Author

Yiming Zhang

The University of Tokyo

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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Bioinformatics· 2 Cell Biology· 1 Neuroscience· 1 Physiology· 1

Signature Assays, Organisms & Methods

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Organism:mouse· 5 Organism:human· 3 Assay:CITE-seq· 2 Approach:deep learning· 2 Approach:experimental assay· 2 Assay:long-read sequencing· 2 Research Focus:sequence-to-function modeling· 2 Approach:transformer / foundation model· 2

Frequent Co-Authors

Bian BianiD· 2 shared Yutaka Saito· 2 shared Aidan C. ManningiD· 1 shared Alejandra Patino-GuerreroiD· 1 shared Alicyn I. Stothard· 1 shared Allyson L. Mayer· 1 shared Benjamin M. Swarts· 1 shared Brian J. DeBosch· 1 shared

Activity by Year

2018-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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2 shared papersBioinformatics

Bian BianORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

The Onset of Breathing at Birth Switches Off Regenerative Capacity

Xuan Song, Xinyi Cai, Shane Hegarty, Davide Speri, Masahiro Yasuda, Ryan Donahue, Joanna Stanicka, Ting Yan, Susu Mao, Sarah Yang, Jiawen Chen, Junjie Zhu, James Kiraly, Cheng-Hao Chien, Evgenii Kegeles, , Zhigang He

The paper shows that breathing at birth triggers CO2 exhalation, which reduces mTOR activity and limits regenerative capacity in CNS neurons and other tissues, but this effect is reversible with CO2 inhalation or Snrk deletion.

bioRxiv · Oct 11, 2026 · PreprintNeuroscience

A tRNA-derived small RNA orchestrates cardioprotection through distinct cell-type-specific mechanisms

Tian Hao, Jin Li, Kaushik V Amancherla, Lingfei Sun, Priyanka Gokulnath, Alejandra Patino-Guerrero, Ritin Sharma, Krystine Garcia‐Mansfield, Chunyang Xiao, Aidan C. Manning, Emeli Chartterjee, Xiaoting Yu, Richard Xu, Yiming Zhang, Zhihong Yang, , Guoping Li

This study identifies a tRNA-derived small RNA that reduces cardiac fibrosis and hypertrophy through cell-type-specific mechanisms in mouse and human cardiac cells.

bioRxiv · Sep 29, 2026 · PreprintCell Biology

Designing mRNA coding sequence via multimodal reverse translation language modeling with Pro2RNA

Bian Bian, Yiming Zhang, Jichen Zhang, Kiyoshi Asai, Yutaka Saito

Pro2RNA generates species-adapted mRNA coding sequences from protein sequences using a multimodal language model, outperforming existing methods in benchmark tests.

bioRxiv · Mar 20, 2026 · PreprintBioinformatics

Large generative mRNA language foundation model for efficient coding sequence generation and design with mRNA-GPT

Bian Bian, Yiming Zhang, Hongmin Li, Jiuzhou Zhong, Yutaka Saito

The paper introduces mRNA-GPT, a generative mRNA language model trained on sequences from bacteria, eukaryotes, and archaea, showing improved translation efficiency and stability in mRNA design.

bioRxiv · Dec 24, 2025 · PreprintBioinformatics

ALOXE3 is a hepatic fasting-responsive lipoxygenase that enhances insulin sensitivity via hepatic PPARγ

Cassandra B. Higgins, Yiming Zhang, Allyson L. Mayer, Hideji Fujiwara, Alicyn I. Stothard, Mark J. Graham, Benjamin M. Swarts, Brian J. DeBosch

This study identifies ALOXE3 as a fasting-responsive lipoxygenase that improves insulin sensitivity and metabolism through PPARγ activation in the liver.

bioRxiv · Feb 19, 2018 · PreprintPhysiology