Biosketch

Dr. Fang received his Ph.D. from Peking University. He had postdoctoral training in Columbia University and the Children’s Hospital of Philadelphia. In November 2022, he joined Sun Yat-sen University and won the Yat-sen Scholar Award. He is now an Associate Professor in Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine. Dr. Fang is a bioinformatics researcher with expertise in human genetic variation. His research interests include the development of computational tools for detection and annotation of genetic variants that may be involved in human diseases.

Selected Publications

1. Jiang T, Fang L#, Wang K#. Deciphering “the language of nature”: A transformer-based language model for deleterious mutations in proteins. The Innovation. 2023. (#corresponding author, IF: 32.1)
   DOI: 10.1016/j.xinn.2023.100487
2. Ahsan MU, Liu Q, Perdomo JE, Fang L, Wang K. A survey of algorithms for the detection of genomic structural variants from long-read sequencing data. Nature Methods. 2023. (IF: 48.0)
   DOI: 10.1038/s41592-023-01932-w
3. Fang L*, Monteys AM*, Dürr A, Keiser M, Cheng C, Harapanahalli A, et al. Haplotyping SNPs for allele-specific gene editing of the expanded huntingtin allele using long-read sequencing. Human Genetics and Genomics Advances. 2023;4(1):100146 (*co-first author)
   DOI: 10.1016/j.xhgg.2022.1001466
4. Fang L, Wang K. Polishing high-quality genome assemblies. Nature Methods. 2022;19(6):649-50. (IF: 48.0)
   DOI: 10.1038/s41592-022-01515-1
5. Fang L*, Liu Q*, Monteys AM, Gonzalez-Alegre P, Davidson BL, Wang K. DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing. Genome Biology. 2022;23(1):108. (*co-first author, IF: 17.9)
   DOI: 10.1186/s13059-022-02670-6
6. Fang L, Kao C, Gonzalez MV, Mafra FA, Pellegrino da Silva R, Li M, et al. LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data. Nature Communications. 2019;10(1):5585. (IF: 17.694)
   DOI: 10.1038/s41467-019-13397-7
7. Zhao M*, Havrilla JM*, Fang L*, Chen Y, Peng J, Liu C, Wu C, Sarmady M, Botas P, Isla J, Lyon GJ, Weng C, Wang K. Phen2Gene: rapid phenotype-driven gene prioritization for rare diseases. NAR Genomics and Bioinformatics. 2020;2(2):lqaa032. (*co-first author)
   DOI: 10.1093/nargab/lqaa032
8. Fang L, Wang K. Identification of Copy Number Variants from SNP Arrays Using PennCNV. Methods in Molecular Biology. 2018;1833:1-28. (Springer book series)
   DOI: 10.1007/978-1-4939-8666-8_1

Online Preprint

• Fang L*, Chen Q*, Wei CH, Lu Z, Wang K. Bioformer: an efficient transformer language model for biomedical text mining. 2023. Preprint at Arxiv https://doi.org/10.48550/arXiv.2302.01588 (*co-first author)

Contact Information

Email: fangli9@mail.sysu.edu.cn
Address: North Campus of Sun Yat-sen University, Guangzhou, 510080, China