Author

Junke Zhang

Cornell UniversityORCID 0000-0002-2178-1307Unclaimed ORCID profile · follow to get notified of new preprints

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Junke Zhang1 paper · Cornell University

Biology Disciplines

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Bioinformatics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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

Frequent Co-Authors

Abdullah OzeriD· 2 shared Alden King-Yung LeungiD· 2 shared Haiyuan YuiD· 2 shared John T. LisiD· 2 shared Xiuqi Pan· 2 shared Yutong ZhuiD· 2 shared Alejandro BarreraiD· 1 shared Avery Willis· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersBioinformatics

Abdullah OzerORCID

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2 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