Author

Yuli Zhang

Huazhong University of Science and TechnologyPrimary ORCID profile (0000-0001-6267-4244 · 1 paper)Unclaimed ORCID profile · follow to get notified of new preprints

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

Yuli ZhangiD1 paper · Huazhong University of Science and Technology

Biology Disciplines

Click to filter author papers

Bioinformatics· 3 Bioengineering· 1 Microbiology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Assay:metagenomics· 4 Approach:deep learning· 3 Research Focus:benchmarking· 2 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Research Focus:drug response / drug discovery· 2 Organism:human· 2 Approach:transformer / foundation model· 2

Frequent Co-Authors

Haohong Zhang· 4 shared Kang NingiD· 4 shared Ronghua YangiD· 3 shared Zixin KangiD· 2 shared Amatzia GantziD· 1 shared Dimitria Bonizol CamasãoiD· 1 shared Jiayun Xiong· 1 shared Jin Han· 1 shared

Activity by Year

2025-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 18 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

4 shared papersBioinformatics

Haohong Zhang

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

MGM2 as a Multimodal Foundation Model for Microbial Community States and Responses

Haohong Zhang, Yuli Zhang, Yuxuan Qi, Tianao Liu, Linfeng Zhao, Ronghua Yang, Kang Ning

The paper introduces MGM2, a multimodal foundation model for microbial communities that predicts responses to interventions and interprets community changes using shared representations of molecular identity and context.

bioRxiv · Sep 30, 2026 · PreprintBioinformatics

Microbial general model: Leveraging large language model for contextualized microbiome analysis

Haohong Zhang, Yuli Zhang, Zixin Kang, Jiayun Xiong, Ronghua Yang, Kang Ning

The paper introduces MGM, a foundation model for microbiome analysis, showing improved classification and detection of dynamic patterns across diverse contexts.

Advanced Science · Jan 25, 2026Peer-reviewedBioinformatics

Expansion of functional human salivary acinar cell spheroids with reversible thermo-ionically crosslinked 3D hydrogels

José G. Munguia-López, Sangeeth Pillai, Yuli Zhang, Amatzia Gantz, Dimitria Bonizol Camasão, Showan N. Nazhat, Joseph Matthew Kinsella, Simon D. Tran

This study evaluates AG-based hydrogels for expanding human salivary gland spheroids, finding AGHA gels support larger, viable, and functionally active spheroids with sustained protein expression.

International Journal of Oral Science · May 9, 2025Peer-reviewedBioengineering

MicroProphet: A Digital Twin Framework for Predicting Microbial Community Dynamics with Personalized Precision

Yuli Zhang, Kouyi Zhou, Xiaoke Chen, Haohong Zhang, Jin Han, Kang Ning

MicroProphet predicts microbial community dynamics from sparse longitudinal data, enabling personalized health monitoring and intervention planning.

bioRxiv · May 8, 2025 · PreprintMicrobiology

Towards a Generative Paradigm for Large-scale Microbiome Analysis by Generative Language Model

Haohong Zhang, Zixin Kang, Yuli Zhang, Ronghua Yang, Kang Ning

This paper introduces MGM 2.0, a generative language model for microbiome analysis that uses sentence-like representations to predict microbial colonization, generate disease-specific profiles, and improve donor selection for fecal microbiota transplantation.

bioRxiv · Jan 15, 2025 · PreprintBioinformatics