General

Beijing Institute of Genomics, Chinese Academy of Sciences

No.1 Beichen West Road, Chaoyang District, Beijing 100101, China

Email: leihx@big.ac.cn

Office: (86)-010-8409-7276, Mobile: (86)-137-1859-0608


Research Areas

Alzheimer's disease

Stem cell

Big data in biomedicine

Education

Ph.D., Biochemistry, Kansas State University, Advisor: Dr. Paul E. Smith, May 2003

B.E., Biomed. Eng., Huazhong University of Science and Technology, China, June 1991


Experience

   
Work Experience

2008-present:          Professor in Computational Systems Biology, Beijing Institute of Genomics, Chinese Academy of Sciences
2004-2008:               Postdoctoral ResearchGenome center, University of California at Davis, Computational Structural Biology    (Mentor: Dr. Yong Duan)
2003-2004:               Department of chemistry and biochemistry, University of Delaware (Mentor: Dr. Yong Duan)

2008:                        100-Talent of Chinese Academy of Sciences (****)
2014-present:   Adjunct professor, Beijing institute for brain disorders
2012-present:   Associate Editor, Journal of Alzheimer’s Disease.
2011-present:           Associate Editor-in-Chief, Genomics, Proteomics & Bioinformatics.


Teaching Experience

Professor, Big data in biomedicine, 2016

Professor, Systems biology and network analysis for neurological disorders, 2013-2015

Professor, Frontiers in systems and synthetic biology, 2011 and 2012

Professor, Structural bioinformatics: from genome to drug design, 2009 and 2010


Publications

   
Papers

60.  X. Peng, P.-Q. Xing, X.-H. Li, Y. Qian, F.-H. Song, Z.-X. Bai, G.-C. Han and H.-X. Lei*. (2016) Toward Personalized Intervention for Alzheimer's Disease. Genomics Proteomics & Bioinformatics. 14: 289-297

59.  F.-H. Song, Y. Qian, X. Peng, G.-C. Han, J.-J. Wang, Z.-X. Bai, P.J. Crack and H.-X. Lei*. (2016) Perturbation of the transcriptome: implications of the innate immune system in Alzheimer’s disease. Curr Opin Pharmacology 26: 47-53. 

58.  H.-B. Luo, G.-C. Han, J.-J. Wang, F. Zeng, Y.-M. Li, S.-J. Saho, F.-H. Song, Z.-X. Bai, X. Peng, Y.-J. Wang, X.-Q. Shi and H.-X. Lei*. (2016) Common aging signature in the peripheral blood of vascular dementia and Alzheimer’s disease. Mol Neurobiol. 536):3596-605

57.  F.-H. Song, G.-C. Han, Z.-X. Bai, X. Peng, J.-J. Wang and H.-X. Lei*. (2015) Alzheimer’s disease: genomics and beyond. Int Rev Neurobiol 1211-24.

56.  T. Wei, X. Peng, L.-L. Ye, J.-J. Wang, F.-H. Song Z.-X. Bai, G.-C. Han, F.-M. Ji and H.-X. Lei*. (2015) Web resources for stem cell research. Genomics Proteomics & Bioinformatics 13(1):40-45.

55.  Z.-X. Bai, G.-C. Han, B. Xie, J.-J. Wang, F.-H. Song, X. Peng and H.-X. Lei*. (2016) AlzBase: an integrative database for gene dysregulation in Alzheimer’s disease. Mol Neurobiol 53(1), 310-319.

54.  G.-C. Han, J.-Y. Sun, J.-J. Wang, Z.-X. Bai, F.-H. Song and H.-X. Lei*. (2014) Genomics in neurological disorders. Genomics Proteomics & Bioinformatics 12: 156-163.

53.  J.-Y. Sun, F.-H. Song, J.-J. Wang, G.-C. Han, Z.-X. Bai, B. Xie, X.-M. Feng, J.-P. Jia, Y. Duan and H.-X. Lei*. (2014) Hidden risk genes with high order intragenic epistasis in Alzheimer’s disease. J Alzheimers Dis, 41:1039-1056.

