Author

Shanshan Zhang

Harvard 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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Microbiology· 3 Immunology· 2 Bioengineering· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Assay:bulk RNA-seq· 3 Research Focus:cell type annotation· 3 Research Focus:differential expression· 3 Organism:E. coli· 3 Approach:deep learning· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2

Frequent Co-Authors

Nan Wu· 3 shared Shuang Liu· 3 shared Wenhong Zhang· 3 shared Ying Zhang· 3 shared Antoine FreuchetiD· 2 shared Charlotte J. ImianowskiiD· 2 shared Christophe O. BenoistiD· 2 shared David ZemmouriD· 2 shared

Activity by Year

2018-2026 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersMicrobiology

Nan Wu

Mutual co-authors in cluster

Author profile →

7 papers

Recent·Most cited

The ammonia-senescence ratchet drives an adaptation-senescence-ammonioptosis transition in liver cancer

Yubin Han, Miao Huang, Yulin Xie, Shanshan Zhang, 王金申, Lin Han, Chunxia Li, Yong Zhang

This study identifies an ammonia-senescence ratchet mechanism that drives tumor cells from metabolic adaptation to senescence and ultimately to ammonioptosis.

bioRxiv · Oct 13, 2026 · PreprintBioengineering

A Reference Landscape of Regulatory T Cell States in Mice

Antoine Freuchet, Nitya Mehrotra, Ian Magill, Odhran Casey, Xinxin Chi, Shanshan Zhang, Charlotte J. Imianowski, Jacob A. Myers, Jun R. Huh, Laurent Brossay, Dario A.A. Vignali, Christophe O. Benoist, David Zemmour, the immgenT project

The paper defines a unified framework for Treg heterogeneity using a joint RNA-protein model, identifying eight conserved clusters across tissues and conditions.

bioRxiv · Sep 2, 2026 · PreprintImmunology

immgenT: A Comprehensive Reference of Convergent T-cell States in the Mouse

Ian Magill, Odhran Casey, Dania Mallah, Siba Smarak Panigrahi, Leon Lee Zhou, Olga Barreiro del Río, Derek J. Bangs, Gavyn Chern Wei Bee, Samantha M. Borys, Josh Choi, Can Ergen, Enxhi Ferraj, Maurizio Fiusco, Antoine Freuchet, Giovanni Galletti, , the immgenT project

immgenT creates a comprehensive T-cell molecular atlas across mouse organs and disease states, identifying 8 lineages and 107 clusters using deep generative models and integrating external datasets.

bioRxiv · Sep 2, 2026 · PreprintImmunology

Cross-platform Hi-C meta-analysis identifies functional insulators that actively block enhancer-promoter interactions

Jian Cui, Wanying Xu, Xiaodong Lang, Shanshan Zhang, Leina Lu, Xiaoxiao Liu, Yan Li, Fulai Jin

The paper identifies functional insulators (FINs) through Hi-C meta-analysis, showing they block enhancer-promoter interactions and are distinct from TAD boundaries.

Nature Communications · Jul 16, 2026Peer-reviewedGenomics

Identification of small regulatory RNAs involved in persister formation

Shanshan Zhang, Shuang Liu, Nan Wu, Wenhong Zhang, Ying Zhang

This study identifies seven small regulatory RNAs involved in type II persister formation in uropathogenic E. coli.

bioRxiv · Apr 30, 2018 · PreprintMicrobiology

Identification of novel genes including rpmF and yjjQ critical for Type II persister formation in Escherichia coli

Shuang Liu, Nan Wu, Shanshan Zhang, Yumeng Zhang, Wenhong Zhang, Ying Zhang

This study identifies novel genes critical for Type II persister formation in E. coli by analyzing transcriptome changes during persister emergence and abundance and validating their roles through knockout and overexpression experiments.

bioRxiv · Apr 30, 2018 · PreprintMicrobiology

Identification of Polynucleotide Phosphorylase (PNPase) in Escherichia coli Involved in Persister Formation

Nan Wu, Yumeng Zhang, Shanshan Zhang, Youhua Yuan, Shuang Liu, Peng Cui, Wenhong Zhang, Ying Zhang

This study identifies PNPase as a key regulator of persister formation in E. coli by negatively regulating the crp operon at the post-transcriptional level.

bioRxiv · Apr 30, 2018 · PreprintMicrobiology