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厦门大学生物信息学辅助药物开发研究组

Bioinfmatics-Aided Drug Discovery Group, Xiamen University

The BADD group focuses its research on two areas: (1) Bioinformatics-aided virtual drug discovery, especially on mechanistic understanding and prediction of drug efficacy, bioactivity and toxicity; development of a high-throughput virtual screening workflow or system for new drug discovery. (2) Data mining and "-omics", especially on development of novel methods and applications to seek meaningful clues from high throughput data, e.g. microarray and RNA-seq.

Pharmacoinformatics and Drug Design
ADReCS
 Adverse Drug Reaction Classification System（ADReCS）is an ADR ontology database that provides standardization and hierarchical classification of ADRs.
ADRAlert
 Adverse Drug Reaction Alert（ADRAlert） is an on-line server developed for rapid quantitative assessment of clinical ADRs. It is constructed on a genome wide drug-gene-ADR association network, predicting potential clinical ADRs with frequency estimation via seeking associations between drug-induced significant genes and ADRs.
ADReCS-Target
 Adverse Drug Reaction Classification System-Target Profile（ADReCS-Target）provides comprehensive information about ADRs caused by drug interaction with protein, gene and genetic variation.
ADMETNet
 Absorption, Distribution, Metabolism, Exctretion and Toxicity Network Database（ADMETNet）is a comprehensive, interaction, visual nwtwork database containing 1,541 FDA approved small molecule drugs, more than 1,974 non-redunant protein as well as more than 9,246 drug ADMET pathways found in humans.

Bioinformatics and Systems Biology
IncDNA
 We constructed an Integrative transcript library-Branchiostoma floridae, IncDNA-BF from heterogenous RNA-seq datasets and EST data. Transcriptome assembled by referring to this library show superior to that by genome-based or de novo methods. It will be particularly useful for systematic and dynamic exploration of gene behavior, regardless of the genome quality.
PaGeFinder
 Pattern Gene Finder （PaGeFinder）is a free web-based server to provide interactive pattern analysis of user-submitted gene expression profiles generated by high throughput technologies, e.g. microarray, next generation sequencing or SAGE.
PaGenBase
 Pattern Gene Database （PaGenBase）is a novel repository that collects information of spatiotemporal pattern genes derived from literature and data mining of more than 123,000 gene expression profiles over 1,004 samples among 11 model organisms. It provides information of specific genes, housekeeping genes, selective genes and repressed genes in different conditions.

Publication List

  1. Yue QX, Ding RF, Chen WH, Wu LY, Liu K, Ji ZL*. Mining Real-World Big Data to Characterize Adverse Drug Reaction Quantitatively: Mixed Methods Study. Journal of Medical Internet Research. 2024 May 3;26:e48572.

  2. Tong MS, Liu Z, Li JA, Wei X, Shi WH, Liang CY, Yu CY, Huang RT, Lin YX, Wang XK, Wang S, Wang Y, Huang JL, Wang YN, Li TT*, Qin J*, Zhan DD*, Ji ZL*. PhosMap: An ensemble bioinformatic platform to empower interactive analysis of quantitative phosphoproteomics. Computers in Biology and Medicine. 2024 May;174:108391.

  3. Zhao MX, Ding RF, Chen Q, Meng JH, Li FL, Fu SS, Huang BL, Liu Y, Ji ZL*, Zhao YF*. Nphos: Database and Predictor of Protein N-phosphorylation. Genomics, Proteomics & Bioinformatics. 2024. doi: 10.1093/gpbjnl/qzae032.

  4. Shi H, Li QY, Li H, Wang HY, Fan CX, Dong QY, Pan BC*, Ji ZL*, Li JY*. ROS-induced oxidative stress is a major contributor to sperm cryoinjury. Human Reproduction. 2024 Feb 1;39(2):310-325.

  5. Li YF, Li QY, Wu LY, Wang HY, Shi H, Yang CH, Gu YQ*, Li JY*, Ji ZL*. SperMD: the expression atlas of sperm maturation. BMC Bioinformatics. 2024 Jan 17;25(1):29.