52.  X.-M. Feng, Z.-X. Bai, J.-J. Wang, B. Xie, J.-Y. Sun, G.-C. Han, F.-H. Song, P.J. Crack, Y. Duan and H.-X. Lei*. (2014) Robust gene dys-regulation in Alzheimer’s brains. J Alzheimers Dis, 41:587-597.

51.  Z.-X. Bai, B. Stamova, H. Xu, B. P. Ander, J.-J. Wang, G. C. Jickling, X. Zhan, G.-C. Han, L.-W. Jin, C. DeCarli, H.-X. Lei and F. R. Sharp. (2014) Distinctive RNA expression profiles in blood associated with Alzheimer's disease after accounting for white matter hyperintensities. Alzheimer Dis Assoc Disord, 28(3):226-233.

50.  H.-X. Lei*, J.-Y. Sun, E.P. Baldwin, D.J. Segal and Y. Duan. (2014) Conformational elasticity can facilitate TALE-DNA recognition. Adv Protein Chem Str94: 347-364.

49.  J.-J. Wang, X.-M. Feng, Z.-X. Bai, L.-W. Jin, Y. Duan and H.-X. Lei*. (2014) Chromosome 19p in Alzheimer’s disease: when genome meets transcriptome. J Alzheimers Dis, 38: 245-250.

48.  B. Xie, D.-P. Wang, Y. Duan, J. Yu and H.-X. Lei*, (2013) The functional network of human divergently paired genes (DPGs). PLoS Onee78896

47.  G.-C. Han, J.-J. Wang, F. Zeng, X.-M. Feng, J. Yu, H.-Y. Cao, X. Yi, H.-D. Zhou, L.-W. Jin, Y. Duan, Y.-J. Wang and H.-X. Lei*. (2013) Characteristic transformation of blood transcriptome in Alzheimer’s disease. J Alzheimers Dis, 35: 373-386.

46.  J.-Y. Sun, Y.-Y. Pan, X.-M. Feng, H.-J. Zhang, Y. Duan and H.-X. Lei*. (2013) iBIG: an integrative network tool for supporting human disease mechanism studies. Genomics Proteomics & Bioinformatics 11: 166-171.

45.  D.-P. Liang, G.-C. Han, X.-M. Feng, J.-Y. Sun, Y. Duan and H.-X. Lei*. (2012) Concerted perturbation observed in a hub network in Alzheimer’s disease. PLoS One7(7): e40498

44.  H.-X. Lei*, X.-F. Wang and C. Wu. (2012) Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations. J Mol Graph Mod38: 279-289.

43.  J.-Y. Sun, X.-M. Feng, D.-P. Liang, Y. Duan and H.-X. Lei*. (2012) Down-regulation of energy metabolism in Alzheimer’s disease is a protective response of neurons to the microenvironment. J Alzheimers Dis28, 389-402

42.  D.-P. Wang, Y. Su, H.-X. Lei* and J. Yu. (2012) Transposon-Derived and Satellite-Derived Repetitive Sequences Play Distinct Functional Roles in Mammalian Intron Size Expansion. Evol Bioinfo8, 301-319

41.  H.-X. Lei*, C.-J. Chen, Y. Xiao and Y. Duan. (2011)The folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel. J Chem Phys134205104.

40.  J. Wang, P. Cieplak, J. Li, J. Wang, Q. Cai, M.J. Hsieh, H.-X. Lei, R. Luo, and Y. Duan. (2011) Development of Polarizable Models for Molecular Mechanical Calculations II: Induced Dipole Models Significantly Improve Accuracy of Intermolecular Interaction Energies. J. Phys. Chem. B, 115 (12): 3100–3111

39.  H.-X. Lei* and Y Duan. (2011) Kinetics and thermodynamics of protein folding. InTechbook title “Thermodynamics 2”, Chapter 5.

