Search
back BACK
Publications


Yaoqi Zhou LabBack to Top
 In Press 

103.   Xu, B.*, Yang, Y.*, Liang, H. and Zhou, Y., An all-atom knowledge-based energy function for protein-DNA threading, decoy discrimination, and prediction of transcription-factor binding profiles, Proteins, in Press (2009) [DDNA 2 Download ] [List of Protein-DNA complexes]

102.  Liang, S., Wang, G., and Zhou, Y., Refining near-native protein-protein docking decoys by local re-sampling and energy minimization, Proteins, in Press (2009). [PDF-TBA]

 2009 

101.  Zhou, Y. and Faraggi, E., Prediction of one-dimensional structural properties of proteins by integrated neural network (Book Chapter), Protein Structure Prediction: Method and Algorithms, edited by H. Rangwala and G. Karypis, Wiley, 2009.

100.  Xue, B., Faraggi, E., and Zhou, Y., Predicting residue-residue contact maps by a two-layer, integrated neural-network method., Proteins 76, 176-183 (2009) [SPINE-2D server ] [PDF]

99.  Liang, S., Li, L., Hsu, W. L., Uversky, V. N., Zhou, Y., Dunker, A. K. and Meroueh, S. O., Exploring the molecular design of protein interaction sites with molecular dynamics and free energy calculations, Biochemistry 48, 399-414 (2009). [PDF]

98.  Liang, S., Meroueh, S. O., Wang, G., Qiu, C. and Zhou, Y., Consensus scoring for enriching near-native structures from protein-protein docking decoys, Proteins 75, 397-403 (2009). [ENDES download] [PDF]

97.  Faraggi, E., Xue, B., and Zhou, Y., Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by fast guided-learning through a two-layer neural network. Proteins 74, 857-871 (2009). [Real-SPINE 3.0 server] [PDF]

 2008 

96.  Lei, H., Wu, C., Wang, Z. X., Zhou, Y., and Duan, Y., 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, 235105 (2008). [PDF]

95.  Luo, Z., Ding, J. and Zhou, Y., Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations, J. Chem. Phys. 128, 225103 (2008). [PDF]

94.  Zhang, W., Liu, S. and Zhou, Y., SP5: Improving protein fold recognition by using predictedtorsion angles and profile-based gap penalty, PLoS ONE 3, e2325 (2008). [PDF] [SP5 server] [List of Prefab pairs]

93.  Yang, Y. and Zhou, Y., Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely-related all-atom statistical energy functions., Protein Science 17 1212-1219, (2008). [PDF] [DFIRE 2.0]

92.  Yang, Y. and Zhou, Y., Specific interactions for ab initio folding of protein terminal regions with secondary structures., Proteins 72, 793-803 (2008). [PDF] [dDFIRE]

91.  Xue, B., Dor, O., Faraggi, E. and Zhou, Y., Real value prediction of backbone torsion angles., Proteins 72, 427-433 (2008). [Real-SPINE 2.0 server ] [PDF]

90.  Zhang, W., Dunker, A. K., and Zhou, Y., Assessing secondary-structure assignment of protein structures by using pairwise sequence-alignment benchmarks., Proteins 71, 61--67 (2008). [SKSP server ][PDF] [List of Prefab pairs (Table IV)]

 2007 

89.  Luo, Z., Ding, J., and Zhou, Y., Temperature-Dependent Folding Pathways of Pin1 WW Domain: An All-Atom Molecular Dynamics Simulation of a Gō Model., Biophys. J.93, 2152--2161 (2007) [PDF]

88.  Liang, S., Liu, S., Zhang, C. and Zhou, Y., A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys., Proteins 69, 244--253 (2007). [PDF] [Server [On the Cover]

87.  Chen, Y., Zhou, Y. and Ding, J., The helix-coil transition revisited., Proteins 69, 58--68 (2007). [PDF]

86.  Zhou, H., Xue, B., and Zhou, Y., DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile, Protein Sci.16,947--955 (2007)[DDOMAIN server] [PDF]

85.  Liu, S., Zhang, C., Liang, S., and Zhou, Y., Fold Recognition by Concurrent Use of Solvent Accessibility and Residue Depth, Proteins68, 636--645, (2007)[SP4 Server] [PDF] [On the Cover]

84.  Dor, O. and Zhou, Y., Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training, Proteins 66, 838--845, (2007)[SPINE Server] [PDF]

83.  Dor, O. and Zhou, Y., Real-SPINE: An integrated system of neural networks forreal-value prediction of protein structural properties, Proteins 68, 76--81, (2007)[SPINE/Real-SPINE Server] [PDF]

 2006 

82.  Zhou, Y., Zhou, H., and Karplus, M., Cooperativity in Scapharca dimeric hemoglobin: Simulation of binding intermediates and elucidation of the role of interfacial water, Rend. Fis. Acc. Lincei, 17:191-211 (2006) Reprinted from #54].

81.  Liang, S., Zhang, C., Liu, S. and Zhou, Y., Protein binding site prediction with an empirical scoring function, Nucl. Acids Res. 34, 3698-3707 (2006). [PINUP Server] [PDF]

80.  Zhang, C., Liu, S. and Zhou, Y., MC2: Identifying high-quality protein-interaction modules by clique merging, J. Proteome Res. 5, 801--807 (2006). [MC2 Server] [PDF]

79.  Liu, S., Zhang, C. and Zhou, Y., Uneven size distribution of mammalian genes in the number of tissues expressed and in the number of co-expressed genes, Human Molec. Genetics 15, 1313--1318 (2006) [Cover Article]. [Abstract.] [PDF]

78.  Zhou, Y., Zhou, H., Zhang, C. and Liu, S., What is a desirable statistical energy function for proteins and how can it be obtained?, Cell Biochem. Biophys. 46, 165--174 (2006). Review. [PDF]

77.  Xu, Z. and Zhang, C. and Liu, S. and Zhou, Y., QBES: Predicting real values of solventaccessibility from sequences by efficient, constrained energyoptimization, Proteins 63, 961--966 (2006). [PDF]

 2005 

76.  Zhou, Z., Feng, H., Zhou, H., Zhou, Y. and Y. Bai, Design and folding of a multi-domain protein, Biochemistry 44, 12107--12112 (2005). [PDF]

75.  Zhou, H. and Zhou, Y., SPEM: Improving multiple-sequence alignment withsequence profiles and predicted secondary structures, Bioinformatics 21, 3615--3621 (2005). [PDF] [SPEM Server]

74.  Zhou, H. and Zhou, Y., SPARKS 2 and SP3 servers in CASP 6., Proteins (Supplement CASP issue), Suppl 7 152--156 (2005). [ PDF]

73.  Li, H., and Zhou, Y., Fold helical proteins by energy minimization in dihedral space and a DFIRE-based statistical energy function, J. Bioinfo. Comput. Biol. 3, 1151-1170 (2005). [ PDF]

72.  Pandey, B. P., Zhang, C., Yuan, X., Zi, J. and Zhou, Y., Protein flexibility prediction by an all-atom mean-field statistical theory, Protein Science 14, 1772--1777 (2005). [PDF]

71.  H. Li and Zhou, Y., SCUD: Fast structure clustering of decoys usingreference state to remove overall rotation, J. Comput. Chem. 26, 1189-1192 (2005). [ PDF] [SCUD Server]

70.  Zhou, H., Zhang, C., Liu, S., and Zhou, Y., Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis, and comparative analysis of domain combinations, Nucl. Acids Res. (Server issue) 33, W193--W197 (2005). [PDF]

69.  Zhang, C., Liu, S., and Zhou, Y., Docking prediction using biological information, ZDOCK sampling technique and clustering guided by the DFIRE statistical energy function, Proteins (Special CAPRI issue) 60, 314--318 (2005) Invited, Peer-reviewed Conference Paper. [PDF]

68.  Zhang, C., Liu, S., Zhu, Q. and Zhou, Y., A knowledge-based energy function for protein-ligand, protein-protein and protein-DNA complexes, J. Med. Chem. 48, 2325-2335 (2005). [PDF] [DDNA Server]

67.  Liu, S., Zhang, C., and Zhou, Y., Domain Graph of Arabidopsis thaliana Proteome by comparative analysis, J. Proteome Res. 4, 435-444 (2005). [PDF] [DOGMA Server/Database]

66.  Zhou, H., and Zhou, Y., Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments., Proteins. 58, 321-328 (2005). [ PDF] [Server] [ Independent LiveBench Performance [ CAFASP4 [CASP6] [Ranked #2 in CM (SPARKS 2 as #1) and #5 in FR/H targets in 49 servers assessed at CASP6 ]

 2004 

65.  Bai, Y., Zhou, H., and Zhou, Y., Critical nucleation size in the folding of small apparently two-state proteins., Protein Sci. 13, 1173-1181 (2004). [ PDF]

64.  Zhang, C., Liu, S., Zhou, H., and Zhou, Y., The dependence of all-atom statistical potentials on training structural database., Biophys. J. 86, 3349-3358 (2004). [ PDF]

