Publications | Jeong Lab

Preprints

A cross-species single-cell epigenome kidney atlas identifies epithelial cells as a driver of epigenetic aging

Hyeonsoo Jeong, Blue B Lake, Dinh Diep, Xuwen Li, and 7 more authors

bioRxiv, Jan 2026

Nature Aging, accepted

@article{jeong2026kidney,
  title = {A cross-species single-cell epigenome kidney atlas identifies epithelial cells as a driver of epigenetic aging},
  author = {Jeong, Hyeonsoo and Lake, Blue B and Diep, Dinh and Li, Xuwen and Yan, Qi and Gisch, Debora L and Reinert, Stephanie and Eadon, Michael T and Gaut, Joseph P and Jain, Sanjay and Zhang, Kun},
  journal = {bioRxiv},
  year = {2026},
  month = jan,
  doi = {10.64898/2026.01.22.700871},
  url = {https://www.biorxiv.org/content/10.64898/2026.01.22.700871v1},
  publisher = {Cold Spring Harbor Laboratory}
}

Peer-reviewed Publications

2025

PopGen
Structural polymorphism and diversity of human segmental duplications

Hyeonsoo Jeong^*, Philip C Dishuck^*, DongAhn Yoo^*, William T Harvey, and 10 more authors

Nature genetics, 2025

Abs DOI Bib

Segmental duplications (SDs) contribute significantly to human disease, evolution and diversity but have been difficult to resolve at the sequence level. We present a population genetics survey of SDs by analyzing 170 human genome assemblies (from 85 samples representing 38 Africans and 47 non-Africans) in which the majority of autosomal SDs are fully resolved using long-read sequence assembly. Excluding the acrocentric short arms and sex chromosomes, we identify 173.2 Mb of duplicated sequence (47.4 Mb not present in the telomere-to-telomere reference) distinguishing fixed from structurally polymorphic events. We find that intrachromosomal SDs are among the most variable, with rare events mapping near their progenitor sequences. African genomes harbor significantly more intrachromosomal SDs and are more likely to have recently duplicated gene families with higher copy numbers than non-African samples. Comparison to a resource of 563 million full-length isoform sequencing reads identifies 201 novel, potentially protein-coding genes corresponding to these copy number polymorphic SDs.
@article{jeong2025structural, title = {Structural polymorphism and diversity of human segmental duplications}, author = {Jeong, Hyeonsoo and Dishuck, Philip C and Yoo, DongAhn and Harvey, William T and Munson, Katherine M and Lewis, Alexandra P and Kordosky, Jennifer and Garcia, Gage H and (HGSVC), Human Genome Structural Variation Consortium and Yilmaz, Feyza and Hallast, Pille and Lee, Charles and Pastinen, Tomi and Eichler, Evan E.}, journal = {Nature genetics}, volume = {57}, number = {2}, pages = {390--401}, year = {2025}, dimensions = {true}, doi = {10.1038/s41588-024-02051-8}, pubmed = {39779957}, publisher = {Nature Publishing Group US New York} }
Disease

Human brain aging is associated with dysregulation of cell type epigenetic identity

Hyeonsoo Jeong, Isabel Mendizabal, and Soojin V Yi

GeroScience, 2025

DOI
PopGen

Human de novo mutation rates from a four-generation pedigree reference

David Porubsky, Harriet Dashnow, Thomas A Sasani, Glennis A Logsdon, and 8 more authors

Nature, 2025
Evolution

Complete sequencing of ape genomes

DongAhn Yoo, Arang Rhie, Prajna Hebbar, Francesca Antonacci, and 8 more authors

Nature, 2025

DOI

2024

Evolution

The complete sequence and comparative analysis of ape sex chromosomes

Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, and 8 more authors

Nature, 2024

DOI Bib

@article{makova2024complete,
  title = {The complete sequence and comparative analysis of ape sex chromosomes},
  author = {Makova, Kateryna D and Pickett, Brandon D and Harris, Robert S and Hartley, Gabrielle A and Cechova, Monika and Pal, Karol and Nurk, Sergey and Yoo, DongAhn and Li, Qiuhui and Hebbar, Prajna and Jeong, Hyeonsoo and others},
  journal = {Nature},
  volume = {630},
  number = {8016},
  pages = {401--411},
  year = {2024},
  dimensions = {true},
  doi = {10.1038/s41586-024-07473-2},
  publisher = {Nature Publishing Group UK London}
}

