decker, J. E., & Schnabel, R. D. (2016) · Genetics Selection Evolution · doi:10.1186/s12711-016-0237-6 · Cited by 30

Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with high-altitude pulmonary hypertension

Heaton, M. P., Smith, T. P. L., Carnahan, J. K., Basnayake, V. R., Qiu, J., Simpson, B., & Kalbfleisch, T. (2016) · F1000Research · doi:10.12688/f1000research.9254.1 · Cited by 28

Microsatellite Analysis of Genetic Population Structure of Zebu Cattle (Bos indicus) Breeds from North-Western Region of India

Sodhi, M., Mukesh, M., Mishra, B., Ahlawat, S., Prakash, B., & Sobti, R. C. (2011) · Animal Biotechnology · doi:10.1080/10495398.2011.536091 · Cited by 22

Variations in mitochondrial cytochrome b region among Ethiopian indigenous cattle populations assert Bos taurus maternal origin and historical dynamics

Tarekegn, G. M., Ji, X., Bai, X., Liu, B., Zhang, W., Birungi, J., Djikeng, A., & Tesfaye, K. (2018) · Asian-Australasian Journal of Animal Sciences · doi:10.5713/ajas.17.0596 · Cited by 22

Quantitative Analysis of Cytokine mRNA Expression and Protozoan DNA Load in Theileria parva-Infected Cattle

Yamada, S., Konnai, S., Imamura, S., Simuunza, M. C., Chembensofu, M., Chota, A., Nambota, A. M., Onuma, M., & Ohashi, K. (2009) · Journal of Veterinary Medical Science · doi:10.1292/jvms.71.49 · Cited by 19

The Archaeology of Herding in Southernmost Africa

Sadr, K. (2013) · Oxford University Press eBooks · doi:10.1093/oxfordhb/9780199569885.013.0044 · Cited by 19

The Bos taurus–Bos indicus balance in fertility and milk related genes

Kasarapu, P., Porto-Neto, L. R., Fortes, M. R. S., Lehnert, S. A., Mudadu, M. A., Coutinho, L. L., Regitano, L. C. D. A., George, A. W., & Reverter, A. (2017) · PLoS ONE · doi:10.1371/journal.pone.0181930 · Cited by 18

PABP Interacting Protein 2 (Paip2) Is a Major Translational Regulator Involved in the Maturation of Male Germ Cells and Male Fertility.

Delbès, G., Yanagiya, A., Sonenberg, N., & Robaire, B. (2009) · Biology of Reproduction · doi:10.1093/biolreprod/81.s1.167 · Cited by 3

Novel Functional Sequences Uncovered through a Bovine Multiassembly Graph

Crysnanto, D., Leonard, A. S., Fang, Z.-H., & Pausch, H. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2101056118 · Cited by 96

Assembly of a Pangenome for Global Cattle Reveals Missing Sequences and Novel Structural Variations, Providing New Insights into Their Diversity and Evolutionary History

Zhou, Y., Yang, L., Han, X., Han, J., Hu, Y., Li, F., Xia, H., Peng, L., Boschiero, C., Rosen, B. D., et al. (2022) · Genome Research · doi:10.1101/gr.276550.122 · Cited by 89

Global Genetic Diversity, Introgression, and Evolutionary Adaptation of Indicine Cattle Revealed by Whole Genome Sequencing

Chen, N., Xia, X., Hanif, Q., Zhang, F., Dang, R., Huang, B., Lyu, Y., Luo, X., Zhang, H., Yan, H., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43626-z · Cited by 83

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Leonard, A. S., Crysnanto, D., Fang, Z., Heaton, M. P., Ley, B. L. V., Herrera, C., Bollwein, H., Bickhart, D. M., Kuhn, K. L., Smith, T. P. L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30680-2 · Cited by 78

Pangenome graphs and their applications in biodiversity genomics

Secomandi, S., Gallo, G. R., Rossi, R., Fernandes, C., Jarvis, E. D., Bonisoli‐Alquati, A., Gianfranceschi, L., & Formenti, G. (2025) · Nature Genetics · doi:10.1038/s41588-024-02029-6 · Cited by 83

Integrative Population and Functional Genomics of Trypanotolerance in Hybrid African Cattle

McHugo, G. P. (2025) · Research Repository UCD (University College Dublin)

Genome-wide local ancestry and the functional consequences of admixture in African and European cattle populations

McHugo, G. P., Ward, J. A., Ng’ang’a, S. I., Frantz, L., Salter‐Townshend, M., Hill, E. W., O’Gorman, G. M., Meade, K. G., Hall, T. J., & MacHugh, D. E. (2024) · Heredity · doi:10.1038/s41437-024-00734-w · Cited by 4

Distinct adaptation and ancestral retention signals in African and European indigenous cattle genomes

Gao, J., Ginja, C., Liu, Y., Kantanen, J., Ghanem, N., Kugonza, D. R., Makgahlela, M. L., Okwasiimire, R., Bovenhuis, H., Groenen, M. A. M., et al. (2026) · Communications Biology · doi:10.1038/s42003-026-09856-9 · Cited by 1

A genomic history of African cattlePreprint

Frantz, L., Ng’ang’a, S. I., Ward, J. A., McHugo, G. P., Jones, M., Thalmann, O., Achukwi, M. D., Adeola, A. C., Biginagwa, T., Sow, R. S., et al. (2026) · Research Square · doi:10.21203/rs.3.rs-10317902/v1

African cattle adaptations

Koch, L. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-00293-w · Cited by 2