Publications

1. Xiang Li, and Jie Liang.(2005) Geometric cooperativity and anti-cooperativity of three-body interactions in native proteins.
   Proteins. In press.
2. Xiang Li, and Jie Liang.(2005) Computational design of combinatorial peptide library for modulating protein-protein interactions.
   Pacific Symposium of Biocomputing. In press.
3. Xiang Li, Ozlem Keskin, Buyong Ma, Ruth Nussinov and Jie Liang. (2004) Protein-protein interactions: Hot spots and structurally conserved residues often locate in complemented pockets that are pre-organized in the unbound states. Implications to docking
   J. Mol. Biol. 344:781-795
4. Nathan Stitziel, Brenton G. Mar, Jie Liang, and Carol Westbrook.(2004) Membrane-associated and secreted genes in breast cancer.
   Cancer Research. 64:8682-8687.
5. Changyu Hu, Xiang Li, and Jie Liang.(2004) Developing optimal nonlinear scoring function for protein design
   Bioinformatics. 20(17):3080-3098.
6. Moon Jung Song, Seungmin Hwang, Wendy Wong, June Round, DeeAnn Martinez-Guzman1, Yaron Turpaz, Jie Liang, Ben Wong, Reid C. Johnson, Michael Carey, and Ren Sun. (2004) The DNA architectural protein HMGB1 facilitates RTAmediated viral gene expression in gamma2 herpesviruses.
   J. Virology. In press.
7. Jinfeng Zhang, Yu Chen, Rong Chen and Jie Liang (2004) Importance of chirality and reduced flexibility of protein side chains: A study with square and tetrahedral lattice models.
   J. Chem. Phys. 121:592-603.
8. T. Andrew Binkowski, Patrick Freeman and Jie Liang (2004) pvSOAR: Detecting similar surface patterns of Pocket and Void Surfaces of Amino Acid Residues on proteins.
   Nucleic Acid Research. 32:W555-W558.
9. Yan Yuan Tseng and Jie Liang (2004) Are residues in a protein folding nucleus evolutionarily conserved?
   J. Mol. Biol. 335:869-880.
10. Nathan O. Stitziel, T. Andrew Binkowski, Yan Yuan Tseng, Simon Kasif and Jie Liang (2004) topoSNP: A topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association.
    Nucleic Acid Research. 32:D520-D522.
11. Sema Kachalo, Zarema Arbieva and Jie Liang (2003) Assessing effect of cross-hybridization on oligonucleotide microarrays. Methods of microarray data analysis III (Papers from CAMDA'02). Edited by Kimberly F. Johnson, Simon M. Lin. Kluwer Academic Publishers, Boston, 2003, p.185-198.
12. Xiang Li, Changyu Hu, and Jie Liang. (2003). Simplicial edge representation of protein structures and alpha contact potential with confidence measure.
    Proteins. 53:792-805.
13. T. Andrew Binkowski, Larisa Adamian and Jie Liang. (2003) Inferring functional relationship of proteins from local sequence and spatial surface patterns.
    J. Mol. Biol. 332:505-526.
14. T. Andrew Binkowski, Shapor Naghibzadeh, and Jie Liang. (2003). CASTp: computed atlas of surface topography of proteins.
    Nucleic Acid Research. 31(13):3352-3355. Abstract
15. Nathan O. Stitziel, Yan Yuan Tseng, Dimitri Pervouchine, David Goddeau, Simon Kasif, and Jie Liang. (2003) Structural location of disease-associated single nucleotide polymorphisms.
    J. Mol. Biol. 327:1021-1030.
16. J. D. Lear, H. Gratkowski, L. Adamian, J. Liang, and W.F. DeGrado. (2003) Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles.
    Biochemistry. 2003 42(21):6400-6407.
17. Larisa Adamian, and Jie Liang. (2003) Interhelical hydrogen bonds in transmembrane region are important for function and stability of Ca2+-transporting ATPase.
    Cell Biochemistry and Biophysics. 39:1-12.
18. Larisa Adamian, Ronald Jackups, Jr, T. Andrew Binkowski, and Jie Liang. (2003)
    Higher order interhelical spatial interactions in membrane proteins.
    J. Mol. Biol. 327:251-272.
19. Jinfeng Zhang, Rong Chen, Chao Tang, and Jie Liang. (2003)
    Origin of scaling behavior of protein packing density: A sequential Monte Carlo study of compact long chain polymers.
    J. Chem. Phys. 118(13):6102-6109. (eprint in arxiv)
    Data: (SAWs in pdb format and Z_alpha data are here.)
    Selected by ( Virtual Journal of Biological Physics Research--April 1, 2003 Volume 5, Issue 7 ).
20. Jie Liang. (2002)
    Experimental and computational studies of the determinants of membrane protein folding.
    Current Opinion in Chemical Biology, 6:878-884
21. Jie Liang, Jinfeng Zhang and Rong Chen. (2002)
    Statistical geometry of packing defects of lattice chain polymer from enumeration and sequential Monte Carlo method.
    J. Chem. Phys., 117:3511-3521. Selected by ( Virtual Journal of Biological Physics Research--August 1, 2002 Volume 4, Issue 3 ).
22. Jie Liang and Sema Kachalo. (2002)
    Computational Analysis of Microarray Gene Expression Profiles Clustering, Classification, and Beyond.
    Chemometrics and Intelligent Laboratory Systems, 62:199-216.
