Jie Liang

Summary

Affiliation: University of Illinois at Chicago
Country: USA

Publications

  1. pmc CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
    Joe Dundas
    Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA
    Nucleic Acids Res 34:W116-8. 2006
  2. pmc Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES
    Hsiao Mei Lu
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, USA
    PLoS Comput Biol 5:e1000526. 2009
  3. pmc Pattern of amino acid substitutions in transmembrane domains of β-barrel membrane proteins for detecting remote homologs in bacteria and mitochondria
    David Jimenez-Morales
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
    PLoS ONE 6:e26400. 2011
  4. pmc Mechanisms of regulating cell topology in proliferating epithelia: impact of division plane, mechanical forces, and cell memory
    Yingzi Li
    School of Biomedical Engineering and Med X Research Institute, Shanghai Jiao Tong University, Shanghai, China
    PLoS ONE 7:e43108. 2012
  5. pmc Weakly stable regions and protein-protein interactions in beta-barrel membrane proteins
    Hammad Naveed
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, 60607, USA
    Curr Pharm Des 20:1268-73. 2014
  6. pmc Computational studies of membrane proteins: models and predictions for biological understanding
    Jie Liang
    Department of Bioengineering, Chicago, IL 60607, USA
    Biochim Biophys Acta 1818:927-41. 2012
  7. pmc Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability
    Youfang Cao
    Shanghai Center for Systems Biomedicine SCSB, Shanghai Jiao Tong University, Shanghai, 200240, China
    BMC Syst Biol 2:30. 2008
  8. pmc Protein surface analysis for function annotation in high-throughput structural genomics pipeline
    T Andrew Binkowski
    Department of Bioengineering, The University of Illinois, 851 South Morgan St, Room 218, Chicago, IL 60607, USA
    Protein Sci 14:2972-81. 2005
  9. pmc Geometry of protein shape and its evolutionary pattern for function prediction and characterization
    Jie Liang
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA
    Conf Proc IEEE Eng Med Biol Soc 2009:2324-7. 2009
  10. ncbi request reprint The membrane-water interface region of membrane proteins: structural bias and the anti-snorkeling effect
    Jie Liang
    Department of Bioengineering, University of Illinois at Chicago, M C563, 835 S Wolcott Avenue, Chicago, IL 60612 7340, USA
    Trends Biochem Sci 30:355-7. 2005

Collaborators

Detail Information

Publications83

  1. pmc CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
    Joe Dundas
    Program in Bioinformatics, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA
    Nucleic Acids Res 34:W116-8. 2006
    ..The updated CASTp web server can be used to study surface features, functional regions and specific roles of key residues of proteins...
  2. pmc Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES
    Hsiao Mei Lu
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, USA
    PLoS Comput Biol 5:e1000526. 2009
    ..This approach is general and can be applied to other large macromolecular machineries such as the virus capsid and ribosomal complex...
  3. pmc Pattern of amino acid substitutions in transmembrane domains of β-barrel membrane proteins for detecting remote homologs in bacteria and mitochondria
    David Jimenez-Morales
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
    PLoS ONE 6:e26400. 2011
    ..The estimated substitution pattern will also help to identify key elements important for the structural and functional integrity of β-barrel membrane proteins, and will aid in the design of mutagenesis studies...
  4. pmc Mechanisms of regulating cell topology in proliferating epithelia: impact of division plane, mechanical forces, and cell memory
    Yingzi Li
    School of Biomedical Engineering and Med X Research Institute, Shanghai Jiao Tong University, Shanghai, China
    PLoS ONE 7:e43108. 2012
    ..We conclude that both division plane orientation and mechanical forces play important roles in cell topology in animal proliferating epithelia. Moreover, cell memory is also essential for generating specific topological distributions...
  5. pmc Weakly stable regions and protein-protein interactions in beta-barrel membrane proteins
    Hammad Naveed
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, 60607, USA
    Curr Pharm Des 20:1268-73. 2014
    ....
  6. pmc Computational studies of membrane proteins: models and predictions for biological understanding
    Jie Liang
    Department of Bioengineering, Chicago, IL 60607, USA
    Biochim Biophys Acta 1818:927-41. 2012
    ..This article is part of a Special Issue entitled: Protein Folding in Membranes...
