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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
...are needed in order to properly capture the genetic composition of populations. Here, we explore deep learning techniques, namely, variational autoencoders (VAEs), to process genomic data from a population perspective. We show the power of VAEs for a variety of tasks relating to the interpretation...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...drive rare variant discovery and assess the geographic distribution of canine diversity, which identifies Asia as a major source of missing variation. Finally, we review recent comparative genomic analyses that will facilitate annotation of the noncoding in dogs.The domestic dog has increasingly been...
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Research: Copy number variation underlies complex phenotypes in domestic dog breeds and other canids
- Aitor Serres-Armero,
- Brian W. Davis,
- Inna S. Povolotskaya,
- Carlos Morcillo-Suarez,
- Jocelyn Plassais,
- David Juan,
- Elaine A. Ostrander,
- and Tomas Marques-Bonet
Genome Res. May 2021 31: 762-774; Published in Advance April 16, 2021, doi:10.1101/gr.266049.120
....marques@upf.eduAbstractExtreme phenotypic diversity, a history of artificial selection, and socioeconomic value make domestic dog breeds a compelling subject for genomic research. Copy number variation (CNV) is known to account for a significant part of inter-individual genomic diversity in other systems. However, a comprehensive -wide...
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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
...to human-dominated landscapes.To test the “introgression fueled adaptation” hypothesis, we conducted a comprehensive genomic analysis of 48 historical (1912–2005) and 97 contemporary samples of Iberian wolves, alongside 67 worldwide wolves and 131 dogs (Fig. 1A,B; Supplemental Table S1). We used these data...
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Research: A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids
- Bridgett M. vonHoldt,
- John P. Pollinger,
- Dent A. Earl,
- James C. Knowles,
- Adam R. Boyko,
- Heidi Parker,
- Eli Geffen,
- Malgorzata Pilot,
- Wlodzimierz Jedrzejewski,
- Bogumila Jedrzejewska,
- Vadim Sidorovich,
- Claudia Greco,
- Ettore Randi,
- Marco Musiani,
- Roland Kays,
- Carlos D. Bustamante,
- Elaine A. Ostrander,
- John Novembre,
- and Robert K. Wayne
Genome Res. August 2011 21: 1294-1305; Published in Advance May 12, 2011, doi:10.1101/gr.116301.110
...inference. To better resolve population structure and admixture within wolf-like canids, we assayed 48,036 SNPs in a panel of 208 gray wolves (C. lupus) representing their worldwide distribution (Eurasia and North America), 57 coyotes and 12 red wolves (Fig. 2; Supplemental Table S2). To our knowledge...
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Research: Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells
- Tate Tunstall,
- Richard Kock,
- Jiri Vahala,
- Mark Diekhans,
- Ian Fiddes,
- Joel Armstrong,
- Benedict Paten,
- Oliver A. Ryder,
- and Cynthia C. Steiner
Genome Res. June 2018 28: 780-788; Published in Advance May 24, 2018, doi:10.1101/gr.227603.117
...populations (Tsplit) are shown. Genomics of the northern white rhinoceros Genome Research 783 www..org on the method used (Zhou and Teo 2015); therefore, the variation in divergent estimates may be due to the fact that ∂a∂i infers split time from a population’s allele frequency spectrum, while PSMC makes...
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Research: Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia
- Xiao Gou,
- Zhen Wang,
- Ning Li,
- Feng Qiu,
- Ze Xu,
- Dawei Yan,
- Shuli Yang,
- Jia Jia,
- Xiaoyan Kong,
- Zehui Wei,
- Shaoxiong Lu,
- Linsheng Lian,
- Changxin Wu,
- Xueyan Wang,
- Guozhi Li,
- Teng Ma,
- Qiang Jiang,
- Xue Zhao,
- Jiaqiang Yang,
- Baohong Liu,
- Dongkai Wei,
- Hong Li,
- Jianfa Yang,
- Yulin Yan,
- Guiying Zhao,
- Xinxing Dong,
- Mingli Li,
- Weidong Deng,
- Jing Leng,
- Chaochun Wei,
- Chuan Wang,
- Huaming Mao,
- Hao Zhang,
- Guohui Ding,
- and Yixue Li
Genome Res. August 2014 24: 1308-1315; Published in Advance April 10, 2014, doi:10.1101/gr.171876.113
...have a close but different genetic background with other indigenous dogs living at high altitude (Fig. 1), though their origin and relationship with plateau wolves need further studies. We also found the existence of admixture among TM and indigenous dogs (Fig. 1), which raised the demands for genetic...

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