Beijing Institute of Genomics, Chinese Academy of Sciences

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


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

Research Areas

Alzheimer's disease

Stem cell

Big data in biomedicine


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


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



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



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