38.  H.-X. Lei* and Y. Duan. (2011) Protein folding by computer: How far have we gone? ACTA BIOPHYSICA SINICA27(3): 187-194

37.  Y.-Q. Zhou, Y. Duan, Y.-D. Yang, E. Faraggi and H.-X. Lei. (2011) Trends in template/fragment-free protein structure prediction. Theor Chem Acc, 128(1), 3-16

36.  H.-X. Lei*, Y. Su, L. Jin and Y. Duan. (2010) The folding network of villin headpiece subdomain. Biophys J99: 3374-3384

35.  H.-X. Lei*. (2010) Amyloid and Alzheimer’s disease. Protein & Cell1(4), 312-314

34.  H.-X. Lei, Z.-X. Wang, C. Wu and Y. Duan. (2009) Dual folding pathways of an a/b protein from all-atom ab initio folding simulations. J. Chem. Phys., 131, 165105

33.  H.-X. Lei, X.-J. Deng, Z.-X. Wang, and Y. Duan. (2008) The fast-folding HP35 double mutant has a substantially reduced primary folding free energy barrier. J. Chem. Phys.129(15), 155104

32.  C. Wu, Z.-X. Wang, H.-X. Lei, Y. Duan, M. T. Bowers, and J.-E. Shea, (2008) The binding of thioflavin T and its neutral analog BTA-1 to protofibrils of the Alzheimer's disease Abeta(16-22) peptide probed by molecular dynamics simulations. J Mol Biol., 384(3): 718-29.

(2003-2008, #9-31)

31.  H.-X. Lei, C. Wu, Z.-X. Wang, Y.-Q. Zhou, and Y. Duan. (2008) Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations. J Chem Phys, 128(23): 235105

30.  H.-G. Liu, S.G. Dastidar, H.-X. Lei, W. Zhang, M.C. Lee and Y. Duan. (2008) Protein Conformational changes in protein functions. in Molecular Modeling of Proteins. Methods in Molecular Biology book series. Human Press Inc, Vol 443

29.  H.-X. Lei and Y. Duan. (2008) Protein Folding and Unfolding by All-atom Molecular Dynamics. in Molecular Modeling of Proteins. Methods in Molecular Biology book series. Human Press Inc, Vol 443

28.  H.-X. Lei, C. Wu, H.-G. Liu and Y. Duan. (2007) Folding free energy landscape of HP35 from molecular dynamics simulations. PNAS, 104(12): 4925-4930

27.  H.-X. Lei and Y. Duan. (2007) Two-stage folding of HP-35 from Ab initio simulation. J. Mol. Biol., 370:196-206 (cover story)

26.  H.-X. Lei and Y. Duan. (2007) Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation. J Phys Chem B, 111: 5458-5463.

25.  H.-X. Lei and Y. Duan. (2007) Improved sampling methods for molecular dynamics. Curr Opin Struct Biol, 17: 187-191

24.  C. Wu, Z.-X. Wang, H.-X. Lei, W. Zhang and Y. Duan. (2007) Dual binding modes of congo red to amyloid protofibril surface observed in molecular dynamics simulations. J Am Chem Soc, 129: 1225-1232

23.  Z.-X. Wang, C. Wu, H.-X. Lei, W. Zhang and Y. Duan. (2007) Accurate ab initio study on the hydrogen bond pairs in protein secondary structures. J Chem Theory Comput., 3(4): 1527-1537

22.  H.-X. Lei; S.G. Dastidar and Y. Duan. (2006) Folding transition state and denatured state ensembles of FSD-1 from folding and unfolding simulations. J Phys Chem B, 110: 22001-22008

21.  H.-X. Lei; C. Wu; Z.-X. Wang and Y. Duan. (2006) Molecular dynamics simulations and free energy analyses on the dimer formation of an amyloidgenic heptamer peptide from human β2-microglobulin: implication to the protofibril structure. J. Mol. Biol., 356: 1049-1063

20.  C. Wu, H.-X. Lei, Z.-X. Wang, W. Zhang and Y. Duan. (2006) Phenol red interacts with the protofibrils oligomers of an amyloidogenic hexapeptide NFGAIL through both hydrophobic and aromatic contacts and acts as a chemical chaperon. Biophys J, 91: 3664-3672

19.  Z.-X. Wang, W. Zhang, C. Wu, H.-X. Lei, P. Cieplak, and Y. Duan. (2006) Strike a Balance: optimization of backbone torsion parameters of AMBER polarizable force field (ff05pol) for simulations of proteins and peptides. J. Comp. Chem., 27: 781-790