63.  Zhang, C., Liu, S., Zhou, H., and Zhou, Y., An accurate residue-level pair potential of mean force for folding and binding based on the distance-scaled ideal-gas reference state., Protein Sci. 13, 400-411 (2004). [PDF]

62.  Zhang, C., Liu, S., and Zhou, Y., Accurate and efficient loop selections using DFIRE-based all-atom statistical potential., Protein Sci. 13, 391-399 (2004). [ PDF] [ Supplement Materials] [Server]

61.  Liu, S., Zhang, C., Zhou, H., and Zhou, Y., A physical reference state unifies the structure-derived potential of mean force for protein folding and binding., Proteins 56, 93-101 (2004). [ PDF] [Server]

60.  Jang, H., Hall, C. K., and Zhou, Y., Thermodynamics and stability of a beta-sheet complex: Molecular dynamics simulations on simplified off-lattice protein models, Protein Sci., 13, 40-53 (2004) [ PDF]

59.  Zhou, H. and Zhou, Y., Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition, Proteins, 55, 1005-1013 (2004). Subject Area:Bioinformatics] [Server] [Abstract [ PDF] **Ranked #1 in CM targets in 49 servers assessed in CASP6 - [ Independent LiveBench Performance [CASP6]

58.  Jang, H., Hall, C. K., and Zhou, Y., Assembly and kinetic folding pathways of a tetrameric beta-sheet complex: Molecular dynamics simulations on simplified off-lattice protein models, Biophys. J., 86, 31-49 (2004). Subject Area:Folding Kinetics/Thermodynamcs] [PDF]

57.  Zhou, H. and Zhou, Y., Quantifying the effect of burial of amino acid residues on proteinstability, Proteins, 54, 315-322 (2004). SubjectArea:Bioinformatics [PDF ] [List of 200 PDB structures]

 2003 

56.  Zhou, H. and Zhou, Y., Predicting the topology of transmembrane helical proteins usingmean burial propensity and a hidden-Markov-model based method, Protein Sci., 12, 1547-1555 (2003). Subject Area:Bioinformatics [THUMBUP Server] [UMBHMM Server] [Abstract] [PDF] [73 protein sequences] [topologies] [pdb list]

55.  Zhou, Y., Zhang, C., Stell, G., and J. Wang, Temperature dependence of thedistribution of the first passage time: Results from all-atomdiscontinuous molecular dynamics simulations of the second -hairpin fragment of protein G", J. Am.Chem. Soc., 125, 6300-6305 (2003). Subject Area:Folding kinetics [PDF]

54.  Zhou, Y., Zhou, H., and Karplus, M., Cooperativity in Scapharca dimerichemoglobin: Simulation of binding intermediates and elucidation ofthe role of interfacial water, J. Mol. Biol., 326,593--606 (2003). Subject Area: BindingCooperativity, Protein Dynamics] [Abstract] [PDF]

 2002 

53.  Zhou, H. and Zhou, Y., Folding rate prediction using total contact distance., Biophys. J. 82, 458--463 (2002). Subject Area: Folding Kinetics] [Server] [Abstract] [ Residue ranges for some proteins] [PDF]

52.  Zhou, Y. and Linhananta, A., Thermodynamics of an all-atom off-lattice model of the fragment B of Staphylococcal protein A: Implication for the origin of the cooperativity of protein folding, J. Phys. Chem. B, 106, 1481-1485 (2002). Subject Area: Folding Thermodynamics, Folding Cooperativity. [Abstract] [PDF]

51.  Linhananta, A., Zhou, H. and Zhou, Y., The dual role of a loop with low loop contact distance infolding and domain swapping, Protein Science, 11,1695-1701 (2002). Subject Area: Folding Mechanism, Folding Kinetics, Bioinformatics [Abstract] [PDF]

50.  Linhananta, A. and Zhou, Y., The role of sidechain packing and native contact interactions infolding: Discontinuous molecular dynamics folding simulations of anall-atom Go model of fragment B of Staphylococcal proteinA, J. Chem. Phys., 117, 8983--8995 (2002). Subject Area: Folding Mechanism, FoldingKinetics, Protein Dynamics] [PDF]

49.  Zhou, H. and Zhou, Y., Distance-scaled, finite ideal-gas reference state improvesstructure-derived potentials of mean force for structure selectionand stability prediction, Protein Science, 11,2714--2726 (2002). Subject Area: Bioinformatics, Folding Stability, StructurePrediction [The895 mutation list] [ Abstract] [PDF] [CORRECTIONS] Protein Science, 12, 2121 (2003). [DMONMER Server] [DMUTANT Server]

48.  Zhou, H. and Zhou, Y., Thestability scale and atomic solvation parameters extracted from 1023mutation experiments, Proteins, 49, 483--492 (2002). Subject Area: Bioinformatics, Folding Stability [The 1023 mutation list] [PDF]

47.  Jang, H., Hall, C. K., and Zhou, Y. Protein folding pathways and kinetics: Molecular dynamics simulations of -strand motifs, Biophys. J. 83, 819-835 (2002). [Subject Area: FoldingMechanism, Folding Kinetics] [PDF]

46.  Zhou, Y. and Linhananta, A., Role of hydrophilic and hydrophobic contacts in folding of the second -hairpin fragment of protein G: Molecular dynamics simulation studies of an all-atom model, Proteins, 47, 154-162 (2002). Subject Area: Folding Mechanism, Folding Kinetics] [Abstract] [PDF]

45.  Jang, H., Hall, C. K., and Zhou, Y. Folding thermodynamics of model four-strand antiparallel -sheet proteins, Biophys. J. 82, 646-659 (2002). Subject Area: Folding Thermodynamics [PDF]

44.  Zhou, Y., Karplus, M., Ball, K. D. and Berry, R. S., The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers,J. Chem. Phys., 116, 2323-2329 (2002). [Subject Area: Polymer Thermodynamics, Statistical Mechanics] [PDF]

 2001 

43.  Zhou, Y., Fast and accurate thermodynamics of square-well systems from umbrella-sampling simulations of hard-sphere systems., J. Chem. Phys. 115, 7550-7553 (2001). [Subject Area: Polymer Thermodynamics, Statistical Mechanics] [PDF]

 2000 

42.  Zhou, Y., Cook, M., and Karplus, M., Protein motions at zero-total angular momentum: The importance of long-range correlations., Biophys. J. 79, 2902-2908 (2000). [PDF]

 1999 

41.  Zhou, Y., Vitkup, D., and Karplus, M., Native proteins are surface-molten solids: Application of the Lindemann criterion for the solid versus liquid state., J. Molec. Biol. 285 , 1371 (1999). [PDF]

40.  Zhou, Y. and Karplus, M., Folding of a model three-helix bundle protein: A thermodynamic and kinetic analysis., J. Molec. Biol. 293, 917-951 (1999). [PDF]

39.  Zhou, Y. and Karplus, M., Interpreting the folding kinetics of helical proteins., Nature 401, 400-403 (1999). [PDF]

38.  Zhou, Y., Hall, C. K., and Karplus, M., The calorimetric criterion for a two-state process revisited., Protein Science 8, 1064 (1999). [PDF]

 1998 

37.  Zhou, Y. Salt effects on protein titration and binding. J. Phys. Chem. 102, 10615 (1998). [PDF]

 1997 

36.  Zhou, Y. and Karplus, M., Folding thermodynamics of a model three-helix bundle protein., Proc. Natl. Acad. Sci. (USA) 94, 14429 (1997). [PDF]

35.  Zhou, Y., Karplus, M., Wichert, J. M., and Hall, C. K., Equilibrium thermodynamics of homopolymers and clusters: Molecular dynamics and Monte Carlo simulation studies of systems with square-well interactions., J. Chem. Phys. 107, 10691 (1997). [PDF]

 1996 

34.  Zhou, Y., Hall, C. K., and Karplus, M., A first-order disorder-to-order transition in an isolated homopolymer model., Phys. Rev. Lett. 77 , 2822 (1996). [PDF]

33.  Zhou, Y. and Karplus, M., Exact results for the effect of bond flexibility on the structure and the collapse transition of isolated square-well trimers., Molec. Phys. 89, 1707 (1996).

32.  Zhou, Y. and Hall, C. K., Solute excluded-volume effects on the stability of globular proteins: A statistical thermodynamic theory., Biopolymers 38 , 273 (1996).

31.  Yeh, S., Zhou, Y., and Stell, G., Phase separation of ionic fluids: An extended Ebeling-Grigo approach., J. Phys. Chem. (Friedman, H. L. Issue) 100 , 1415 (1996). [PDF]

 1995 

30.  Zhou, Y., Hall, C. K., and Stell, G., Exact results for isolated sticky chains., Molec. Phys. 86 , 1485 (1995).

29.  Zhou, Y., S. W. Smith, and Hall, C. K., Linear dependence of thermodynamic properties of tangent hard-sphere chains on chain length., Molec. Phys. 86, 1157 (1995).

28.  Zhou, Y., Hall, C. K., and Stell, G., The thermodynamic perturbation theory for fused hard-sphere chain fluids., J. Chem. Phys. 103 , 2688 (1995).