  7. pmc Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability
    Youfang Cao
    Shanghai Center for Systems Biomedicine SCSB, Shanghai Jiao Tong University, Shanghai, 200240, China
    BMC Syst Biol 2:30. 2008
    ..However, there are neither closed-form solutions nor algorithms fully describing all microstates for a given molecular network...
  8. pmc Protein surface analysis for function annotation in high-throughput structural genomics pipeline
    T Andrew Binkowski
    Department of Bioengineering, The University of Illinois, 851 South Morgan St, Room 218, Chicago, IL 60607, USA
    Protein Sci 14:2972-81. 2005
    ....
  9. pmc Geometry of protein shape and its evolutionary pattern for function prediction and characterization
    Jie Liang
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60612, USA
    Conf Proc IEEE Eng Med Biol Soc 2009:2324-7. 2009
    ....
  10. ncbi request reprint The membrane-water interface region of membrane proteins: structural bias and the anti-snorkeling effect
    Jie Liang
    Department of Bioengineering, University of Illinois at Chicago, M C563, 835 S Wolcott Avenue, Chicago, IL 60612 7340, USA
    Trends Biochem Sci 30:355-7. 2005
    ..The results have revealed that this interface region has an important role in constraining protein secondary structure. This study raises new questions and opens up new directions for studying membrane proteins...
  11. pmc Are proteins well-packed?
    J Liang
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607 7052, USA
    Biophys J 81:751-66. 2001
    ..And we find that the enthalpies of folding (per amino acid) are independent of the packing density of a protein, indicating that van der Waals interactions are not a dominant component of the folding forces...
  12. ncbi request reprint Prediction of buried helices in multispan alpha helical membrane proteins
    Larisa Adamian
    Department of Bioengineering, University of Illinois, Chicago, Illinois 60612 7340, USA
    Proteins 63:1-5. 2006
    ..68. A server for this tool (RANTS) is available online at http://gila.bioengr.uic.edu/lab/...
  13. pmc Chapter 4. Predicting and characterizing protein functions through matching geometric and evolutionary patterns of binding surfaces
    Jie Liang
    Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, China
    Adv Protein Chem Struct Biol 75:107-41. 2008
    ..In addition, we briefly discuss how the negative image of a binding pocket can be casted, and how such information can be used to facilitate drug discovery...
  14. ncbi request reprint Developing optimal non-linear scoring function for protein design
    Changyu Hu
    Department of Bioengineering, SEO, MC 063, University of Illinois at Chicago, 851 S Morgan Street, Room 218, Chicago, IL 60607 7052, USA
    Bioinformatics 20:3080-98. 2004
    ..To select the correct sequences and to guide the search process, a design scoring function is critically important. Such a scoring function should be able to characterize the global fitness landscape of many proteins simultaneously...
  15. ncbi request reprint Higher-order interhelical spatial interactions in membrane proteins
    Larisa Adamian
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
    J Mol Biol 327:251-72. 2003
    ..On the basis of the analysis of the archaeal rhodopsin family of proteins, tightly packed triplet interactions can be achieved with several different choices of amino acid residues...
  16. ncbi request reprint Evolutionary patterns of retinal-binding pockets of type I rhodopsins and their functions
    Larisa Adamian
    University of Illinois at Chicago, Bioengineering Bioinformatics, Chicago, IL, USA
    Photochem Photobiol 82:1426-35. 2006
    ..The approach we describe in this paper may be useful for large-scale functional prediction of rhodopsins...
  17. ncbi request reprint Automated method for predicting enzyme functional surfaces and locating key residues with accuracy and specificity
    Yan Yuan Tseng
    Dept of Bioeng, Illinois Univ, Chicago, IL 60607 7052, USA
    Conf Proc IEEE Eng Med Biol Soc 1:4552-5. 2006
    ..We discuss application of our methods to amylase, dioxygenase, deaminase, dehalogenase, and hydratase. A large scale cross-validated prediction study shows that our method is sensitive and specific...
  18. ncbi request reprint Are residues in a protein folding nucleus evolutionarily conserved?
    Yan Yuan Tseng
    Department of Bioengineering, SEO, MC 063, University of Illinois at Chicago, 851 S Morgan Street, Room 218, Chicago, IL 60607 7052, USA
    J Mol Biol 335:869-80. 2004
    ..We further reconstruct candidate ancestral residues of the folding nucleus and suggest possible test tube mutation studies for testing folding behavior of ancient folding nucleus...
