北京大学分子心血管学教育部重点实验室
北京大学医学部生物医学信息学系
北京市学院路38号
电话: +86-10-82801585
传真: +86-10-82801001
研究综述
崔庆华博士主要研究兴趣为非编码RNA(noncoding RNA)生物信息学和网络药理学及其在心血管疾病等复杂疾病中的应用。发表SCI论文50余篇，其中第一/责任作者发表SCI文论32篇（第一作者7篇，责任作者25篇），总IF约155，其中5篇论文单篇IF>9.0，11篇论文单篇IF>5.0，总SCI引用1000余次，Google scholar引用1800余次，其中三篇论文单篇SCI引用超过100次。单篇论文最高SCI引用207次（责任作者）。
教育背景
1995.9-1999.7，本科，河北工业大学机械电子工程系 专业：机械电子工程
1999.9-2002.7, 硕士，河北工业大学机器人与自动化研究所 研究方向：机器人视觉系统
2002.9-2005.7，博士，中科院自动化所模式识别国家重点实验室 研究方向：生物信息学和系统生物学
工作经历
2005.7-2007.7，加拿大国家研究委员会生物技术研究所博士后（加拿大，蒙特利尔）
2007.8-2012.8，北京大学基础医学院生物医学信息学系 副教授
2007.8-今，北京大学教育部分子心血管学教育部重点实验室心血管生物信息学学研究组组长，PI
2009.6-2013.12，北京大学基础医学院生物医学信息学系 代理主任
2012.8-今，北京大学基础医学院生物医学信息学系 教授，博士研究生导师
2013.12-今，北京大学基础医学院生物医学信息学系 主任
承担的科研项目
ü 国家自然科学基金委“优青”（2015-2017）
ü 国家自然科学基金重大研究计划（培育），基于转录组的腹主动脉瘤治疗药物的筛选策略研究（2014-2016）
ü 863（co-PI），人类非编码RNA的系统识别与功能分析平台建设 （2014-2018）
ü 973（骨干），脂代谢紊乱导致脂肪肝及高脂血症发生的机制（2012-2015），
ü 教育部新世纪优秀人才基金，miRNA分子稳定性的系统生物学研究（2011-2014）
ü 国家自然科学基金，基于生物信息学的microRNA和人类疾病关联研究（2010-2012），
ü 北京大学985基金，microRNA单核苷酸多态性的生物信息学研究（2008-2009）
ü 教育部博士点基金，基于生物信息学的人类microRNA和疾病关联数据的研究（2010-2012）
ü 教育部留学回国人员启动基金，心血管疾病相关microRNA的系统生物学分析（2009-2011）
技术服务及任职
ü
学术期刊编委:
The Scientific World
Journal (IF=1.7), Lead Guest Editor of 《BioMed Research
International》(IF=2.88)。
ü
下列期刊或会议的审稿人:
Chemical Society
Review, Genome Research, Nucleic Acids Research, Bioinformatics, Scientific
Reports, Journal of Translational Medicine, PLoS ONE,
Molecular BioSystems, Molecular Oncology, BMC Systems
Biology, BMC Bioinformatics, BMC Genomics, FEBS letter, DATABASE, Chromosome
Research, Disease Markers, Genome Biology and Evolution, IEEE Transactions on
Autonomous Mental Development, BMC Research Notes, Journal of Biomedical
Informatics, IET Systems Biology, GENE, African Journal of Biotechnology，Journal of Genetics and
Genomics，Journal of
Diabetes，Science China
Life Sciences,《中国生物化学与分子生物学报》，《生理科学进展》
ü
国自然评审专家、国自然“十三五””生命科学中的数学理论与方法”战略规划研究专家组成员、科技部科技支撑计划验收专家组
ü
学术会议程序委员会（Program
committee）:
（1）2010，Program committee of IEEE
International Conference on Bioinformatics & Biomedicine；
（2）2010，Program committee of ACM
IHI 2011；
（3）April 22-24,
2012, Program committee of International Conference on Intelligent Biology and
Medicine, Vanderbilt University, USA；
（4）June 13-15,2012,
13th WSEAS International Conference on MATHEMATICS AND COMPUTERS IN BIOLOGY AND
CHEMISTRY (MCBC '12) "G. Enescu"
University, Iasi, Romania
（5）January 28-30,
2012, Program committee of the ACM SIGHIT International Health Informatics
Symposium (IHI 2012), Miami, FL, USA.