  6. Lin Z, Qin YM, Chen H, Shi D, Zhong MD, An T, Chen LS, Wang YQ, Lin F*, Li G*, Ji ZL*. TransIntegrator: capture nearly full protein-coding transcript variants via integrating Illumina and PacBio transcriptomes. Briefings in Bioinformatics. 2023 Sep 22;24(6):bbad334.

  7. Ding RF, Zhang Y, Wu LY, You P*, Fang ZX, Li ZY, Zhang ZY, Ji ZL*. Discovering Innate Driver Variants for Risk Assessment of Early Colorectal Cancer Metastasis. Frontiers in Oncology. 2022 Jun 20;12:898117.

  8. Zhou J, Wu LY, Xu PY, Li Y, Ji ZL*, Kang XM*. Filamin A Is a Potential Driver of Breast Cancer Metastasis via Regulation of MMP-1. Frontiers in Oncology. 2022 Mar 11;12:836126.

  9. Zhao MX, Ding RF, Liu Y, Ji ZL*, Zhao YF*. Determination of the Amino Acid Recruitment Order in Early Life by Genome-Wide Analysis of Amino Acid Usage Bias. Biomolecules. 2022 Jan 21;12(2):171.

  10. Chen XW, Li YF, Huang QY, Lin XM, Wang XD, Wang YF, Liu Y, He QS, Liu YH, Wang T*, Ji ZL*, Li QG*. Segmental duplication as potential biomarkers for non-invasive prenatal testing of aneuploidies. EBioMedicine. 2021 Aug 2;70:103535.

  11. Liu K, Ding RF, Xu H, Qin YM, He QS, Du F, Zhang Y, Yao LX, You P, Xiang YP, Ji ZL*. Broad‐Spectrum Profiling of Drug Safety via Learning Complex Network. Clinical Pharmacology & Therapeutics. 2020 Feb 28;107(6):1373-1382.

  12. Huang LH, He QS, Liu K, Cheng J, Zhong MD, Chen LS, Yao LX, Ji ZL*. ADReCS-Target: target profiles for aiding drug safety research and application. Nucleic Acids Research. 2018 Jan; 46: D911-17.

  13. Liu Y, Li YB, Gao X, Yu YF, Liu XX, Ji ZL*, Ma Y, Li YM, Zhao YF*. Evolutionary relationships between seryl-histidine dipeptide and modern serine proteases from the analysis based on mass spectrometry and bioinformatics. Amino Acids. 2017 Oct 25. doi: 10.1007/s00726-017-2487-1.

  14. Tong ML, Zhao Q, Liu LL, Zhu XZ, Gao K, Zhang HL, Lin LR, Niu JJ*, Ji ZL*, Yang TC*. Whole genome sequence of the Treponema pallidum subsp. pallidum strain Amoy: An Asian isolate highly similar to SS14. PLoS One. 2017 Aug 7;12(8): e0182768. doi: 10.1371/journal.pone.0182768. eCollection 2017.

  15. Xu Q, Liu K, Lin X, Qin Y, Chen L, Cheng J, Zhong M, He Q, Li Y, Wang T, Pan J, Peng M, Yao L, Ji Z*. ADMETNet: The knowledge base of pharmacokinetics and toxicology network. Journal of Genetics & Genomics. 2017 May 20;44(5):273-276.

  16. Wei L, Xing P, Shi G, Ji ZL*, Zou Q*. Fast prediction of protein methylation sites using a sequence-based feature selection technique. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2017 Feb 16. doi: 10.1109/TCBB.2017.2670558.

  17. Zhang J, Wang S, Jiang B, Huang L, Ji Z, Li X, Zhou H, Han A, Chen A, Wu Y, Ma H, Zhao W, Zhao Q, Xie C, Sun X, Zhou Y, Huang H, Suleman M, Lin F, Zhou L, Tian F, Jin M, Cai Y, Zhang N, Li Q*. c-Src phosphorylation and activation of hexokinase promotes tumorigenesis and metastasis. Nature Communications. 2017 Jan 5; 8:13732. doi: 10.1038/ncomms13732.