Evolution

Structurally divergent and recurrently mutated regions of primate genomes

Yafei Mao, William T Harvey, David Porubsky, Katherine M Munson, and 8 more authors

Cell, 2024

DOI Bib

@article{mao2024structurally,
  title = {Structurally divergent and recurrently mutated regions of primate genomes},
  author = {Mao, Yafei and Harvey, William T and Porubsky, David and Munson, Katherine M and Hoekzema, Kendra and Lewis, Alexandra P and Audano, Peter A and Rozanski, Allison and Yang, Xiangyu and Zhang, Shilong and Jeong, Hyeonsoo and others},
  journal = {Cell},
  volume = {187},
  number = {6},
  pages = {1547--1562},
  year = {2024},
  dimensions = {true},
  doi = {10.1016/j.cell.2024.01.052},
  publisher = {Elsevier}
}

2022

PopGen

Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows

Hyeonsoo Jeong^*, Nicole M Baran^*, Dan Sun, Paramita Chatterjee, and 4 more authors

Elife, 2022

DOI Bib

@article{jeong2022dynamic,
  title = {Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows},
  author = {Jeong, Hyeonsoo and Baran, Nicole M and Sun, Dan and Chatterjee, Paramita and Layman, Thomas S and Balakrishnan, Christopher N and Maney, Donna L and Yi, Soojin V},
  journal = {Elife},
  volume = {11},
  pages = {e79387},
  year = {2022},
  dimensions = {true},
  doi = {10.7554/elife.79387},
  publisher = {eLife Sciences Publications Limited}
}

2021

Evolution
Evolution of DNA methylation in the human brain

Hyeonsoo Jeong^*, Isabel Mendizabal^*, Stefano Berto, Paramita Chatterjee, and 9 more authors

Nature communications, 2021

Abs DOI Bib

DNA methylation is a critical regulatory mechanism implicated in development, learning, memory, and disease in the human brain. Here we have elucidated DNA methylation changes during recent human brain evolution. We demonstrate dynamic evolutionary trajectories of DNA methylation in cell-type and cytosine-context specific manner. Specifically, DNA methylation in non-CG context, namely CH methylation, has increased (hypermethylation) in neuronal gene bodies during human brain evolution, contributing to human-specific down-regulation of genes and co-expression modules. The effects of CH hypermethylation is particularly pronounced in early development and neuronal subtypes. In contrast, DNA methylation in CG context shows pronounced reduction (hypomethylation) in human brains, notably in cis-regulatory regions, leading to upregulation of downstream genes. We show that the majority of differential CG methylation between neurons and oligodendrocytes originated before the divergence of hominoids and catarrhine monkeys, and harbors strong signal for genetic risk for schizophrenia. Remarkably, a substantial portion of differential CG methylation between neurons and oligodendrocytes emerged in the human lineage since the divergence from the chimpanzee lineage and carries significant genetic risk for schizophrenia. Therefore, recent epigenetic evolution of human cortex has shaped the cellular regulatory landscape and contributed to the increased vulnerability to neuropsychiatric diseases.
@article{jeong2021evolution, title = {Evolution of DNA methylation in the human brain}, author = {Jeong, Hyeonsoo and Mendizabal, Isabel and Berto, Stefano and Chatterjee, Paramita and Layman, Thomas and Usui, Noriyoshi and Toriumi, Kazuya and Douglas, Connor and Singh, Devika and Huh, Iksoo and Preuss, Todd M. and Konopka, Genevieve and Yi, Soojin V.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2021}, year = {2021}, doi = {10.1038/s41467-021-21917-7}, url = {https://www.nature.com/articles/s41467-021-21917-7}, dimensions = {true}, publisher = {Nature Publishing Group UK London} }

Epigenomics

Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows

Dan Sun, Thomas S Layman, Hyeonsoo Jeong, Paramita Chatterjee, and 4 more authors

Molecular Ecology, 2021

DOI Bib

@article{sun2021genome,
  title = {Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows},
  author = {Sun, Dan and Layman, Thomas S and Jeong, Hyeonsoo and Chatterjee, Paramita and Grogan, Kathleen and Merritt, Jennifer R and Maney, Donna L and Yi, Soojin V},
  journal = {Molecular Ecology},
  volume = {30},
  number = {14},
  pages = {3453--3467},
  year = {2021},
  dimensions = {true},
  doi = {10.1111/mec.15793},
  publisher = {Wiley Online Library}
}

