Insights into human genetic variation and population history from 929 diverse genomes

Fast and accurate short read alignment with Burrows-Wheeler transform

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

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

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A global reference for human genetic variation

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BEAST: Bayesian evolutionary analysis by sampling trees

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Mathematical model for studying genetic variation in terms of restriction endonucleases.

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Fast model-based estimation of ancestry in unrelated individuals

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dbSNP: the NCBI database of genetic variation

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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

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Population history and gene divergence in native Mexicans inferred from 76 human exomes

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Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations

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A genetic history of the Balkans from Roman frontier to Slavic migrations

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Genetic variation across and within individuals

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Comprehensive whole-genome sequence analyses provide insights into the genomic architecture of cerebral palsy

Fehlings, D. L., Zarrei, M., Engchuan, W., Sondheimer, N., Thiruvahindrapuram, B., MacDonald, J. R., Higginbotham, E. J., Thapa, R., Behlim, T., Aimola, S., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01686-x · Cited by 50

The genetic origins and impacts of historical Papuan migrations into Wallacea

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Integrated analysis of the complete sequence of a macaque genome

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Multiple Human Population Movements and Cultural Dispersal Events Shaped the Landscape of Chinese Paternal Heritage

Wang, M., Huang, Y., Liu, K., Wang, Z., Zhang, M., Yuan, H., Duan, S., Wei, L., Yao, H., Sun, Q., et al. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae122 · Cited by 51

Including diverse and admixed populations in genetic epidemiology research

Caliebe, A., Ayele, F. T., Darst, B. F., Wang, X., Song, Y. E., Gui, J., Sebro, R., Balding, D. J., Saad, M., & Dubé, M. (2022) · Genetic Epidemiology · doi:10.1002/gepi.22492 · Cited by 46

Limits and convergence properties of the sequentially Markovian coalescent

Sellinger, T. P. P., Awad, D. A., & Tellier, A. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13416 · Cited by 52

Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa

Vallini, L., Marciani, G., Aneli, S., Bortolini, E., Benazzi, S., Pievani, T., & Pagani, L. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac045 · Cited by 48

Reconstruction of the personal information from human genome reads in gut metagenome sequencing data

Tomofuji, Y., Sonehara, K., Kishikawa, T., Maeda, Y., Ogawa, K., Kawabata, S., Nii, T., Okuno, T., Oguro-Igashira, E., Kinoshita, M., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01381-3 · Cited by 45

Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations

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A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition

Altınışık, N. E., Kazancı, D. D., Aydoğan, A., Gemici, H. C., Erdal, Ö. D., Sarıaltun, S., Vural, K. B., Koptekin, D., Gürün, K., Sağlıcan, E., et al. (2022) · Science Advances · doi:10.1126/sciadv.abo3609 · Cited by 47

Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean

Koptekin, D., Yüncü, E., Varela, R., Altınışık, N. E., Psonis, N., Kashuba, N., Yorulmaz, S., George, R., Kazancı, D. D., Kaptan, D., et al. (2022) · Current Biology · doi:10.1016/j.cub.2022.11.034 · Cited by 44

Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers

Liu, Y.-C., Hunter-Anderson, R. L., Cheronet, O., Eakin, J., Camacho, F. A., Pietrusewsky, M., Rohland, N., Ioannidis, A. G., Athens, J. S., Douglas, M. T., et al. (2022) · Science · doi:10.1126/science.abm6536 · Cited by 46

Phenome-wide analysis of Taiwan Biobank reveals novel glycemia-related loci and genetic risks for diabetes

Lee, C., Chen, T., Lim, A. M. W., Chang, C.-C., Sie, J. J., Chen, P., Chang, S., Wu, S.-J., Hsu, C., Hsieh, A., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-04168-0 · Cited by 44

Evolution of Homo in the Middle and Late Pleistocene

Harvati, K., & Reyes‐Centeno, H. (2022) · Journal of Human Evolution · doi:10.1016/j.jhevol.2022.103279 · Cited by 51

ManyDogs Project: A Big Team Science Approach to Investigating Canine Behavior and Cognition