  18. Fan F, He Z, Kong LL, Chen Q, Yuan Q, Zhang S, Ye J, Liu H, Sun X, Geng J, Yuan L, Hong L, Xiao C, Zhang W, Sun X, Li Y, Wang P, Huang L, Wu X, Ji Z, Wu Q, Xia NS, Gray NS, Chen L, Yun CH, Deng X, Zhou D*. Pharmacological targeting of kinases MST1 and MST2 augments tissue repair and regeneration. Science Translational Medicine. 2016 Aug 17;8(352):352ra108. doi: 10.1126/scitranslmed.aaf2304.

  19. Qin Y, Pan J, Cai M, Yao L, Ji Z*. Pattern Genes Suggest Functional Connectivity of Organs. Sci Rep. 2016 May 26; 6: 26501. doi: 10.1038/srep26501.

  20. Chen L, Zhang YH, Zou Q, Chu C, Ji Z*. Analysis of the chemical toxicity effects using the enrichment of Gene Ontology terms and KEGG pathways. Biochim Biophys Acta. 2016 Nov;1860(11 Pt B):2619-26. doi: 10.1016/j.bbagen.2016.05.015.

  21. Shi S, Liu K, Chen Y, Zhang S, Lin J, Gong C, Jin Q, Yang XJ, Chen R, Ji Z*, Han A*. Competitive inhibition of lysine acetyltransferase 2B by a small motif of the adenoviral oncoprotein E1A. Journal of Biological Chemistry. 2016 May 2. pii: jbc.M115.697300.

  22. He C, Jiang S, Jin H, Chen S, Lin G, Yao H, Wang X, Mi P, Ji Z, Lin Y, Lin Z, Liu G*. Mitochondrial electron transport chain identified as a novel molecular target of SPIO nanoparticles mediated cancer-specific cytotoxicity. Biomaterials. 2016 Mar; 83: 102-14. doi: 10.1016/j.biomaterials.2016.01.010.

  23. Zhang ZF, Ma PF, Jing Y, Yan Y, Cai MC, Zhang MY, Zhang SZ, Peng HX, Ji ZL, Di W, Gu ZY, Gao WQ, Zhuang GL*. BET Bromodomain Inhibition as a Therapeutic Strategy in Ovarian Cancer by Downregulating FoxM1. Theranostics. 2016; 6(2): 219-230. doi: 10.7150/thno.13178.

  24. Lin S*, Cheng S, Song B, Zhong X, Lin X, Li W, Li L, Zhang Y, Zhang H, Ji Z, Cai M, Zhuang Y, Shi X, Lin L, Wang L, Wang Z, Liu X, Yu S, Zeng P, Hao H, Zou Q, Chen C, Li Y, Wang Y, Xu C, Meng S, Xu X, Wang J, Yang H, Campbell DA, Sturm NR, Dagenais-Bellefeuille S, Morse D. The Symbiodinium kawagutii genome illuminates dinoflagellate gene expression and coral symbiosis. Science. 2015 Nov 6;350(6261):691-4. doi: 10.1126/science.aad0408.

  25. Cui YZ, Xu Q, Luan J, Hu SC, Pan JB, Han JX*, Ji ZL*. MVsCarta: A protein database of matrix vesicles to aid understanding of biomineralization. BioScience Trends. 2015 ;9(3):190-192. doi: 10.5582/ bst.2015.01061.

  26. Cai MC, Xu Q, Pan YJ, Pan W, Ji N, Li YB, Jin HJ, Liu K and Ji ZL*. ADReCS: an ontology database for aiding standardization and hierarchical classification of adverse drug reaction terms. Nucleic Acids Research.,2015 Jan 28;43(Database issue):D907-13.

  27. Xiang YP, Liu K, Cheng XY, Cheng C, Gong F, Pan JB, Ji ZL*. Rapid Assessment of Adverse Drug Reactions by Statistical Solution of Gene Association Network. IEEE Transactions on Computational Biology and Bioinformatics. 2015 Jul-Aug;12(4):844-50. doi: 10.1109/TCBB.2014.2338292.

