Bioinformatics Laboratory for Precision Medicine


Selected Publication:

  • HuanYang1,LiliCheZhiqiangCheng MingleiYang1,JianboWang1,ChenghaoLin1,YuefengWang2,LeileiHuang2, YangshanChen2,SuiPengZunfuKe andWeizhongLi* Deep learning-based six-type classifier for lung cancer and mimics from histopathological whole slide images: a retrospective study (2021)BMC Medicin https://doi.org/10.1186/s12916-021-01953-2
  • wenliang Zhang, Binghui Zeng, Huancai Lin, Wen Guan, Jing Mo, Song Wu,Yanjie Wei, Qianshen Zhang, Dongsheng Yu, Weizhong Li & Godfrey Chi-FungChan CanImmunother: a manually curated databasefor identification of cancer immunotherapiesassociating with biomarkers, targets, and clinicaleffects (2020)OncoImmunology https://doi.org/10.1080/2162402X.2021.1944553
  • Guocai Yao, Wenliang Zhang, Minglei Yang, Huan Yang, Jianbo Wang, Haiyue Zhang, Lai Wei, Zhi Xie, Weizhong Li†  (2021) MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes.   Genomics, Proteomics & Bioinformatics. https://doi.org/10.1016/j.gpb.2020.11.001.
  • Zhang W, Zeng B, Yang M, Yang H, Wang J, Deng Y, Zhang H, Yao G, Wu S, Li W†  (2020) ncRNAVar: A Manually Curated Database for Identification of Noncoding RNA Variants Associated with Human Diseases.   J Mol Biol 2020 Dec 1. doi: 10.1016/j.jmb.2020.166727.
  • Zhang W, Yao G, Wang J, Yang M, Wang J, Zhang H, Li W.†  (2020) 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.
  • Pei S, Liu T, Ren X, Li W, Chen C, Xie Z. Benchmarking variant callers in next-generation and third-generation sequencing analysis [published online ahead of print, 2020 Jul 23]. Brief Bioinform. 2020;bbaa148. doi:10.1093/bib/bbaa148
  • Minglei Yang, Wenliang Zhang, Guocai Yao, Haiyue Zhang, Weizhong Li*. Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D. Database (2019) Vol. 2019: article ID baz092; doi:10.1093/database/baz092
  • Wenliang Zhang, Haiyue Zhang, Huan Yang, Miaoxin Li, Zhi Xie, Weizhong Li*. Computational resources associating diseases with genotypes, phenotypes and exposures. Briefings in Bioinformatics. 2018 Aug. PMID: 30102366
  • Chensi Cao,Feng Liu,Hai Tan,Deshou Song,Wenjie Shu, WeiZhong Li,Yiming Zhou,Xiaochen Bo,Zhi xie. Deep learning and it's applications in biomedicine.Genomics Proteomics Bioinformatics. 2017 Jul.

  • Pearson WR, Li W, Lopez R. Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold. Nucleic Acids Res. 2016 Dec . PMID: 27923999.

  • 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;43(W1) W580-4. PMID: 25845596

  • 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;7 539. PMID: 21988835

  • UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 2015 Jan;43(Database issue) D204-12. PMID: 25348405

  • 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. PMID: 19884134

  • Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR. PSI-Search: iterative HOE-reduced profile SSEARCH searching. Bioinformatics. 2012 Jun;28(12) 1650-1651. PMID: 22539666

  • Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R. A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res. 2010 Jul;38(Web Server issue) W695-9. PMID: 20439314

  • 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. PMID: 23671338

  • 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;30(9) 1236-1240. PMID: 24451626

  • 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;10 560. PMID: 19939286

  • Li W, Kondratowicz B, McWilliam H, Nauche S, Lopez R. The annotation-enriched non-redundant patent sequence databases. Database (Oxford). 2013;2013 bat005. PMID: 23396323

  • Silvester N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Ten Hoopen P, Kay S, Leinonen R, Li W, Liu X, Lopez R, Pakseresht N, Pallreddy S, Plaister S, Radhakrishnan R, Rossello M, Senf A, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Content discovery and retrieval services at the European Nucleotide Archive. Nucleic Acids Res. 2015 Jan;43(Database issue) D23-9. PMID: 25404130

  • 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;43(W1) W585-8. PMID: 25855807

  • Pakseresht N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Gur T, Jang M, Kay S, Leinonen R, Li W, Liu X, Lopez R, McWilliam H, Oisel A, Pallreddy S, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Squizzato S, ten Hoopen P, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Assembly information services in the European Nucleotide Archive. Nucleic Acids Res. 2014 Jan;42(Database issue) D38-43. PMID: 24214989

  • McWilliam H, Valentin F, Goujon M, Li W, Narayanasamy M, Martin J, Miyar T, Lopez R. Web services at the European Bioinformatics Institute-2009. Nucleic Acids Res. 2009 Jul;37(Web Server issue) W6-10. PMID: 19435877

  • 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;101(48) 16970-16975. PMID: 15550548

  • Williams DR, Epperson LE, Li W, Hughes MA, Taylor R, Rogers J, Martin SL, Cossins AR, Gracey AY. Seasonally hibernating phenotype assessed through transcript screening. Physiol Genomics. 2005 Dec;24(1) 13-22. PMID: 16249311

  • Gonzalez SF, Chatziandreou N, Nielsen ME, Li W, Rogers J, Taylor R, Santos Y, Cossins A. Cutaneous immune responses in the common carp detected using transcript analysis. Mol Immunol. 2007 Mar;44(7) 1664-1679. PMID: 17049603.

