Author

Xiekui Cui

University of California, San Francisco

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· 3 Genetics· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Research Focus:gene regulatory network inference· 3 Organism:human· 3 Assay:ChIP-seq· 2 Assay:CRISPR screen· 2 Research Focus:variant effect prediction· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Ian Richard JonesiD· 3 shared Yin SheniD· 3 shared Jia WeniD· 2 shared Ming HuiD· 2 shared Xiaoyu YangiD· 2 shared Yun LiiD· 2 shared Aaron A Coley· 1 shared Alejandro BarreraiD· 1 shared

Activity by Year

2020-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 27 mutual co-author links

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3 shared papersGenomics

Ian Richard JonesORCID

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4 papers

Recent·Most cited

Interrogation of noncoding schizophrenia risk variants using CRISPR-based functional genomics

Marisa C. Hamilton, Julia W. Riley, Alexander C. Nelson, Boxun Li, Sophie F. Dornbaum, Alexias Safi, Xiekui Cui, Ian Richard Jones, Aaron A Coley, Kevin T. Hagy, Ruhi Rai, Alejandro Barrera, Andrew S. Allen, Yin Shen, Richard I. Sherwood, , Gregory E. Crawford

The paper uses CRISPR-based functional genomics to identify noncoding regulatory elements and variants affecting schizophrenia-associated gene expression.

bioRxiv · Sep 17, 2026 · PreprintGenomics

Capture-C MPRA: A high-throughput method to simultaneously characterize promoter interactions and regulatory activity

Coline Arnould, Pia Keukeleire, Fumitaka Inoue, Xiekui Cui, Kelly An, Elizabeth Murray, Xuhuiqun Zhang, Radoje Drmanac, Brock A. Peters, Jay Shendure, Yin Shen, Martin Kircher, Nadav Ahituv

This paper introduces ccMPRA, a method that combines Capture-C and MPRA to study promoter interactions and regulatory activity, identifying enhancers and silencers.

bioRxiv · Jun 11, 2025 · PreprintGenomics

Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons

Xiaoyu Yang, Ian Richard Jones, Poshen B. Chen, Han Kwang Yang, Xingjie Ren, Lina Zheng, Bin Li, Yang Eric Li, Quan Sun, Jia Wen, Cooper Beaman, Xiekui Cui, Yun Li, Wei Wang, Ming Hu, , Yin Shen

The paper identifies functional CREs in iPSCs and neurons and links them to neuropsychiatric disease risk variants.

bioRxiv · Aug 30, 2023 · PreprintGenetics

3D Epigenomic Characterization Reveals Insights Into Gene Regulation and Lineage Specification During Corticogenesis

Michael Song, Mark-Phillip Pebworth, Xiaoyu Yang, Armen Abnousi, Changxu Fan, Jia Wen, Jonathan D. Rosen, Mayank N. K. Choudhary, Xiekui Cui, Ian Richard Jones, Seth Bergenholtz, Ugomma C. Eze, Ivan Jurić, Bingkun Li, Lenka Maliskova, , Yin Shen

This study characterizes 3D epigenomic landscapes during human corticogenesis, revealing chromatin looping and super interactive promoters involved in lineage-specific gene regulation.

Nature · Oct 14, 2020Peer-reviewedGenomics