2020

Epigenomics

Lineage and parent-of-origin effects in DNA methylation of honey bees (Apis mellifera) revealed by reciprocal crosses and whole-genome bisulfite sequencing

Xin Wu, David A Galbraith, Paramita Chatterjee, Hyeonsoo Jeong, and 2 more authors

Genome Biology and Evolution, 2020

DOI Bib

@article{wu2020lineage,
  title = {Lineage and parent-of-origin effects in DNA methylation of honey bees (Apis mellifera) revealed by reciprocal crosses and whole-genome bisulfite sequencing},
  author = {Wu, Xin and Galbraith, David A and Chatterjee, Paramita and Jeong, Hyeonsoo and Grozinger, Christina M and Yi, Soojin V},
  journal = {Genome Biology and Evolution},
  volume = {12},
  number = {8},
  pages = {1482--1492},
  year = {2020},
  dimensions = {true},
  doi = {10.1093/gbe/evaa133},
  publisher = {Oxford University Press}
}

Evolution

Bacterial origin and reductive evolution of the CPR group

Rijja Hussain Bokhari, Nooreen Amirjan, Hyeonsoo Jeong, Kyung Mo Kim, and 2 more authors

Genome biology and evolution, 2020

DOI Bib

@article{bokhari2020bacterial,
  title = {Bacterial origin and reductive evolution of the CPR group},
  author = {Bokhari, Rijja Hussain and Amirjan, Nooreen and Jeong, Hyeonsoo and Kim, Kyung Mo and Caetano-Anoll{\'e}s, Gustavo and Nasir, Arshan},
  journal = {Genome biology and evolution},
  volume = {12},
  number = {3},
  pages = {103--121},
  year = {2020},
  dimensions = {true},
  doi = {10.1093/gbe/evaa024},
  publisher = {Oxford University Press}
}

2019

Epigenomics

Cell type-specific epigenetic links to schizophrenia risk in the brain

Isabel Mendizabal, Stefano Berto, Noriyoshi Usui, Kazuya Toriumi, and 9 more authors

Genome biology, 2019

DOI Bib

@article{mendizabal2019cell,
  title = {Cell type-specific epigenetic links to schizophrenia risk in the brain},
  author = {Mendizabal, Isabel and Berto, Stefano and Usui, Noriyoshi and Toriumi, Kazuya and Chatterjee, Paramita and Douglas, Connor and Huh, Iksoo and Jeong, Hyeonsoo and Layman, Thomas and Tamminga, Carol A and Preuss, Todd M. and Konopka, Genevieve and Yi, Soojin V.},
  journal = {Genome biology},
  volume = {20},
  number = {1},
  pages = {135},
  year = {2019},
  dimensions = {true},
  doi = {10.1186/s13059-019-1747-7},
  publisher = {Springer}
}

Evolution

Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation

Hyeonsoo Jeong, Bushra Arif, Gustavo Caetano-Anollés, Kyung Mo Kim, and 1 more author

Scientific reports, 2019

DOI Bib

@article{jeong2019horizontal,
  title = {Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation},
  author = {Jeong, Hyeonsoo and Arif, Bushra and Caetano-Anoll{\'e}s, Gustavo and Kim, Kyung Mo and Nasir, Arshan},
  journal = {Scientific reports},
  volume = {9},
  number = {1},
  pages = {5953},
  year = {2019},
  dimensions = {true},
  doi = {10.1038/s41598-019-42227-5},
  publisher = {Nature Publishing Group UK London}
}

2018

Disease

Gene network dysregulation in the trigeminal ganglia and nucleus accumbens of a model of chronic migraine-associated hyperalgesia

Hyeonsoo Jeong, Laura S Moye, Bruce R Southey, Alvaro G Hernandez, and 6 more authors

Frontiers in Systems Neuroscience, 2018

DOI Bib

@article{jeong2018gene,
  title = {Gene network dysregulation in the trigeminal ganglia and nucleus accumbens of a model of chronic migraine-associated hyperalgesia},
  author = {Jeong, Hyeonsoo and Moye, Laura S and Southey, Bruce R and Hernandez, Alvaro G and Dripps, Isaac and Romanova, Elena V and Rubakhin, Stanislav S and Sweedler, Jonathan V and Pradhan, Amynah A and Rodriguez-Zas, Sandra L},
  journal = {Frontiers in Systems Neuroscience},
  volume = {12},
  pages = {63},
  year = {2018},
  dimensions = {true},
  doi = {10.3389/fnsys.2018.00063},
  publisher = {Frontiers Media SA}
}

