遗传与生物医学信息学研究中心

Highlighted Publications

Li Y#, Zhang K#, Chen H#, Sun F, Xu J, Wu Z, Li P, Zhang L, Du Y, Luan H, Li X, Wu L, Li H, Wu H, Li X, Li X, Zhang X, Gong L, Dai L, Sun L, Zuo X, Xu J, Gong H, Li Z, Tong S, Wu M, Li X, Xiao W, Wang G, Zhu P, Shen M, Liu S, Zhao D, Liu W, Wang Y, Huang C, Jiang Q, Liu G, Liu B, Hu S, Zhang W, Zhang Z, You X, Li M, Hao W, Zhao C, Leng X, Bi L, Wang Y, Zhang F, Shi Q, Qi W, Zhang X, Jia Y, Su J, Li Q, Hou Y, Wu Q, Xu D, Zheng W, Zhang M, Wang Q, Fei Y, Zhang X, Li J, Jiang Y, Tian X, Zhao L, Wang L, Zhou B, Li Y, Zhao Y, Zeng X, Ott J, Wang J, Zhang F. (2013). A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren’s syndrome at 7q11.23. Nature Genetics 45(11):1361-1365. doi:10.1038/ng.2779 第一个中国人群干燥综合征GWAS，首次鉴别出干燥综合征的易感基因区域7q11.23。
Zhang K#, Qu S#, Chang S#, Li G, Cao C, Fang K, Olff M, Wang L, Wang J. (2017). An overview of posttraumatic stress disorder genetic studies by analyzing and integrating genetic data into genetic database PTSDgene. Neuroscience and Biobehavioral Reviews 83:647-656. doi:10.1016/j.neubiorev.2017.08.021 Li G, Zhang K, Wang L, Cao C, Fang R, Liu P, Luo S, Liberzon I. (2019). The preliminary investigation of orexigenic hormone gene polymorphisms on posttraumatic stress disorder symptoms. Psychoneuroendocrinology 100:131-136. doi:10.1016/j.psyneuen.2018.09.042 构建了国际上第一个创伤后应激障碍遗传学数据库PTSDgene，发现了创伤后应激障碍中促食欲基因的基因-基因交互作用。
左玲，陈建新，王伟，汪思佳，张昆林。（2022）。中医信息学与表型组学：症状的遗传突变与证候的生物学基础初探。北京中医药大学学报* 45(2):140-147。DOI：10.3969/j.issn.1006-2157.2022.02.007 张昆林，孙鹏程，陈雪梅，陈建新，张妍，王一，王济，王琦。（2021）。基于生物信息学方法的祛风解表中药干预过敏体质机制研究。天津中医药 38(3):273-279。DOI:10.11656/j.issn.1672-1519.2021.03.01
Gao J#, Zhang K#, Wang Y#, Guo R, Liu H, Jia C, Sun X, Wu C, Wang W, Du J, Chen J. (2020). A Machine Learning-driven Study Indicates Emodin Improves Cardiac Hypertrophy by Modulation of Mitochondrial SIRT3 Signaling. Pharmacological Research* 155:104739. doi:10.1016/j.phrs.2020.104739 用人工智能，结合分子细胞实验和动物模型，进行了大黄素通过调节线粒体SIRT3信号改善心肌肥厚的药理学研究。
Zhang K#, Chang S#, Guo L, Wang J. (2015). I-GSEA4GWAS v2: a web server for functional analysis of SNPs in trait-associated pathways identified from genome-wide association study. Protein & Cell* 6(3):221-224. doi:10.1007/s13238-014-0114-4 构建了GWAS数据通路分析的网络平台。

Publication List

1. Zhang J, Li G, Yang H, Cao C, Fang R, Liu P, Luo S, Zhao G, Zhang Y, Zhang K* and Wang L*. (2022). The main effect and gene-environment interaction effect of the ADCYAP1R1 polymorphism rs2267735 on the course of posttraumatic stress disorder symptoms—A longitudinal analysis. Frontiers in Psychiatry 13:1032837. doi: 10.3389/fpsyt.2022.1032837