ManyDogs Project, Alberghina, D., Bray, E. E., Buchsbaum, D., Byosiere, S., Espinosa, J., Gnanadesikan, G. E., Guran, C.-N. A., Hare, E., Horschler, D. J., et al. (2023) · Comparative Cognition & Behavior Reviews · doi:10.3819/ccbr.2023.180004 · Cited by 45

The Precision Toxicology initiative

The PrecisionTox Consortium (2023) · Toxicology Letters · doi:10.1016/j.toxlet.2023.05.004 · Cited by 47

Neural ADMIXTURE for rapid genomic clustering

Mantes, A. D., Montserrat, D. M., Bustamante, C. D., Giró-i-Nieto, X., & Ioannidis, A. G. (2023) · Nature Computational Science · doi:10.1038/s43588-023-00482-7 · Cited by 44

Forensic investigative genetic genealogy: expanding pedigree tracing and genetic inquiry in the genomic era

Wang, M., Chen, H., Luo, L., Huang, Y., Duan, S., Yuan, H., Tang, R., Liu, C., & He, G. (2024) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2024.06.016 · Cited by 44

An integrated personal and population-based Egyptian genome reference

Wohlers, I., Künstner, A., Munz, M., Olbrich, M. R., Fähnrich, A., Calonga‐Solís, V., Ma, C., Hirose, M., El-Mosallamy, S., Salama, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17964-1 · Cited by 47

Local adaptation and archaic introgression shape global diversity at human structural variant loci

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Applications of massively parallel sequencing in forensic genetics

Carratto, T. M. T., Moraes, V. M. S., Recalde, T. S. F., de Oliveira, M. L. G., & Mendes‐Junior, C. T. (2022) · Genetics and Molecular Biology · doi:10.1590/1678-4685-gmb-2022-0077 · Cited by 54

Lake-centred sedentary lifestyle of early Tibetan Plateau Indigenous populations at high elevation 4,400 years ago

Yang, X., Gao, Y., Wangdue, S., Ran, J., Wang, Q., Chen, S., Yang, J., Wang, T., Gu, Z., Zhang, Y., et al. (2024) · Nature Ecology & Evolution · doi:10.1038/s41559-024-02539-w · Cited by 44

Revisiting the demographic history of Central African populations from a genetic perspective

Breton, G., Fortes‐Lima, C., & Schlebusch, C. M. (2021) · Human Population Genetics and Genomics · doi:10.47248/hpgg2101010004 · Cited by 42

Architecture of the outbred brown fat proteome defines regulators of metabolic physiology

Xiao, H., Bozi, L. H. M., Sun, Y., Riley, C. L., Philip, V. M., Chen, M., Li, J., Zhang, T., Mills, E. L., Emont, M. P., et al. (2022) · Cell · doi:10.1016/j.cell.2022.10.003 · Cited by 46

Distinguished biological adaptation architecture aggravated population differentiation of Tibeto-Burman-speaking people

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Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals

Harris, D., Platt, A., Hansen, M. E. B., Fan, S., McQuillan, M. A., Nyambo, T., Mpoloka, S. W., Mokone, G. G., Belay, G., Fokunang, C., et al. (2023) · Current Biology · doi:10.1016/j.cub.2023.09.066 · Cited by 42

Deep history of cultural and linguistic evolution among Central African hunter-gatherers

Padilla‐Iglesias, C., Blanco-Portillo, J., Pricop, B., Ioannidis, A. G., Bickel, B., Manica, A., Vinicius, L., & Migliano, A. B. (2024) · Nature Human Behaviour · doi:10.1038/s41562-024-01891-y · Cited by 42

Multivariate statistical approach and machine learning for the evaluation of biogeographical ancestry inference in the forensic field

Alladio, E., Poggiali, B., Cosenza, G., & Pilli, E. (2022) · Scientific Reports · doi:10.1038/s41598-022-12903-0 · Cited by 39

Evolutionary History of Endogenous Human Herpesvirus 6 Reflects Human Migration out of Africa

Aswad, A., Aimola, G., Wight, D. J., Roychoudhury, P., Zimmermann, C., Hill, J. A., Laßner, D., Xie, H. J., Huang, M.-L. W., Parrish, N. F., et al. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa190 · Cited by 41

