Author

Qingya Shi

Tsinghua UniversityORCID 0000-0001-9724-3743Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Approach:deep learning· 1 Research Focus:gene regulatory network inference· 1 Assay:long-read sequencing· 1 Assay:scRNA-seq· 1 Research Focus:sequence-to-function modeling· 1 Approach:statistical model· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Anyue Cheng· 1 shared Bing LiuiD· 1 shared David H. PerlmutteriD· 1 shared Fen PeiiD· 1 shared Gary A. SilvermaniD· 1 shared Guangye Lv· 1 shared İvet BahariD· 1 shared Jack X. Chen· 1 shared

Activity by Year

2020-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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1 shared paperMolecular Biology

Anyue Cheng

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2 papers

Recent·Most cited

Molecular BiologybioRxivPreprintMar 24, 2026

A Long-Context Generative Foundation Model Deciphers RNA Design Principles

Yanjie Huang, Guangye Lv, Anyue Cheng…·Shuangjia Zheng

EVA is a long-context generative RNA model trained on 114 million sequences, achieving state-of-the-art performance in RNA design tasks and structural modeling.

1 citation

long-read sequencingscRNA-seq

𝕏 PostBluesky

Systems BiologyInternational Journal of Molecular SciencesPeer-reviewedApr 19, 2020

Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis

Qingya Shi, Fen Pei, Gary A. Silverman…·İvet Bahar

The paper performs a quantitative systems pharmacology analysis of 225 autophagy modulators to uncover their molecular mechanisms and regulatory pathways.

32 citations

statistical modelbenchmarking

𝕏 PostBluesky