PI

Weihua Pan, Professor, PhD advisor, Shenzhen Overseas High-level Talent. He graduated from University of California, Riverside in 2019 and received a Ph.D. degree in Computer Science and a master degree in Statistics. He subsequently worked as a Lane Fellow in School of Computer Science, Carnegie Mellon University. He has been working on genomics for a long time, especially focusing on algorithm design related to genome sequence analysis. His major achievements have been published in top conferences such as RECOMB, ISMB and professional journals like National Science Review, Molecular Plant, Bioinformatics, Genomics Proteomics & Bioinformatics, Plant Physiology. He is leading a few research programs such as National Natural Science Foundation of China and Shenzhen Outstanding Science and Technology Innovation Talent Cultivation Project. He is a member of the Special Committee on Bioinformatics Algorithms of the Chinese Society of Bioinformatics, and a member of the Special Committee on Computational Biology and Bioinformatics of the Chinese Society of Bioengineering. He is a guest editor of Frontiers in Plant Science and Genes.

Research Experience

2020.09-Present: Agricultural Genomics Institute at Shenzhen-CAAS Professor

2019.09-2020.08: Carnegie Mellon University, Lane Fellow

Education

2014.09-2019.09: University of California, Riverside, Computer Science, Ph.D.

2016.09-2018.06: University of California, Riverside, Statistics, M.S.

2011.09-2014.06: University of Science and Technology of China, Computer Software and Theory, M.E.

2007.09-2011.06: Nanjing Normal University, Computer Science and Technology, B.E.

Research Interest

Our research focuses on designing algorithms to solve key problems in genomics such as genome assembly, haplotype phasing and variant calling. We integrate cutting-edge genomics technologies such as Pacbio HiFi, Oxford Nanopore, Hi-C, BioNano and 10x Genomics with computational methods such as combinatorial optimization algorithms, graph theory, statistics and machine learning to develop novel, accurate and efficient algorithms to solve computational problems like polyploid genome assembly, haplotype reconstruction, telomere to telomere assembly and metagenome assembly. And we apply computational methods developed to important scientific discovery.

Selected Publication

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. The full version of this article was published in the 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. The full version of this article was published in the 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.