A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants

Choi, J., Kim, S., Kim, J., Son, H., Yoo, S., Kim, C.-U., Park, Y. J., Moon, S., Cha, B., Jeon, M. C., et al. (2023) · Science Advances · doi:10.1126/sciadv.adg6319 · Cited by 34

The GenoPred pipeline: a comprehensive and scalable pipeline for polygenic scoring

Pain, O., Al‐Chalabi, A., & Lewis, C. M. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae551 · Cited by 36

Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data

de la Puente, M., Ruiz-Ramírez, J., Ambroa-Conde, A., Xavier, C., Amigo, J., Cal, M. Á. C. D., Gómez‐Tato, A., Carracedo, Á., Parson, W., Phillips, C., et al. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.581041 · Cited by 38

Inferring archaic introgression from hominin genetic data

Gopalan, S., Atkinson, E. G., Buck, L. T., Weaver, T. D., & Henn, B. M. (2021) · Evolutionary Anthropology Issues News and Reviews · doi:10.1002/evan.21895 · Cited by 37

Whole-genome resequencing of Chinese pangolins reveals a population structure and provides insights into their conservation

Wang, Q., Lan, T., Li, H., Sahu, S. K., Shi, M., Zhu, Y., Han, L., Yang, S., Li, Q., Zhang, L., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03757-3 · Cited by 39

Pilot work of the 10K Chinese People Genomic Diversity Project along the Silk Road suggests a complex east-west admixture landscape and biological adaptations

He, G., Yao, H., Duan, S., Luo, L., Sun, Q., Tang, R., Chen, J., Wang, Z., Sun, Y., Li, X., et al. (2025) · Science China Life Sciences · doi:10.1007/s11427-024-2748-4 · Cited by 41

The proteome of the late Middle Pleistocene Harbin individual

Fu, Q., Bai, F., Rao, H., Chen, S., Ji, Y., Liu, A., Bennett, E. A., Liu, F., & Ji, Q. (2025) · Science · doi:10.1126/science.adu9677 · Cited by 40

The Genetics of Spondyloarthritis

Díaz‐Peña, R., Castro, P. G., Durán, J., Santiago, C., & Lucía, A. (2020) · Journal of Personalized Medicine · doi:10.3390/jpm10040151 · Cited by 38

Multi-Indel: A Microhaplotype Marker Can Be Typed Using Capillary Electrophoresis Platforms

Qu, S., Lv, M., Xue, J., Zhu, J., Wang, L., Jian, H., Liu, Y., Zhang, R., Zha, L., Liang, W., et al. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.567082 · Cited by 37

Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool

de la Puente, M., Ruiz-Ramírez, J., Ambroa-Conde, A., Xavier, C., Pardo‐Seco, J., Álvarez‐Dios, J. A., Freire-Aradas, A., Mosquera‐Miguel, A., Gross, T. E., Cheung, E. Y. Y., et al. (2021) · Genes · doi:10.3390/genes12081284 · Cited by 37

Interpreting Clinical Trials With Omega-3 Supplements in the Context of Ancestry and FADS Genetic Variation

Chilton, F. H., Manichaikul, A. W., Yang, C., O’Connor, T. D., Johnstone, L. M., Blomquist, S. A., Schembre, S. M., Sergeant, S., Zec, M. M., Tsai, M. Y., et al. (2022) · Frontiers in Nutrition · doi:10.3389/fnut.2021.808054 · Cited by 43

The Thousand Polish Genomes—A Database of Polish Variant Allele Frequencies

Kaja, E., Lejman, A., Sielski, D., Sypniewski, M., Gambin, T., Dawidziuk, M., Suchocki, T., Golik, P., Wojtaszewska, M. L., Mroczek, M., et al. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23094532 · Cited by 38

Fine-scale population structure and demographic history of British Pakistanis

Arciero, E., Dogra, S. A., Malawsky, D. S., Mezzavilla, M., Tsismentzoglou, T., Huang, Q. Q., Hunt, K. A., Mason, D., Sharif, S. M., van Heel, D. A., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27394-2 · Cited by 36

Plasma phospho-tau217 as a predictive biomarker for Alzheimer’s disease in a large south American cohort