2. 张萦倩，赵光义，韩雨薇，张静怡，曹成琦，王力，张昆林*。（2022）。创伤后应激障碍的组蛋白修饰机制。心理科学进展 30(1):98-114。doi: 10.3724/SP.J.1042.2022.00098
3. 左玲，陈建新，王伟，汪思佳，张昆林*。（2022）。中医信息学与表型组学：症状的遗传突变与证候的生物学基础初探。北京中医药大学学报 45(2):140-147。DOI：10.3969/j.issn.1006-2157.2022.02.007
4. 张昆林，孙鹏程，陈雪梅，陈建新，张妍，王一，王济*，王琦*。（2021）。基于生物信息学方法的祛风解表中药干预过敏体质机制研究。天津中医药 38(3):273-279。DOI:10.11656/j.issn.1672-1519.2021.03.01
5. Wang L, Zhang J, Li G, Cao C, Fang R, Liu P, Luo S, Zhao G, Zhang Y, & Zhang K*. (2021). The ADCYAP1R1 Gene Is Correlated With Posttraumatic Stress Disorder Symptoms Through Diverse Epistases in a Traumatized Chinese Population. Frontiers in Psychiatry 12:665599.
6. Zhang K, Ji G, Zhao M, Wang Y*. (2021). Candidate l-methionine target piRNA regulatory networks analysis response to cocaine-conditioned place preference in mice. Brain and Behavior 11(8):e2272. doi: 10.1002/brb3.2272. Epub 2021 Jul 1.
7. Gao J#, Zhang K#, Wang Y#, Guo R, Liu H, Jia C, Sun X, Wu C, Wang W, Du J, Chen J*. (2020). A Machine Learning-driven Study Indicates Emodin Improves Cardiac Hypertrophy by Modulation of Mitochondrial SIRT3 Signaling. Pharmacological Research 155:104739. doi:10.1016/j.phrs.2020.104739
8. Liu X, Jia C, Wu C, Wang N, Jia Y, Zhu Y*, Li P*, Ghulam M*, Zhang K*. (2020). Discovering Traditional Chinese Medicinal Herbs for Neurodegenerative Disorders. Indian Journal of Pharmaceutical Sciences 82(2)Spl issue3:70-76.
9. Zhang K, Wang L*, Li G, Cao C, Fang R, Liu P, Luo S, Zhang X. (2020). Correlation between hypothalamic-pituitary-adrenal axis gene polymorphisms and posttraumatic stress disorder symptoms. Hormones and Behavior 117:104604. doi: 10.1016/j.yhbeh.2019.104604
10. Zhang K, Li G, Wang L*, Cao C, Fang R, Luo S, Liu P, Zhang XY. (2019). An epistasis between dopaminergic and oxytocinergic systems confers risk of post-traumatic stress disorder in a traumatized Chinese cohort. Scientific Reports 9(1):19252. doi: 10.1038/s41598-019-55936-8
11. Li G, Zhang K*, Wang L*, Cao C, Fang R, Liu P, Luo S, Liberzon I. (2019). The preliminary investigation of orexigenic hormone gene polymorphisms on posttraumatic stress disorder symptoms. Psychoneuroendocrinology 100:131-136. doi: 10.1016/j.psyneuen.2018.09.042
12. Zhang K, Wang L*, Cao C, Li G, Fang R, Liu P, Luo S, Zhang X, Liberzon I. (2018) A DRD2/ANNK1-COMT interaction, consisting of functional variants, confers risk of post-traumatic stress disorder in traumatized Chinese. Frontiers in Psychiatry 9:170. doi: 10.3389/fpsyt.2018.00170.
