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For: Lorente-Galdos B, Lao O, Serra-Vidal G, Santpere G, Kuderna LFK, Arauna LR, Fadhlaoui-Zid K, Pimenoff VN, Soodyall H, Zalloua P, Marques-Bonet T, Comas D. Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations. Genome Biol 2019;20:77. [PMID: 31023378 PMCID: PMC6485163 DOI: 10.1186/s13059-019-1684-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/28/2019] [Indexed: 12/30/2022]  Open
Number Cited by Other Article(s)
1
Tran LN, Sun CK, Struck TJ, Sajan M, Gutenkunst RN. Computationally Efficient Demographic History Inference from Allele Frequencies with Supervised Machine Learning. Mol Biol Evol 2024;41:msae077. [PMID: 38636507 PMCID: PMC11082913 DOI: 10.1093/molbev/msae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]  Open
2
Foley RA, Mirazón Lahr M. Ghosts of extinct apes: genomic insights into African hominid evolution. Trends Ecol Evol 2024;39:456-466. [PMID: 38302324 DOI: 10.1016/j.tree.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 02/03/2024]
3
Hünemeier T. Biogeographic Perspectives on Human Genetic Diversification. Mol Biol Evol 2024;41:msae029. [PMID: 38349332 PMCID: PMC10917211 DOI: 10.1093/molbev/msae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 03/08/2024]  Open
4
D'Atanasio E, Risi F, Ravasini F, Montinaro F, Hajiesmaeil M, Bonucci B, Pistacchia L, Amoako-Sakyi D, Bonito M, Onidi S, Colombo G, Semino O, Destro Bisol G, Anagnostou P, Metspalu M, Tambets K, Trombetta B, Cruciani F. The genomic echoes of the last Green Sahara on the Fulani and Sahelian people. Curr Biol 2023;33:5495-5504.e4. [PMID: 37995693 DOI: 10.1016/j.cub.2023.10.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/28/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023]
5
Bondzi-Simpson A, Ribeiro T, Coburn NG, Hallet J. Integrating equity frameworks into surgical quality improvement and health administrative databases: A narrative review. Am J Surg 2023:S0002-9610(23)00394-X. [PMID: 37640638 DOI: 10.1016/j.amjsurg.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/05/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023]
6
Choi J, Kim S, Kim J, Son HY, Yoo SK, Kim CU, Park YJ, Moon S, Cha B, Jeon MC, Park K, Yun JM, Cho B, Kim N, Kim C, Kwon NJ, Park YJ, Matsuda F, Momozawa Y, Kubo M, Kim HJ, Park JH, Seo JS, Kim JI, Im SW. A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants. SCIENCE ADVANCES 2023;9:eadg6319. [PMID: 37556544 PMCID: PMC10411914 DOI: 10.1126/sciadv.adg6319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/06/2023] [Indexed: 08/11/2023]
7
Ragsdale AP, Thornton KR. Multiple Sources of Uncertainty Confound Inference of Historical Human Generation Times. Mol Biol Evol 2023;40:msad160. [PMID: 37450583 PMCID: PMC10404577 DOI: 10.1093/molbev/msad160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]  Open
8
Nam CH, Youk J, Kim JY, Lim J, Park JW, Oh SA, Lee HJ, Park JW, Won H, Lee Y, Jeong SY, Lee DS, Oh JW, Han J, Lee J, Kwon HW, Kim MJ, Ju YS. Widespread somatic L1 retrotransposition in normal colorectal epithelium. Nature 2023;617:540-547. [PMID: 37165195 DOI: 10.1038/s41586-023-06046-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
9
Ragsdale AP, Weaver TD, Atkinson EG, Hoal EG, Möller M, Henn BM, Gravel S. A weakly structured stem for human origins in Africa. Nature 2023;617:755-763. [PMID: 37198480 PMCID: PMC10208968 DOI: 10.1038/s41586-023-06055-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/05/2023] [Indexed: 05/19/2023]
10
Fan S, Spence JP, Feng Y, Hansen MEB, Terhorst J, Beltrame MH, Ranciaro A, Hirbo J, Beggs W, Thomas N, Nyambo T, Mpoloka SW, Mokone GG, Njamnshi A, Folkunang C, Meskel DW, Belay G, Song YS, Tishkoff SA. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation. Cell 2023;186:923-939.e14. [PMID: 36868214 PMCID: PMC10568978 DOI: 10.1016/j.cell.2023.01.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 10/16/2022] [Accepted: 01/30/2023] [Indexed: 03/05/2023]
11