（6）August 11-13,
2013, Program committee of the International Conference on Intelligent Biology
and Medicine, ICIBM 2013, Nashville/Vanderbilt University, USA
（7）September 20-22,
2013, Program committee of the 12th International Conference on Bioinformatics
of the Asia-Pacific Bioinformatics Network, Taicang,
China
ü
2009，Reviewer panel of senior scientist for the Early Career Fellowship
application of The Wellcome Trust (UK) /DBT India
Alliance in biomedical research
ü
2010，Panel of foreign examiner to evaluate Ph.D thesis
for Anna University, Coimbatore, Tamil Nadu, India
ü
2010.12-今，国际计算生物学会会员，Member of ISCB
(International Society for Computational Biology)
生物信息学平台
1.
LncTar, lncRNA的RNA靶基因预测软件，2014年创建
1.
HMDD, miRNA疾病数据库，2007年创建
2.
LncRNADisease， lncRNA疾病数据库和lncRNA-疾病关系分析生物信息学方法集成平台，2012年创建
3.
TransmiR， miRNA转录因子数据库，2009年创建
4.
miREnvironment， miRNA-环境因子相互作用数据库和生物信息分析集成平台，2011年创建
5.
TAM，miRNA功能和关联疾病富集分析工具，2010年创建
6.
MISIM，miRNA功能相似度计算和关联疾病预测工具，2010年创建
7.
CEPRED，内含子miRNA和宿主基因共表达分析及关联疾病预测工具，2008年创建
8.
miRUPnet，miRNA功能和关联疾病预测工具，2012年创建
l 发表论文（*表明为责任作者, #为共同第一作者，按时间顺序排列）
1. Li J*, Ma
W, Zeng P, Wang J, Geng B, Yang J, and Cui Q*.
LncTar: a tool for predicting the RNA targets of long noncoding
RNAs. Briefings in Bioinformatics
2014 (in press).
2. Li J*, Gao
C, Wang Y, Ma W, Tu J, Wang J, Chen Z, Kong W, and Cui Q*.
A bioinformatics method for predicting long noncoding
RNAs associated with vascular disease. Science China Life Sciences
2014 57(8):852-7.
3. Jin L, Tu
J, Jia J, An W, Tan H*, Cui Q*,
and Li Z*. Drug-repurposing identified the combination of Trolox
C and Cytisine for the treatment of type 2 diabetes. Journal
of Translational Medicine 2014 12:153.
4. Jia S, Chen Z, Li J, Chi Y, Wang J,
Li S, Luo Y, Geng B, Wang
C, Cui Q,
Guan Y, Yang J. FAM3A promotes vascular smooth muscle cell proliferation and
migration and exacerbates neointima formation in rat
artery after balloon injury. J Mol Cell Cardiol
2014 74C:173-182.
5. Liu M, Chen X, Cui Q*,
and Yan G*. A framework to infer the disease associated with human long noncoding RNAs. PLoS
ONE 2014 9(1): e84408.
6. Chen Z, Jia
S, Li D, Cai J, Tu J, Geng B, Cui Q*, and Yang J*. (2013) Silencing of Long Noncoding RNA AK139328 Attenuates Ischemia/Reperfusion
Injury in Mouse Livers. PLoS
ONE 8(11): e80817, 2013.
7. Li Y, Qiu
C, Tu J, Geng B, Yang J,
Jiang T*, and Cui
Q*.HMDD v2. 0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Research , 2014,
42(D1), D1070-D1074.
8. Li X, Wang J, Jia
Z, Cui Q,
Zhang C, Wang W, Chen P, Ma K, and Zhou C*. MiR-499 Regulates Cell
Proliferation and Apoptosis during Late-Stage Cardiac Differentiation via Sox6
and Cyclin D1. PLoS
ONE 8(9): e74504, 2013.
9. Zheng X, Li A, Zhao L, Zhou T, Shen Q, Cui Q, and Qin X*. Key role of microRNA-15a in
the KLF4 suppressions of proliferation and angiogenesis in endothelial and
vascular smooth muscle cells. Biochemical and Biophysical Research
Communications. Volume 437, Issue 4, 9 August 2013, Pages 625–631
10. Geng B, Cai
B, Liao F, Zheng Y, Zeng Q,
Fan X, Gong Y, Yang J, Cui Q, Tang C, Xu GH.
Increase or decrease hydrogen sulfide exert opposite lipolysis, but reduce global insulin resistance in high
fatty diet induced obese mice. PLoS
One 2013 8(9):e73892.
11. Xu W, Geng
B, Cui Q,
Guan Y, and Yang J*. Intracellular and extracellular ATP in regulation of
insulin secretion from pancreatic β cells. Journal of Diabetes, 2013 6(2):113-9.
12. Li D, Chen G, Yang J, Fan X, Gong
Y, Xu G, Cui Q*, and Geng B*. Transcriptome Analysis Reveals Distinct Patterns of Long Noncoding RNAs in Heart and Plasma of Mice with Heart
Failure. PLoS
ONE 2013
8(10): e77938.