27.  Costa, L. A., Zhou, Y., Hall, C. K., and Carr, S., Fused hard-sphere chain molecules: Comparison between monte carlo simulation for the bulk pressure and generalized Flory theories., J. Chem. Phys. 102, 6212 (1995).

26.  Zhou, Y. and Stell, G., Criticality of charged systems: II. The binary mixture of hard spheres and ions., J. Chem. Phys. 102, 5796 (1995).

25.  Zhou, Y., Yeh, S., and Stell, G., Criticality of charged systems: I. The restricted primitive model., J. Chem. Phys. 102, 5785 (1995).

24.  Zhou, Y. and Stell, G., Chemical association in simple models of molecular and ionic fluids IV. New approximation for the cavity function and an application to the theory of weak electrolytes., J. Chem. Phys. 102, 8089 (1995).

 1993 

23.  Zhou, Y. and Stell, G., Analytical approach to molecular liquids: V. Symmetric dissociative dipolar dumbbells with the bonding length, /2 and related systems., J. Chem. Phys. 98, 5777 (1993).

 1992 

22.  Stell, G. and Zhou, Y., Microscopic modeling of association., Fluid Phase Equilibria 79, 1 (1992).

21.  Zhang, Y., Zhou, Y., Luo, Z., and Hanson, D., Electron rearrangement and energy relaxation due to a core hole creation in molecules., J. Phys. Chem. 96, 2949 (1992).

20.  Zhou, Y. and Stell, G., Chemical association in simple models of molecular and ionic fluids III. The cavity functions., J. Chem. Phys. 96, 1507 (1992).

19.  Zhou, Y. and Stell, G., Chemical association in simple models of molecular and ionic fluids II. Thermodynamic properties., J. Chem. Phys. 96, 1504 (1992).

 1991 

18.  Raineri, F. O., Zhou, Y., Friedman, H. L., and Stell, G., Ion solvation dynamics in an interaction site model solvent., Chem. Phys. 152, 201 (1991).

17.  Zhou, Y., Friedman, H. L., and Stell, G., Outer-sphere electron transfer reactions in model molecular solvents: The mean spherical approximation., Chem. Phys. 152, 185 (1991).

 1990 

16.  Zhou, Y. and Stell, G., Nonlocal integral-equation approximations: II. The Lennard-Jones fluid., J. Chem. Phys. 92, 5544 (1990).

15.  Zhou, Y. and Stell, G., Nonlocal integral-equation approximations: I. The hydrostatic approximation with applications., J. Chem. Phys. 92, 5533 (1990).

 1989 

14.  Zhou, Y. and Stell, G., Fluids inside a pore -- an integral-equation approach III. Water-in-oil microemulsions., Molec. Phys. 68, 1265 (1989).

13.  Zhou, Y., Friedman, H. L., and Stell, G., Analytical approach to molecular liquids: IV. Solvation dynamics and electron-transfer reactions., J. Chem. Phys. 91, 4885 (1989).

12.  Zhou, Y., Friedman, H. L., and Stell, G., Analytical approach to molecular liquids: III. The Born solvation free energy of two fixed ions in a dipolar solvent., J. Chem. Phys. 91, 4879 (1989).

11.  Zhou, Y. and Stell, G., Analytical approach to molecular liquids: II. Solvation of ions in molecular fluids., J. Chem. Phys. 91, 4869 (1989).

10.  Stell, G. and Zhou, Y., Analytical approach to molecular liquids: I. Site-site interaction model using an extended mean-spherical approximation., J. Chem. Phys. 91, 4861 (1989).

9.  Stell, G. and Zhou, Y., Chemical association in simple models of molecular and ionic fluids., J. Chem. Phys. 91, 3618 (1989).

8.  Zhou, Y. and Stell, G., The theory of semipermeable vesicles and membranes: An integral-equation approach. III. Vesicles with internal nonpermeating ions., J. Chem. Phys. 91, 3208 (1989).

7.  Zhou, Y. and Stell, G., Fluids inside a pore -- an integral-equation approach II. Cylindrical pores., Molec. Phys. 66, 791 (1989).

6.  Zhou, Y. and Stell, G., Fluids inside a pore -- an integral-equation approach I. General formalism and hard-spheres inside spherical and slit pores., Molec. Phys. 66, 767 (1989).

 1988 

5.  Zhou, Y. and Stell, G., The theory of semipermeable vesicles and membranes: An integral-equation approach. II. Donnan equilibrium., J. Chem. Phys. 89, 7020 (1988).

4.  Zhou, Y. and Stell, G., The theory of semipermeable vesicles and membranes: An integral-equation approach. I. General formalism and application to a hard-sphere mixture., J. Chem. Phys. 89, 7010 (1988).

3.  Zhou, Y. and Stell, G., Equations of state for hard-sphere fluids., Int. J. Thermophys. 9, 953 (1988).

2.  Zhou, Y., Stell, G., and Friedman, H. L., Note on standard free energy of transfer and partitioning of ionic species between two fluid phases., J. Chem. Phys. 89, 3836 (1988).

1.  Zhou, Y. and Stell, G., The hard-sphere fluid: New exact results with applications., J. Stat. Phys., Howard Reiss Issue 52, 1389 (1988).

Keith Dunker LabBack to Top
 In Press 

49.  Xie, H., Vucetic, S., Iakoucheva, L.M., Oldfield, C.J., Dunker, A.K., Uversky, V.N., and Obradovic, Z. Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome. Res. (In press, 2007)

48.  Vucetic, S., Xie, H., Iakoucheva, L.M., Oldfield, C.J., Dunker, A.K., Obradovic, Z. and Uversky, V.N., Functional anthology of intrinsic disorder. II. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J. Proteome. Res. (In press, 2007)

47.  Midic, U. Dunker, K. and Obradovic, Z. Exploring alternative knowledge representations for protein secondary-structure prediction. Int’l Journal of Data Mining and Bioinformatics. (In press)

46.  Uversky, V. N., Dunker, A.K. Understanding protein non-folding. To fold or not to fold: Some current concepts of protein chemistry. (Zbilut, J., Scheibel, T., eds.) (2006) Nova Science Publishers, Inc. Hauppauge, NY. (In Press)

45.  Xie, H., Vucetic, S., Iakoucheva, L.M., Oldfield, C.J., Dunker, A.K., Obradovic, Z. and Uversky, V.N. Functional anthology of intrinsic disorder. III. Biological processes and functions of proteins with long disordered regions. J. Proteome. Res. (In press, 2007)

44.  Uversky V.N., Dunker A.K., Intrinsically Disordered Proteins. Vol. 1: Longhi S., Measles Virus Nucleoprotein. Nova Science Publishers, Inc., Hauppauge, NY, USA. (In press, 2007)

43.  Uversky, Radivojac, P., V.N., Iakoucheva, L.M., Obradovic, Z., Dunker, A.K. Prediction of Intrinsic Disorder in Functional Proteomics. In: Methods in Molecular Biology: Gene Function Analysis. (Michael F. Ochs, ed.) Humana Press. Totowa, NJ. (In Press, 2007)

42.  Oldfield, C.J., Van, Y. Dunker, A.K. Prediction of intrinsic protein disorder: applications in structural genomics. In: Methods Mol. Biol. Structural Genomics (M.A. Kennedy, ed.). (In Press, 2007)

41.  Vacic, V., Oldfield, C.J., Mohan, A., Radivojac, P., Cortese, M.S., Uversky, V.N., and Dunker, A.K. Characterization of molecular recognition features, MoRFs, and their binding partners. Journal of Proteome Research (In Press, 2007)

40.  Dunker, A.K. Disordered Proteins. In: Encyclopedia for the Life Sciences. John Wiley & Sons. London (In Press, 2007)

39.  Radivojac, P., Iakoucheva, L. M., Oldfield, C.J., Obradovic, Z., Uversky, V.N., Dunker, A.K. Intrinsic Disorder and Functional Proteomics. Biophys. J. (In press, 2007).