Brasil MF, Monson TA, Taylor CE, Yohler RM, Hlusko LJ. A Pleistocene assemblage of near-modern Papio hamadryas from the Middle Awash study area, Afar Rift, Ethiopia. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023;180:48-76. [PMID: 36790648 DOI: 10.1002/ajpa.24634] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/15/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022]
12
Vespasiani DM, Jacobs GS, Cook LE, Brucato N, Leavesley M, Kinipi C, Ricaut FX, Cox MP, Gallego Romero I. Denisovan introgression has shaped the immune system of present-day Papuans. PLoS Genet 2022;18:e1010470. [PMID: 36480515 PMCID: PMC9731433 DOI: 10.1371/journal.pgen.1010470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 10/10/2022] [Indexed: 12/13/2022]  Open
13
Reilly PF, Tjahjadi A, Miller SL, Akey JM, Tucci S. The contribution of Neanderthal introgression to modern human traits. Curr Biol 2022;32:R970-R983. [PMID: 36167050 PMCID: PMC9741939 DOI: 10.1016/j.cub.2022.08.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
14
Osman A, Jonasson J. Cross-ethnic analysis of common gene variants in hemostasis show lopsided representation of global populations in genetic databases. BMC Med Genomics 2022;15:69. [PMID: 35337356 PMCID: PMC8957123 DOI: 10.1186/s12920-022-01220-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/21/2022] [Indexed: 11/12/2022]  Open
15
Zhang C, Hansen MEB, Tishkoff SA. Advances in integrative African genomics. Trends Genet 2022;38:152-168. [PMID: 34740451 PMCID: PMC8752515 DOI: 10.1016/j.tig.2021.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022]
16
Montinaro F, Pankratov V, Yelmen B, Pagani L, Mondal M. Revisiting the out of Africa event with a deep-learning approach. Am J Hum Genet 2021;108:2037-2051. [PMID: 34626535 PMCID: PMC8595897 DOI: 10.1016/j.ajhg.2021.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]  Open
17
Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0. Nat Commun 2021;12:6232. [PMID: 34716342 PMCID: PMC8556419 DOI: 10.1038/s41467-021-26503-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/06/2021] [Indexed: 12/30/2022]  Open
18
A reference database of forensic autosomal and gonosomal STR markers in the Tigray population of Ethiopia. Forensic Sci Int Genet 2021;56:102618. [PMID: 34735940 DOI: 10.1016/j.fsigen.2021.102618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 11/20/2022]
19
Breton G, Johansson ACV, Sjödin P, Schlebusch CM, Jakobsson M. Comparison of sequencing data processing pipelines and application to underrepresented African human populations. BMC Bioinformatics 2021;22:488. [PMID: 34627144 PMCID: PMC8502359 DOI: 10.1186/s12859-021-04407-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/27/2021] [Indexed: 11/10/2022]  Open
20
Ahlquist KD, Bañuelos MM, Funk A, Lai J, Rong S, Villanea FA, Witt KE. Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture. Genome Biol Evol 2021;13:evab115. [PMID: 34028527 PMCID: PMC8480178 DOI: 10.1093/gbe/evab115] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/07/2021] [Accepted: 05/22/2021] [Indexed: 11/30/2022]  Open
21
Clemente F, Unterländer M, Dolgova O, Amorim CEG, Coroado-Santos F, Neuenschwander S, Ganiatsou E, Cruz Dávalos DI, Anchieri L, Michaud F, Winkelbach L, Blöcher J, Arizmendi Cárdenas YO, Sousa da Mota B, Kalliga E, Souleles A, Kontopoulos I, Karamitrou-Mentessidi G, Philaniotou O, Sampson A, Theodorou D, Tsipopoulou M, Akamatis I, Halstead P, Kotsakis K, Urem-Kotsou D, Panagiotopoulos D, Ziota C, Triantaphyllou S, Delaneau O, Jensen JD, Moreno-Mayar JV, Burger J, Sousa VC, Lao O, Malaspinas AS, Papageorgopoulou C. The genomic history of the Aegean palatial civilizations. Cell 2021;184:2565-2586.e21. [PMID: 33930288 PMCID: PMC8127963 DOI: 10.1016/j.cell.2021.03.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/17/2020] [Accepted: 03/18/2021] [Indexed: 12/30/2022]
22
Hollfelder N, Breton G, Sjödin P, Jakobsson M. The deep population history in Africa. Hum Mol Genet 2021;30:R2-R10. [PMID: 33438014 PMCID: PMC8117439 DOI: 10.1093/hmg/ddab005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 12/28/2022]  Open
23