13. Li Y, Li Z, Zhou S, Wen J, Geng B, Yang J, and Cui Q*.
Genome-Wide Analysis of Human MicroRNA Stability. BioMed Research International 2013:368975,
2013.
14. Chen G, Wang Z, Wang D, Qiu C, Liu M, Chen X, Zhang Q, Yan G*, and Cui Q*.
LncRNADisease: a database for long noncoding RNA associated diseases. Nucleic Acids Research.
41, 983-986, 2013. (SCI引用42次)
15. Chen G, Wang J*, and Cui Q*. Could circulating microRNAs contribute to cancer therapy.
Trends
in Molecular Medicine .
19 (2), 71-73, 2013.
16. Chen G, Qiu
C, Zhang Q, Liu B*, and Cui Q*.
Genome-wide analysis of human SNPs at long intergenic
noncoding RNAs. Human Mutation .34 (2),
338-344, 2013.
17. Chen X, Liu M, Cui Q*,
and Yan G*. Prediction of
Disease-Related Interactions between MicroRNAs and
Environmental Factors Based on a Semi-Supervised Classifier. PLOS
ONE 2012, 7(8) e43425 DOI: 10.1371/journal.pone.0043425
18. Qiu C, Chen G, and Cui Q*.
Towards the understanding of microRNA and
environmental factor interactions and their relationships to human diseases. Scientific
Reports 2012:2.DOI: 10.1038/srep00318.
19. Qiu C, Wang D,
Wang E, and Cui
Q*. An
upstream interacting context based framework for the computational inference of
microRNA functions. Molecular BioSystems
2012, 8(5) 1492-1498.
20. Li X, Gao
L, Cui Q,
Gary BD, Dyess DL, Taylor W, Shevde-Samant
LR, Samant RS, Dean-Colomb
W,
21. Cui X, Wang C, Li L, Fan D, Zhou
Y, Wu D, Cui Q,
Fu F, Wu L. Insulin decreases myocardial adiponectin
receptor 1 expression via PI3K/Akt and FoxO1 pathway.
Cardiovasc Res. 93, 69-78, 2012.
22. Wang J*, Zhang J, Li K, Zhao W, and
Cui Q.
SpliceDisease database: linking RNA splicing and
disease. Nucleic Acids Research. 40, 1055-1059, 2012.
23. Qiu C, Wang J, and Cui Q*.
miR2Gene: Pattern discovery of single gene, multiple genes, and pathways by
enrichment analysis of their microRNA regulators. BMC
Systems Biology 5 (Suppl 2):S9, 2011.
24. Yang Q, Qiu
C, Yang J, Wu Q, and Cui Q*. miREnvironment
Database: providing a bridge for microRNAs,
environmental factors, and phenotypes. Bioinformatics 2011 27:
3329-3330.
25. Wang J*, Li Z, Qiu C, Wang D, and Cui Q*. The relationship between rational drug
design and drug side effects. Briefings in Bioinformatics . 13, 377-382, 2012.
26. Cui Q*. A network of cancer genes with co-occurring
and anti-co-occurring mutations. PLoS
ONE 2010 5(10): e13180. doi:10.1371/
journal.pone.0013180.
27. Wang D, Qiu
C, Zhang H, Wang J, Cui Q*, and Yin Y*. Human microRNA
oncogenes and tumor suppressors show significantly
different biological patterns: from functions to targets. PLoS
ONE 2010 5(9): e13067. doi:
10.1371/journal.pone.0013067. (SCI引用31次)
28. Lu M, Shi B, Wang J, Cao Q, Cui Q*.
TAM: A method for enrichment and depletion analysis of a microRNA
category in a list of microRNAs. BMC Bioinformatics.
2010, 11:419 (9 August 2010). (SCI引用32次)
29. Li J, Lenferink
A, Deng Y, Collins C, Cui Q, Purisima E,
O’Connor-McCourt M, and Wang E. Identification of high quality cancer
prognostic markers and metastasis network modules. Nat. Commun.
2010 1: 34. (SCI引用45次)
30. Chang N, Yi J, Guo G, Liu X, Shang Y, Tong T, Cui Q, Zhan M, Gorospe
M, Wang W. HuR uses AUF1 as a cofactor to promote
p16INK4 mRNA decay. Mol Cell Biol. 30, 3875-3886, 2010. (SCI引用40次)
31. Qiu C, Wang J,
32. Wang D, Wang, J, Lu M, Song F,
and Cui Q*.
