Author

Xiuqi Pan

Cornell University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Assay:ChIP-seq· 2 Approach:experimental assay· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:deconvolution· 1 Approach:deep learning· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Abdullah OzeriD· 3 shared Alden King-Yung LeungiD· 3 shared Haiyuan YuiD· 3 shared John T. LisiD· 3 shared Jin Hua LiangiD· 2 shared Junke ZhangiD· 2 shared Nathaniel D. TippensiD· 2 shared Yao LiiD· 2 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 44 mutual co-author links

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3 shared papersGenomics

Abdullah OzerORCID

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3 papers

Recent·Most cited

High-resolution reconstruction of cell-type specific transcriptional regulatory processes from bulk sequencing samples

Yao Li, Sagar R Shah, Abdullah Ozer, Yutong Zhu, Xiuqi Pan, Tianyu Xia, Junke Zhang, Alden King-Yung Leung, Meihan Wei, John T. Lis, Haiyuan Yu

This paper introduces DeepDETAILS, a method to reconstruct cell-type-specific genomic signals from bulk data, outperforming traditional methods and providing insights into disease mechanisms.

Nature Biotechnology · Jul 13, 2026Peer-reviewedBioinformatics

Comprehensive Evaluation of Diverse Massively Parallel Reporter Assays to Functionally Characterize Human Enhancers Genome-wide

Junke Zhang, Alden King-Yung Leung, Yutong Zhu, Li Yao, Avery Willis, Xiuqi Pan, Abdullah Ozer, Zhou Zhou, Keith Siklenka, Alejandro Barrera, Jin Hua Liang, Nathaniel D. Tippens, Timothy E. Reddy, John T. Lis, Haiyuan Yu

This study evaluates multiple MPRA and STARR-seq datasets to identify enhancers, finding inconsistencies due to technical factors and proposing a unified pipeline to improve cross-assay agreement.

Genome biology · Nov 3, 2025Peer-reviewedGenomics

Simultaneous measurement of intrinsic promoter and enhancer potential reveals principles of functional duality and regulatory reciprocity

Mauricio I. Paramo, Alden King-Yung Leung, Sagar R. Shah, Junke Zhang, Nathaniel D. Tippens, Jin Hua Liang, Yao Li, Yiyang Jin, Xiuqi Pan, Abdullah Ozer, John T. Lis, Haiyuan Yu

The paper develops a dual reporter assay to measure promoter and enhancer potential, finding that they share regulatory logic and can function reciprocally.

bioRxiv · Mar 14, 2025 · PreprintGenomics