 2007 

38.  Le Gall, T., Romero, P., Cortese, M.S., Uversky, V.N., and Dunker, A.K., Intrinsic disorder in the Protein Data Bank. J. Biomol. Struct. Dyn. 24: 325-42. (2007)

37.  Sickmeier, M., Hamilton, J.A., LeGall, T., Vacic, V., Cortese, M.S., Tantos, A., Szabo, B., Tompa, P., Chen, J., Uversky, V.N., Obradovic, Z., and Dunker, A.K. DisProt: The database of disordered proteins. Nucleic Acids Res. 35 (Database issue): D786-93. (2007)

 2006 

36.  Chen, J.W., Romero, P., Uversky, V.N., and Dunker, A.K. Conservation of intrinsic disorder in protein domains and families: I. A database of conserved predicted disordered regions, J. Proteome Res.5: 879-887 (2006)

35.  Chen, J.W., Romero, P., Uversky, V.N., and Dunker, A.K. Conservation of intrinsic disorder in protein domains and families: II. Functions of conserved disorder, J. Proteome Res. 5: 888-898 (2006)

34.  Cheng Y., Le Gall T., Oldfield C.J., Dunker A.K., Uversky V.N. Abundance of intrinsic disorder in proteins associated with cardiovascular disease. Biochemistry. 45: 10448-10460 (2006)

33.  Cheng, Y., LeGall, T., Oldfield, C.J., Mueller, J.P., Van, Y.Y., Romero, P., Cortese, M.S, Uversky, V.N., and Dunker, A.K. Rational drug design via intrinsically disordered protein. Trends Biotechnol. 24: 435-42. (2006)

32.  Dosztányi, Z., Chen, J., Dunker, A.K., Simon, I., and Tompa, P. Disorder and sequence repeats in hub proteins and their implications for network evolution. J. Proteome Res. 5: 2985-95 (2006)

31.  Liu, J., Perumal, N.B., Uversky, V.N., Oldfield, C.J., Su, E.W., Dunker, A.K. Intrinsic disorder in transcription factors. Biochemistry 45: 6873-6888 (2006)

30.  Mohan, A., Radivojac, P., Oldfield, C.J., Vacic, V., Cortese, M.S., Uversky, V.N., Dunker, A.K. A dataset of molecular recognition features (MoRFs). J. Mol. Biol. 362: 1043-59 (2006)

29.  Peng, K., Radovojac, P., Vucetic, S., Dunker, A.K., and Obradovic, Z. Length-dependent prediction of protein intrinsic disorder, BMC Bioinformatics 7: 208 (2006)

28.  Radivojac, P., Iakoucheva, L.M., Oldfield, C.J., Obradovic, Z., Uversky, V.N., and Dunker, A.K. Intrinsic Disorder and Functional Proteomics. Biophys J. [Epub ahead of print]. (2006)

27.  Radivojac, P., Vucetic, S., O’Connor, T.R., Uversky, V.N., Obradovic, Z., and Dunker, A.K. Calmodulin signaling: analysis and prediction of a disorder-dependent molecular recognition mechanism. Proteins: Structure, Function, and Bioinformatics 63: 398-410 (2006)

26.  Romero, P. R., Zaidi, S., Fang, Y.Y., Uversky, V.N., Radivojac, P., Cortese, M., Sickmeier, M., Obradovic, Z., and Dunker, A.K. Alternative splicing in concert with protein intrinsic disorder enables functional diversity in multicellular organisms. Proc. Nat’l. Acad. Sci. USA 103: 8390-8395 (2006)

25.  Romero, P., S. Zaidi, S., and Dunker, A. K. Roles of Intrinsic Disorder in Protein Families and Isozymes; Proceedings of the 13th International Congress on Genes, Gene Families and Isozymes (Xiong X.G., Yan Z.Z., Liang W.Y., eds.) Medimond Publishers, Bologna, Italy, pp 7-13 (2006)

24.  Uversky, V.N., Roman, A., Oldfield, C.J., Dunker, A.K. Protein intrinsic disorder and human papillomaviruses: Increased amount of disorder in E6 and E7 oncoproteins from high risk HPVs. J. Proteome Res. 5: 1829-1842 (2006)

 2005 

23.  Cortese, M.C., Baird, J.P., Uversky, V.N., and Dunker, A.K. Uncovering the unfoldome: enriching cell extracts for unstructured proteins by acid treatment. J. Proteome Res. 4: 1610-1618 (2005)

22.  Daly, K., Radivojac, P., and Dunker, A. K. Intrinsic disorder and protein modifications: building an SMV predictor for methylation. Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2005, pp. 475-481, San Diego, California, USA, (2005)

21.  Midic, U., Dunker, A.K., and Obradovic, Z. Improving Protein Secondary-Structure Prediction by Predicting Ends of Secondary-Structure Segments. Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2005, pp. 490-497, San Diego, California, USA, (2005)

20.  Obradovic, Z., Peng, K., Vucetic, S., Radivojac, P., and Dunker, A.K. Exploiting heterogeneous sequence properties improves prediction of protein disorder. Proteins: Structure, Function, Bioinformatics. 61: 176-182 (2005)

19.  Oldfield, C.J., Cheng, Y., Cortese, M., Romero, P., Uversky, V.N., and Dunker, A.K. Coupled folding and binding with -helical molecular recognition elements. Biochemistry. 44: 12454-12470 (2005).

18.  Oldfield, C.J., Cheng, Y., Cortese, M.S., Brown, C.J., Uversky, V.N., and Dunker, A.K. Comparing and combining predictors of mostly disordered proteins. Biochemistry. 44: 1989-2000. (2005).

17.  Oldfield, C.J., Ulrich, E.L., Cheng, Y., Dunker, A.K., and Markley, J.L. Addressing the intrinsic disorder bottleneck in structural proteomics. Proteins: Structure, Function, and Bioinformatics. 59: 444-453 (2005).

16.  Park, I.Y., Kim, E.J., Park, H.J., Fields, K., Dunker, A.K., Kang, C.H. Interaction between cardiac calsequestrin and drugs with known cardiotoxicity. Mol. Pharmacol. 67: 97-104 (2005).

15.  Peng, K., Vucetic, S., Radivojac, P., Brown, C.J., Dunker, A.K., Obradovic, Z. Optimizing long intrinsic disorder predictors with protein evolutionary information. J. Bioinform. and Comp. Bio. 3: 35-60. (2005).

14.  Vucetic, S., Obradovic, Z., Vacic, V., Radivojac, P., Peng, K., Iakoucheva, L.M., Lawson, J.D., Brown, C.J., Sikes, J.G., Newton, C.D., Dunker, A.K. DisProt: a database of protein disorder. Bioinformatics. 21: 137-140. (2005).

 2004 

13.  Park, H., Park, I.Y., Kim, E., Youn, B., Fields, K., Dunker, A.K., and Kang, C. Comparing skeletal and cardiac calsequestrin structures and their calcium binding: a proposed mechanism for coupled calcium binding and protein phosphorylation. J. Biol. Chem. 279(17): 18026-18033. 2004.

12.  Bourhis J-M, Johansson K, Receveur-Brechot V, Oldfield CJ, Dunker KA, Canard B, Longhi S. The C-terminal domain of measles virus nucleoprotein belongs to the class of intrinisically disordered proteins that fold upon binding to their physiological partner. Virus Res. 99(2): 157-167. 2004.

11.  Iakoucheva, L.M., Radivojac, P., Brown, C.J., O’Connor, T.R., Sikes, J.G., Obradovic, Z., and Dunker, A.K. The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Research. 32(3): 1037-1049. 2004

10.  Radivojac, P., Obradovic, Z., Smith, D.K., Zhu, G., Vucetic, S., Brown, C.J., Lawson, J.D., and Dunker, A.K. Protein flexibility and intrinsic disorder. Protein Sci. 13(1): 71-80. 2004.

9.  Radivojac, P., Chawla, N.V., Dunker, A.K., Obradovic, Z. Classification and knowledge discovery in protein databases. Journal of Biomedical Informatics. 37: 224-239 (2004).

8.  Radivojac, P., Obradovic, Z., Dunker, A.K., Vucetic, S. Feature selection filters based on the permutation test. 15th European Conference on Machine Learning. ECML 2004: 334-345 (2004).

 2003 

7.  Iakoucheva LM, Dunker AK. Order, disorder, and flexibility: prediction from protein sequence. Structure. 11:1316-1317. 2003.

6.  Obradovic Z, Kang P, Vucetic S, Radivojac P, Brown CJ, Dunker AK. Predicting intrinsic disorder from amino acid sequence. Proteins: Structure, Function, and Genetics. 53:566-572. 2003.

5.  Vucetic, S., Brown, C.J., Dunker, A.K., and Obradovic, Z. Flavors of protein disorder. Proteins. 52(4): 573-584. 2003.

4.  Park, H.J., Wu, S., Dunker, A.K., and Kang, C.H. Polymerization of calsequestrin: implications for calcium regulation. J. Biol. Chem. 278: 16176-16182 (2003).

3.  Radivojac, P., Obradovic, Z., Brown, C.J. and Dunker A.K. Prediction of boundaries between intrinsically ordered and disordered protein. Pac. Symp. Biocomput. 8: 216-227 (2003).

2.  Smith, D.K., Radivojac, P., Obradovic, Z., Dunker, A.K., and Zhu, G. Improved amino acid flexibility parameters. Protein Science. 12: 1060-1072 (2003).

1.  Yang, J., Powers, J.R., Clark, S., Dunker, A.K. & Swanson, B.G. Ligand and flavor binding functional properties of β-lactoglobulin in the molten globule state induced by high pressure. J. Food Science. 68: 444-452 (2003).

Bioinformatics CoreBack to Top
 2013 

3.  Kolchinsky A, Lourenço A, Li L, Rocha LM. 1. Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions. Pac Symp Biocomput. 2013:409-20.

2.  Xu C., Quinney S.K., Guo Y., Hall S.D., Li L., Desta Z. CYP2B6 pharmacogenetics-based in vitro-in vivo extrapolation (IVIVE) of efavirenz clearance by PBPK modeling. 2013, Drug Metabolism and Disposition, accepted.

