Author

Jingyi Li

Pennsylvania State 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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Biophysics· 2 Ecology· 2 Microbiology· 1 Neuroscience· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Research Focus:ecology & biodiversity· 2 Approach:experimental assay· 2 Approach:statistical model· 2 Research Focus:database / resource· 1 Approach:diffusion model· 1 Approach:graph neural network· 1 Organism:human· 1

Frequent Co-Authors

Jian WangiD· 2 shared Nikolay V. DokholyaniD· 2 shared Adrian A. Barnett· 1 shared Ajuan ZhangiD· 1 shared Alexine KeuroghlianiD· 1 shared Ana Carolina AntunesiD· 1 shared Ana Paula de Almeida CorreaiD· 1 shared Ana Yoko Ykeuti MeigaiD· 1 shared

Activity by Year

2018-2026 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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2 shared papersBiophysics

Jian WangORCID

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

Energetic and functional development of soil food webs along secondary succession

Ajuan Zhang, Chengwei Tu, Yuanfei Wang, Jingyi Li, Zheng Zhou, Ruyi Luo, Karin Hohberg, Zhe Chen, Bingxue Zhu, Xueyong Pang, Nico Eisenhauer, Anton Potapov

This study examines energy flux changes in soil food webs during secondary succession, finding shifts from herbivory to detritivory and differences between plantation and natural forest types.

bioRxiv · Nov 6, 2026 · PreprintEcology

The neural geometry of naturalistic surprise: Graded boundary breakthroughs in the human brain

Yunqiang Hao, Jingyi Li, Chao Jiang

This paper shows that more surprising events cause whole-brain neural states to move further from non-surprise states, measured as boundary breakthrough depth in bits.

bioRxiv · Sep 23, 2026 · PreprintNeuroscience

Forest degradation reshapes trophic functioning in vertebrate food webs across Amazonian forests

Ana Carolina Antunes, Ulrich Brose, Anelise Montanarin, Benjamin Rosenbaum, Carlos A. Peres, Carsten Meyer, Henrique M. Pereira, Jes Hines, Jingyi Li, Tainara Sobroza, Emilio Berti, Benoît Gauzens, Adrian A. Barnett, Alexine Keuroghlian, Antônio Carlos da Silva Zanzini, , R. C. Oliveira

The paper quantifies how forest degradation affects trophic functioning in Amazonian vertebrate food webs, showing shifts in carnivory and herbivory despite stable biodiversity metrics.

bioRxiv · Jul 14, 2026 · PreprintEcology

ChironRNA: Steric Clashes Resolution in RNA Structures via E(3)-Equivariant Diffusion

Jingyi Li, Jian Wang, Nikolay V. Dokholyan

ChironRNA resolves steric clashes and reconstructs missing atoms in RNA structures using an E(3)-equivariant diffusion model, achieving high precision on test data.

bioRxiv · Mar 19, 2026 · PreprintBiophysics

ATLAS: Graph-based 3D RNA Motif Library Incorporating non-Watson-Crick Interactions

Jingyi Li, Jian Wang, Srinivasan Ekambaram, Nikolay V. Dokholyan

The paper introduces ATLAS, a 3D RNA motif library with graph representations and non-Watson-Crick interactions, enabling motif-based RNA structure prediction and design.

bioRxiv · Feb 19, 2026 · PreprintBiophysics

The reduced prevalence of macrolide resistance in Mycoplasma pneumoniae clinical isolates from pediatric patients in Beijing in 2016

Xiujun Tian, Ran Wei, Junyan Shao, Hong Wang, Jing Li, Wei Zhou, Xuanguang Qin, Yinghui Hu, Haiwei Dou, Dongxing Guo, Jingyi Li, Dan Li, Baoping Xu, Deli Xin

The study reports macrolide resistance rates in Mycoplasma pneumoniae isolates from pediatric patients in Beijing, 2016, and identifies specific mutations associated with resistance.

bioRxiv · Jun 7, 2018 · PreprintMicrobiology