  28. Zou Q, Mao Y, Hu L, Wu Y, Ji ZL*. miRClassify: An advanced web server for miRNA family classification and annotation. Computers in Biology and Medicine. 2014 Feb; 45: 157-160.

  29. Zhang HP, Pan JB, Zhang C, Ji N, Wang H, Ji ZL*. Network understanding of herb medicine via rapid identification of ingredient-target interactions. Sci Rep. 2014 Jan 16;4:3719. doi: 10.1038/srep03719.

  30. Wang Q, Wei L, Guan X, Wu Y, Zou Q, Ji ZL*. Briefing in family characteristics of microRNAs and their applications in cancer research. Biochim Biophys Acta. 2014 Jan;1844 (1 Pt B): 191-7. doi: 10.1016/j.bbapap.2013.08.002.

  31. Pan JB, Hu SC, Shi D, Cai MC, Li YB, Zou Q, Ji ZL*. PaGenBase: a pattern gene database for the global and dynamic understanding of gene function. PLoS ONE. 2013 Dec 2;8(12):e80747. doi: 10.1371/journal.pone.0080747.

  32. Pan JB, Ji N, Pan W, Hong R, Wang H, Ji ZL*. High-throughput Identification of Off-Targets for the Mechanistic Study of Severe Adverse Drug Reactions Induced by Analgesics. Toxicol Appl Pharmacol. 2014 Jan 1;274(1):24-34 . doi: 10.1016/j.taap.2013.10.017.

  33. Cheng XY, Huang WJ, Hu SC, Zhang HL, Wang H, Zhang JX, Lin HH, Chen YZ, Zou Q, Ji ZL*. A global characterization and identification of multifunctional enzymes. PLoS ONE. 2012;7(6):e38979. doi: 10.1371/journal.pone.0038979.

  34. Pan JB, Hu SC, Wang H, Zou Q, Ji ZL*. PaGeFinder: quantitative identification of spatiotemporal pattern genes. Bioinformatics. 2012 Jun 1;28(11):1544-5.

  35. Huang QS, Xie XL, Liang G, Gong F, Wang Y, Wei XQ, Wang Q, Ji ZL*, Chen QX*. The GH18 Family of Chitinases: Their Domain Architectures, Functions, and Evolutions. Glycobiology 2012 Jan;22(1):23-34.

  36. Han DX, Wang HY, Ji ZL, Hu AF, Zhao YF. Amino Acid Homochirality may be Linked to the Origin of Phosphate-Based Life. Journal of Molecular Evolution. 2010 Jun; 70(6): 572-82.

  37. Xiao SJ, Zhang C, Ji ZL*. TiSGeD: a Database for Tissue-Specific Genes. Bioinformatics. 2010 May 1;26(9):1273-5.

  38. Liu XX, Zhang JX, Ni F, Dong X, Han BC, Han DX, Ji ZL*, Zhao YF*. Genome wide exploration of the origin and evolution of amino acids. BMC Evolutionary Biology 2010, 10:77. (IF: 4.294)

  39. Kumar P, Han BC, Shi Z, Jia J, Wang YP, Zhang YT, Liang L, Liu QF, Ji ZL, Chen YZ. Update of KDBI: Kinetic Data of Bio-molecular Interaction database. Nucleic Acids Res. 2009 Jan;37:D636-41.

  40. Quan Y, JiZL* , Wang X, Tartakoff AM, Tao T*. Evolutionary and Transcriptional Analysis of Karyopherin Superfamily Proteins. Mol Cell Proteomics. 2008 Jul;7(7):1254-69.

  41. Han LY, Ma XH, Lin HH, Jia J, Zhu F, Xue Y, Li ZR, Cao ZW, Ji ZL, Chen YZ. A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor. J Mol Graph Model. 2008 Jun; 26 ( 8 ): 1276-86.

  42. Yap CW, Li H, Ji ZL, Chen YZ. Regression methods for developing QSAR and QSPR models to predict compounds of specific pharmacodynamic, pharmacokinetic and toxicological properties. Mini Rev Med Chem.2007 Nov; 7(11):1097-107.