18.  C. Wu, H.-X. Lei, and Y. Duan. (2005) Elongation of ordered peptide aggregate of an amyloidgenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent. J Am Chem Soc, 127: 13530-13537

17.  A.J. Fischer, N.C. Rockwell, A.Y. Jang, L.A. Ernst, A.S. Waggoner, Y. Duan, H.-X. Lei, and J.C. Lagarias. (2005) Multiple Roles of a Conserved GAF Domain Tyrosine Residue in Cyanobacterial and Plant Phytochromes. Biochemistry, 44: 15203-15215

16.  S. Chowdhury, H.-X. Lei, and Y. Duan. (2005) Denatured state ensemble and the early stage folding of the G29A mutant of the B-domain of protein A. J Phys Chem B, 109(18): 9073-9081

15.  C. Wu, H.-X. Lei, and Y. Duan. (2005) The role of Phe in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent. Biophys J, 88: 2897-2906

14.  H.-X. Lei and Yong Duan. (2004) Incorporating intermolecular distance into protein-protein docking. Protein Eng Des Sel, 17(12): 837-845 (cover story)

13.  H.-X. Lei and Y. Duan. (2004) The role of plastic β-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein. J Chem Phys, 121(23): 12014-12111

12.  C. Wu, H.-X. Lei, and Y. Duan. (2004) Formation of partially ordered oligomers of amyloidogenic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations. Biophys J, 87:3000-3009

11.  W. Zhang, H.-X. Lei, S. Chowdhury, and Y. Duan. (2004) Fs-21 Peptides Can Form Both Single Helix and Helix-Turn-Helix. J Phys Chem B, 108(22): 7479-7489

10.  H.-X. Lei and P. E. Smith. (2003) The role of the unfolded state in hairpin stability. Biophys J, 85(6): 3513-3520

9.    H.-X. Lei and P. E. Smith. (2003) The Effects of Internal Water Molecules on the Structure and Dynamics of Chymotrypsin Inhibitor 2. J Phys Chem B., 107: 1395-1402

 (1993-1998, #1-8)

8.       Li W.-J., Lei H.-X., Pei W.-H. and Wu J.-J., (1998) GeneDn: for high-level expression design of heterologous genes in a prokaryotic system. Bioinformatics, 14(10): 884-885

7.       Wu J.-J., Lei H.-X., Du Y. and Wang L.-G.. (1998) Comparison of the 3-D structures in hematopoietic cytokine family. Chinese J. Exp. Hematology, 6(2): 111-119

6.       Lei H.-X., Li W.-J., Zhang L.-X., Wu J.-J. and Li C.-H., (1997) Computer-aided gene design and its application in molecular biology., Current Advance in Tumor Biology. pp 59-62. Chinese Medical Sciences Press.

5.       Lei H.-X., Wu J.-J. and Shen B.-F., (1997) Design and structure modeling of the ricin toxin A chain mutant. ACTA BIOPHYSICA SINICA, 13(1): 24-28

4.       Lei H.-X. and Wu J.-J., (1995) Progress in viroid research. Foreign Medical Sciences, , 12(2): 53-56

3.       Wu J.-J., Li W.-J., Lei H.-X. and Sun T., (1994) Software for sequence analysis-GOLDKEY. Lett. in Biotech., 5(4): 189-193

2.       Sun T., Jiang X.-C., Wu J.-J., He L.-T. and Lei H.-X., (1994) Application of computer in study on infrared spectrum analysis of condensed phase organic phosphate. Chinese J. Anal. Chem., 22(7): 679-682

1.       Lei H.-X., Wu J.-J., Li W.-J.. (1993) Prediction of the solubility of recombinant protein in E. Coli.  ACTA BIOPHYSICA SINICA, 9(3): 504-506


Students

已指导学生

孙继亚  02  19183  

裴玉超  02  19187  

潘玉云  02  19187  

苏尧  01  19187  

梁大鹏  01  19187  

孙继亚  01  19187  

谢彬  01  19187  

韩光春  01  19187  

汪嘉葭  01  19187  

白周现  01  67687  

现指导学生

宋福海  01  67687  

李秀辉  02  63228  

邢培琪  02  67687  

彭星  01  67687  

陈传远   02  67687  

钱颖  01  67687