  • Zhang W#, Shi H#, Zhang M, Liu B, Mao S, Li L, Tong F, Liu G, Yang S, and Wang H*. Poly C binding protein 1 represses autophagy through downregulation of LC3B to promote tumor cell apoptosis in starvation. International Journal of Biochemistry and Cell Biology, 2016,73,127-136. IF=4.056.(# Co-first author)

  • ZHANG Wenliang, ZHANG Mingming, LIU Bin, SHI Hongshun, WANG Haihe*. Optimal timing of autophagy occurrence induced by earle’s balanced salts solution in DLD-1, HCT-116, A2780, CHO, Hep G2 and SMMC7721 cancer cell lines. Acta Scientiarum Naturalium Universitatis Sun Yat-seni, 2016, 55(4), 108-117.(Chinese core, English articles)

  • Li L, Shi H, Zhang M, Guo X, Tong Fang,Zhang W, Zhou J, Wang H*, and Yang S*. Upregulation of metastasis-associated PRL-3 initiates chordoma in zebrafish. International Journal of Oncology,2016,48(4)1541-1552.  IF=3.03. 

  • Huan Yang, Hua Tang, Xin-Xin Chen, Chang-Jian Zhang, Pan-Pan Zhu, Hui Ding, Wei Chen*, Hao Lin*. (2016) Identification of secretory proteins in mycobacterium tuberculosis using pseudo amino acid composition. BioMed Research International, 2016: 5413903. (2015 IF: 2.134)

  • Zhi-Yong Liang, Hong-Yan Lai, Huan Yang, Chang-Jian Zhang, Hui Yang, Huan-Huan Wei, Xin-Xin Chen, Ya-Wei Zhao, Zhen-Dong Su, Wen-Chao Li, En-Ze Deng, Hua Tang, Wei Chen*, Hao Lin* (2017) Pro54DB: a database for experimentally verified sigma-54 promoters. Bioinformatics, 33(3): 467-469. (2016 IF: 7.307)

  • Ting Zhang, Puwen Tan, Liqiang Wang, Nana Jin, Yana Li, Lin Zhang, Huan Yang, Zhenyu Hu, Lining Zhang, Chunyu Hu, Chunhua Li, Kun Qian, Changjian Zhang, Yan Huang, KongningLi*, Hao Lin*, Dong Wang*. (2017) RNALocate: a resource for RNA Subcellular Localizations. Nucleic Acids Research, 45(D1): D135-D138. (2016 IF: 10.162)

  • 杨明磊,晁江涛,王大伟,胡军华,龚达平,吴华,刘贯山.烟草C2H2基因家族成员鉴定及表达分析[J]. 遗传, 2016,38 (4): 337-349(生物信息学分析)

  • 向小华, 吴新儒, 晁江涛, 杨明磊, 杨帆, 陈果, 刘贯山, 王元英. 普通烟草WRKY基因家族的鉴定及表达分析[J] . 遗传, 2016, 38 (9): 840-856

  • 张艳艳,王倩,李晓旭,孙亭亭,龚达平,杨明磊,刘贯山.普通烟草MATE基因家族分析及功能预测[J].植物遗传资源学报,2015,16(6):1307-1314.

  • 胡军华,王大伟,杨明磊,王新,吴新儒,吴华,刘贯山.普通烟草DREB转录因子的序列鉴定与表达分析. 中国烟草科学. 2017 ,01: 1-7

Book Chapters:

  • 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.  
  • 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.  
  • 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
  • 普世医学, 标识肺部结节的候选框过滤、融合和自动更新方法、系统及存储介质 已申请未授权 发明专利 202010252924.6  
  • 普世医学, 基于深度学习的肺结节识别与分割方法及计算机设备 已申请未授权 发明专利 202011425293.X  
  • 普世医学,一种新冠肺炎磨玻璃病灶造影解析方法、系统及存储介质 已申请未授权 发明专利 202010433448.8  
  • 普世医学,基于基因变异与疾病表型自动关联匹配的遗传病预测系统 已申请未授权 发明专利 201810539136.8  


  • 普世医学,CT数据同步传输与自动扫描一体化系统 已获得软著证书 2020SR0371858
  • 普世医学,肺部CT影像深度智能筛查系统 已获得软著证书 2019SR0460891 
  • 普世医学,胸部CT影像深度智能辅助筛查系统 已获得软著证书 2020SR0373665
  • 普世医学,基于胸部CT影像的新冠肺炎智能辅助筛查系统 已获得软著证书 2020SR1035331 


  • Li W2019年广州市创新领军人才 


  • 数字病理图像分析方法、系统、设备及存储介质 PCT/CN2021/090360
  • 胚胎光镜图像中细胞的识别方法和系统、设备及存储介质 PCT/CN2021/090357
  • 代谢特征谱推断方法、系统、计算机设备及存储介质 PCT/CN2021/102060


  • 医学信息技术基础教程 科学出版社 出版年份:2020 编著情况:中山大学、南方医科大学参与编著 排序:编委之一 成效:成为5所高等院校的指定教材
  • 医学信息技术基础实验指导 科学出版社 出版年份:2020 编著情况:中山大学、南方医科大学参与编著 排序:编委之一 成效:成为5所高等院校的指定教材