1.  Ramamoorthy A., Liu Y., Philips S., Desta Z., Lin H., Goswami C., Gaedigk A., Li L., Flockhart D.A., Skaar T. Regulation of miRNA expression by rifampin in human hepatocytes. Drug Metabolism and Disposition. (accepted).

Lang Li LabBack to Top
 In Revision 

147.  Schelleman H., Han X., Brensinger C.M., Quinney S.K., Bilker W.B., Flockhart D.A., Li L., Hennessy S. Pharmacoepidemiologic and in Vitro Evaluation of Potential Drug-Drug Interactions of Sulfonylureas with Fibrates and Statins. Science CPT (revised) (Li L. is the co-senior author with equal contribution).

146.  Hocevar BA, Kamendulis LM, Pu X, Perkins SM, Wang ZY, Johnston EL, DeWitt JM, Li L., Loehrer PJ, Klaunig JE, Chiorean G. Contribution of environment and genetics to pancreatic cancer susceptibility. (revised).

 In Press 

145.  Liu, D., Zhou, D., Wang, B., Knabe, W. E., and Meroueh, S. O. (2015) A New Class of Orthosteric uPAR•uPA Small-Molecule Inhibitors Are Allosteric Modulators of the uPAR•Vitronectin Interaction. ACS Chem. Biol. In Press

144.  Wang G., Wang, Yadong Wang, Changy Shen, Yi-wen Huang, Kun Huang, Tim Huang, Kenneth Nephew, Lang Li, and Yunlong Liu, RNA Polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation, Plos One 2011 (in press).

143.  Fang F, Balch C, Schilder J, Breen T, Zhang S, Shen C, Li L., Kulesavage C, Snyder AJ, Nephew KP, Matei DE.A phase 1 and pharmacodynamic study of decitabine in combination with carboplatin in patients with recurrent, platinum-resistant, epithelial ovarian cancer. Cancer. 2011 (in press).

142.  Friedman AN, Yu Z, Juliar BE, Nguyen JT, Strother M, Quinney SK, Li L, Inman M, Gomez G, Shihabi Z, Moe S. Independent influence of dietary protein on markers of kidney function and disease in obesity. Kidney Int. 2011 (in press).

141.  Hayes DF, Skaar TC, Rae JM, Henry NL, Nguyen AT, Stearns V, Li L, Philips S, Desta Z, and Flockhart DA. Estrogen receptor genotypes, menopausal status, and the effects of tamoxifen on lipid levels: revised and updated results. The Journal of Clinical Pharmacology and Therapeutics 2011 (in press).

140.  Wang X., Hickey R., Malkas L., Koch M., Li L., Zhang S., Sandusky GE, Grignon DJ, Eble JN, Cheng L. Elevated expression of cancer-associated proliferating cell nuclear antigen in high-grade prostatic intraepithelial neoplasia and prostate cancer. The Prostate 2011 (in press).

139.  Zhou F., Zhao Q., Edenberg H. J., Goodlett C. R., Liu Y., Li L. Microarray and gene set enrichment analysis of differential gene expression upon alcohol exposure at early neurulation. BMC Genomics 2011 (in press).

138.  Li L., Borges-Gonzales S, Robarge J., Sheng C., Desta Z., and Flockhart D. A Penalized mixture model approach in genotype/phenotype association analysis for quantitative phenotype. Cancer Informatics, 2010, 9, 93-103.

137.  Hahn N., Kelley M., Klaunig J. E., Koch M. O., Li L., and Sweeney, C.J. Prostate Cancer Germline Pharmacogenetics - Diagnostic, Prevention, and Therapeutic Application. Future Medicine, 2009 (in press).

136.  Henry NL, Giles JT, Ang D, Mohan M, Dadabhoy D, Robarge J, Hayden J, Lemler S, Shahverdi K, Powers P, Li L, Flockhart D, Stearns V, Hayes DF, Storniolo AM, Clauw DJ. Prospective characterization of musculoskeletal symptoms in early stage breast cancer patients treated with aromatase inhibitors. Breast Cancer Res Treatment, 2009, (in press)

135.  Schneider B., Radovivh M., Flockhart DA., Carpenter JS., Li L., Robarge JD., Storniolo AM,Hancock BA, Skaar TC, Sledge GW. Exploratory study evaluating the association of polymorphisms of angiogenesis genes with hot flashes. Breast Cancer Research and Treatment, 2009, 116, 543-549.

134.  Li M., Paik H., Balch C., Kim Y., Li L., Huang H-M. T., Nephew P. K., Kim, S. Enriched transcription factor binding sites in hypermethylated gene promoters in cancer cells. Bioinformatics 2009, (in press).

133.  Zhou F., Zhao Q., Edenberg H. J., Goodlett C. R., Liu Y., Li L. Microarray and gene set enrichment analysis of differential gene expression upon alcohol exposure at early neurulation. ACER 2009 (in press).

132.  Kim S., Hall S.D., and Li L. Optimal MCMC algorithm in the nonlinear mixed models. Journal of Biopharmaceutical Statistics. 2009 (in press).

131.  Yu M., Ni L., Walsh J.P., Robarge J.D., Desta Z., and Li L. Two-stage designs for predictive marker validation in randomized clinical trials. Biometrics, 2009, (in press).

130.  Desta Z., Li L., Flockhart D. A. A breath test for CYP2C19. Journal of Pharmacologic Experimental Therapeutics, 2009 (in press).

129.  Wang Z., Luis R., Quinney S., Kim S., and Li L. Pharmacokinetics parameter data mining – A case study. Journal of Medical Informatics, 2009 (in press).

 Submitted 

128.  Kreutz RP, Nystrom P, Kreutz Y, Miao J, Desta Z, Breall JA, Li L, Chiang C, Kovacs R, Flockhart DA, Jin Y. Influence of paraoxonase-1 Q192R and cytochrome P450 2C19 polymorphisms on clopidogrel response. Clin Pharmacol. 2012;4:13-20.

127.  Henry NL, Azzouz F, Desta Z, Li L, Nguyen AT, Lemler S, Hayden J, Tarpinian K, Yakim E, Flockhart DA, Stearns V, Hayes DF, Storniolo AM. Predictors of aromatase inhibitor discontinuation as a result of treatment-emergent symptoms in early-stage breast cancer. J Clin Oncol. 2012, 20;30(9):936-42.

126.  Ramamoorthy A, Li L, Gaedigk A, Bradford LD, Benson EA, Flockhart DA, Skaar TC. Comparison of Changes in the Lipid Profile of Postmenopausal Women With Early Stage Breast Cancer Treated With Exemestane or Letrozole. Drug Metab Dispos. 2012, 40(4):726-33.

 2013 

125.  117. Wu H., Karnik S.D., Subhadarshini A., Wang Z., Philips S., Han X., Chiang C., Liu L., Boustani M., Rocha L.M., Flockhart D., Quinney S.K., Li L. An Integrated Pharmacokinetics Ontology and Corpus for Text Mining. BMC Bioinformatics, 2013, 14:35.

124.  Haas DM, Dantzer J, Lehmann AS, Philips S, Skaar TC, McCormick CL, Hebbring SJ, Jung J, Li L. The impact of glucocorticoid polymorphisms on markers of neonatal respiratory disease after antenatal betamethasone administration. Am J Obstet Gynecol, 2013;208:215.e1-6.

123.  Schneider BP, Gray RJ, Radovich M, Shen F, Vance G, Li L, Jiang G, Miller KD, Gralow JR, Dickler MN, Cobleigh MA, Perez EA, Shenkier TN, Vang Nielsen K, Müller S, Thor A, Sledge GW Jr, Sparano JA, Davidson NE, Badve SS. Prognostic and Predictive Value of Tumor Vascular Endothelial Growth Factor Gene Amplification in Metastatic Breast Cancer Treated with Paclitaxel with and without Bevacizumab; Results from ECOG 2100 Trial. Clin Cancer Res. 2013 Mar 1;19(5):1281-1289.

122.  Henry NL, Skaar TC, Dantzer J, Li L, Kidwell K, Gersch C, Nguyen AT, Rae JM, Desta Z, Oesterreich S, Philips S, Carpenter JS, Storniolo AM, Stearns V, Hayes DF, Flockhart DA Genetic associations with toxicity-related discontinuation of aromatase inhibitor therapy for breast cancer. Breast Cancer Res Treat. 2013 Apr;138(3):807-16.R

121.  Wang G, Qi K, Zhao Y, Li Y, Juan L, Teng M, Li L, Liu Y, Wang Y. 1. Identification of regulatory regions of bidirectional genes in cervical cancer. BMC Med Genomics. 2013;6 Suppl 1:S5.

120.  Kim S. and Li L. Statistical identifiability and convergence evaluation for nonlinear pharmacokinetic models with particle swarm optimization. 2013, Computer Methods and Programs in Biomedicine, accepted.

119.  Quinney S.K., Knopp S., Chang C., Hall S.D. and Li L. Integration of in vitro binding mechanism into the semi-physiologically based pharmacokinetic interaction model between ketoconazole and midazolam. 2013, Pharmacometrics and System Pharmacology, accepted.

