潘玮华课题组

潘玮华课题组

Pan Weihua Lab

课题组长

潘玮华，研究员，博士生导师。2019年获美国加州大学河滨分校计算机科学博士学位和统计学硕士学位。2019-2020年在美国卡内基梅隆大学计算机学院计算生物学系担任Lane Fellow（博士后）。长期从事基因组学，尤其是基因组序列分析相关的生物信息算法研究。主要成果发表在顶级会议RECOMB、ISMB和专业期刊Genome Research、Plant Physiology、National Science Review、Molecular Plant、Bioinformatics、Genomics Proteomics & Bioinformatics等。主持国家自然科学基金面上项目、青年科学基金项目、深圳市优秀科技创新人才培养项目等科研项目。担任中国生物信息学学会（筹）生物信息算法专委会委员、中国生物工程学会计算生物学与生物信息学专委会委员等。担任Frontiers in Plant Science和Genes等期刊客座编辑。

课题组联系方式：潘玮华（panweihua@caas.cn）、蒋和灵（jiangheling@caas.cn）

工作经历

2020.09-至今           中国农业科学院（深圳）农业基因组研究所，研究员

2019.09-2020.08     美国卡内基梅隆大学，Lane Fellow（博士后）

教育经历

2014.09-2019.09        美国加州大学（河滨分校）, 计算机科学, 博士

2016.09-2018.06        美国加州大学（河滨分校）, 统计学, 硕士

2011.09-2014.06        中国科学技术大学, 计算机软件与理论, 硕士

2007.09-2011.06        南京师范大学, 计算机科学与技术, 学士

研究方向

本团队主要从事基因组学相关的生物信息学算法研究。目前尤其关注于基因组组装、单体分型、变异检测等关键性计算问题。将前沿的基因组学技术，如PacBio HiFi，Oxford Nanopore，Hi-C，BioNano，10x Genomics等，与先进的计算技术，如组合优化算法、图论、概率统计、机器学习等相结合，开发新颖、准确、高效的算法用于攻克本领域尚未解决或完全解决的难题，如多倍体基因组组装、端到端组装、单体型组装、宏基因组组装等。并将开发的算法技术应用于科研项目，辅助解决重大科研问题。

论文发表情况

1. D. Xu†, J. Yang†, H. Wen†, W. Feng†, X. Zhang, X. Hui, J. Yue, Y. Xu*, F. Chen*, W. Pan*. CentIER: Accurate centromere identification for plant genomes, Plant Communications, vol. 5, no. 10, 2024.

2. Y. Lu†, J. Yang†, C. Li†, Y. Tian, R. Chang, D. Kong, S. Yang, Y. Wang, Y. Zhang, X. Zhu*, W. Pan*, S. Kong*. Efficient and easy-to-use capturing three-dimensional metagenome interactions with GutHi-C, iMeta, 2024.

3. W. Yu†, H. Luo†, J. Yang†, S. Zhang†, H. Jiang†, X. Zhao, X. Hui, D. Sun, L. Li, X. Wei*, S.Lonardi*, W. Pan*. “Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes.” Genome Research, 2024.

4. L. Ding†, S. Wu†, Z. Hou†, A. Li, Y. Xu, H. Feng, W. Pan*, J. Ruan*. “Improving Error-Correcting Capability in DNA Digital Storage Via Soft-Decision Decoding.” National Science Review, 2023.

5. L. Shang†*, W. He†, T. Wang†, Y. Yang†, Q. Xu†, X. Zhao†, L. Yang, H. Zhang, X. Li, Y. Lv, W. Chen, S. Cao, X. Wang, B. Zhang, X. Liu, X. Yu, H. He, H. Wei, Y. Leng, C. Shi, M. Guo, Z. Zhang, B. Zhang, Q. Yuan, H. Qian, X. Cao, Y. Cui, Q. Zhang, X. Dai, C. Liu, L. Guo, Y. Zhou, X. Zheng, J. Ruan, Z. Cheng, W. Pan*, Q. Qian*. “A complete assembly of the rice Nipponbare reference genome.” Molecular Plant, vol 16, 2023.

6. D. Xu†, Y. Yang†, D. Gong†, X. Chen†, K. Jin, H. Jiang, W. Yu, J. Li*, J. Zhang*, W. Pan*. “GFAP: ultra-fast and accurate gene functional annotation software for plants.” Plant Physiology, 2023. 

7. D. Xu†, J. Zhang†, X. Zhao†, Y. Hou, H. Jiang, W. He*, X. Ma*, W. Pan*. “CIDP: a multi-functional platform for designing CRISPR sgRNAs.” Horticulture Research, vol 10, 2023.

8. J. Yang†, X. Zhao†, H. Jiang†, Y. Yang†, Y. Hou, W. Pan*. “RAfilter: an algorithm for detecting and filtering false-positive alignments in repetitive genomic regions.” Horticulture Research, vol 10, 2023. 

9. D. Xu†, Y. Song†, X. Zhao, D. Gong, Y. Yang*, W. Pan*. “RAviz: a visualization tool for detecting false-positive alignments in repetitive genomic regions.” Horticulture Research, vol 9, 2022

10. W. Pan*, J. Ruan*. “En Route to Completion: What Is An Ideal Reference Genome?” Genomics, Proteomics & Bioinformatics, vol. 20, no. 1, pp. 1-3, 2022.

11. W. Pan, T. Jiang, S. Lonardi*. “OMGS: Optical Map-based Genome Scaffolding.” Proceedings of Conference on Research in Computational Molecular Biology (RECOMB), pp. 190-207, Washington, DC, 2019. 该文完整版发表于Journal of Computational Biology, vol. 27, no. 4, pp. 519-533, 2020. 

12. W. Pan, S. Lonardi*. “Accurate detection of chimeric contigs via Bionano optical maps.” Bioinformatics, vol. 35, no. 10, pp. 1760-1762, 2019. 

13. W. Pan, S. Wanamaker, A. Ah-Fong, H. Judelson, S. Lonardi*. “Novo&Stitch: Accurate Reconciliation of Genome Assemblies via Optical Maps.” Proceedings of Conference on Intelligent Systems for Molecular Biology (ISMB), Chicago, IL, 2018. 该文完整版发表于Bioinformatics, vol. 34, no. 13, pp. i43-i51, 2018.

14. W. Pan, B. Chen, Y. Xu*. “MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing.” Interdisciplinary Sciences: Computational Life Sciences, vol. 7, no. 4, pp. 405-413, 2015. 

15. W. Pan, Y. Zhao, Y. Xu*, F. Zhou*. “WinHAP2: an extremely fast haplotype phasing program for long genotype sequences.” BMC bioinformatics vol. 15, no. 1, pp. 164, 2014.

潘玮华课题组更新于2024年3月