  19. pmc topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association
    Nathan O Stitziel
    Department of Bioengineering, University of Illinois at Chicago, M C 063, 851 S Morgan Street, Chicago, IL 60607, USA
    Nucleic Acids Res 32:D520-2. 2004
    ..TopoSNP includes an interactive structural visualization web interface, as well as downloadable batch data. The database will be updated at regular intervals and can be accessed at: http://gila.bioengr.uic.edu/snp/toposnp...
  20. pmc Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns
    Yan Yuan Tseng
    Department of Bioengineering, University of Illinois at Chicago, 851 S Morgan Street, Room 218, SEO, MC 063, Chicago, IL 60607 7052, USA
    J Mol Biol 387:451-64. 2009
    ..955, close to the perfect value of 1.00. The best Matthews coefficient is 86.6%. Our method also works well in predicting the biochemical functions of orphan proteins from structural genomics projects...
  21. pmc Lipid-binding surfaces of membrane proteins: evidence from evolutionary and structural analysis
    Larisa Adamian
    Department of Bioengineering, Univeristy of Illinois, Chicago, IL, USA
    Biochim Biophys Acta 1808:1092-102. 2011
    ..Overall, we find that the residues forming specific lipid binding sites on the surfaces of membrane proteins often experience strong purifying selection pressure...
  22. pmc Structural model of rho1 GABAC receptor based on evolutionary analysis: Testing of predicted protein-protein interactions involved in receptor assembly and function
    Larisa Adamian
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60612, USA
    Protein Sci 18:2371-83. 2009
    ....
  23. ncbi request reprint Interhelical hydrogen bonds in transmembrane region are important for function and stability of Ca2+-transporting ATPase
    Larisa Adamian
    Department of Bioengineering, University of Illinois at Chicago, IL 60607, USA
    Cell Biochem Biophys 39:1-12. 2003
    ..Interhelical hydrogen bonds in the transmembrane regions play important roles for the stability and specificity of helix-helix interactions in proteins where change of conformation is required for transport of ions or small molecules...
  24. pmc Accuracy of functional surfaces on comparatively modeled protein structures
    Jieling Zhao
    Department of Bioengineering, University of Illinois at Chicago, 851 S Morgan Street, Room 218, MC 063, Chicago, IL 60607, USA
    J Struct Funct Genomics 12:97-107. 2011
    ..5 Å, and contain 48% or more of the binding surface atoms, with nearly all of the important atoms in the signatures of binding pockets captured...
  25. pmc pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins
    T Andrew Binkowski
    Department of Bioengineering, The University of Illinois at Chicago, Chicago, IL 60607 7052, USA
    Nucleic Acids Res 32:W555-8. 2004
    ..We present an example using pvSOAR to explore the biological roles of a protein whose structure was solved by the structural genomics project. The pvSOAR web server is available at http://pvsoar.bioengr.uic.edu/...
  26. pmc Detecting remote homologues using scoring matrices calculated from the estimation of amino acid substitution rates of beta-barrel membrane proteins
    David Jimenez-Morales
    Department of Bioengineering, University of Illinois at Chicago, 60612, USA
    Conf Proc IEEE Eng Med Biol Soc 2008:1347-50. 2008
    ..Our results demonstrate that bbTM matrices have higher selectivity towards transmembrane beta-barrel proteins and may be used with higher confidence in database searches for remote homologues of this class of proteins...
  27. pmc Topology independent protein structural alignment
    Joe Dundas
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607 7053, USA
    BMC Bioinformatics 8:388. 2007
    ..The resulting structural alignment is sequence order independent. Our method is also insensitive to insertions, deletions, and gaps...
  28. ncbi request reprint Empirical potential function for simplified protein models: combining contact and local sequence-structure descriptors
    Jinfeng Zhang
    Department of Bioengineering, University of Illinois, Chicago, Illinois, USA
    Proteins 63:949-60. 2006
    ..Our results also suggest that local sequence-structure correlation may play important role in reducing the entropic cost of protein folding...
  29. pmc Prediction of geometrically feasible three-dimensional structures of pseudoknotted RNA through free energy estimation
    Jian Zhang
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607, USA
    RNA 15:2248-63. 2009
    ..These close-to-native structures can be used as starting points for further refinement to derive accurate three-dimensional structures of RNA molecules, including those with pseudoknots...
