Author

Jian Chen

Commonwealth Scientific and Industrial Research Organisation

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· 1 Cancer Biology· 1 Genomics· 1 Microbiology· 1 Plant Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 2 Approach:deep learning· 2 Organism:human· 2 Research Focus:protein structure prediction· 2 Assay:whole-genome sequencing· 2 Organism:Arabidopsis· 1 Approach:benchmark study· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Peter N. DoddsiD· 2 shared An YuiD· 1 shared Beibei XiniD· 1 shared Boštjan KobeiD· 1 shared Bozhen HuiD· 1 shared Bryan Y. J. LimiD· 1 shared Camilla Langlands-PerryiD· 1 shared Carlotta Domeniconi· 1 shared

Activity by Year

2026-2026 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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2 shared papersMicrobiology

Peter N. DoddsORCID

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Author profile →

5 papers

Recent·Most cited

GPBench: A benchmark framework for genomic prediction

Xiaowei Zhang, Hanwen Luo, Geng Li, Xuerui Zhang, Siying Wang, Liliang Liu, Maozu Guo, Qiaoyu Tan, Carlotta Domeniconi, Jian Chen, Jun Wang, Guoxian Yu

GPBench provides a standardized benchmark framework for genomic prediction, evaluating 21 models across 16 species and offering tools for analysis and comparison.

bioRxiv · Nov 4, 2026 · PreprintGenomics

DeepD enables efficient genome modeling and controllable long-context sequence generation across domains of life

Jinsheng Lai, Beibei Xin, Zijian Wang, An Yu, Ziyang Chen, Yucheng Guo, Mingpei Zhang, Bozhen Hu, Chonghang Ye, Jian Chen, Qiujie Liu, Haiming Zhao, Weibin Song, Nanqing Dong, Fan Yang, , Hainan Zhao

DeepD is a genome foundation model that enables accurate sequence-to-function prediction and controllable genome-scale sequence generation across domains of life.

bioRxiv · Oct 18, 2026 · PreprintBioinformatics

EffectorGeneP: accurate gene annotation in pathogen genomes from infection transcriptomes

Jana Sperschneider, Camilla Langlands-Perry, Jian Chen, Jibril Lubega, Taj Arndell, David Lewis, Eva C. Henningsen, Cheryl Blundell, Thomas Vanhercke, Kanyuka Kostya, Melania Figueroa, Peter N. Dodds

EffectorGeneP improves gene annotation in pathogen genomes by predicting coding sequences from transcript data, outperforming existing methods and expanding the predicted secretome.

bioRxiv · May 5, 2026 · PreprintMicrobiology

CEACAM5/6+ Tumor Cells and IL-1β+ Macrophages Drive Resistance to Chemo-immunotherapy in Gastric Cancer

Jian Chen, Liudeng Zhang, Yikai Luo, Xu Han, Muxing Kang, Jing Chen, Wei Liu, Zhenzhen Xun, Guofeng Chen, Ke Chen, Shenbin Xu, Yu Zhang, Zhiwei Wu, Wenxuan Wu, Z. R. Hao, , Han Liang

The paper identifies two resistance mechanisms in gastric cancer to chemo-immunotherapy, involving CEACAM5/6+ tumor cells and IL-1β+ macrophages, and suggests them as biomarkers and therapeutic targets.

bioRxiv · Mar 8, 2026 · PreprintCancer Biology

Structural basis of canonical TIR-NLR activation in plant innate immunity

Natsumi Maruta, Weixi Gu, Bryan Y. J. Lim, Mitchell Sorbello, Dalton H. Y. Ngu, Chacko Jobichen, Jeffrey D. Nanson, Yan Li, Jian Chen, Megan A. Outram, Maud Bernoux, Md Motiur Rahman, Thi Danh Vu, Hongyi Xu, Lei Wang, , Boštjan Kobe

The paper determines cryo-EM structures of a plant TNL NLR, revealing its activation mechanism and NAD+ recognition, which informs engineering disease-resistant crops.

bioRxiv · Feb 6, 2026 · PreprintPlant Biology