  43. Li G, Zhang QJ, Ji ZL, Wang YQ. Origin and evolution of vertebrate ABCA genes: A story from Amphioxus. Gene. 2007 Dec 15;405(1-2):88-95 .

  44. Xu JR, Zhang JX, Han BC, Liang L, Ji ZL*. CytoSVM: An Advanced Server for Identification of Cytokine-Receptor Interactions. Nucleic Acids Research 2007 Jul 1; 35: W538-42.

  45. Zhang JX, Huang WJ, Huang WH, Wang Y, Zhao R, Han BC, Liu QF, Chen YZ, Ji ZL*. DITOP: Drug-Induced Toxicity Related Protein Database. Bioinformatics 2007, 23 (13): 1710–1712.

  46. Liang L, Han LY, Cai CZ, Huang WH, Chen YZ*, Ji ZL*. Functional Annotation of ORFs in Viral Genomes from Primary Sequence by Support Vector Machine Approach. Journal of Computational Information Systems,2007; 3 (2): 667-673.

  47. Yao LX, Wu ZC, Ji ZL, Chen YZ, Chen X. Internet resources related to drug action and human response: a review. Appl Bioinformatics. 2006; 5(3):131-9.

  48. 王潇，王玉鹏，全宇，纪志梁，陶涛. 细胞核质转运受体 Importin β家族与转运调控研究进展 . 细胞生物学杂志2006; 28(5): 637-645.

  49. 王怡，曾雅明，杨淑佳，纪志梁*. 生物信息学在药物不良反应研究中的应用. 中国药学杂志 2007; 42 (21): 1605-1609.

  50. Wang YP, Liang L, Han BC, Quan Y, Wang X, Tao T, Ji ZL*. GEPS: Gene Expression Pattern Scanner. Nucleic Acids Research 2006 July; 34: W492-W497.

  51. Ji ZL*, Wang Y, Yu L, Han LY, Zheng CJ and Chen YZ. In silico Search of Putative Adverse Drug Reaction Related Proteins as a Potential Tool for Facilitating Drug Adverse Effect Prediction. Toxicology Letters 2006 July 1; 164 (2): 104-112.

  52. Han LY, Cui J, Lin HH, Ji ZL, Cao ZW, Li YS, and Chen YZ. Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity. Proteomics 2006 June 21; 6(14): 4023-4037.

  53. Zheng CZ, Han LY, Yap CY, Ji ZL, Cao ZW and Chen YZ. Therapeutic Targets: Progress of Their Exploration and Investigation of Their Characteristics. Pharmacological Reviews 2006 Jun;58(2):259-79.

  54. Ji ZL, Li ZR, Wang JF, Cai CZ, Han LY, Zheng CJ, and Chen YZ. Increasing the Odds of Drug Hit Identification by Screening Against Receptor Homologs? Letters in Drug Design & Discovery 2006 April;3(3):200-204.

  55. Ji ZL, Zhou H, Wang JF, Han LY, Zheng CJ, and Chen YZ. Traditional Chinese Medicine Information Database.Journal of Ethnopharmacology 2006 Feb 20;103 (3):501.

  56. Lin HH, Han LY, Cai CZ, Ji ZL and Chen YZ. Prediction of Transporter Family by Support Vector Machine Approach. Proteins. 2006 Jan 1; 62(1):218-31.

  57. 黄文晖, 纪志梁*. 生物信息学在免疫学上的应用. 细胞与分子免疫学杂志. 2006: 22 (1):129-132.

  58. Ji ZL, Han LY, Zheng CJ, Cao ZW and Chen YZ. Prediction of Putative Adverse Drug Reaction Related Proteins from Primary Sequence By Support Vector Machines. International Journal of Pharmaceutical Medicine 2005; 19(6): 317-322.

  59. Cui J, Han LY, Cai CZ, Zheng CJ, Ji ZL, and Chen YZ. Prediction of Functional Class of Novel Bacterial Proteins without the Use of Sequence Similarity by a Statistical Learning Method. Journal of Molecular Microbiology and Biotechnology 2005;9(2): 86-100.

  60. Zhou H, Zarubin T, Ji ZL, Min Z, Zhu W, Downey JS, Lin S, Han J. Frequency and Distribution of AP-1 Sites in the Human Genome. DNA Research. 2005;12(2):139-50.