  30. ncbi request reprint Predicting enzyme functional surfaces and locating key residues automatically from structures
    Yan Yuan Tseng
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607 7052, USA
    Ann Biomed Eng 35:1037-42. 2007
    ..A large scale cross-validated prediction study shows that our method is sensitive and specific. Our method can used to study enzyme function, drug design, and engineering novel biochemical function...
  31. pmc Combinatorial model for sequence and spatial motif discovery in short sequence fragments: examples from beta-barrel membrane proteins
    Ronald Jackups
    Dept of Bioeng, Illinois Univ, Chicago, IL 60607 7052, USA
    Conf Proc IEEE Eng Med Biol Soc 1:3470-3. 2006
    ..In this study, we develop combinatorial models for assessing statistically significant sequence and spatial patterns. We show our method can uncover previously unknown sequence and spatial motifs in beta-barrel membrane proteins...
  32. ncbi request reprint Inferring functional relationships of proteins from local sequence and spatial surface patterns
    T Andrew Binkowski
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607 7052, USA
    J Mol Biol 332:505-26. 2003
    ....
  33. pmc CASTp: Computed Atlas of Surface Topography of proteins
    T Andrew Binkowski
    Department of Bioengineering, MC 063, University of Illinois at Chicago, 851 S Morgan Street, Chicago, IL 60607, USA
    Nucleic Acids Res 31:3352-5. 2003
    ..CASTp includes a graphical user interface, flexible interactive visualization, as well as on-the-fly calculation for user uploaded structures. CASTp is updated daily and can be accessed at http://cast.engr.uic.edu...
  34. ncbi request reprint Geometric cooperativity and anticooperativity of three-body interactions in native proteins
    Xiang Li
    Department of Bioengineering, SEO, MC 063, University of Illinois at Chicago, Chicago, Illinois 60607 7052, USA
    Proteins 60:46-65. 2005
    ..In addition, analysis of cooperative 3-body interaction may reveal spatial motifs that can suggest specific protein functions...
  35. pmc Prediction of transmembrane helix orientation in polytopic membrane proteins
    Larisa Adamian
    Department of Bioengineering, University of Illinois at Chicago, M C 563, 835 S, Wolcott St, Chicago, IL 60612 7340, USA
    BMC Struct Biol 6:13. 2006
    ..Therefore, it is important to develop reliable computational methods to predict structures of membrane proteins...
  36. ncbi request reprint Estimation of amino acid residue substitution rates at local spatial regions and application in protein function inference: a Bayesian Monte Carlo approach
    Yan Y Tseng
    Department of Bioengineering, Science and Engineering Offices, MC 063, University of Illinois at Chicago, USA
    Mol Biol Evol 23:421-36. 2006
    ..We show with examples that our method is effective in identifying functionally related proteins that have overall low sequence identity, a task known to be very challenging...
  37. ncbi request reprint Experimental and computational studies of determinants of membrane-protein folding
    Jie Liang
    Department of Bioengineering, University of Illinois at Chicago, SEO 218, MC 063 851, South Morgan Street, Chicago, IL 60607, USA
    Curr Opin Chem Biol 6:878-84. 2002
    ..Further details of the energetics of helix-helix association and interhelical packing geometry are being mapped out. Many sequence motifs and a few spatial motifs promoting helical associations have also been identified...
  38. pmc Generating properly weighted ensemble of conformations of proteins from sparse or indirect distance constraints
    Ming Lin
    Department of Information and Decision Science, University of Illinois at Chicago, 845 S Morgan St, Chicago, Illinois 60607, USA
    J Chem Phys 129:094101. 2008
    ..We show that our approach can faithfully generate conformations that satisfy the given constraints, which approach the native structures when distance constraints for all residue pairs are given...
  39. pmc Engineered oligomerization state of OmpF protein through computational design decouples oligomer dissociation from unfolding
    Hammad Naveed
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
    J Mol Biol 419:89-101. 2012
    ..Furthermore, the conserved site near G57 and G59 is important for the PPI interface and might provide the essential scaffold for PPIs...