Pandey, N., Yang, Z., Cieza, B., Reyes‐Dumeyer, D., Kang, M. S., Montesinos, R., Soto‐Añari, M., Custodio, N., Honig, L. S., & Tosto, G. (2025) · Alzheimer s Research & Therapy · doi:10.1186/s13195-024-01655-w · Cited by 39

50,000 years of evolutionary history of India: Impact on health and disease variation

Kerdoncuff, E., Skov, L., Patterson, N., Banerjee, J., Khobragade, P., Chakrabarti, S. S., Chakrawarty, A., Chatterjee, P., Dhar, M., Gupta, M., et al. (2025) · Cell · doi:10.1016/j.cell.2025.04.027 · Cited by 36

Shared paternal ancestry of Han, Tai‐Kadai ‐speaking, and Austronesian‐speaking populations as revealed by the high resolution phylogeny of O1a‐M119 and distribution of its sub‐lineages within China

Sun, J., Li, Y., Ma, P., Yan, S. L., Cheng, H., Fan, Z., Deng, X., Ru, K., Wang, C., Chen, G., et al. (2021) · American Journal of Physical Anthropology · doi:10.1002/ajpa.24240 · Cited by 34

Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression

Garg, P., Martin-Trujillo, A., Rodriguez, O. L., Gies, S. J., Hadelia, E., Jadhav, B., Jain, M., Paten, B., & Sharp, A. J. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.03.016 · Cited by 36

Human inbreeding has decreased in time through the Holocene

Ceballos, F. C., Gürün, K., Altınışık, N. E., Gemici, H. C., Karamurat, C., Koptekin, D., Vural, K. B., Mapelli, I., Sağlıcan, E., Sürer, E., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.06.027 · Cited by 41

Race and prostate cancer: genomic landscape

Gallo, C. A., Owiredu, J. N., Weinstein, I., Lewicki, P., Basourakos, S. P., Vince, R., Awamlh, B. A. H. A., Schumacher, F. R., Spratt, D. E., Barbieri, C. E., et al. (2022) · Nature Reviews Urology · doi:10.1038/s41585-022-00622-0 · Cited by 36

The Evolution of Human Social Behavior

Grinde, B. (2024) · Encyclopedia · doi:10.3390/encyclopedia4010029 · Cited by 36

The Propagation of Racial Disparities in Cardiovascular Genomics Research

Clarke, S. L., Assimes, T. L., & Tcheandjieu, C. (2021) · Circulation Genomic and Precision Medicine · doi:10.1161/circgen.121.003178 · Cited by 35

Epidemiological aspects of hereditary fructose intolerance: A database study

Pinheiro, F. C., Sperb‐Ludwig, F., & Schwartz, I. V. D. (2021) · Human Mutation · doi:10.1002/humu.24282 · Cited by 35

A Southeast Asian origin for present-day non-African human Y chromosomes

Hallast, P., Agdzhoyan, A., Balanovsky, O. P., Xue, Y., & Tyler‐Smith, C. (2020) · Human Genetics · doi:10.1007/s00439-020-02204-9 · Cited by 36

The evolution of human ritual behavior as a cooperative signaling platform

Lang, M., & Kundt, R. (2023) · Religion Brain & Behavior · doi:10.1080/2153599x.2023.2197977 · Cited by 42

Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary Statistics

Privé, F. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac348 · Cited by 33

A genealogical estimate of genetic relationships

Fan, C., Mancuso, N., & Chiang, C. W. K. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.03.016 · Cited by 33

Development and evaluations of the ancestry informative markers of the VISAGE Enhanced Tool for Appearance and Ancestry

Ruiz-Ramírez, J., de la Puente, M., Xavier, C., Ambroa-Conde, A., Álvarez-Dios, J., Freire-Aradas, A., Mosquera‐Miguel, A., Ralf, A., Amory, C., Katsara, M., et al. (2023) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2023.102853 · Cited by 33

The landscape of human SVA retrotransposons

Chu, C., Lin, E. W., Tran, A. V., Jin, H., Ho, N. I., Veit, A. D., Cortés‐Ciriano, I., Burns, K. H., Ting, D. T., & Park, P. J. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad821 · Cited by 33

