学科专业：生物信息学、医学人工智能、精准医学大数据
                  
研究方向
1、    基于单细胞多组学的人体细胞图谱构建与复杂疾病诊疗应用
2、    人工智能在生命组学和医学大数据的研究与应用
3、    精准医学大数据的关键信息技术研发与整合

个人简介
李伟忠，中山大学医学院长聘教授、博导，毕业于中山大学（学士）、英国利物浦大学（博士）；入选广东省珠江人才计划、广州市创新领军人才，现任广东省生物信息学会秘书长、中国人工智能学会生物信息学与人工生命专委会委员、国际期刊Precision Clinical Medicine 编委。曾主持国家重点研发计划课题、国自然面上项、广东省重点等项目多项；在Nature Communications, PNAS, Genome Medicine, Nucleic Acids Research, BMC Medicine, Artificial Intelligence in Medicine等国际权威期刊发表论文40余篇，总SCI引用近1万，Google学者引用近3万5千, 影响广泛；担任Nature Machine Intelligence, Cell Reports Medicine等国际权威期刊评审。曾任欧洲生物信息研究所（EMBL-EBI）高级软件工程师，深度参与了多个国际性大型研究项目，包括UniProt、ENA、Ensembl Genomes、JDispatcher等。近年围绕肺部重大疾病的免疫耐药及其微环境特征等前沿科学问题，进行了生物信息学和医学人工智能的深入研究，尝试开拓生物信息在医学研究和应用的新范式，建立了多个疾病相关的知识图谱、数据平台和AI算法，助力揭示肺部疾病的分子机制和精准诊治，国家发明专利申请12项，已授权7项。

欢迎由计算机、生物、医学、数学背景的同学报考本实验室的硕士、博士研究生。
实验室网站：http://lilab2.sysu.edu.cn/ & http://www.liwzlab.cn
电子邮件：liweizhong at mail.sysu.edu.cn

