publications

2025

1. 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}
   }

2. Disease

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

   Hyeonsoo Jeong, Isabel Mendizabal, and Soojin V Yi

   GeroScience, 2025

   DOI
3. 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
4. Evolution

   Complete sequencing of ape genomes

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

   Nature, 2025

   DOI

2024

1. 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}
   }

2. 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

1. 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

1. 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}
   }

2. 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

1. 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}
   }

2. 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

1. 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}
   }

2. 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

1. 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}
   }

2. 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

1. 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}
   }

2. 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

1. 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}
   }

2. 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

1. 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}
   }