13. Zhang K#, Qu S#, Chang S#, Li G, Cao C, Fang K, Olff M, Wang L*, Wang J*. (2017). An overview of posttraumatic stress disorder genetic studies by analyzing and integrating genetic data into genetic database PTSDgene. Neuroscience and Biobehavioral Reviews 83:647-656. doi: 10.1016/j.neubiorev.2017.08.021.
14. Qu S, Du Y, Chang S, Guo L, Fang K, Li Y, Zhang F, Zhang K*, Wang J*. (2017). Common variants near IKZF1 are associated with primary Sjögren's syndrome in Han Chinese. PLoS ONE 12(5):e0177320.
15. Zhang K#, Fan Z#, Wang Y, Faraone SV, Yang L*, Chang S*. (2017). Genetic analysis for cognitive flexibility in the trail-making test in attention deficit hyperactivity disorder patients from single nucleotide polymorphism, gene to pathway level. The World Journal of Biological Psychiatry. doi: 10.1080/15622975.2017.1386324.
16. Piao W#, Guo J#, Bao Y, Wang F, Zhang T, Huo J*, Zhang K*. (2016). Analysis of polymorphisms of genes associated with folate-mediated one-carbon metabolism and neural tube defects in Chinese Han population. Birth Defects Research Part A: Clinical and Molecular Teratology 106(4):232-239.
17. Zhang K#, Chang S#, Guo L, Wang J*. (2015). I-GSEA4GWAS v2: a web server for functional analysis of SNPs in trait-associated pathways identified from genome-wide association study. Protein & Cell 6(3):221-224. doi:10.1007/s13238-014-0114-4
18. Li Y#, Zhang K#, Chen H#, Sun F, Xu J, Wu Z, Li P, Zhang L, Du Y, Luan H, Li X, Wu L, Li H, Wu H, Li X, Li X, Zhang X, Gong L, Dai L, Sun L, Zuo X, Xu J, Gong H, Li Z, Tong S, Wu M, Li X, Xiao W, Wang G, Zhu P, Shen M, Liu S, Zhao D, Liu W, Wang Y, Huang C, Jiang Q, Liu G, Liu B, Hu S, Zhang W, Zhang Z, You X, Li M, Hao W, Zhao C, Leng X, Bi L, Wang Y, Zhang F, Shi Q, Qi W, Zhang X, Jia Y, Su J, Li Q, Hou Y, Wu Q, Xu D, Zheng W, Zhang M, Wang Q, Fei Y, Zhang X, Li J, Jiang Y, Tian X, Zhao L, Wang L, Zhou B, Li Y, Zhao Y, Zeng X, Ott J, Wang J*, Zhang F*. (2013). A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren's syndrome at 7q11.23. Nature Genetics 45(11):1361-1365. doi:10.1038/ng.2779
19. Zhang K, Chang S, Cui S, Guo L, Zhang L, Wang J*. (2011). ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework. Nucleic Acids Research 39(Web Server issue):W437-443.
20. Zhang K, Zhang L, Zhang W, Wang J*. (2011). Pathway-based analysis for genome-wide association studies of schizophrenia to provide new insight in schizophrenia study. Chinese Science Bulletin 56(32):3398-3402.
21. Yang L#, Zhang K#, Dai W, He X, Zhao Q, Wang J*, Sun ZS*. (2011). Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array. BMC Genomics 12:10.
22. Zhang K#, Cui S#, Chang S, Zhang L, Wang J*. (2010). i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study. Nucleic Acids Research 38 Web Server issue):W90-95.
23. Zhang K-L, Mangeat B, Ortiz M, Zoete V, Trono D, Telenti A*, Michielin O*. (2007). Model structure of human APOBEC3G. PLoS ONE 2(4):e378.
24. Zhang K, Luo JC, Liu CQ*. (2005). Exploring consensus mRNA secondary (folding) structure units by stochastic sampling and folding simulation. Journal of Molecular Structure: THEOCHEM 715(1-3):15-20.
25. Zhang K-L, Zhang J*, Luo JC. (2005). Potential Transcriptional Synergy between Upstream Regions and Introns of Yeast Genes. Progress in Biochemistry and Biophysics 32(1):46-52.
