Author

Yu Cai

Columbia University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

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Biology Disciplines

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Bioinformatics· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Organism:Arabidopsis· 1 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Assay:DNA methylation· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Adriana Rosas-VillegasiD· 1 shared Alexandra E. DeFoeiD· 1 shared Artyom KoppiD· 1 shared Ben R. HopkinsiD· 1 shared Brittney D WickiD· 1 shared Can YangiD· 1 shared Cheng JiniD· 1 shared Danqing ZhuiD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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1 shared paperGenomics

Adriana Rosas-VillegasORCID

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2 papers

Recent·Most cited

A single-nucleus transcriptomic atlas of the adult Aedes aegypti mosquito

Olivia V. Goldman, Alexandra E. DeFoe, Yanyan Qi, Yaoyu Jiao, Shih‐Che Weng, Brittney D Wick, Leah Houri-Zeevi, Priyanka Lakhiani, Takeshi Morita, Jacopo Razzauti, Adriana Rosas-Villegas, Yael N. Tsitohay, Madison M. Walker, Ben R. Hopkins, Joshua X.D. Ang, , Nadav Shai

The paper presents a single-nucleus RNA sequencing atlas of Aedes aegypti mosquitoes, identifying novel cell types and sexual dimorphism in gene expression across tissues.

Cell · Oct 30, 2025Peer-reviewedGenomics

Genomic Touchstone: Benchmarking Genomic Language Models in the Context of the Central Dogma

Yihui Wang, Zhiyuan Cai, Qian Zeng, Yihang Gao, Jiarui Ouyang, Yingxue Xu, Shu Yang, Sunan He, Yuxiang Nie, Yu Cai, Fengtao Zhou, Cheng Jin, Xi Wang, Zhi Xie, Danqing Zhu, , Hao Chen

Genomic Touchstone evaluates genomic language models across 36 tasks and 88 datasets, revealing insights on model performance, scaling, and pretraining strategies.

bioRxiv · Jun 25, 2025 · PreprintBioinformatics