Author

Wei Zhu

Duke University

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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Bioinformatics· 3 Genomics· 3

Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Organism:human· 3 Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Assay:ChIP-seq· 1

Frequent Co-Authors

Charles A. GersbachiD· 2 shared Gregory E. CrawfordiD· 2 shared Raluca GordâniD· 2 shared Samantha E Miller· 2 shared Samuel J. Reisman· 2 shared Alexander J. HarteminkiD· 1 shared Alexey Zakharov· 1 shared Alexias SafiiD· 1 shared

Activity by Year

2020-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 18 mutual co-author links

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2 shared papersGenomics

Charles A. GersbachORCID

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6 papers

Recent·Most cited

Cellular composition and the interpretation of candidate RNA readouts of trogocytosis in colorectal cancer

Jinglin Wang, Pan Sun, Lei XU, Yao Wang, Wei Zhu, Yan Zhang, Yao Tang, Juan Yang

The paper evaluates an eight-gene module associated with trogocytosis in CRC, finding its correlation with T-cell fraction is typical of random modules, suggesting it reflects cellular composition rather than trogocytosis.

bioRxiv · Nov 4, 2026 · PreprintBioinformatics

Quantitative profiling of intrinsic dCas9-DNA recognition reveals key determinants of guide RNA performance

Wei Zhu, Michael Tian, Yuncheng Duan, Samuel J. Reisman, Samantha E Miller, Evan Corden, Maria A. ter Weele, Lingyun Song, Jameson Blount, Alexias Safi, Jacob Matthew Schreiber, Charles A. Gersbach, Gregory E. Crawford, Raluca Gordân

This study quantifies intrinsic dCas9-DNA recognition using TANGO, identifying key factors affecting gRNA performance and revealing new aspects of dCas9 specificity.

bioRxiv · Aug 10, 2026 · PreprintGenomics

Mismatch tolerance of a gRNA for CRISPR-based gene activation confers broad activity critical for cell reprogramming

Samuel J. Reisman, Wei Zhu, Samantha E Miller, Dahlia Halabi, Nicholas Sangvai, Gregory E. Crawford, Raluca Gordân, Charles A. Gersbach

The paper identifies a CRISPRa gRNA with broad off-target activity that enables genome-wide transcriptional reprogramming, showing that mismatch tolerance and PAM-proximal bases determine binding specificity.

bioRxiv · Feb 3, 2026 · PreprintGenomics

Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication

Vinay Tripuraneni, Gönen Memişoğlu, Heather K. MacAlpine, Trung Q. Tran, Wei Zhu, Alexander J. Hartemink, James E. Haber, David M. MacAlpine

The paper investigates how nucleosome dynamics and eviction after a double-strand break are reversible via NHEJ repair in yeast, showing re-establishment of chromatin structure in G1-arrested cells.

Genome Research · May 1, 2021Peer-reviewedGenomics

Discovery of TMPRSS2 inhibitors from virtual screening

Xin Hu, Jonathan H. Shrimp, Hui Guo, Miao Xu, Catherine Z. Chen, Wei Zhu, Alexey Zakharov, Sankalp Jain, Paul Shinn, Anton Simeonov, Matthew D. Hall, Min Shen

This study identifies novel TMPRSS2 inhibitors through virtual screening and experimental validation, offering potential drug candidates for COVID-19 treatment.

bioRxiv · Dec 28, 2020 · PreprintBioinformatics

DeepPSC (protein structure camera): computer vision-based reconstruction of proteins backbone structure from alpha carbon trace as a case study

Xing Zhang, Junwen Luo, Yi Cai, Wei Zhu, Xiaofeng Yang, Hongmin Cai, Zhanglin Lin

This paper introduces DeepPSC, a deep learning method that reconstructs protein backbone structures from alpha carbon traces, outperforming existing methods.

bioRxiv · Aug 12, 2020 · PreprintBioinformatics