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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
..., characterizing ancestry as a set of discrete, predefined labels can be limiting, as individuals are at some level all admixed, stemming from ancestors belonging to multiple ancestral population groups (Supplemental Methods S1). For instance, the s of numerous African-Americans have variable proportions...
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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...in the non-African population for each position (gray line). (C) Reference-free methods do not rely on an archaic reference to infer introgressed segments. Instead, they use a control panel with negligible introgressed ancestry (e.g., Africans) and a target panel hypothesized to have received introgression...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...knowledge about the population for which ancestry inference is required (Supplemental Methods; Supplemental Fig. S14). Although some methods (Zhang et al. 2008; Chen et al. 2013; Bansal and Libiger 2015), such as SNPweights and iAdmix, can estimate ancestry without determining an optimal K value by relying...
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Method: Inferring ancestry with the hierarchical soft clustering approach tangleGen
- Klara Elisabeth Burger,
- Solveig Klepper,
- Ulrike von Luxburg,
- and Franz Baumdicker
Genome Res. December 2024 34: 2244-2255; Published in Advance October 21, 2024, doi:10.1101/gr.279399.124
...significantly improved our ability to infer ancestries. However, these methods typically work with a fixed number of independent ancestral populations. As a result, they provide insight into genetic admixture, but do not include a hierarchical interpretation. In particular, the intricate ancestral population...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...inference without requiring phased data or a prior window size definition (Guan 2014). ELAI can also infer an unsampled reference population based on allele frequencies of the admixed population (Seixas et al. 2018). Given the absence of a true Iberian wolf reference population, we ran ELAI considering...
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Research: Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations
- Juan L. Rodriguez-Flores,
- Khalid Fakhro,
- Francisco Agosto-Perez,
- Monica D. Ramstetter,
- Leonardo Arbiza,
- Thomas L. Vincent,
- Amal Robay,
- Joel A. Malek,
- Karsten Suhre,
- Lotfi Chouchane,
- Ramin Badii,
- Ajayeb Al-Nabet Al-Marri,
- Charbel Abi Khalil,
- Mahmoud Zirie,
- Amin Jayyousi,
- Jacqueline Salit,
- Alon Keinan,
- Andrew G. Clark,
- Ronald G. Crystal,
- and Jason G. Mezey
Genome Res. February 2016 26: 151-162; Published in Advance January 4, 2016, doi:10.1101/gr.191478.115
...population structure, which have inferred that the Q1 (Bedouin) s have the greatest proportion of Arab genetic ancestry, even when compared to Bedouins from outside Qatar and to Arabs in surrounding countries, including Yemen and Saudi Arabia (Hodgson et al. 2014; Shriner et al. 2014). To confirm a similarly...
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Method: An efficient method to identify, date, and describe admixture events using haplotype information
- Pongsakorn Wangkumhang,
- Matthew Greenfield,
- and Garrett Hellenthal
Genome Res. August 2022 32: 1553-1564; Published in Advance July 6, 2022, doi:10.1101/gr.275994.121
...that Equation 3 is monotonically increasing with g, whereas Equation 4 is monotonically decreasing with g. As the true admixing sources A and B are unknown, we instead consider the probability that two segments separated by distance g are inferred to share most recent ancestry with reference populations U and V...
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RECOMB Special/Methods: Panel construction for mapping in admixed populations via expected mutual information
- Sivan Bercovici,
- Dan Geiger,
- Liran Shlush,
- Karl Skorecki,
- and Alan Templeton
Genome Res. April 2008 18: 661-667; Published in Advance March 18, 2008, doi:10.1101/gr.073148.107
...for the identification of genomic regions harboring disease susceptibility genes in recently admixed populations. We develop an information-theory-based measure, called expected mutual information (EMI), which computes the impact of a set of markers on the ability to infer ancestry at each chromosomal location. We...
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Resource: A harmonized public resource of deeply sequenced diverse human genomes
- Zan Koenig,
- Mary T. Yohannes,
- Lethukuthula L. Nkambule,
- Xuefang Zhao,
- Julia K. Goodrich,
- Heesu Ally Kim,
- Michael W. Wilson,
- Grace Tiao,
- Stephanie P. Hao,
- Nareh Sahakian,
- Katherine R. Chao,
- Mark A. Walker,
- Yunfei Lyu,
- gnomAD Project Consortium,
- Heidi L. Rehm,
- Benjamin M. Neale,
- Michael E. Talkowski,
- Mark J. Daly,
- Harrison Brand,
- Konrad J. Karczewski,
- Elizabeth G. Atkinson,
- and Alicia R. Martin
Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
..., and genotype QC (Chen et al. 2024), including ancestry outlier removal (Methods) (Supplemental Table S2), we identified 153,894,851 high-quality variants across 4094 individuals, 3400 of whom are inferred to be unrelated (Methods) (Supplemental Table S3). We computed the mean coverage within each population...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...to African, and three individuals similar to admixed populations from The 1000 Genomes Project (Fig. 1A; Supplemental Fig. 1; Supplemental Table 1; The 1000 Genomes Project Consortium 2015). We generated an average of 85 million high-quality aligned ATAC-seq read pairs per individual (Supplemental Tables 2...

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