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，深圳市海外高层次人才。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National Science Review、Molecular Plant、Bioinformatics、Genomics Proteomics & Bioinformatics、Plant Physiology等。主持国家自然科学基金、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（[email protected]）、蒋和灵（[email protected]）
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. 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.
2. 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.
3. 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.
4. 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.
5. 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.
6. 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
7. 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.
8. 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.
9. W. Pan, S. Lonardi*. “Accurate detection of chimeric contigs via Bionano optical maps.” Bioinformatics, vol. 35, no. 10, pp. 1760-1762, 2019.
10. 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.
11. 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.
12. 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1月