Inferring the human microRNA functional similarity
and functional network based on microRNA-associated
diseases. Bioinformatics 2010 26: 1644-1650. (SCI引用27次)
33. Qin X, Wang X, Wang Y, Tang Z, Cui Q,
Xi J, Li YS, Chien S, Wang N. (2010) Proc
Natl Acad Sci U S A. 107(7):3240-3244, 2010. (SCI引用63次)
34. Wang J, Lu M, Qiu
C, and Cui Q*. TransmiR:
a transcription factor-microRNA regulation database. Nucleic
Acids Research. 38, 119-122, 2010. (SCI引用74次)
35. Shi G, Cui Q*,
and Youyi Zhang*. MicroRNA Set:
36. Wang D, Lu M,
Miao J, Li T, Wang E, and Cui Q*. Cepred: Predicting the Co-Expression
Patterns of the Human Intronic microRNAs
with Their Host Genes. PLoS
ONE 2009 4(2): e4421. (SCI引用23次，被Science杂志引用)
37. Zhao H, Wang D,Liu
B, Jiang X, Zhang J, Fan M, Fan Z, Chen Y, Song SW, Gao
W, Jiang T*, Cui Q*. Recombination rates
of human microRNA. Biochem Biophys Res Commun.
2009 Feb 13;379(3):702-5.
38. Zhang F, Lu M, Zhang Q, Zhang F, Gao W, and Cui Q*. Predicting cardiovascular
disease associated microRNAs by bioinformatics. Journal
of
39. Cui Q, Purisima
EO, Wang E*, Protein evolution on a human signaling network. BMC
Systems Biology 2009, 3:21. (SCI引用23次)
40. Miao J, Fan Q, Cui Q,
Zhang H, Chen L, Wang S, Guan N, Guan Y, Ding J: Newly
identified cytoskeletal components are associated
with dynamic changes of podocyte foot processes. Nephrol Dial Transplant 2009,
24(11):3297-3305.
41. Lu M, Zhang Q, Deng M, Miao J, Guo Y, Gao W, Cui Q*.
An analysis of human microRNA and disease
associations. PLoS
ONE. 2008;3(10):e3420. (该研究是国际上从“计算”和“信息学”角度探讨microRNA和疾病关系的第一个工作。SCI引用207次，并被Cell, Nature Reviews Genetics, Nature Methods等著名杂志多次引用，其中网络生物医学奠基人Barabasi在Nature Reviews Genetics关于网络生物医学的综述用一小节的篇幅对该工作进行了介绍)
42. Cui Q, Ma Y, Jaramillo M, Bari H, Awan A, Yang S, Zhang S, Liu L, Lu M, O'Connor-McCourt M, Purisima EO, Wang E*. A map of human cancer
signaling. Mol Syst Biol
2007 3:152. (SCI引用120次)
43. Cui
Q#, Yu Z#, Purisima EO, Wang E*. MicroRNA regulation and interspecific variation of gene expression. Trends
Genet 2007 23:372-375. (SCI引用37次)
44. Cui
Q#, Yu Z#, Pan Y, Purisima EO, Wang E*. MicroRNAs preferentially target the genes
with high transcriptional regulation complexity. Biochem Biophys Res Commun
2007 352:733-738. (SCI引用63次)
45. Awan A, Bari H, Yoksong
S, Chowdhury S, Cui Q,
Yu Z, Purisima EO, Wang E*. Regulatory network
motifs and hotspots of cancer genes in a mammalian cellular signalling
network. IET Syst Biol
2007 1: 292-7.
46. Cui
Q#, Yu Z#, Purisima EO, Wang E*. Principles of microRNA
regulation of a human cellular signaling network. Mol Syst
Biol 2006 2:46. (SCI引用148次)
47. Cui Q, Liu B, Jiang T*, Ma S.
Characterizing the dynamic connectivity between genes by variable parameter
regression and Kalman filtering based on temporal
gene expression data. Bioinformatics 2005
21:1538-1541.
48. Liu B, Cui Q, Jiang T*, Ma S. A combinational feature
selection and ensemble neural network method for classification of gene
expression data. BMC Bioinformatics 2004 5: 136. (SCI引用50次)
49. Cui
Q, Jiang T*,
Liu B, Ma S. Esub8: a novel tool to predict protein subcellular
localizations in eukaryotic organisms. BMC Bioinformatics 2004 5:66. (SCI引用22次)
50. Huang H, Zhang
L, Cui Q, Jiang T, Ma S, Gao Y*. Finding Potential Ligands for PDZ Domains by Tailfit,
a JAVA program. Chinese Medical Sciences Journal 2004 19: 97-104.
51. Jiang T*, Cui Q, Shi G, Ma S. Protein Folding Simulations
of the Hydrophobic-Hydrophilic Model by Combining Tabu
Search with Genetic Algorithms. Journal of Chemical Physics
2003 119: 4592-4596. (SCI引用35次)