精准医学生物信息实验室

学术论著与教材

Selected Publication:

• Minglei Yang, Chenghao Lin, Yanni Wang, Kang Chen, Yutong Han, Haiyue Zhang, Weizhong Li#, Cytokine storm promoting T cell exhaustion in severe COVID-19 revealed by single cell sequencing data analysis, Precision Clinical Medicine, Volume 5, Issue 2, June 2022. 点击跳转
• 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. 点击跳转
• 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. 点击跳转
• 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. 点击跳转
• 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. 2021:S1672-0229(20)30169-8. 点击跳转
• 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. 2020:166727. 点击跳转
• 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.  点击跳转
• Yang M, Zhang W, Yao G, Zhang H, Li W.† (2019) Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D. Database (Oxford). baz092.
• 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 Bioinf, 20(6):2098-2115.
• Pearson WR, Li W., Lopez R. (2017) Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold. Nucleic Acids Res. 45(7):e46.  点击跳转
• The UniProt Consortium. (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res. 45(D1):D158-D169. 点击跳转
• Li W.*, Cowley A*, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R. (2015) The EMBL-EBI bioinformatics web and programmatic tools framework, Nucleic Acids Res. 43:W580-4.
• Squizzato, S, Park, Y.M., Buso, N., Gur, T., Cowley, A., Li, W., et al. (2015) The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI, Nucleic Acids Res., 43:W585-8. 点击跳转
• Jones, P., Binns, D., Chang, HY, Fraser, M, Li, W., et al. (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics.  点击跳转
• Li, W., Kondratowicz, B., McWilliam, H., Nauche, S. and Lopez, R. (2013) The Annotation-enriched Non-redundant Patent Sequence Databases. Database (Oxford) 2013:bat005. 点击跳转
• McWilliam, H., Li, W., Uludagi, M., Squizzato, S., Park, Y.M., Buso, N., Cowley, A.P., Lopez, R. (2013) Analysis tool web services from the EMBL-EBI. Nucleic Acids Res. 41:W597-600.  点击跳转
• Li, W., McWilliam, H., Goujon, M., Cowley, A., Lopez, R., and Pearson, W.R. (2012) PSI-Search: iterative HOE-reduced profile SSEARCH searching. Bioinformatics 28:1650-1651. 点击跳转
• Sievers, F., et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology. 点击跳转
• Li W., McWilliam, H., Richart de la Torre, A., Grodowski, A., Benediktovich, I., Goujon, M., Nauche, S., Lopez, R. (2010) Non-redundant patent sequence databases with value-added annotations at two levels. Nucleic Acids Res. 38:D52-D56.
• Li, W., Olohan, L., Williams, D., Hughes, M., Gracey, A., Cossins, A. (2009) Application of ESTs in Microarray Analysis. Methods in Molecular Biology 533:1-21. 点击跳转
• Li, W., Gracey, A.Y., Vieira Mello, L., Brass, A. and Cossins, A.R. (2009) ExprAlign - the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles. BMC Genomics 10:560  点击跳转
• Gracey, A. Y., Fraser, E. J., Li, W., Fang, Y., Taylor, R. R., Rogers, J., Brass, A. (2004). Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc. Natl. Acad. Sci. USA. 101: 16970-16975. 点击跳转
• 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  点击跳转
• 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 点击跳转
• 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. 点击跳转
• 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