Author

Jingjing Zhao

Second Affiliated Hospital of Zhejiang 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· 1 Biophysics· 1 Cancer Biology· 1 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 2 Approach:deep learning· 2 Research Focus:gene regulatory network inference· 2 Assay:protein structure· 2 Organism:bacteria (other)· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Assay:ChIP-seq· 1

Frequent Co-Authors

Dongge Ma· 2 shared Jiahua Peng· 2 shared Kaining LiuiD· 2 shared Qiuting Qian· 2 shared Yifei Yao· 2 shared Betty M Booker· 1 shared David C. HayiD· 1 shared Feifei Zhang· 1 shared

Activity by Year

2016-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 18 mutual co-author links

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2 shared papersBiophysics

Dongge Ma

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

Molecular dynamics descriptors for 1,079 post-translationally modified protein systems

Kaining Liu, Qiuting Qian, Jiahua Peng, Dongge Ma, Yifei Yao, Jingjing Zhao, Ying Chi

The paper provides a resource of 1,079 post-translationally modified protein systems with molecular dynamics simulations and descriptors for research and method evaluation.

bioRxiv · Aug 24, 2026 · PreprintBiophysics

Harnessing Tumor-Specific Transcript Diversity Uncovers a Shared Neoantigen Reservoir for Pancreatic Ductal Adenocarcinoma

Jingjing Zhao, Qiaojuan Li, Peng Lin, Yu Yang, Hongwu Yu, Yifan Wen, Wenqian Yu, Huiyi He, Sichen Tao, Feifei Zhang, Yan Li, Zhixiang Hu, Jing Xie, Zhen Chen, Shenglin Huang

This paper introduces NeoAPP, a tool to identify tumor-specific transcript-derived neoantigens in PDAC, revealing a large neoantigen reservoir that could improve immunotherapy.

MedComm · Jul 30, 2026Peer-reviewedCancer Biology

ProteinFlux: accurate, rapid and scalable generative prediction of protein dynamics driven by post-translational modifications

Qiuting Qian, Jiahua Peng, Dongge Ma, Kaining Liu, Yihan Cheng, Yanqi Deng, Jingjing Zhao, Shen Su, Yifei Yao, Yuan Qu, Rao Fu, Jinliang Liu, Make Zhao, Yu Xiao, Keying Wang, , Y G

ProteinFlux predicts protein conformational dynamics influenced by post-translational modifications using a generative framework, outperforming traditional methods in speed and accuracy.

bioRxiv · May 11, 2026 · PreprintBioinformatics

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus

Betty M Booker, Tara Friedrich, Mandy K Mason, Julia E VanderMeer, Jingjing Zhao, Walter L Eckalbar, Malcolm Logan, Nicola Illing, Katherine S Pollard, Nadav Ahituv

The paper identifies bat-specific enhancer regions in the HoxD locus that show differential activity in bat and mouse limbs, potentially contributing to bat wing development.

PLOS Genetics · Mar 28, 2016Peer-reviewedEvolutionary Biology