Welcome!

I’m Kaining Hu (胡恺宁). I obtained my PhD in Crop Genetics and Breeding from the Huazhong Agricultural University in 2019, under the guidance of Prof. Jinxing Tu. My doctoral dissertation investigated rolling-cycle DNA transposon (Helitron) in Brassicaceae species and the gene evolution of Brassica napus.

In March 2021, I joined the Xiaochang Zhang lab at the University of Chicago as a postdoc scholar in bioinformatics. My research focused on the evolution of cassette exons and nonsense-mediated mRNA decay (NMD) associated with alternative splicing in brain development.

Since April 2026, I have been an Associate Professor at the Zhe Ji lab, Center for Excellence in Molecular Cell Science, CAS. My research focuses on evolution and microprotein functions.

Interests
  • RNA
  • Evolution
  • Deep Learning
Education

  • PhD in Crop Genetics and Breeding, 2019

    Huazhong Agricultural University

  • BSc in Plant Science and Technology, 2012

    Huazhong Agricultural University

Skills

AI & Deep Learning

Deep Learning Specialization · AI+Science Summer School · Prompting Essentials

Programming & Infrastructure

R (Shiny) · Python · Perl · Shell (Linux/Unix) · Server & Website Management

Transcriptomics & RNA Biology

RNA-seq · ChIP-seq · CLIP-seq · Alternative Splicing · ASO Design

Genomics & Evolution

Genome Assembly · GWAS · BSA · Evolution Analysis · TE/Helitron

Experience

 
 
 
 
 
X. Zhang Lab, Department of Human Genetics, University of Chicago
Postdoc scholar
X. Zhang Lab, Department of Human Genetics, University of Chicago
Mar 2021 – Feb 2026 Chicago, USA

Software

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All Machine Learning Genomics RNA Biology
EANMD
XGBoost-based prediction of alternative splicing-induced nonsense-mediated mRNA decay.
Code Web App
EAHelitron
Whole-genome search and analysis of Helitron transposons.
Code

Recent Publications

Hu, Kaining , Yang, Runwei , Qiu, Jiaming , Feng, Xinran , LaPre, Kayleigh J. , Tanouye, Jessica , Yang, Yalan , Zhang, Xiaochang (2026). Alternative splicing-triggered mRNA decay informs splice-switching targets for neurodevelopmental disorders. The Journal of Clinical Investigation.

Cite DOI URL

Ruan, Xiangbin , Hu, Kaining , Yang, Yalan , Yang, Runwei , Tseng, Elizabeth , Kang, Bowei , Kauffman, Aileen , Zhong, Rong , Zhang, Xiaochang (2025). Cell-Type–Specific Splicing of Transcription Regulators and Ptbp1 by Rbfox1/2/3 in the Developing Neocortex. Journal of Neuroscience.

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Kang, Bowei , Yang, Yalan , Hu, Kaining , Ruan, Xiangbin , Liu, Yi-Lin , Lee, Pinky , Lee, Jasper , Wang, Jingshu , Zhang, Xiaochang (2023). Infernape uncovers cell type–specific and spatially resolved alternative polyadenylation in the brain. Genome Research.

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Chen, Jiao , Zhang, Sihao , Li, Bao , Zhuo, Chenjian , Hu, Kaining , Wen, Jing , Yi, Bin , Ma, Chaozhi , Shen, Jinxiong , Fu, Tingdong , Tu, Jinxing (2023). Fine mapping of BnDM1—the gene regulating indeterminate inflorescence in Brassica napus. Theoretical and Applied Genetics.

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Ruan, Xiangbin , Hu, Kaining , Zhang, Xiaochang (2023). PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing. Nature Communications.

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