  40. pmc Mechanical forces mediate localized topological change in epithelia
    Yingzi Li
    Department of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
    Conf Proc IEEE Eng Med Biol Soc 2011:178-81. 2011
    ..We conclude that mechanical forces in addition to localized differential proliferation are required to produce the distorted topological change which significantly impacts the overall cell shape and tissue morphogenesis...
  41. pmc Predicting weakly stable regions, oligomerization state, and protein-protein interfaces in transmembrane domains of outer membrane proteins
    Hammad Naveed
    Department of Bioengineering, University of Illinois, Chicago, IL 60607, USA
    Proc Natl Acad Sci U S A 106:12735-40. 2009
    ....
  42. pmc Structural signatures of enzyme binding pockets from order-independent surface alignment: a study of metalloendopeptidase and NAD binding proteins
    Joe Dundas
    Department of Bioengineering, University of Illinois at Chicago, 835 South Wolcott, Chicago, IL 60612, USA
    J Mol Biol 406:713-29. 2011
    ..In both cases, we show that signatures and signature basis set reveal significant biological insight...
  43. pmc Discrete state model and accurate estimation of loop entropy of RNA secondary structures
    Jian Zhang
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607, USA
    J Chem Phys 128:125107. 2008
    ..The discrete model and the program used to calculate loop entropy can be downloaded at http://gila.bioengr.uic.edu/resources/RNA.html...
  44. pmc Detecting positively selected sites from amino Acid sequences: an implicit codon model
    Zheng Ouyang
    Department of Bioengineering, SEO, MC 063 University of Illinois Chicago, 851 S Morgan Street, Chicago, IL 60607 7052, USA
    Conf Proc IEEE Eng Med Biol Soc 2007:5302-6. 2007
    ..The object is that sampled DNA sequences should fit the same phylogenetic tree as well as the native DNA sequences. Data set of Beta-globin sequences from vertebrates is used to verify our model...
  45. ncbi request reprint Simplicial edge representation of protein structures and alpha contact potential with confidence measure
    Xiang Li
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607 7052, USA
    Proteins 53:792-805. 2003
    ..This result suggests that the geometry of packing plays an important role, but the specific residue types are often interchangeable...
  46. pmc Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda
    Youfang Cao
    Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
    Proc Natl Acad Sci U S A 107:18445-50. 2010
    ..The landscape approach computed from dCME is general and can be applied to study broad issues in systems biology...
  47. pmc Predicting three-dimensional structures of transmembrane domains of β-barrel membrane proteins
    Hammad Naveed
    Department of Bioengineering, University of Illinois at Chicago, 835 South Wolcott Avenue, Chicago, Illinois 60607, USA
    J Am Chem Soc 134:1775-81. 2012
    ..These results suggest that our model captures key components of the organization principles of β-barrel membrane protein assembly...
  48. ncbi request reprint Importance of chirality and reduced flexibility of protein side chains: a study with square and tetrahedral lattice models
    Jinfeng Zhang
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607, USA
    J Chem Phys 121:592-603. 2004
    ..Our results suggest that side chain entropy may be an important factor contributing to the formation of alpha helices for compact conformations...
  49. ncbi request reprint Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction
    Ronald Jackups
    Department of Bioengineering, SEO, MC 063, University of Illinois at Chicago, 851 S Morgan Street, Room 218, Chicago, IL 60607 7052, USA
    J Mol Biol 354:979-93. 2005
    ..The propensity scales developed in this study will also be useful for computational structure prediction and for folding simulations...
  50. pmc Statistical geometry of lattice chain polymers with voids of defined shapes: sampling with strong constraints
    Ming Lin
    Department of Information and Decision Science, University of Illinois at Chicago, 845 S Morgan St, Chicago, Illinois 60607, USA
    J Chem Phys 128:084903. 2008
    ..Our model is highly effective, and these results indicate that voids representing functional sites can be used as an improved model for studying the evolution of protein functions and how protein function relates to protein stability...
  51. ncbi request reprint Sequence motifs and antimotifs in beta-barrel membrane proteins from a genome-wide analysis: the Ala-Tyr dichotomy and chaperone binding motifs
    Ronald Jackups
    Department of Bioengineering, SEO, MC 063, University of Illinois at Chicago, 851 S Morgan Street, Room 218, Chicago, IL 60607 7052, USA
    J Mol Biol 363:611-23. 2006
    ..Our results also suggest several experiments that can help to elucidate the mechanisms of in vitro and in vivo folding of beta-barrel membrane proteins...