代表性学术论著与教材：
Selected Publication （SCI论文40+篇，SCI总引用~1万, Google总引用 ~3万5千）（时间倒序排列）:
通讯作者文章：
•    Deng Y, Yao Y, Wang Y, Yu T, Cai W, Zhou D, Yin F, Liu W, Liu Y, Xie C, Guan J, Hu Y, Huang P, Li W#. An end-to-end deep learning method for mass spectrometry data analysis to reveal disease-specific metabolic profiles. Nature Communications. 2024 Aug 20;15(1):7136. doi: 10.1038/s41467-024-51433-3. PMID: 39164279; PMCID: PMC11335749.
•    Chen K, Han Y, Wang Y, Zhou D, Wu F, Cai W, Zheng S, Xiao Q, Zhang H, Li W#. scMoresDB: A comprehensive database of single-cell multi-omics data for human respiratory system. iScience. 2024 Mar 26;27(4):109567. doi: 10.1016/j.isci.2024.109567. PMID: 38617561; PMCID: PMC11015448.
•    Liao Z*, Yan C*, Wang J*,  Zhang N, Yang H, Lin C, Zhang H, Wang W#, Li W#,, A clinical consensus-compliant deep learning approach to quantitatively evaluate human in vitro fertilization early embryonic development with optical microscope images, Artificial Intelligence in Medicine, 2024 Jan 19;149:102773. doi: 10.1016/j.artmed.2024.102773.
•    Wu F, Lin C, Han Y, Zhou D, Chen K, Yang M, Xiao Q, Zhang H, Li W#. Multi-omic analysis characterizes molecular susceptibility of receptors to SARS-CoV-2 spike protein. Comput Struct Biotechnol J. 2023 Nov 10;21:5583-5600. doi: 10.1016/j.csbj.2023.11.012. PMID: 38034398; PMCID: PMC10681948. 
•    Li W#, Yan C. GLUE multimodal single cell data. Precis Clin Med. 2023 Mar 20;6(1):pbad007. doi: 10.1093/pcmedi/pbad007. PMID: 37007746; PMCID: PMC10052360.
•    Yang M, Lin C, Wang Y, Chen K, Zhang H, Li W#. Identification of a cytokine-dominated immunosuppressive class in squamous cell lung carcinoma with implications for immunotherapy resistance. Genome Medicine. 2022 Jul 8;14(1):72. doi: 10.1186/s13073-022-01079-x. PMID: 35799269; PMCID: PMC9264601.
•    Yang H, Chen L, Cheng Z, Yang M, Wang J, Lin C, Wang Y, Huang L, Chen Y, Peng S, Ke Z, Li W#. Deep learning-based six-type classifier for lung cancer and mimics from histopathological whole slide images: a retrospective study. BMC Medicine. 2021 Mar 29;19(1):80. doi: 10.1186/s12916-021-01953-2. PMID: 33775248; PMCID: PMC8006383.
•    Yang M, Lin C, Wang Y, Chen K, Han Y, Zhang H, Li W#. Cytokine storm promoting T cell exhaustion in severe COVID-19 revealed by single cell sequencing data analysis. Precis Clin Med. 2022 May 23;5(2):pbac014. doi: 10.1093/pcmedi/pbac014. PMID: 35694714; PMCID: PMC9172646.
•    Yao G, Zhang W, Yang M, Yang H, Wang J, Zhang H, Wei L, Xie Z, Li W#. MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes. Genomics Proteomics Bioinformatics. 2020 Dec;18(6):760-772. doi: 10.1016/j.gpb.2020.11.001. Epub 2021 Jan 6. PMID: 33418085; PMCID: PMC8377004. 
•    Zhang W, Zhang H, Yang H, Li M, Xie Z, Li W#. Computational resources associating diseases with genotypes, phenotypes and exposures. Brief Bioinform. 2019 Nov 27;20(6):2098-2115. doi: 10.1093/bib/bby071. PMID: 30102366; PMCID: PMC6954426.
•    Zhang W#, Zeng B, Lin H, Guan W, Mo J, Wu S, Wei Y, Zhang Q, Yu D, Li W#, Chan GC#. CanImmunother: a manually curated database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects. Oncoimmunology. 2021 Jul 16;10(1):1944553. doi: 10.1080/2162402X.2021.1944553. PMID: 34345532; PMCID: PMC8288037.
•    Chen Y, Yang H, Cheng Z, Chen L, Peng S, Wang J, Yang M, Lin C, Chen Y, Wang Y, Huang L, Chen Y, Li W#, Ke Z#. A whole-slide image (WSI)-based immunohistochemical feature prediction system improves the subtyping of lung cancer. Lung Cancer. 2022 Jan 10;165:18-27. doi: 10.1016/j.lungcan.2022.01.005. Epub ahead of print. PMID: 35065344. 
•    Zhang W, Zeng B, Yang M, Yang H, Wang J, Deng Y, Zhang H, Yao G, Wu S, Li W#. ncRNAVar: A Manually Curated Database for Identification of Noncoding RNA Variants Associated with Human Diseases. J Mol Biol. 2021 May 28;433(11):166727. doi: 10.1016/j.jmb.2020.166727. Epub 2020 Dec 1. PMID: 33275967. 
•    Zhang W, Yao G, Wang J, Yang M, Wang J, Zhang H, Li W#. ncRPheno: a comprehensive database platform for identification and validation of disease related noncoding RNAs. RNA Biol. 2020 Jul;17(7):943-955. doi: 10.1080/15476286.2020.1737441. Epub 2020 Mar 26. PMID: 32122231; PMCID: PMC7549653. 
•    Yang M, Zhang W, Yao G, Zhang H, Li W#. Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D. Database (Oxford). 2019 Jan 1;2019:baz092. doi: 10.1093/database/baz092. PMID: 31317184; PMCID: PMC6637259.
第一作者文章：
•    Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R. The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res. 2015 Jul 1;43(W1):W580-4. doi: 10.1093/nar/gkv279. Epub 2015 Apr 6. PMID: 25845596; PMCID: PMC4489272.
•    Li W, McWilliam H, de la Torre AR, Grodowski A, Benediktovich I, Goujon M, Nauche S, Lopez R. Non-redundant patent sequence databases with value-added annotations at two levels. Nucleic Acids Res. 2010 Jan;38(Database issue):D52-6. doi: 10.1093/nar/gkp960. Epub 2009 Nov 1. PMID: 19884134; PMCID: PMC2808894.
•    Li W, Kondratowicz B, McWilliam H, Nauche S, Lopez R. The annotation-enriched non-redundant patent sequence databases. Database (Oxford). 2013 Feb 9;2013:bat005. doi: 10.1093/database/bat005. PMID: 23396323; PMCID: PMC3568390.
•    Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR. PSI-Search: iterative HOE-reduced profile SSEARCH searching. Bioinformatics. 2012 Jun 15;28(12):1650-1. doi: 10.1093/bioinformatics/bts240. Epub 2012 Apr 25. PMID: 22539666; PMCID: PMC3371869.
•    Li W, Gracey AY, Mello LV, Brass A, Cossins AR. ExprAlign--the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles. BMC Genomics. 2009 Nov 26;10:560. doi: 10.1186/1471-2164-10-560. PMID: 19939286; PMCID: PMC2790474.
•    Li W, Olohan L, Williams D, Hughes M, Gracey A, Cossins A. Application of ESTs in microarray analysis. Methods Mol Biol. 2009;533:289-309. doi: 10.1007/978-1-60327-136-3_14. PMID: 19277566.
重点参与文章：
•    Pearson WR, Li W, Lopez R. Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold. Nucleic Acids Res. 2017 Apr 20;45(7):e46. doi: 10.1093/nar/gkw1207. PMID: 27923999; PMCID: PMC5605230.
•    McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R. Analysis Tool Web Services from the EMBL-EBI. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W597-600. doi: 10.1093/nar/gkt376. Epub 2013 May 13. PMID: 23671338; PMCID: PMC3692137.
•    Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75. PMID: 21988835; PMCID: PMC3261699.
•    Gracey AY, Fraser EJ, Li W, Fang Y, Taylor RR, Rogers J, Brass A, Cossins AR. Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci U S A. 2004 Nov 30;101(48):16970-5. doi: 10.1073/pnas.0403627101. Epub 2004 Nov 18. PMID: 15550548; PMCID: PMC534716.
•    Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014 May 1;30(9):1236-40. doi: 10.1093/bioinformatics/btu031. Epub 2014 Jan 21. PMID: 24451626; PMCID: PMC3998142.
•    Squizzato S, Park YM, Buso N, Gur T, Cowley A, Li W, Uludag M, Pundir S, Cham JA, McWilliam H, Lopez R. The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. Nucleic Acids Res. 2015 Jul 1;43(W1):W585-8. doi: 10.1093/nar/gkv316. Epub 2015 Apr 8. PMID: 25855807; PMCID: PMC4489232.