  61. Cui JA, Han LY, Lin HH, Tang ZQ, Ji ZL, Cao ZW, Li YX, Chen YZ. Advances in exploration of machine learning methods for predicting functional class and interaction profiles of proteins and peptides irrespective of sequence homology. Current Bioinformatics May 2007, 2(2):95-112.

  62. Cao ZW, Han LY, Zheng CJ, Ji ZL, Chen X, Lin HH and Chen YZ. Computer prediction of drug resistance mutations in proteins. Drug Discovery Today 2005;10 (7):521-529.

  63. Han LY, Cai CZ, Ji ZL, Chen YZ. Prediction of Functional Class of Novel Viral Proteins by a Statistical Learning Method Irrespective of Sequence Similarity. Virology 2005 Jan 5;331(1):136-43.

  64. Han LY, Cai CZ, Ji ZL, Cao ZW, Cui J, Chen YZ. Predicting Functional Family of Novel Enzymes Irrespective of Sequence Similarity: A Statistical Learning Approach. Nucleic Acids Research 2004 Dec 7;32(21):6437-44.

  65. Zheng CJ, Sun LZ, Han LY, Ji ZL, Chen X, and Chen YZ. Drug ADME-Associated Protein Database as a Resource for Facilitating Pharmacogenomics Research. Drug Development Research 2004; 62:134–142.

  66. Cai CZ, Han LY, Ji ZL, Chen YZ. Enzyme Family Classification by Support Vector Machines. Proteins.2004; 55(1):66-76.

  67. Cai CZ, Han LY, Ji ZL, Chen X, Chen YZ. SVM-Prot: Web-Based Support Vector Machine Software for Functional Classification of a Protein from Its Primary Sequence. Nucleic Acids Research 2003; 31 (13): 3692-3697.

  68. Ji ZL, Han LY, Yap CW, Sun LZ, Chen X, and Chen YZ. DART: Drug Adverse Reaction Target Database. Drug Safety 2003; 26 (10): 685-690.

  69. Ji ZL, Sun LZ, Chen X, Zheng CJ, Yao LX, Han LY, Cao ZW, Wang JF, Yeo WK, Cai CZ, and Chen YZ. Internet Resources for Proteins Associated with Drug Therapeutic Effects, Adverse Reactions, and ADME. Drug Discovery Today 2003; 8 (12): 526-529.

  70. Ji ZL, Chen X, Zhen CJ, Yao LX, Han LY, Yeo WK, Chung PC, Puy HS, Tay YT, Muhammad A, and Chen YZ. KDBI: Kinetic Data of Bio-molecular Interactions database. Nucleic Acids Research 2003; 31: 255-257.

  71. Sun LZ, Ji ZL, Chen X, Wang JF, Chen YZ. ADME-AP: a database of ADME associated proteins. Bioinformatics 2002; 18(12): 1699-1700.

  72. Chen X, Ji ZL, Zhi DG, Chen YZ. CLiBE: a database of computed ligand binding energy for ligand-receptor complexes. Journal of Computational Chemistry 2002; 26(6): 661-6.

  73. Sun LZ, Ji ZL, Chen X, Wang JF and Chen YZ. ADME Associated Protein Database. Clinical Pharmacology & Therapeutics 2002; 71: 5.

  74. Chen X, Ji ZL and Chen YZ. TTD: Therapeutic Target Database. Nucleic Acids Research 2002; 30: 412-415.

  75. Moe TK, Ji ZL, Barathi A, Beuerman RW. Differential Expression of Glyceraldehyde-3-phophate dehydrogenase (GAPDH), beta actin and hypoxanthine phosphoribosyltransferase (HPRT) in postnatal rabbit sclera. Current Eye Research 2001; 23 (1): 44-50.

  76. Song KP, Chan TK, Ji ZL and Wong SW. Rapid Identification of Pseudomonas aeruginosa from Ocular isolates by PCR Using Exotoxin A-specific Primers. Molecular and Cellular Probes 2000; 14: 199-204.