潘瑋華課題組

Pan Weihua Lab

課題組長

潘瑋華，研究員,，博士生導(dǎo)師,。2019年獲美國加州大學(xué)河濱分校計算機科學(xué)博士學(xué)位和統(tǒng)計學(xué)碩士學(xué)位。2019-2020年在美國卡內(nèi)基梅隆大學(xué)計算機學(xué)院計算生物學(xué)系擔(dān)任Lane Fellow（博士后）,。長期從事基因組學(xué),，尤其是基因組序列分析相關(guān)的生物信息算法研究。主要成果發(fā)表在頂級會議RECOMB,、ISMB和專業(yè)期刊Genome Research,、Plant Physiology、National Science Review,、Molecular Plant,、Bioinformatics,、Genomics Proteomics & Bioinformatics等。主持國家自然科學(xué)基金面上項目,、青年科學(xué)基金項目,、深圳市優(yōu)秀科技創(chuàng)新人才培養(yǎng)項目等科研項目。擔(dān)任中國生物信息學(xué)學(xué)會（籌）生物信息算法專委會委員,、中國生物工程學(xué)會計算生物學(xué)與生物信息學(xué)專委會委員等,。擔(dān)任Frontiers in Plant Science和Genes等期刊客座編輯。

課題組聯(lián)系方式：潘瑋華（[email protected]）,、蔣和靈（[email protected]）

工作經(jīng)歷

2020.09-至今           中國農(nóng)業(yè)科學(xué)院（深圳）農(nóng)業(yè)基因組研究所,，研究員

2019.09-2020.08     美國卡內(nèi)基梅隆大學(xué)，Lane Fellow（博士后）

教育經(jīng)歷

2014.09-2019.09        美國加州大學(xué)（河濱分校）, 計算機科學(xué), 博士

2016.09-2018.06        美國加州大學(xué)（河濱分校）, 統(tǒng)計學(xué), 碩士

2011.09-2014.06        中國科學(xué)技術(shù)大學(xué), 計算機軟件與理論, 碩士

2007.09-2011.06        南京師范大學(xué), 計算機科學(xué)與技術(shù), 學(xué)士

研究方向

本團隊主要從事基因組學(xué)相關(guān)的生物信息學(xué)算法研究,。目前尤其關(guān)注于基因組組裝,、單體分型、變異檢測等關(guān)鍵性計算問題,。將前沿的基因組學(xué)技術(shù),，如PacBio HiFi，Oxford Nanopore,，Hi-C,，BioNano，10x Genomics等,，與先進的計算技術(shù),，如組合優(yōu)化算法、圖論,、概率統(tǒng)計,、機器學(xué)習(xí)等相結(jié)合,，開發(fā)新穎,、準確、高效的算法用于攻克本領(lǐng)域尚未解決或完全解決的難題,，如多倍體基因組組裝,、端到端組裝、單體型組裝,、宏基因組組裝等,。并將開發(fā)的算法技術(shù)應(yīng)用于科研項目，輔助解決重大科研問題,。

論文發(fā)表情況

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. 該文完整版發(fā)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. 該文完整版發(fā)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.

潘瑋華課題組更新于2024年3月