Author

jinren Ni

Peking UniversityORCID 0000-0002-9114-8347Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Organism:bacteria (other)· 1 Research Focus:chromatin & epigenetic regulation· 1 Research Focus:database / resource· 1 Approach:deep learning· 1 Approach:experimental assay· 1 Research Focus:host-pathogen & immune response· 1 Assay:metagenomics· 1

Frequent Co-Authors

Pengwei LiiD· 2 shared Alexander J. ProbstiD· 1 shared Anna RasmusseniD· 1 shared Bethany Cristine KolodyiD· 1 shared Bradley B. TolariD· 1 shared Cheng WangiD· 1 shared Christopher A. FrancisiD· 1 shared Chunfang Deng· 1 shared

Activity by Year

2026-2026 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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Curved chords = mutual co-authorship

2 shared papersMicrobiology

Pengwei LiORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

CRISPR mapping unveils global prevalence of viral predators of Myxobacteria

Pengwei Li, Jinren Ni

The paper uses CRISPR spacer analysis to identify 790 myxophages across 3,229 myxobacterial genomes, revealing six new viral lineages and their functional roles in host interactions.

bioRxiv · Sep 16, 2026 · PreprintMicrobiology

ProteinSage: From implicit learning to explicit structural constraints for efficient protein language modeling

Lingdong Shen, Linlin Chao, Tang Liu, Qi Liu, Guowei Zhou, Hao Wang, Xinyue Dong, Tianhong Li, Xiaoming Zhang, jinren Ni

ProteinSage uses structural constraints during pretraining to improve protein language modeling with less data, achieving competitive performance on structure-aware tasks.

bioRxiv · Sep 9, 2026 · PreprintBioinformatics

Functional profiling of ESKAPE viromes uncovers resistance-limiting phage-host dynamics

Pengwei Li, Quan Liu, Chunfang Deng, Jinren Ni

The paper constructs a comprehensive ESKAPE virome resource, revealing phages' dual roles in targeting pathogens and limiting resistance spread through antagonizing plasmids and ARGs.

bioRxiv · Aug 19, 2026 · PreprintMicrobiology

The origin and evolution of archaeal Borg extrachromosomal elements

Ling-Dong Shi, Petar I. Penev, Bethany Cristine Kolody, Leylen Miloslavich, Shufei Lei, Rohan Sachdeva, Anna Rasmussen, Bradley B. Tolar, Christopher A. Francis, Alexander J. Probst, Xabier Vázquez-Campos, Timothy E. Payne, Zhou Jiang, J Li, Cheng Wang, , Jillian F. Banfield

The paper identifies and characterizes Borgs and mini-Borgs in Methanoperedens archaea, revealing their evolutionary origins and genomic relationships.

bioRxiv · May 23, 2026 · PreprintMicrobiology