26. Zhang K-L, Zhang J*, Luo J-C. (2005). Possible Short- and Long-Range Transcriptional Synergistic Regulation between Upstream Regions and Introns in Yeast Genes. Acta Biophysica Sinica (《生物物理学报》) 21(4):277-283. (in Chinese)
27. Qi F, Liu Y, Zhang K, Zhang Y, Xu K, Zhou M, Zhao H, Zhu S, Chen J*, Li P*, Du J*. (2022). Artificial Intelligence Uncovers Natural MMP Inhibitor Crocin as a Potential Treatment of Thoracic Aortic Aneurysm and Dissection. Frontiers in Cardiovascular Medicine 9:871486.
28. Shi L#, Wang Y#, Li C, Zhang K, Du Q, Zhao M*. (2021). AddictGene: An integrated knowledge base for differentially expressed genes associated with addictive substance. Computational and Structural Biotechnology Journal 19:2416-2422. doi: 10.1016/j.csbj.2021.04.027. eCollection 2021.
29. Li G, Wang L*, Zhang K, Cao C, Cao X, Fang R, Liu P, Luo S, Zhang X. (2019). FKBP5 Genotype Linked to Combined PTSD-Depression Symptom in Chinese Earthquake Survivors. Canadian Journal of Psychiatry 64(12):863-871. doi: 10.1177/0706743719870505.
30. Zhao M*, Hou L, Teng H, Li J, Wang J, Zhang K, Yang L*. (2019). Whole-Exome Sequencing Identified a Novel Compound Heterozygous Genotype in ASL in a Chinese Han Patient with Argininosuccinate Lyase Deficiency. Biomed Research International 2019:3530198. doi: 10.1155/2019/3530198.
31. Yang L#, Chang S#, Lu Q, Zhang Y, Wu Z, Sun X, Cao Q, Qian Y, Jia T, Xu B, Duan Q, Li Y, Zhang K, Gunter S, Lu L, Liu D*, Wang J*, Wang Y*, Lu L. (2018). A new locus regulating MICALL2 expression was identified for association with executive inhibition in children with attention deficit hyperactivity disorder. Molecular Psychiatry 23(4):1014-1020. doi: 10.1038/mp.2017.74.
32. Xue Y, Lameijer EW, Ye K, Zhang K, Chang S, Wang X, Wu J, Gao G, Zhao F, Li J, Han C, Xu S, Xiao J, Yang X, Ying X, Zhang X, Chen WH, Liu Y, Zhang Z, Huang K, Yu J*. (2016). Precision Medicine: What Challenges Are We Facing? Genomics, Proteomics & Bioinformatics 14(5):253-261.
33. Wang J, Qu S, Wang W, Guo L, Zhang K, Chang S*, Wang J*. (2016). A combined analysis of genome-wide expression profiling of bipolar disorder in human prefrontal cortex. Journal of Psychiatric Research 82:23-9.
34. Fang K, Zhang K, Wang J*. (2015). Network-assisted analysis of primary Sjögren's syndrome GWAS data in Han Chinese. Scientific Reports 5:18855.
35. Chang S#, Wang J#, Zhang K, Wang J*. (2015). Pathway-based analysis for genome-wide association study data of bipolar disorder provides new insights for genetic study. Protein & Cell 6(12):912-5. doi: 10.1007/s13238-015-0201-1.
36. Chang S#, Fang K#, Zhang K, Wang J*. (2015). Network-based analysis of schizophrenia genome-wide association data to detect the joint functional association signals. PLoS ONE 10(7):e0133404.
37. Guo L#, Du Y#, Chang S, Zhang K, Wang J*. (2014). rSNPBase: a database for curated regulatory SNPs. Nucleic Acids Research 42(Database issue):D1033-D1039.
38. Zhang W-N, Chang S-H, Guo L-Y, Zhang K-L, Wang J*. (2013). The neural correlates of reward-related processing in major depressive disorder: a meta-analysis of functional magnetic resonance imaging studies. Journal of Affective Disorders 151(2):531-539.
