Author

Manman Shi

Tempus Labs (United States)

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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Bioinformatics· 1 Genomics· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 3 Research Focus:gene regulatory network inference· 3 Organism:human· 3 Assay:ChIP-seq· 2 Approach:statistical model· 2 Research Focus:variant effect prediction· 2 Assay:ATAC-seq· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Donghoon LeeiD· 3 shared Jason J. LiuiD· 3 shared Jennifer R. MoraniD· 3 shared Jing ZhangiD· 3 shared Kevin P. WhiteiD· 3 shared Mark GersteiniD· 3 shared Ahyeon HwangiD· 2 shared Daniel H. GeschwindiD· 2 shared

Activity by Year

2020-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersGenomics

Donghoon LeeORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Single-cell genomics and regulatory networks for 388 human brains

Prashant S. Emani, Jason J. Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che-Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur R. Galeev, Ahyeon Hwang, , Gregory M. Cooper

The paper processes single-nuclei multi-omics data from 388 human brains to identify regulatory elements and build cell-type networks, revealing changes in aging and neuropsychiatric disorders.

Science · May 23, 2024Peer-reviewedGenomics

Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq

Sophia C. Gaynor-Gillett, Lijun Cheng, Manman Shi, Jason J. Liu, Gaoyuan Wang, Megan Spector, Mary Flaherty, Martha Wall, Ahyeon Hwang, Mengting Gu, Zhanlin Chen, Yuhang Chen, Jennifer R. Moran, Jing Zhang, Donghoon Lee, , Kevin P. White

The paper identifies and validates enhancer regions in primary human neural progenitor cells using capture STARR-seq, linking them to genes involved in psychiatric disease pathways.

bioRxiv · Mar 14, 2024 · PreprintNeuroscience

STARRPeaker: Uniform processing and accurate identification of STARR-seq active regions

Donghoon Lee, Manman Shi, Jennifer R. Moran, Martha Wall, Jing Zhang, Jason J. Liu, Dominic Fitzgerald, Yasuhiro Kyono, Lijia Ma, Kevin P. White, Mark Gerstein

The paper introduces STARRPeaker, a processing pipeline for STARR-seq data that improves enhancer detection by addressing sequencing biases and RNA stability effects.

Genome biology · Dec 1, 2020Peer-reviewedBioinformatics