  52. ncbi request reprint Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins
    Larisa Adamian
    Department of Bioengineering, University of Illinois at Chicago, Illinois 60612 7340, USA
    Proteins 59:496-509. 2005
    ..We also compare performance of TMLIP with another lipid propensity scale, kPROT, and with several hydrophobicity scales using hydrophobic moment analysis...
  53. ncbi request reprint Protein folding dynamics via quantification of kinematic energy landscape
    Sema Kachalo
    Department of Bioengineering, MC 063, University of Illinois at Chicago, Chicago, Illinois 60305, USA
    Phys Rev Lett 96:058106. 2006
    ....
  54. pmc Stochastic probability landscape model for switching efficiency, robustness, and differential threshold for induction of genetic circuit in phage lambda
    Youfang Cao
    Shanghai Center for Systems Biomedicine, Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
    Conf Proc IEEE Eng Med Biol Soc 2008:611-4. 2008
    ..Our study has revealed likely mechanism of the phage switch network that was previously unknown...
  55. ncbi request reprint Membrane-associated and secreted genes in breast cancer
    Nathan O Stitziel
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, USA
    Cancer Res 64:8682-7. 2004
    ....
  56. ncbi request reprint Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking
    Xiang Li
    Department of Bioengineering, University of Illinois at Chicago, MC 063, Chicago, IL 60607, USA
    J Mol Biol 344:781-95. 2004
    ..The root-mean-squared deviations of the atoms lining the pockets between the bound and unbound states is as small as 0.9A, suggesting that such pockets constitute features of the populated native state that may be used in docking...
  57. ncbi request reprint Transitions in chronic low back pain in Japanese older adults: a sociomedical perspective
    N Muramatsu
    School of Public Health, University of Illinois at Chicago, USA
    J Gerontol B Psychol Sci Soc Sci 52:S222-34. 1997
    ..The results suggest that social relationships have both favorable and unfavorable effects on chronic low back pain...
  58. pmc Geometric order in proliferating epithelia: impact of rearrangements and cleavage plane orientation
    Hammad Naveed
    Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, IL 60607, USA
    Conf Proc IEEE Eng Med Biol Soc 2010:3808-11. 2010
    ..Our off-lattice cellular model provides an improvement over existing topological for studying the dynamics of proliferating epithelium...
  59. ncbi request reprint Interhelical hydrogen bonds and spatial motifs in membrane proteins: polar clamps and serine zippers
    Larisa Adamian
    Department of Bioengineering, The University of Illinois at Chicago, Chicago, Illinois 60607, USA
    Proteins 47:209-18. 2002
    ..With the examples of halorhodopsin, calcium-transporting ATPase, and bovine cytochrome c oxidase, we discuss the roles of hydrogen bonds in stabilizing helical bundles in polytopic membrane proteins and in protein functions...
  60. ncbi request reprint A model study of protein nascent chain and cotranslational folding using hydrophobic-polar residues
    Hsiao Mei Lu
    Department of Bioengineering, MC 063 University of Illinois at Chicago, Chicago, Illinois 60607, USA
    Proteins 70:442-9. 2008
    ....
  61. pmc Ionizable side chains at catalytic active sites of enzymes
    David Jimenez-Morales
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
    Eur Biophys J 41:449-60. 2012
    ..It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes...
  62. pmc Predicting protein folding rates from geometric contact and amino acid sequence
    Zheng Ouyang
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607, USA
    Protein Sci 17:1256-63. 2008
    ..Second, we show that folding rates can also be predicted from amino acid sequences directly, without the need to know the native topology or other structural properties...
  63. pmc On simplified global nonlinear function for fitness landscape: a case study of inverse protein folding
    Yun Xu
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, United States of America
    PLoS ONE 9:e104403. 2014
    ..Our results can be generalized to construct other types of fitness landscape. ..
  64. pmc Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method
    Youfang Cao
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois 60607, USA
    J Chem Phys 139:025101. 2013
    ..The ABSIS method is general and can be applied to study rare events of other stochastic networks with complex probability landscape. ..
  65. pmc Mechanisms of regulating tissue elongation in Drosophila wing: impact of oriented cell divisions, oriented mechanical forces, and reduced cell size
    Yingzi Li
    School of Biomedical Engineering and Med X Research Institute, Shanghai Jiao Tong University, Shanghai, China Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
    PLoS ONE 9:e86725. 2014
    ..Our simulation results suggest that cell divisions without cell growth play essential roles in tissue elongation. ..