39. Zhang L#, Chang S#, Li Z, Zhang K, Du Y, Ott Y, Wang J*. (2012). ADHDgene: a genetic database for attention deficit hyperactivity disorder. Nucleic Acids Research 40(Database issue):D1003-1009.
40. Fang K#, Zhao H#, Sun C, Lam C M-C, Chang S, Zhang K, Panda G, Godinho M, Martins dos Santos VA*, Wang J*. (2011). Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction. BMC systems Biology 5:83.
41. Fellay J#, Ge D#, Shianna KV, Colombo S, Ledergerber B, Cirulli ET, Urban TJ, Zhang K, Gumbs CE, Smith JP, Castagna A, Cozzi-Lepri A, De Luca A, Easterbrook P, Günthard HF, Mallal S, Mussini C, Dalmau J, Martinez-Picado J, Miro JM, Obel N, Wolinsky SM, Martinson JJ, Detels R, Margolick JB, Jacobson LP, Descombes P, Antonarakis SE, Beckmann JS, O'Brien SJ, Letvin NL, McMichael AJ, Haynes BF, Carrington M, Feng S, Telenti A*, Goldstein DB*; NIAID Center for HIV/AIDS Vaccine Immunology (CHAVI). (2009). Common genetic variation and the control of HIV-1 in humans. PLoS Genetics 5:e1000791.
41. Ge D*, Zhang K, Need AC, Martin O, Fellay J, Telenti A, Goldstein DB*. (2008). WGAViewer: A software tool for genomic annotation of whole genome association studies. Genome Research 18(4):640-3.
43. Ortiz M, Kaessmann H, Zhang K, Bashirova A, Carrington M, Quintana-Murci L, Telenti A*. (2008). The evolutionary history of the CD209 (DC-SIGN) family in humans and non-human primates. Genes & Immunity 9(6):483-92.
44. Fellay J, Shianna KV, Ge D, Colombo S, Ledergerber B, Weale M, Zhang K, Gumbs C, Castagna A, Cossarizza A, Cozzi-Lepri A, Luca AD, Easterbrook P, Francioli P, Mallal S, Martinez-Picado J, Miro JM, Obel N, Smith JP, Wyniger J, Descombes P, Antonarakis SE, Letvin NL, McMichael AJ, Haynes BF, Telenti A*, Goldstein DB*. (2007). A Whole-Genome Association Study of Major Determinants for Host Control of HIV-1. Science (ScienceXpress, 19 July 2007) 317(5840):944-7.
45. Rotger M#, Saumoy M#, Zhang K, Flepp M, Sahli R, Decosterd L, Telenti A*, the Swiss HIV Cohort Study. (2007). Partial deletion of CYP2B6 owing to unequal crossover with CYP2B7. Pharmacogenetics and Genomics 17(10):885-90.
46. Zhou W, Chen X-F, Zhang K-L, Liu C-Q*. (2005). The identification and quantification of highly stable ‘common hairpin’ in the dynamic process of co-transcriptional mRNA folding. Journal of Molecular Structure: THEOCHEM 722(1-3):41-50.
47. Zhong L, Zhang K, Huang X, Ni P, Han Y, Wang K, Wang J, Li S*. (2003). A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts. Genomics, Proteomics & Bioinformatics 1(1):43-51.
48. Yu J#, Hu S#, Wang J#, Wong GK#, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L*, Yuan L*, Yang H*. (2002). A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296(5565):79-92.
49. Wang J*, Wong GK*, Ni P, Han Y, Huang X, Zhang J, Ye C, Zhang Y, Hu J, Zhang K, Xu X, Cong L, Lu H, Ren X, Ren X, He J, Tao L, Passey DA, Wang J, Yang H, Yu J, Li S. (2002). RePS: a sequence assembler that masks exact repeats identified from the shotgun data. Genome Research 12(5):824-31.