118.  Chakroborty A., Jiang G., Boustani M., Skaar T., Liu Y., Li L. Simultaneous inferences based on empirical Bayes methods and false discovery rates in eQTL data analysis. 2013, BMC Genomics, accepted.

117.  Jiang G., Chakraborty A., Wang Z, Boustani M., Liu Y., Skaar T., and Li L. New aQTL SNPs for the CYP2D6 Identified by a Novel Mediation Analysis of Genome-wide SNP Arrays, Gene Expression Arrays and CYP2D6 Activity. 2013, Journal of Computational Biology and Bioinformatics, accepted.

116.  Campbell N.L, Dexter P., Perkins A.J., Gao S., Li L., Skaar T.C., Frame A., Hendrie H.C., Callahan C.M. and Boustani M.A. Medication adherence and tolerability of Alzheimer disease medications: study protocol for a randomized controlled trial. Trials, 2013, 14:125.

115.  131. Mourad R., Shen C., Zhang P., Koneru P., Lin H., Juan L., Hsu P., Liu Y., Nephew K., Huang T.H., Li L. Spatio-temporal analysis of chromatin interactions in MCF-7 breast cancer cells after estradiol stimulation. 2013 (submitted).

114.  Mourad R., Shen C., Zhang P., Koneru P., Lin H., Juan L., Hsu P., Liu Y., Nephew K., Huang T.H., Li L. Estrogen induces global reorganization of chromatin structure in human breast cancer cells 2013 (submitted).

113.  Unthank JL, McClintick JN, Labarrere CA, Li L., DiStasi MR, Miller SJ. Molecular Basis for Impaired Collateral Artery Growth in the Spontaneously Hypertensive Rat: Insight from Microarray Analysis. (submitted).

 2012 

112.  Hartmaier RJ, Richter AS, Gillihan RM, Sallit JZ, McGuire SE, Wang J, Lee AV, Osborne CK, O'Malley BW, Brown PH, Xu J, Skaar TC, Philips S, Rae JM, Azzouz F, Li L, Hayden J, Henry NL, Nguyen AT, Stearns V, Hayes DF, Flockhart DA, Oesterreich S. A SNP in steroid receptor coactivator-1 disrupts a GSK3β phosphorylation site and is associated with altered tamoxifen response in bone. Mol Endocrinol. 2012 Feb; 26(2):220-7.

111.  Haas DM, Lehmann AS, Skaar T, Philips S, McCormick CL, Beagle K, Hebbring SJ, Dantzer J, Li L, Jung J. The impact of drug metabolizing enzyme polymorphisms on outcomes after antenatal corticosteroid use. Am J Obstet Gynecol. 2012, 206(5):447.e17-24.

110.  Badve S., Goswami C., Polar Y., Nelson R.P., Henley J., Miller N., Zaheer N.A., Sledge G.W., Li L., Kesler K.A., Loehrer P.J. Molecular Analysis of Thymoma. PLoS One, 2012, 7, e42669.

109.  Polar Y., Sanders KL, Goswami C., Cano OD, Zaheer NA, Jain RK, Kesler KA, Nelson RP, Vance GH, Smith D., Li L., Cardoso AA, Badve S., Loehrer PJ, Sledge GW. Establishment and characterization of a novel cell line derived from human thymoma AB tumor. 2012, 1-10.

108.  Kim S. and Li L. A switching Markov chain Monte Carlo method for statistical identifiability of nonlinear pharmacokinetics models. Statistics in Sinica, 2012, 22, 1199-1215.

107.  Quinney S.K., Mohammed A. N., Herbert M.F., Hass D.M., Clark S., Umans J.G., Caritis S.N., and Li L. A Semi-Mechanistic Metabolism Model of CYP3A Substrates in Pregnancy: Predicting Changes in Midazolam and Nifedipine Pharmacokinetic. CPT: Pharmacometrics and System Pharmacology 2012, 1, e2.

106.  Teng M., Wang Y., Kim S., Li L., Shen C., Liu Y., Huang T., Nephew K. P., and Balch C. Empirical Bayes Model Comparisons for Differential Methylation Analysis. Comparative and Functional Genomics, 2012, 2012:376706.

105.  Duke J., Han X., Wang Z., Overhage M., Subhadarshini A., Karnik SD, Rocha L.M., Li X., Strother M., Flockhart D., Quinney SK, and Li L. Literature based drug interaction discovery and its validation in the electronic medical record system. PLoS Computational Biology, 2012, 8(8):e1002614.

104.  Zhang P., Mourad R., Xiang Y., Huang K., Huang T., Nephew K., Liu Y. and Li L., A dynamic time order network for time-series gene expression data analysis, BMC System Biology, 2012, 6 Suppl 3:S9.

103.  Wu H., Zhang P., Nephew K., Huang T., Liu Y., Li L., A mediator based ERα regulatory network model of MCF7 cells. BMC Genomics, 2012, 13 Suppl 6:S6.).

102.  Zhou A., Breese M.R., Hao Y., Edenberg H.J., L. Li, Skaar T.C., and Liu Y., Alt Event Finder: A tool for extracting alternative splicing events from RNA-seq data. BMC Genomics, 2012, 13 Suppl 8:S10.

101.  Zhang J., Dhakal I.B., Zhao Z., Li L. Trend in mortality from cancers of the breast, colon, prostate, esophagus, and stomach in east Asia: role of nutrition transition. European Journal of Cancer Prevention, 2012, 21, 480-489.

100.  Wei R., Yang F., Urban T., Li L., Chalasani N., Flockhart DA, and Liu W. Impact of the interaction between 3’-UTR SNPs and microRNA on the expression of human xenobiotic metabolism enzyme (XMEs) genes. Frontiers in Pharmacogenetics and Pharmacogenomics, 2012; 3:248.

 2011 

99.  Wessels AM, Flockhart DA, Carpenter JS, Radovich M, Li L, Miller KD, Sledge GW, Storniolo AM, Otte JL, Lemler SM, Schneider BP. 7. Cytochrome P450 polymorphisms and their relationship with premature ovarian failure in premenopausal women with breast cancer receiving doxorubicin and cyclophosphamide. Breast J. 2011, 17(5):536-8.

98.  Kim S. and Li L. A novel global search algorithm for nonlinear mixed effect models using particle swarm optimization. Journal of Pharmacokinetics and Pharmacodynamics. 2011, 38, 471-495. PMID: 21717235.

97.  Bell LN, Nguyen AT, Li L, Desta Z, Henry NL, Hayes DF, Wolff AC, Stearns V, Storniolo AM, Flockhart DA; (COBRA) The Consortium on Breast Cancer Pharmacogenomics. 4. J Clin Pharmacol. 2011 Dec 15. Comparison of Changes in the Lipid Profile of Postmenopausal Women With Early Stage Breast Cancer Treated With Exemestane or Letrozole. . 4. J Clin Pharmacol. 2011 Dec 15.

96.  Jeong J., Li L., Liu Y., Nephew K.P., Huang T., Shen C. An Empirical Bayes Model for Gene Expression and Methy- lation Pro files in Antiestrogen Resistant Breast Cancer. BMC Biomedical Genetics, 2010, 3: 55.

95.  98. Desta Z, Kreutz Y, Nguyen AT, Li L, Skaar T, Kamdem LK, Henry NL, Hayes DF, Storniolo AM, Stearns V, Hoffmann E, Tyndale RF, Flockhart DA. 6. Plasma letrozole concentrations in postmenopausal women with breast cancer are associated with CYP2A6 genetic variants, body mass index, and age. Clin Pharmacol Ther. 2011 Nov;90(5):693-700.

94.  Mitra R, Lee J, Jo J, Milani M, McClintick JN, Edenberg HJ, Kesler KA, Rieger KM, Badve S, Cummings OW, Mohiuddin A, Thomas DG, Luo X, Juliar BE, Li L, Mesaros C, Blair IA, Srirangam A, Kratzke RA, McDonald CJ, Kim J, Potter DA. 1.Prediction of postoperative recurrence-free survival in non-small cell lung cancer by using an internationally validated gene expression model. Clin Cancer Res. 2011 May 1;17(9):2934-46.

 2010 

93.  Borges S., Desta Z., Jin Y., Faouzi A., Robarge JD., Philip S., Nguyen A, Stearns V., Hayes D., Rae JM, Skaar TC, Flockhart DA, Li L.. A Composite Functional Genetic and Co-Medication CYP2D6 Activity Score In Predicting Tamoxifen Drug Exposure Among Breast Cancer Patients. Journal of Clinical Pharmacology, 2010, 450-458. NIHMS 220544.

92.  Wang Z. Kim S., and Li L., Non-compartment model/compartment model transformation. BMC System Biology, 2010, 4, 1:S8. NIHMS 254537.