  66. pmc Lysine carboxylation: unveiling a spontaneous post-translational modification
    David Jimenez-Morales
    Department of Bioengineering, University of Illinois at Chicago, 851 South Morgan Street, Room 218, Chicago, IL 60607, USA
    Acta Crystallogr D Biol Crystallogr 70:48-57. 2014
    ..The results also suggest that by switching enzymes on and off under appropriate physicochemical conditions spontaneous PTMs may serve as an important and widely used efficient biological machinery for regulation. ..
  67. pmc Spatial confinement is a major determinant of the folding landscape of human chromosomes
    Gamze Gürsoy
    Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
    Nucleic Acids Res 42:8223-30. 2014
    ..Our results indicate that the overall structure of a human chromosome is dictated by the spatial confinement of the nuclear space, which may undergo significant tissue- and developmental stage-specific size changes. ..
  68. pmc Fast protein loop sampling and structure prediction using distance-guided sequential chain-growth Monte Carlo method
    Ke Tang
    Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
    PLoS Comput Biol 10:e1003539. 2014
    ..Test results on benchmark datasets show that DISGRO performs comparably or better than previous successful methods, while requiring far less computing time. DISGRO is especially effective in modeling longer loops (10-17 residues)...
  69. ncbi request reprint Structural location of disease-associated single-nucleotide polymorphisms
    Nathan O Stitziel
    Department of Bioengineering SEO, MC 063, University of Illinois at Chicago, Room 218, 851, S Morgan Street, Chicago, IL 60607 7052, USA
    J Mol Biol 327:1021-30. 2003
    ..The approach of classifying nsSNPs with alpha shape and HMM developed in this study can be integrated with additional methods to improve the accuracy of predictions of whether a given nsSNP is likely to be disease-associated...
  70. pmc Creation and manipulation of common functional groups en route to a skeletally diverse chemical library
    Jiayue Cui
    Chicago Tri Institutional Center for Chemical Methods and Library Development, Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 108:6763-8. 2011
    ....
  71. ncbi request reprint Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins
    L Adamian
    Department of Bioengineering, University of Illinois at Chicago, 851 S. Morgan Street RM 218, MC-063, Chicago, IL 60607, USA
    J Mol Biol 311:891-907. 2001
    ..This observation may help us to understand the folding mechanism of membrane proteins...
  72. pmc Hydration effects of heparin on antithrombin probed by osmotic stress
    Maria P McGee
    Wake Forest University Medical School, Medicine Department, Medical Center Boulevard, Winston Salem, North Carolina 27157, USA
    Biophys J 82:1040-9. 2002
    ..Together with the structural analyses, results also suggest a direct mechanism linking heparin binding/release to loop expulsion/insertion...
  73. ncbi request reprint Perturbation-based Markovian Transmission Model for macromolecular machinery in cell
    Hsiao Mei Lu
    Department of Bioengineering, SEO, MC 063 University of Illinois at Chicago 851 S Morgan Street, Room 218 Chicago, IL 60607 7052, U S A
    Conf Proc IEEE Eng Med Biol Soc 2007:5029-34. 2007
    ..Further results of selective perturbation on the surface of ATP binding pocket identifies the path of maximal probability flow of signal...
  74. ncbi request reprint Monte Carlo sampling of near-native structures of proteins with applications
    Jinfeng Zhang
    Department of Statistics, Harvard University, Cambridge, Massachusetts, USA
    Proteins 66:61-8. 2007
    ..We also found that the widely used contact potential functions stabilize NNS poorly, whereas potential functions incorporating local structure information significantly increase the stability of NNS...
  75. ncbi request reprint Position-dependence of stabilizing polar interactions of asparagine in transmembrane helical bundles
    James D Lear
    Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104 6059, USA
    Biochemistry 42:6400-7. 2003
    ..Thus, although polar interactions are able to strongly stabilize the folding of membrane proteins, the energetics of association depend on their location within the hydrophobic region of a transmembrane helix...
