主持国家重点研发计划课题和国家自然科学基金项目 参与过多个国际性大型研究项目，设计和实施欧洲生物信息研究所以高性能计算为基础的核心生物大数据分析应用大平台，服务超过180个国家和地区，被同行视为最闪亮的生物信息平台之一 主持和参与国家重点研发项目课题，包括生物医学数据的整合和注释、精准高效检索、大型软件工作流系统以及相关应用大平台开发，通过生物信息和人工智能技术研究基因组与疾病表型（医学影像）的关联。项目课题：
（1）科技部国家重点研发项目课题《精准医学大数据的整合与注释》，500万，主持；

（2）国自然基金委面上项目《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；

（3）科技部国家重点研发项目子课题《精准医学大数据分析应用方法体系》 120万，参与。

，在Nucleic Acids Research、Molecular Systems Biology、PNAS、Bioinformatics等国际权威期刊发表论文近30篇，总影响因子超200，总SCI引用近 5000，Google学者引用近1万5千，国际影响广泛。第一作者论文刊登在2015年的 Nucleic Acids Research (IF 10.162)生物信息顶级期刊上，发表两年来SCI他引超120次， Google Scholar 引用209次。Selected Publication （SCI总引用~5000, Google总引用 ~1万5千）
按时间倒序排列如下:

Zhang W, Zhang H, Yang H, Li M, Xie Z and Li W. (2018) Computational resources associating diseases with genotypes, phenotypes and exposures. Briefings in Bioinformatics, doi: 10.1093/bib/bby071

Cao C, et al. (2018) Deep Learning and its Applications in Biomedicine, Genomics, Proteomics & Bioinformatics, doi: 10.1016/j.gpb.2017.07.003

The UniProt Consortium. (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45(D1):D158-D169. [ doi: 10.1093/nar/gkw1099. PMID: 27899622; PMCID: PMC5210571]

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.


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.