The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal

Vallini, L., Zampieri, C., Shoaee, M. J., Bortolini, E., Marciani, G., Aneli, S., Pievani, T., Benazzi, S., Barausse, A., Mezzavilla, M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46161-7 · Cited by 41

Evolutionary history and biological adaptation of Han Chinese people on the Mongolian Plateau

Li, X., Wang, M., Su, H., Duan, S., Sun, Y., Chen, H., Wang, Z., Sun, Q., Yang, Q., Chen, J., et al. (2024) · hLife · doi:10.1016/j.hlife.2024.04.005 · Cited by 34

Population genomics of Central Asian peoples unveil ancient Trans-Eurasian genetic admixture and cultural exchanges

He, G., Wang, M., Luo, L., Sun, Q., Yuan, H., Lv, H., Feng, Y., Liu, X., Cheng, J., Bu, F., et al. (2024) · hLife · doi:10.1016/j.hlife.2024.06.006 · Cited by 34

Massively parallel sequencing of 165 ancestry-informative SNPs and forensic biogeographical ancestry inference in three southern Chinese Sinitic/Tai-Kadai populations

He, G., Liu, J., Wang, M., Zou, X., Ming, T., Zhu, S., Yeh, H., Wang, C., Wang, Z., & Hou, Y. (2021) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2021.102475 · Cited by 33

Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and mutation signatures

Coll Macià, M., Skov, L., Peter, B. M., & Schierup, M. H. (2021) · Nature Communications · doi:10.1038/s41467-021-25524-4 · Cited by 33

The population genetics characteristics of a 90 locus panel of microhaplotypes

PAKSTIS, A. J., Gandotra, N., Speed, W. C., Murtha, M. T., Scharfe, C., & Kídd, K. K. (2021) · Human Genetics · doi:10.1007/s00439-021-02382-0 · Cited by 33

Genomic Insights Into the Population History and Biological Adaptation of Southwestern Chinese Hmong–Mien People

Liu, Y., Xie, J., Wang, M., Liu, C., Zhu, J., Zou, X., Li, W., Wang, L., Leng, C., Xu, Q., et al. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2021.815160 · Cited by 32

Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture

Ahlquist, K. D., Bañuelos, M. M., Funk, A., Lai, J., Rong, S., Villanea, F. A., & Witt, K. E. (2021) · Genome Biology and Evolution · doi:10.1093/gbe/evab115 · Cited by 36

Climate shifts orchestrated hominin interbreeding events across Eurasia

Ruan, J., Timmermann, A., Raia, P., Yun, K., Zeller, E., Mondanaro, A., Febbraro, M. D., Lemmon, D., Castiglione, S., & Melchionna, M. (2023) · Science · doi:10.1126/science.add4459 · Cited by 32

Rye: genetic ancestry inference at biobank scale

Conley, A. B., Rishishwar, L., Ahmad, M., Sharma, S., Norris, E. T., Jordan, I. K., & Mariño‐Ramírez, L. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad149 · Cited by 29

Population-specific reference panels are crucial for genetic analyses: an example of the CREBRF locus in Native Hawaiians

Lin, M. H., Caberto, C., Wan, P. C., Li, Y., Lum‐Jones, A., Tiirikainen, M., Pooler, L., Nakamura, B. N., Sheng, X., Porcel, J., et al. (2020) · Human Molecular Genetics · doi:10.1093/hmg/ddaa083 · Cited by 32

Origin of ethnic groups, linguistic families, and civilizations in China viewed from the Y chromosome

Yu, X.-E., & Li, H. (2021) · Molecular Genetics and Genomics · doi:10.1007/s00438-021-01794-x · Cited by 31

Opportunities and challenges for the use of common controls in sequencing studies

Wojcik, G. L., Murphy, J. I., Edelson, J. L., Gignoux, C. R., Ioannidis, A. G., Manning, A. K., Rivas, M. A., Buyske, S. G., & Hendricks, A. E. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00487-4 · Cited by 32

Unexpected morphological diversity in ancient dogs compared to modern relatives

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Rare genetic variants explain missing heritability in smoking

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