Method

Genomic landscape of methylation islands in hymenopteran insects

Hyeonsoo Jeong, Xin Wu, Brandon Smith, and Soojin V Yi

Genome biology and evolution, 2018

DOI Bib

@article{jeong2018genomic,
  title = {Genomic landscape of methylation islands in hymenopteran insects},
  author = {Jeong, Hyeonsoo and Wu, Xin and Smith, Brandon and Yi, Soojin V},
  journal = {Genome biology and evolution},
  volume = {10},
  number = {10},
  pages = {2766--2776},
  year = {2018},
  dimensions = {true},
  doi = {10.1093/gbe/evy203},
  publisher = {Oxford University Press}
}

2017

Evolution

A preliminary list of horizontally transferred genes in prokaryotes determined by tree reconstruction and reconciliation

Hyeonsoo Jeong and Arshan Nasir

Frontiers in genetics, 2017

DOI Bib

@article{jeong2017preliminary,
  title = {A preliminary list of horizontally transferred genes in prokaryotes determined by tree reconstruction and reconciliation},
  author = {Jeong, Hyeonsoo and Nasir, Arshan},
  journal = {Frontiers in genetics},
  volume = {8},
  pages = {112},
  year = {2017},
  dimensions = {true},
  doi = {10.3389/fgene.2017.00112},
  publisher = {Frontiers Media SA}
}

PopGen

The genome landscape of indigenous African cattle

Jaemin Kim, Olivier Hanotte, Okeyo Ally Mwai, Tadelle Dessie, and 8 more authors

Genome biology, 2017

DOI

2016

Evolution

Whole genome sequencing of Gyeongbuk Araucana, a newly developed blue-egg laying chicken breed, reveals its origin and genetic characteristics

Hyeonsoo Jeong, Kwondo Kim, Kelsey Caetano-Anollés, Heebal Kim, and 5 more authors

Scientific reports, 2016

DOI Bib

@article{jeong2016whole,
  title = {Whole genome sequencing of Gyeongbuk Araucana, a newly developed blue-egg laying chicken breed, reveals its origin and genetic characteristics},
  author = {Jeong, Hyeonsoo and Kim, Kwondo and Caetano-Anoll{\'e}s, Kelsey and Kim, Heebal and Kim, Byung-ki and Yi, Jun-Koo and Ha, Jae-Jung and Cho, Seoae and Oh, Dong Yep},
  journal = {Scientific reports},
  volume = {6},
  number = {1},
  pages = {26484},
  year = {2016},
  dimensions = {true},
  doi = {10.1038/srep26484},
  publisher = {Nature Publishing Group UK London}
}

Evolution

HGTree: database of horizontally transferred genes determined by tree reconciliation

Hyeonsoo Jeong, Samsun Sung, Taehyung Kwon, Minseok Seo, and 5 more authors

Nucleic acids research, 2016

DOI Bib

@article{jeong2016hgtree,
  title = {HGTree: database of horizontally transferred genes determined by tree reconciliation},
  author = {Jeong, Hyeonsoo and Sung, Samsun and Kwon, Taehyung and Seo, Minseok and Caetano-Anoll{\'e}s, Kelsey and Choi, Sang Ho and Cho, Seoae and Nasir, Arshan and Kim, Heebal},
  journal = {Nucleic acids research},
  volume = {44},
  number = {D1},
  pages = {D610--D619},
  year = {2016},
  dimensions = {true},
  doi = {10.1093/nar/gkv1245},
  publisher = {Oxford University Press}
}

2015

Evolution

Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing

Hyeonsoo Jeong, Ki-Duk Song, Minseok Seo, Kelsey Caetano-Anollés, and 7 more authors

BMC genetics, 2015

DOI Bib

@article{jeong2015exploring,
  title = {Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing},
  author = {Jeong, Hyeonsoo and Song, Ki-Duk and Seo, Minseok and Caetano-Anoll{\'e}s, Kelsey and Kim, Jaemin and Kwak, Woori and Oh, Jae-don and Kim, EuiSoo and Jeong, Dong Kee and Cho, Seoae and others},
  journal = {BMC genetics},
  volume = {16},
  number = {1},
  pages = {104},
  year = {2015},
  dimensions = {true},
  doi = {10.1186/s12863-015-0265-1},
  publisher = {Springer}
}