91.  Henry NL, Nguyen A, Azzouz F, Li L, Robarge J, Philips S, Cao D, Skaar TC, Rae JM, Storniolo AM, Flockhart DA, Hayes DF, Stearns V. Lack of association between oestrogen receptor polymorphisms and change in bone mineral density with tamoxifen therapy. British Journal of Cancer. 2010, 102, 294-300. (PMC2816645)

90.  Henry NL, Pchejetski D, A’Hern R, Nguyen A, Charles P, Waxman J, Li L, Storniolo A, Hayes DF, Flockhart DA, Stearns V, and Stebbing J. A Distinct Inflammatory Signature in Patients with Aromatase Inhibitor-Associated Musculoskeletal Syndrome. British Journal of Cancer. 2010, 103, 291-296. (PMC2920022).

89.  Friedman AN, Strother M, Quinney SK, Hall SD, Perkins SM, Brizendine EJ, Inman M, Gomez G, Shihabi Z, Moe S, and Li L. Measure the glomerular filtration rate in obese individuals without overt kidney disease. Nephron Clinical Practice, 2010, 116, 224-234.

88.  Quinney S.K., Zhang X., Lucksiri A., Gorski J.C., Li L., and Hall S.D. A Physiologically-Based Pharmacokinetic Model of Mechanism-Based Inhibition of CYP3A by Clarithromycin. Drug Metab Dispos, 2010, 38, 241-8.

87.  Atkinson EJ., McDonnell SK, Witte TS., Crawford DC., Fan Y., Fridley B., Li D., Li L., Rodin A., Sadee W., Speed T., Weiss ST., Yang J., Yerges L., and Schaid D.J. Lessons learned from the Fifth Statistical Analysis Workshop of the Pharmacogenetics Research Network. The Pharmacogenetics Journal, 2010, 11, 297-303.

86.  Wang G., Yadong Wang, Mingxiang Teng, Denan Zhang, Lang Li, and Yunlong Liu, Signal Transducers and Activators of Transcription-1 (STAT1) Regulates microRNA Transcription in Interferon gamma-Stimulated HeLa Cells. Plos One, 2010 July 26; 5(7):e11794, PMID: 20668688

 2009 

85.  Hommoud ZT, Badve S., Zhao Q., Li L., Saxena R, Thorat MA, Morimiya A, Rieger KM, Kesler KA. Differential Gene Expression Profiling of Esophageal Adenocarcinoma. The Journal of Thoracic and Cardiovascular Surgery. 2009, 137, 829-843.

84.  Zane Z. T., Li L., Zhao Q., Badve S., Kesler K A. Differential Gene Expression Profiling of Esophageal Adenocarcinoma. The Journal of Thoracic and Cardiovascular Surgery. 2009, 137, 829-843.

83.  Schneider B., Radovivh M., Flockhart DA., Carpenter JS., Li L., Robarge JD., Storniolo AM,Hancock BA, Skaar TC, Sledge GW. Exploratory study evaluating the association of polymorphisms of angiogenesis genes with hot flashes. Breast Cancer Research and Treatment, 2009, 116, 543-549.

82.  Zhou J., Qin Z., Quinney S. K., Kim S., Wang Z., Hall D. S., and Li L. Equivalence Tests between Model based Drug-Drug Interaction Simulations and and Published Drug-Drug Interaction. Journal of Biopharmaceutical Statistics. 2009, 19, 641-657.

81.  Zhou J., Qin Z., Quinney S. K., Kim S., Wang Z., Yu M., Chien J. Y., Lucksiri A., Hall D. S., and Li L. A new probabilistic rule for drug-drug interaction prediction. Journal of Pharmacokinetics and Pharmacodynamics. 2009, 36, 1-18. DOI: 10.1007/s10928-008-9107-3

80.  Srinivasan B.S., Chen J., Cheng C., Conti D., Duan S, Fridley BL, Gu X., Haines JL, Jorgenson E., Kraja A., Lasky-Su J., Li L, Wang D., Rodin A, Province M., and Ritchie M.D. Methods for analysis in pharmacogenomics: Lessons from the Pharmacogenetics Research Network (PGRN) Analysis Group. Pharmacogenomics Journal, 2009, 10, 243-251.

79.  Onitilo AA, McCarty CA, Wilke RA, Glurich I, Engel JM, Flockhart DA, Nguyen A, Li L, Mi D, Skaar TC, and Jin Y. Estrogen receptor genotype is associated with risk of venous thromboembolism during tamoxifen therapy. Breast Cancer Research and Treatment. 2009, 115, 643-650.

78.  Miao J., Jin Y., Marunde R.L., Kim S., Quinney S., Radovich M., Li L., and Hall S.D. Association of Genotypes of the CYP3A Cluster with Midazolam Disposition In Vivo. Pharmacogenomics Journal, 2009, 9, 319-326. (Li L. is the corresponding author).

77.  Mitra R., Srinivasan A., Mesaros C., Thomas D., Mohiuddin A., Li L., Badve S., Edenberg H., Blair I., and Potter D. A. CYP3A5 gene expression is a candidate biomarker for early recurrence of non-small cell lung cancer. Clinical Cancer Research 2009 (revised).

76.  Shen C., Liu Y., Nephew K., Huang T., and Li L. Estrogen regulatory pathway and the impact of selective estrogen receptor modulator. Nature Genetics, 2009 (submitted).

75.  Quinney S.K., Feng W. Miao J., Hall S.D., and Li L. In-vitro/in-vivo Prediction of Midazolam Clearance and Its Variability – A Meta-Analysis Approach. Journal of Pharmacokinetics and Pharmacodynamics, 2009, (submitted).

74.  Quinney S.K., Feng W. Miao J., Hall S.D., and Li L. How much confidence do we have on DDI prediction? – A peek from in-vitro ki prediction. Clinical Pharmacology and Therapeutics, 2009, (submitted).

73.  Quinney S.K., Zhang X., Lucksiri A., Gorski J.C., Li L., and Hall S.D. A Physiologically-Based Pharmacokinetic Model of Mechanism-Based Inhibition of CYP3A by Clarithromycin. Clinical Pharmacokinetics, 2009 (submitted).

72.  Kim S., Quinney S.K., Wang Z., Hall S.D., and Li L. A Population Physiologically-Based Pharmacokinetic Model of Competitive Inhibition of CYP3A by Ketoconazole. Clinical Pharmacology and Therapeutics, 2009 (submitted).

71.  Kim S., Wang Z. and Li L. The application of particle-swamping algorithm in nonlinear mixed model. System Biology 2009 (submitted).

70.  Kim S. and Li L. The optimal MCMC when the model is non-identifiable. Biometrics 2009 (submitted).

69.  Azzouz F. and Li L. An integrated PG/PK/PD model. Biometric 2009 (submitted).

68.  Balch K., Nephew K., and Li L. Which theory is true, Heritable methylation or random methylation? Nucleotide Acid Research, 2009 (sumitted).

67.  Desta Z., Modak A., Nguyen PD, Lemler SM, Kurogi Y, Li L., Flockhart D. A. Rapid identification of the hepatic cytochrome P450 2C19 activity using a novel and noninvasive [13C] pantoprazole breast test. Journal of Pharmacologic Experimental Therapeutics, 2009, 329, 297-305.

66.  Rae JM, Sikora MJ, Henry NL, Li L, Kim S, Oesterreich S, Skaar TC, Nguyen AT, Desta Z, Storniolo AM, Flockhart DA, Hayes DF, Stearns V, Cytochrome P450 2D6 activity predicts discontinuation of tamoxifen therapy in breast cancer patients. 2009, Pharmacogenomics, 9, 258-264.

65.  Henry NL, Rae JM, Li L, Azzouz F, Skaar TC, Desta Z, Sikora MJ, Philips S, Nguyen AT, Storniolo AM, Hayes DF, Flockhart DA, Stearns V. Association between CYP2D6 genotype and tamoxifen-induced hot flashes in a prospective cohort. Breast Cancer Res Treat. 2009 Oct;117(3):571-575.

64.  Wang Z, Kim S, Quinney SK, Guo Y, Hall SD, Rocha LM, Li L. Literature mining on pharmacokinetics numerical data: a feasibility study., J Biomed Inform. 2009, 42, 725-735. NIHMS107535.

63.  Haas DM, Hebert MF, Soldin OP, Flockhart DA, Madadi P, Nocon JJ, Chambers CD, Hankins, GD, Clark S, Wisner KL, Li L, Renbarger JL, Learman LA. Pharmacotherapy and pregnancy: highlights from the Second International Conference for Individualized Pharmacotherapy in Pregnancy. Clinical Translational Science 2009;2:439-43.

 2008 

62.  Schneider BP, Radovich M, Sledge GW, Robarge JD, Li L, Storniolo AM, Lemler S, Nguyen AT, Hancock BA, Stout M, Skaar T, Flockhart DA. Association of polymorphisms of angiogenesis genes with breast cancer. Breast Cancer Research Treatment, 2008, 111, 157-163.

61.  Ntukidem, NI, Nguyen AT, Stearns V., Rehman M., Schott A., Skaar T., Jin Y., Blanche P., Li L., Lemler S., Hayden J., Krauss RM, Desta Z., Flockhart D. A., Hayes D. Estrogen receptor genotypes, menopausal status and the lipid effects of tamoxifen. Journal of Clinical Pharamoclogy and Therapeutics, 2008, 85, 702-710.

