Author

Chongyi Chen

National Institutes of HealthORCID 0000-0002-0504-5369Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Research Focus:gene regulatory network inference· 4 Organism:human· 4 Research Focus:differential expression· 3 Assay:DNA methylation· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Shuai LiiD· 2 shared Abdelmonsif Ahmed· 1 shared Charan VemuriiD· 1 shared Ipsita Biswas· 1 shared Jun LyuiD· 1 shared Jun LyuiD· 1 shared Linying Zhu· 1 shared Qian Yao· 1 shared

Activity by Year

2024-2026 · peak 3/yr

Co-Author Collaboration Network

9 top collaborators · 10 mutual co-author links

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2 shared papersGenomics

Shuai LiORCID

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4 papers

Recent·Most cited

Topoisomerase-mediated resolution of negative DNA supercoiling sustains human transcription and gene activation

Jun Lyu, Abdelmonsif Ahmed, Ipsita Biswas, Shuai Li, Chongyi Chen

This study shows that topoisomerase-mediated resolution of negative DNA supercoiling is essential for productive transcription and gene activation in human cells.

bioRxiv · Oct 2, 2026 · PreprintGenomics

Genome-wide DNA supercoiling arises from transcription and SMC activity and mediates transcriptional negative feedback

Linying Zhu, Qian Yao, Charan Vemuri, Chongyi Chen

The paper shows that genome-wide DNA supercoiling in human cells results from transcription and SMC complexes, and mediates transcriptional negative feedback.

bioRxiv · Oct 2, 2026 · PreprintMolecular Biology

Genome-wide mapping of endogenous topoisomerase cleavage complexes reveals TOP1 at the interface of DNA topological regulation and genome instability

Shuai Li, Chongyi Chen

This study introduces pDAIP-seq, a method to map endogenous topoisomerase cleavage complexes, revealing their genomic distribution and role in DNA breaks and genome instability.

bioRxiv · Oct 2, 2026 · PreprintGenomics

A convenient single-cell newly synthesized transcriptome assay reveals FLI1 downregulation during T-cell activation

Jun Lyu, Xiaoyan Xu, Chongyi Chen

The paper introduces NOTE-seq, a method to profile both regular and newly synthesized transcriptomes in single cells, revealing FLI1 downregulation during T-cell activation.

bioRxiv · Aug 22, 2024 · PreprintGenomics