23. Larisa Adamian, and Jie Liang. (2002)
    Interhelical hydrogen bonds and spatial motif in membrane proteins: Polar clamps and serine zippers.
    Proteins, 47:209-218
24. Maria P. McGee, Jie Liang, and J. Luba. (2002)
    Hydration effects of heparin on antithrombin probed by osmotic stress.
    Biophys. J., 82:1040-1049
25. M. P. McGee and J. Liang. (2002)
    Factor X, Coagulation.
    Wiley Encyclopedia of Molecular Medicine. John Wiley & Sons.
26. L. Adamian and J. Liang. (2001)
    Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins.
    J. Mol. Biol., 311:891-907
27. J. Liang and K.A. Dill. (2001)
    Are proteins well-packed?
    Biophys. J., 81:751-766
28. M. P. McGee and J. Liang. (2001)
    Regulation of glycosaminoglycan function by osmotic potentials. Measurement of water transfer during antithrombin activation by heparin.
    J. Biol. Chem., 276:49275-49282
29. I. Gomes, T. L. Sharma, J. D. Kapp, S. Edassery, N. Fulton, J. Liang, R. Hoffman, and C.A. Westbrook. (2001)
    Highly abundant genes in the transcriptosome of human and baboon CD34 antigen-positive bone marrow cells.
    Blood, 98:93-99.
30. C. Yuan, O. Kuwata, J. Liang, S. Misra, S.P. Balashov, T.G. Ebrey. (1999)
    Chloride binding regulates the Schiff base pK in gecko P521 cone-type visual pigment.
    Biochemistry, 38:4649-4654.
31. M.P. McGee, H. Teuschler and J. Liang. (1999)
    Electrostatic interactions during activation of coagulation factor IX via the tissue factor pathway: effect of univalent salts.
    Biochim. Biophys. Acta, 1453:239-253
32. J. Liang, H. Edelsbrunner, and C. Woodward. (1998)
    Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design.
    Protein Science, 7 , 1884-1897. (8.9 MB)
33. H. Edelsbrunner, M. Facello and J. Liang. (1998)
    On the definition and the construction of pockets in macromolecules.
    Disc. Appl. Math. 88:83-102
34. J. Liang, H. Edelsbrunner, P. Fu, P.V. Sudhakar and S. Subramaniam. (1998)
    Analytical shape computing of macromolecules II: identication and computation of inaccessible cavities inside proteins.
    Proteins. 33, 18-29
35. J. Liang, H. Edelsbrunner, P. Fu, P.V. Sudhakar and S. Subramaniam. (1998)
    Analytical shape computing of macromolecules I: molecular area and volume through alpha shape.
    Proteins. 33, 1-17.
36. J. Liang and M.P. McGee. (1998)
    Mechanisms of coagulation factor Xa inhibition by antithrombin. Correlation between hydration structure and water transfer during reactive loop insertion.
    Biopys. J., 75 , 573-582.
37. M.P. McGee, H. Teuschler, and J. Liang. (1998)
    Effective electrostatic charge of coagulation factor X in solution and on phospholipid membranes: implications for activation mechanisms and structure-function relationships of the Gla domain.
    Biochem. J., 330 , 533-539.
38. J. Liang and S. Subranmaniam. (1997)
    Computation of molecular electrostatics with boundary element methods.
    Biophys. J., 73 , 1830-1841. (6.6 MB)
39. S. Kim, J. Liang, and B.A. Barry. (1997)
    Chemical complementation identies a proton acceptor for redox-active tyrosine D in photosystem II.
    Proc. Natl. Acad. Sci. USA, 94 , 14406-14411.
40. J.W. Lewis, J. Liang, T.G. Ebrey, M. Sheves, N. Livnah, O. Kuwata, S. Jager, and D.S. Kliger. (1997)
    Early photolysis intermediates of gecko and bovine articial visual pigments.
    Biochemistry, 36 , 14593-14600
41. H. Edelsbrunner, M. Facello, P. Fu and J. Liang. (1995)
    Measuring proteins and voids in proteins.
    Proc. 28th Ann. Hawaii Intl. Conf. System Sci. Vol. 5. 256-264. (4.0 MB)
42. T.G. Ebrey and J. Liang. (1995)
    The bleaching of visual pigments.
    Ed. P-S. Song, CRC Handbook of organic photochemistry and photobiology. CRC Press, Boca Raton, Florida. pp. 1484-1491
43. J. Lewis, J. Liang, T.G. Ebrey, M. Sheves and D.S. Kliger. (1995)
    Chloride effect on the early photolysis intermediates of a gecko cone-type visual pigment.
    Biochemistry 34 , 5817-5823. (899 KB)
44. J. Liang, G. Steinberg, N. Livnah, M. Sheves and T.G. Ebrey. (1994)
    The pKa of the protonated Schiff base of gecko cone and octopus visual pigments.
    Biophys. J. 67 , 848-854.
45. J. Liang, R. Govindjee, and T.G. Ebrey. (1993)
    Metarhodopsin intermediates of the gecko cone pigment P521.
    Biochemistry, 32(51) , 14187-14193. (802 KB)
46. W. Lin, C. Ma, Z. Luo, W. Fan, Y. Chen and J. Liang. (1987)
    Study on the radiosensitization of AT1727 on human lung adenocarcinoma cell line SPC-A- 1.
    Chin. J. Radiat. Res. Radiat. Processing, 5 , 58-62.

Last Modified 1/1/2005