Author

Brian J. Zarnegar

Stanford Medicine

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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Molecular Biology· 3 Genomics· 2

Signature Assays, Organisms & Methods

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Approach:experimental assay· 5 Research Focus:cell type annotation· 2 Assay:ChIP-seq· 2 Research Focus:gene regulatory network inference· 2 Organism:mouse· 2 Research Focus:protein structure prediction· 2 Research Focus:cell-cell communication· 1 Assay:CRISPR screen· 1

Frequent Co-Authors

Paul A. KhavariiD· 5 shared Howard Y. ChangiD· 3 shared Diana R. DouiD· 2 shared Douglas F. PorteriD· 2 shared Luca DucoliiD· 2 shared Robin M. MeyersiD· 2 shared Rui LiiD· 2 shared Weili MiaoiD· 2 shared

Activity by Year

2018-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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5 shared papersMolecular Biology

Paul A. KhavariORCID

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5 papers

Recent·Most cited

irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein associations on RNA

Luca Ducoli, Brian J. Zarnegar, Douglas F. Porter, Robin M. Meyers, Weili Miao, Nicholas McIlvain Riley, Suhas Srinivasan, Leandra V. Jackrazi, Yen‐Yu Yang, Zhouxian Li, Yinsheng Wang, Carolyn Ruth Bertozzi, Ryan A. Flynn, Paul A. Khavari

The paper introduces irCLIP-RNP and Re-CLIP methods to identify dynamic RNA-protein assemblies, revealing new patterns of RBP-RNA associations and EGF-induced remodeling.

Nature · Mar 26, 2025Peer-reviewedMolecular Biology

Modified forms of easyCLIP

Douglas F. Porter, Raghav M. Garg, Robin M. Meyers, Weili Miao, Luca Ducoli, Brian J. Zarnegar, Paul A. Khavari

This paper improves the easyCLIP protocol by addressing its limitations and providing a more reproducible analysis workflow.

bioRxiv · Dec 15, 2021 · PreprintMolecular Biology

Structural modularity of the XIST ribonucleoprotein complex

Zhipeng Lu, Jimmy K. Guo, Yuning Wei, Diana R. Dou, Brian J. Zarnegar, Qing Ma, Rui Li, Yang Zhao, Fan Liu, Hani Choudhry, Paul A. Khavari, Howard Y. Chang

The paper demonstrates that the XIST RNA-protein complex has a modular architecture that determines RBP binding and m6A modification, beyond sequence motifs.

Nature Communications · Dec 2, 2020Peer-reviewedMolecular Biology

Spen links RNA-mediated endogenous retrovirus silencing and X chromosome inactivation

Ava C. Carter, Jin Xu, Meagan Y Nakamoto, Yuning Wei, Brian J. Zarnegar, Quanming Shi, James P. Broughton, Ryan C. Ransom, Ankit Salhotra, Surya Nagaraja, Rui Li, Diana R. Dou, Kathryn E. Yost, Seung-Woo Cho, Anil Mistry, , Howard Y. Chang

This study shows Spen binds to endogenous retroviral RNAs and recruits chromatin silencing machinery, linking RNA-mediated retrovirus silencing to X chromosome inactivation.

eLife · May 7, 2020Peer-reviewedGenomics

Coupled single-cell CRISPR screening and epigenomic profiling reveals causal gene regulatory networks

Adam J. Rubin, Kevin R. Parker, Ansuman T. Satpathy, Yanyan Qi, Beijing Wu, Alvin J. Ong, Maxwell R. Mumbach, Andrew L. Ji, Daniel Sunwook Kim, Seung Woo Cho, Brian J. Zarnegar, William James Greenleaf, Howard Y. Chang, Paul A. Khavari

Perturb-ATAC combines CRISPR perturbations with single-cell ATAC-seq to identify gene regulatory networks in human cells.

Cell · Dec 20, 2018Peer-reviewedGenomics