@article{jeong2026kidney,title={A cross-species single-cell kidney epigenome atlas reveals epithelial-dominant aging-like states in disease},author={Jeong, Hyeonsoo and Lake, Blue B. and Diep, Dinh and Li, Xuwen and Yan, Qi and Gisch, Debora L. and Kaushal, Madhurima and Reinert, Stephanie and Eadon, Michael T. and Gaut, Joseph P. and Jain, Sanjay and Zhang, Kun},journal={Nature Aging},year={2026},month=sep,day={24},doi={10.1038/s43587-026-01221-z},url={https://www.nature.com/articles/s43587-026-01221-z},publisher={Springer Nature}}
2025
PopGen
Structural polymorphism and diversity of human segmental duplications
Hyeonsoo Jeong*, Philip C Dishuck*, DongAhn Yoo*, William T Harvey 외 10명
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
@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 외 8명
@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 외 4명
@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 외 9명
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 외 4명
@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 외 2명
@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 외 2명
@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 외 9명
@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 외 1명
@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 외 6명
@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
@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
@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 외 8명
@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 외 5명
@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 외 7명
@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}}