Author

Yin Shen

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.

Same name, identified by ORCID

Biology Disciplines

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Genomics· 3 Genetics· 2 Developmental Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Research Focus:gene regulatory network inference· 3 Organism:human· 3 Organism:mouse· 3 Approach:statistical model· 3 Assay:ChIP-seq· 2 Assay:CRISPR screen· 2 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Axel ViseliD· 2 shared Bin LiiD· 2 shared Bing ReniD· 2 shared Diane E. DickeliD· 2 shared Ian Richard JonesiD· 2 shared Jennifer A. AkiyamaiD· 2 shared Len A. PennacchioiD· 2 shared Lenka MaliskovaiD· 2 shared

Activity by Year

2019-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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2 shared papersDevelopmental Biology

Axel ViselORCID

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Author profile →

6 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

Cell-type specific inference from bulk RNA-sequencing data by integrating single cell reference profiles via EPIC-unmix

Chenwei Tang, Quan Sun, Xinyue Zeng, Gang Li, Xiaoyu Yang, Fei Liu, Jinying Zhao, Yin Shen, Boxiang Liu, Jia Wen, Yun Li

EPIC-unmix improves cell-type specific analysis from bulk RNA-seq by integrating single-cell reference profiles, identifying novel genes and eQTLs in Alzheimer's disease.

Genome biology · Nov 20, 2025Peer-reviewedGenomics

Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis

Rinaldo Catta-Preta, Susan Lindtner, Athéna Rebecca Ypsilanti, Nicolas Seban, James D. Price, Armen Abnousi, Linda Su-Feher, Yurong Wang, Karol Cichewicz, Sally A. Boerma, Ivan Jurić, Ian Richard Jones, Jennifer A. Akiyama, Ming Hu, Yin Shen, , Alex S. Nord

The paper identifies combinatorial TF-cRE interactions in mouse basal ganglia development, revealing modules that drive GABAergic neurogenesis and suppress other fates.

Developmental Cell · Oct 31, 2024Peer-reviewedDevelopmental Biology

CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription

Xingjie Ren, Lina Zheng, Lenka Maliskova, Tsz Wai Tam, Yifan Sun, Hongjiang Liu, Jerry Lee, Maya Asami Takagi, Bin Li, Bing Ren, Wei Wang, Yin Shen

bioRxiv · Oct 8, 2024 · PreprintGenetics

Systematic mapping of chromatin state landscapes during mouse development

David U. Gorkin, Iros Barozzi, Yuan Zhao, Yanxiao Zhang, Hui Huang, Ah Young Lee, Bin Li, Joshua Chiou, André Wildberg, Bo Ding, Bo Zhang, Mengchi Wang, J. Seth Strattan, Jean M. Davidson, Yunjiang Qiu, , Bing Ren

The paper systematically maps chromatin state landscapes during mouse development by profiling histone modifications across 72 tissue-stages, identifying dynamic enhancers and transcriptional regulators.

Nature · Jul 29, 2020Peer-reviewedGenomics

Live-Cell Imaging Reveals Enhancer-dependent Sox2 Transcription in the Absence of Enhancer Proximity

Jeffrey M Alexander, Juan Guan, Bingkun Li, Lenka Maliskova, Michael Song, Yin Shen, Bo Huang, Stavros Lomvardas, Orion David Weiner

This study uses live-cell imaging to show that Sox2 transcription occurs without requiring enhancer proximity in embryonic stem cells.

eLife · May 24, 2019Peer-reviewedGenetics