About Me

I am a joint Ph.D. student focused on Bioinformatics at the Agricultural Genomics Institute at Shenzhen (AGIS, China🇨🇳) and the University of Liège (ULiège, Belgium🇧🇪), primarily supervised by Prof. Sanwen Huang. Before joining AGIS, I received my M.S. in the Department of Plant Science at Kongju National University (KNU, South Korea 🇰🇷), supervised by Prof. Yong-jin Park.

My research focuses on 🥔potato breeding🥔 using bioinformatics and AI. With the rapid growth of genomic data, I aim to uncover hidden insights by integrating multi-omics and AI to decode the “language of life” through genomics and explore evolutionary trajectories in the tree of life.

Selected Publications

• Leveraging a phased pangenome for haplotype design of hybrid potato
  • Lin Cheng*, Nan Wang, Zhigui Bao, Qian Zhou, Andrea Guarracino, Yuting Yang, Pei Wang, Zhiyang Zhang, Dié Tang, Pingxian Zhang, Yaoyao Wu, Yao Zhou, Yi Zheng, Yong Hu, Qun Lian, Zhaoxu Ma, Ludivine Lassois, Chunzhi Zhang, William J. Lucas, Erik Garrison, Nils Stein, Thomas Städler, Yongfeng Zhou & Sanwen Huang†
  • Nature (2025) |Code
• ‘Perfect potato’ designed thanks to unearthed genetic diversity
  • Lin Cheng* & Sanwen Huang†
  • Nature research briefing (2025)
• A 6.49-Mb inversion associated with the purple embryo spot trait in potato
  • Pei Wang, Lin Cheng*, Jun Pan, Lianlian Ma, Xiaojing Hu, Zhong Zhang, Dawei Li, Yanhui Zhu, Shiwei Chang, Pingping Yuan, Philip Kear, Ludivine Lassois, Guangtao Zhu, Sanwen Huang, Hui Du† & Chunzhi Zhang†
  • aBIOTECH (2024)
• Genome evolution and diversity of wild and cultivated potatoes
  • Dié Tang, Yuxin Jia, Jinzhe Zhang, Hongbo Li, Lin Cheng, Pei Wang, Zhigui Bao, Zhihong Liu, Shuangshuang Feng, Xijian Zhu, Dawei Li, Guangtao Zhu, Hongru Wang, Yao Zhou, Yongfeng Zhou, Glenn J. Bryan, C. Robin Buell, Chunzhi Zhang & Sanwen Huang†
  • Nature (2022)
• Graph pangenome captures missing heritability and empowers tomato breeding
  • Yao Zhou, Zhiyang Zhang, Zhigui Bao, Hongbo Li, Yaqing Lyu, Yanjun Zan, Yaoyao Wu, Lin Cheng, Yuhan Fang, Kun Wu, Jinzhe Zhang, Hongjun Lyu, Tao Lin, Qiang Gao, Surya Saha, Lukas Mueller, Zhangjun Fei, Thomas Städler, Shizhong Xu, Zhiwu Zhang, Doug Speed & Sanwen Huang†
  • Nature (2022)
• Signatures of differential selection in chloroplast genome between japonica and indica
  • Lin Cheng*, Jungrye Nam, Sang-Ho Chu, Phitaktansakul Rungnapa, Myeong-hyeon Min, Yuan Cao, Ji-min Yoo, Jee-Su Kang, Kyu-Won Kim† & Yong-Jin Park†
  • Rice (2019)
• Evidence for selection events during domestication by extensive mitochondrial genome analysis between japonica and indica in cultivated rice
  • Lin Cheng*, Kyu-Won Kim & Yong-Jin Park†
  • Scientific Report (2019)

Recent News

• [2025.01] Nature article accepted as a first author🎉.
• [2024.07] Arrivied in Belgium, continuing research.
• [2022.06] Two articles are acceepted by Nature.
• [2021.09] 🎉Ph.D🎉 enrollment in AGIS and University of Liege.

Strengths

• Programming language : Linux, Python and R.

• Bioinformatics: Pangenomes, comparative genomics, transcriptomic, microbiome et al. (All bioinformatics-related analyses are not difficult for me).

  For example: Genome assembly, annotation, variation calling (SNPs, SVs), Differential gene expression, Gene ontology (GO), Synteny analysis, phylogenetic tree, population structure, Principal component analysis (PCA), Bulked Segregant Analysis (BSA), ChIP-seq, 16S, 18S, ITS.

• Language: English: IELTS 6.5 (2019), Beginner (Korean, Japanese and French).
• Personal: Strong self-learning ability, Independent, Diligent, Love life/nature🎾⛰🌊🏂🏻🪂…