Hamdi Y, Zass L, Othman H, Radouani F, Allali I, Hanachi M, Okeke CJ, Chaouch M, Tendwa MB, Samtal C, Mohamed Sallam R, Alsayed N, Turkson M, Ahmed S, Benkahla A, Romdhane L, Souiai O, Tastan Bishop Ö, Ghedira K, Mohamed Fadlelmola F, Mulder N, Kamal Kassim S. Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021;25:213-233. [PMID: 33794662 DOI: 10.1089/omi.2021.0004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
24
Deconvolving Human Evolutionary History: Using Network-Based Approaches to Better Understand Our Past. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11468-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]  Open
25
Pakendorf B, Stoneking M. The genomic prehistory of peoples speaking Khoisan languages. Hum Mol Genet 2020;30:R49-R55. [PMID: 33075813 PMCID: PMC8117426 DOI: 10.1093/hmg/ddaa221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/28/2020] [Accepted: 10/08/2020] [Indexed: 11/14/2022]  Open
26
Sanchez T, Cury J, Charpiat G, Jay F. Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation. Mol Ecol Resour 2020;21:2645-2660. [DOI: 10.1111/1755-0998.13224] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/19/2020] [Accepted: 07/02/2020] [Indexed: 12/28/2022]
27
Schroeder L. Revolutionary Fossils, Ancient Biomolecules, and Reflections in Ethics and Decolonization: Paleoanthropology in 2019. AMERICAN ANTHROPOLOGIST 2020. [DOI: 10.1111/aman.13410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
28
Sankararaman S. Methods for detecting introgressed archaic sequences. Curr Opin Genet Dev 2020;62:85-90. [PMID: 32717667 PMCID: PMC7484293 DOI: 10.1016/j.gde.2020.05.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/12/2020] [Accepted: 05/22/2020] [Indexed: 11/16/2022]
29
Esteller-Cucala P, Maceda I, Børglum AD, Demontis D, Faraone SV, Cormand B, Lao O. Genomic analysis of the natural history of attention-deficit/hyperactivity disorder using Neanderthal and ancient Homo sapiens samples. Sci Rep 2020;10:8622. [PMID: 32451437 PMCID: PMC7248073 DOI: 10.1038/s41598-020-65322-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/24/2020] [Indexed: 11/18/2022]  Open
30
Grün R, Pike A, McDermott F, Eggins S, Mortimer G, Aubert M, Kinsley L, Joannes-Boyau R, Rumsey M, Denys C, Brink J, Clark T, Stringer C. Dating the skull from Broken Hill, Zambia, and its position in human evolution. Nature 2020;580:372-375. [PMID: 32296179 DOI: 10.1038/s41586-020-2165-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/30/2020] [Indexed: 01/15/2023]
31
Genome-wide analyses disclose the distinctive HLA architecture and the pharmacogenetic landscape of the Somali population. Sci Rep 2020;10:5652. [PMID: 32221414 PMCID: PMC7101338 DOI: 10.1038/s41598-020-62645-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/17/2020] [Indexed: 12/16/2022]  Open
32
Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals. Cell 2020;180:677-687.e16. [PMID: 32004458 DOI: 10.1016/j.cell.2020.01.012] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/13/2019] [Accepted: 01/07/2020] [Indexed: 01/27/2023]
33
Gokcumen O. Archaic hominin introgression into modern human genomes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019;171 Suppl 70:60-73. [PMID: 31702050 DOI: 10.1002/ajpa.23951] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 01/01/2023]
34
Serra-Vidal G, Lucas-Sanchez M, Fadhlaoui-Zid K, Bekada A, Zalloua P, Comas D. Heterogeneity in Palaeolithic Population Continuity and Neolithic Expansion in North Africa. Curr Biol 2019;29:3953-3959.e4. [DOI: 10.1016/j.cub.2019.09.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 08/02/2019] [Accepted: 09/19/2019] [Indexed: 01/16/2023]
35
Houldcroft CJ, Rifkin RF, Underdown SJ. Human biology and ancient DNA: exploring disease, domestication and movement. Ann Hum Biol 2019;46:95-98. [DOI: 10.1080/03014460.2019.1629536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
36
Tucci S, Akey JM. The long walk to African genomics. Genome Biol 2019;20:130. [PMID: 31248437 PMCID: PMC6598360 DOI: 10.1186/s13059-019-1740-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
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