Book Chapters:
Lopez R, Cowley A, Li W, McWilliam H. Using EMBL-EBI Services via Web Interface and Programmatically via Web Services. Curr Protoc Bioinformatics. 2014;48 3.12.1-50. PMID: 25501941
Li W*, Olohan L, Williams D, Hughes M, Gracey A, Cossins A. Application of ESTs in microarray analysis. Methods Mol Biol. 2009;533 289-309. PMID: 19277566. 

获奖及荣誉：
广州市创新领军人才（2019年）、广东省珠江人才计划（2017年）

主持项目课题：
（1）科技部国家重点研发计划课题《多器官细胞全息图谱建设与疾病诊疗应用》，主持，2021-2024
（2）科技部国家重点研发计划课题《精准医学大数据的整合与注释》，主持，2016-2021；
（3）国自然面上项目《基于“无拼接组装、无参考基因组”的PB量级组学大数据高速“反向检索”新方法及其高移植性、高可视化平台在基因型分型的应用》，主持，2018-2019；
（4）广东省区域联合重点项目《单细胞多组学数据的整合计算方法》 ，主持，2022-2025；
（5）广东省自然科学基金项目《光镜图像中胚胎细胞的人工智能识别方法与胚胎发育无创评估系统》，主持，2021–2023。

学术兼职：
广东省生物信息学会秘书长
Precision Clinical Medicine 期刊编委
Nature Machine Intelligence、Genome Medicine、Genome Biology, Nucleic Acids Research、Briefings in Bioinformatics、GPB等期刊评审 
欧洲计算生物学大会（ECCB）成果展示评审
中国人工智能学会生物信息与人工生命专委会委员

曾任
- 国际蛋白联盟 UniProt Consortium 成员
- 国际核酸联合会（ INSDC ）欧洲分部成员
- 国际分子生物智能系统大会 (ISMB) 会员