  76. ncbi request reprint An optimal algorithm for enumerating state space of stochastic molecular networks with small copy numbers of molecules
    Youfang Cao
    Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, 800 Dongchuan Road, 200240 Shanghai, China
    Conf Proc IEEE Eng Med Biol Soc 2007:4599-602. 2007
    ..It allows the approach of solving chemical master equation to be applicable to a larger class of stochastic molecular networks. We show an example of application of our method to the MAPK cascade network...
  77. ncbi request reprint Optimal block boundary pre/postfiltering for wavelet-based image and video compression
    Jie Liang
    School of Engineering Science, Simon Fraser University, Burnaby, Canada
    IEEE Trans Image Process 14:2151-8. 2005
    ..Comparisons with other methods demonstrate the advantages of our pre/postfiltering framework...
  78. ncbi request reprint Undersampled boundary pre-/postfilters for low bit-rate DCT-based block coders
    Lu Gan
    Department of Electrical Engineering and Electronics, The University of Liverpool, U K
    IEEE Trans Image Process 16:428-41. 2007
    ..Furthermore, image coding results indicate that the proposed undersampled pre-/postfiltering systems yield excellent and stable performance in low bit-rate image coding...
  79. ncbi request reprint Wiener filter-based error resilient time-domain lapped transform
    Jie Liang
    School of Engineering Science, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
    IEEE Trans Image Process 16:491-502. 2007
    ..Various design examples and multiple description image coding experiments are reported to demonstrate the performance of the proposed method...
  80. ncbi request reprint The transcriptional repression activity of KyoT2 on the Notch/RBP-J pathway is regulated by PIAS1-catalyzed SUMOylation
    Jishu Wang
    State Key Laboratory of Cancer Biology, Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xian 710032, China
    J Mol Biol 370:27-38. 2007
    ..These results suggest that KyoT2 is a substrate of SUMO modification catalyzed by PIAS1, and that SUMOylation may modulate the transcriptional repression effect of KyoT2 on the Notch/RBP-J signaling pathway...
  81. ncbi request reprint Changes of plasma membrane ATPase activities and proline accumulation in twigs of Casuarina under different growth conditions
    Jie Liang
    School of Life Sciences, Xiamen University, Xiamen 361005
    Shi Yan Sheng Wu Xue Bao 36:169-75. 2003
    ..This suggested that Casuarina responded to osmotic stress by increasing osmotic material content and the proton transportation activities of PM ATPase...
  82. doi request reprint Subunit-subunit interactions in the human 26S proteasome
    Chuan Chen
    Key Laboratory for Cell Biology and Tumor Cell Engineering, The Ministry of Education, School of Life Sciences, Xiamen University, Xiamen, China
    Proteomics 8:508-20. 2008
    ..We observed new interactions between the 19S regulatory particle and the beta-rings of the 20S catalytic particle and therefore proposed a modified model of the 26S proteasome...
  83. ncbi request reprint Error resilient pre/post-filtering for DCT-based block coding systems
    Chengjie Tu
    Microsoft Digital Media Division, Microsoft Corporation, Redmond, WA 98052, USA
    IEEE Trans Image Process 15:30-9. 2006
    ..Experiments show that these filtering operators can achieve superior reconstruction performance without sacrificing much coding performance...

Research Grants7

  1. Computational Assembly of Beta Barrel Membrane Protein
    Jie Liang; Fiscal Year: 2007
    ..Because beta-barrel proteins play key roles in the pathogenesis of these infectious diseases, our proposed research will lead to new targets and new strategies in the development of drugs and vaccines. ..
  2. High-Accuracy Models of Proteins from Remote Homology
    Jie Liang; Fiscal Year: 2007
    ..These computational capabilities could have profound impacts to drug design and disease studies. ..
  3. Computational Assembly of Beta Barrel Membrane Protein
    Jie Liang; Fiscal Year: 2009
    ..Because beta-barrel proteins play key roles in the pathogenesis of these infectious diseases, our proposed research will lead to new targets and new strategies in the development of drugs and vaccines. ..
  4. High-Accuracy Models of Proteins from Remote Homology
    Jie Liang; Fiscal Year: 2009
    ..These computational capabilities could have profound impacts to drug design and disease studies. ..
  5. Computational Assembly of Beta Barrel Membrane Protein
    Jie Liang; Fiscal Year: 2010
    ..Because beta-barrel proteins play key roles in the pathogenesis of these infectious diseases, our proposed research will lead to new targets and new strategies in the development of drugs and vaccines. ..