Publications

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Journal Articles

The trajectory of KoRV-A evolution suggests initial integration into the koala germline genome near Coffs Harbour in New South Wales

Published in Genome Biology, 2026

KoRV-A is the youngest transposon in mammals as we know. In this paper, we reconstructed the evolutionary trajectory of this newly invaded ERV transposon after its endogenization.

Recommended citation: Yu et al. "The trajectory of KoRV-A evolution suggests initial integration into the koala germline genome near Coffs Harbour in New South Wales." Genome Biology (Accepted)
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Single-cell transcriptomic and genomic changes in the aging human brain

Published in Nature, 2025

Brain aging is a dynamic process. In this paper, we integrated single-nucleus RNA-seq, single-cell WGS, and spatial transcriptomics, and elucidated genomic and transcriptomic changes of human brain aging.

Recommended citation: Jeffries & Yu et al. "Single-cell transcriptomic and genomic changes in the aging human brain." Nature (2025)
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Evolution of KoRV-A transcriptional silencing in wild koalas

Published in Cell, 2025

KoRV-A is invading the koala germline. As a follow-up of our 2019 paper, this paper described the evolution of an “adaptive” sequence-specific genome immune response to supress endogenous retrovirus transcriptionally.

Recommended citation: Yu et al. "Evolution of KoRV-A transcriptional silencing in wild koalas." Cell 188.8 (2025): 2081-2093.
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Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster

Published in Nucleic Acid Research, 2023

Transposons are the major source of insertional structural variation, but their integration site is not randomly selected. This paper studied the preference of LTR, LINE, and DNA transposon integration site selection, reflecting their underlying replication mechanisms.

Recommended citation: Cao & Yu et al. "Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster." Nucleic Acids Research 51.5 (2023): 2066-2086.
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A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies

Published in Nucleic Acid Research, 2021

Transposon activity is closely related to diseases and can drive evolution. This paper presents a bioinformatics tool TEMP2 for the detection of germline and de novo transposon insertions using short-read whole genome sequencing data.

Recommended citation: Yu et al. "A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies." Nucleic acids research 49.8 (2021): e44-e44.
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Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes

Published in Nature Communications, 2021

In mammals, pachytene piRNA genes produce 24-32nt long piRNAs that are essential for fertility. This paper identified a unique pattern (long and unspliced transcripts) of pachytene piRNA genes distinguished their fate from protein-coding genes.

Recommended citation: Yu & Fan et al. "Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes." Nature communications 12.1 (2021): 73.
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The piRNA response to retroviral invasion of the koala genome

Published in Cell, 2019

KoRV-A is invading the koala germline. This paper illustrated an “innante” genome immune response to specifically supress unspliced retroviral isoform expression.

Recommended citation: Yu & Koppetsch et al. "The piRNA response to retroviral invasion of the koala genome." Cell 179.3 (2019): 632-643.
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Tianxiong (Bear) Yu