50. 于军等。籼稻(Oryza Sativa ssp. indica)全基因组框架序列。(2001). 科学通报 46(23):1937-1941. (in Chinese)
Yu J et al.. A draft sequence of the rice (Oryza sativa ssp. indica) genome. (2001). Chinese Science Bulletin 46(23):1937-1942.
(# co-first author, * corresponding author)

Li Y#, Zhang K#, Chen H#, Sun F, Xu J, Wu Z, Li P, Zhang L, Du Y, Luan H, Li X, Wu L, Li H, Wu H, Li X, Li X, Zhang X, Gong L, Dai L, Sun L, Zuo X, Xu J, Gong H, Li Z, Tong S, Wu M, Li X, Xiao W, Wang G, Zhu P, Shen M, Liu S, Zhao D, Liu W, Wang Y, Huang C, Jiang Q, Liu G, Liu B, Hu S, Zhang W, Zhang Z, You X, Li M, Hao W, Zhao C, Leng X, Bi L, Wang Y, Zhang F, Shi Q, Qi W, Zhang X, Jia Y, Su J, Li Q, Hou Y, Wu Q, Xu D, Zheng W, Zhang M, Wang Q, Fei Y, Zhang X, Li J, Jiang Y, Tian X, Zhao L, Wang L, Zhou B, Li Y, Zhao Y, Zeng X, Ott J, Wang J, Zhang F. (2013). A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren’s syndrome at 7q11.23. Nature Genetics 45(11):1361-1365. doi:10.1038/ng.2779 第一个中国人群干燥综合征GWAS，首次鉴别出干燥综合征的易感基因区域7q11.23。
Zhang K#, Qu S#, Chang S#, Li G, Cao C, Fang K, Olff M, Wang L, Wang J. (2017). An overview of posttraumatic stress disorder genetic studies by analyzing and integrating genetic data into genetic database PTSDgene. Neuroscience and Biobehavioral Reviews 83:647-656. doi:10.1016/j.neubiorev.2017.08.021 Li G, Zhang K, Wang L, Cao C, Fang R, Liu P, Luo S, Liberzon I. (2019). The preliminary investigation of orexigenic hormone gene polymorphisms on posttraumatic stress disorder symptoms. Psychoneuroendocrinology 100:131-136. doi:10.1016/j.psyneuen.2018.09.042 构建了国际上第一个创伤后应激障碍遗传学数据库PTSDgene，发现了创伤后应激障碍中促食欲基因的基因-基因交互作用。
左玲，陈建新，王伟，汪思佳，张昆林。（2022）。中医信息学与表型组学：症状的遗传突变与证候的生物学基础初探。北京中医药大学学报* 45(2):140-147。DOI：10.3969/j.issn.1006-2157.2022.02.007 张昆林，孙鹏程，陈雪梅，陈建新，张妍，王一，王济，王琦。（2021）。基于生物信息学方法的祛风解表中药干预过敏体质机制研究。天津中医药 38(3):273-279。DOI:10.11656/j.issn.1672-1519.2021.03.01
Gao J#, Zhang K#, Wang Y#, Guo R, Liu H, Jia C, Sun X, Wu C, Wang W, Du J, Chen J. (2020). A Machine Learning-driven Study Indicates Emodin Improves Cardiac Hypertrophy by Modulation of Mitochondrial SIRT3 Signaling. Pharmacological Research* 155:104739. doi:10.1016/j.phrs.2020.104739 用人工智能，结合分子细胞实验和动物模型，进行了大黄素通过调节线粒体SIRT3信号改善心肌肥厚的药理学研究。
Zhang K#, Chang S#, Guo L, Wang J. (2015). I-GSEA4GWAS v2: a web server for functional analysis of SNPs in trait-associated pathways identified from genome-wide association study. Protein & Cell* 6(3):221-224. doi:10.1007/s13238-014-0114-4 构建了GWAS数据通路分析的网络平台。