60.  Wang, G., Wang, X., Li, L., Nephew, N.P., Edenberg, H.J., Zhou, F.C., Liu, Y. Identification of transcription factor and microRNA binding sites in responsible to fetal alcohol syndrome. BMC Genomics 1 Jan 2008 9 Suppl 1: p. S19. http://highwire.stanford.edu/cgi/medline/pmid;18366608

59.  Wang, X., Wang, G., Shen, C., Li, L., Edenberg, H.J., Sanford, J., Liu, Y. Using RNase sequence specificity to refine the identification of RNA-protein binding regions. BMC Genomics 1 Jan 2008 9 Suppl 1: p. S17. http://highwire.stanford.edu/cgi/medline/pmid;18366606

58.  55. Shen C., Wang Z., Shanker G., Zhang X., and Li L. A Hierarchical Statistical Model to Assess the Confidence of Peptides and Proteins Inferred from Tandem Mass Spectrometry. Bioinformatics, 2008. 24, 202-208.

57.  Feng W., Liu Y., Wu J., Nephew K.P., Huang T., Li L. A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology. BMC Genomics, 2008, 9, s23. http://www.biomedcentral.com/I47I-2164/9/S2-S23

56.  Jin Y., Hayes D F., Li L., Robarge D., Skaar T. C., Philips S., Nguyen A., Schott A., Hayden J., Lemler S., Storniolo A. M., Flockhart D. A., Stearns V. Menopausal Status and Estrogen Receptor Genotypes Influence Hot Flash Frequency and Composite Score Before and After Tamoxifen Therapy. Journal of Clinical Oncology, 2008, 26, 5849 - 5854.

55.  Li L., Yu M., Robarge J., Shen C., Jin Y., Borges-Gonzales S., Nguyen A., Skaar T., Desta Z., McLeod H., Sweeney C J., and Flockhart D. A penalized mixture model approach in gene-gene and gene-environmental interactions for binary phenotypes. Journal of Pharmaceutical Statistics 2008, 18, 1150-1177. PMID: 1899111, NIHMS 122359.

54.  Yu M., Kim S., Wang Z., Hall S, and Li L. Drug-drug interaction prediction: A Bayesian meta-analysis approach. Journal of Biopharmaceutical Statistics, 2008 18, 1063-1083.

 2007 

53.  52. *Hahn N., Kelley M., Klaunig J. E., Koch M. O., Li L., and Sweeney, C.J. Constitutional polymorphisms of prostate cancer: prognostic and diagnostic implications. Future Oncology, 2007, 665-682.

52.  Li L., Yu M., Chin R., Lucksiri A., Flockhart D., and Hall S. Drug-drug interaction prediction: A Bayesian meta-analysis approach. Statistics in Medicine, 2007, 26, 3700 - 3721.

51.  Khalili A., Potter D., Yan P., Li L., Gray J., Huang T., Lin S. Gamma-Normal-Gamma Mixture Model for Detecting Differentially Methylated Loci in three cancer cell lines. Cancer Informatics, 2007, Journal Link.

50.  Li L, Hui S, Desta Z, Todd S, Nguyen A and Flockhart D. Estimating a positive false discovery rate for variable selection in pharmacogenetic studies. Journal of Pharmaceutical Statistics, 2007, 17, 883-902.

49.  Li L and Hui S. Positive false discovery rate estimate in Step-wise variable selection. Communication in Statistics – Simulation and Computation. 2007, 32, 2.

48.  Jones D. R., Ekins S., Li L., and Hall S. D. Computational approaches that predict metabolic intermediate complex formation with CYP3A4(+b¬¬5). Drug Metab. and Dispos. 2007, 35(9):1466-75

47.  Jin Y., Wang Y-H, Miao J., Li L., Kovacs R J., Marunde R., Hamman M A., Phillips S., Halligoss J., Hall S. D. Cytochrome P450 3A5 Genotype is Associated with Verapamil Response in Healthy Subjects. Journal of Pharmacology and Experimental Therapeutics, 2007, 82, 579-585.

46.  Abbosh P. H., Li X., Li L., Gardner T. A., Kao C., and Nephew K. P. A conditionally replicative, WNT/beta-catenin pathway-based adenovirus therapy for anaplastic thyroid cancer. Cancer Gene Therapy, 2007, 1-10.

45.  Desta Z., Saussele T., Ward B., Blievernicht J., Li L., Klein K., Flockhart D A., Zanger M. U. Impact of CYP2B6 polymorphism on efavirenz metabolism in vitro. Pharmacogenomics. 2007, 8, 547-558.

44.  Robarge J. D., Li L., Desta Z., Nguyen A., and Flockhart D. A. Evaluating genetic nonmenclature of drug metabolizing enzyme. Journal of Clinical Pharmacology and Therapeutics, 2007, 82, 244-248.

43.  Li L. Discussion on parameter estimation for differential equations: a generalized smoothing approach. JRSS B. 2007, 69, 787-788.

42.  Humphrey T. L., Li L., Li X., Janowicz D. M., Fortney K. R., Zhao Q., Li W., McClintick J., Katz B. P., Wilks D. S., Edenberg H. J., Spinola S. M. Dysregulated immune profiles in skin and dendritic cells are associated with increased host susceptibility to Haemophilus ducreyi infection in human volunteers. Journal of Infection and Immunity. 2007, 75, 5686-5697.

 2006 

41.  Cibull TL, Jones TD, Li L, Eble JN, Baldridge LA, Malott SR, Luo Y, Cheng L. Overexpression of PIM-1 during progression of prostatic adenocarcinoma. Journal of Clinical Pathology 2006, 59: 285-288.

40.  Marraffa JM., Li L., Ong G., and Lehman DF. Profound metoprolol induced bradycardia precipitated by Darvocet. Clinical Pharmacology and Therapeutics, 2006, 79, 282-286.

39.  Schneider B. P., Skaar T., Sledge G. W., Badve S., Li L., and Flockhart D. A. Analysis of angiogenesis genes from paraffin-embedded breast tumor and lymph nodes. Breast Cancer Research and Treatment 2006, 96, 209-215.

38.  Li L., Hall S., and Desai M. QT Analysis. Encyclopedia of Biopharmaceutical Statistics. 2006. Marcel Dekker.

37.  Sanda C., Weitzel P., Tsukahara T., Schaley J., Edenberg H., Stephen M., McClintick J., Blatt L., Li L., Brodsky L., and Taylor M. Differential gene induction by type I and II interferons and their combination. Journal of Interferon and Cytokine Research 2006, 26, 462-472.

36.  Srirangam A., Mitra R., Wang M., Gorski C., Badve S., Baldridge L.A., Hamilton J., Hawes J., Li L., Orschell C.M., Srour E.F., Blum J.S., Sledge W.G., Nakshatri H., and Potter D.A. Effect of HIV protease inhibitor ritonavir on Akt-regulated cell proliferation in breast cancer. Clinical Cancer Research, 2006, 12, 1883-1896.

35.  Wei S., Balch C., Paik H., Kim Y, Baldwin R., Liyanarachchi S., Li L., Wang Z., Wan J., Davuluri R., Karlan B., Gifford G., Brown R., Kim S., Huang T., and Nephew K. Prognostic DNA methylation biomarkers in ovarian cancer. Clinical Cancer Research 2006, 12, 2788-2794.

34.  Borges-Gonzulas S., Desta Z., Li L., Skaar, T., Ward B., Nguyen A., Jin Y., Storniolo M., Nikoloff M., Koch W., Hayes D., Stearns V., and Flockhart D. Quantitative effect of CYP2D6 genotype and inhibitors on tamoxifen metabolism: implication for optimization of breast cancer treatment. Clinical Pharmacology and Therapeutics 2006, 80, 61-74.

33.  Shen, C., Li L., and Chen J. A statistical framework to discover true associations from multi-protein complex pull-down proteomics data sets. Proteins: Structure, Function, and Bioinformatics 2006, 64, 436-443.

32.  Lim Y., Li L., Desta D., Zhao Q., Rae, J., Flockhart D. A., and Skaar T. Endoxifen, a secondary metabolite of tamoxifen, and 4-OH-tamoxifen induce similar changes in global gene expression patterns in MCF-7 breast cancer cells. Journal of Pharmacology and Experimental Therapeutics, 2006, 318: 502-513.

31.  Li L., Cheng A. S. L., Jin V., Paik H. H., Fan M., Li X., Zhang W., Robarge J., Balch K., Davuluri R. V., Kim S., Huang T., Nephew K. A Mixture Model Based Discriminate Analysis for Identifying Ordered Transcription Factor Binding Site Pairs in Gene Promoters Directly Regulated by Estrogen Receptor-a. Bioinformatics, 2006, 22: 2210-2216.

30.  Hahn N. M., Marsh S., Fisher W., Langdon R., Zon R., Browning M., Johnson C. S., Scott-Horton T J., Li L., McLeod H L., Sweeney C J. A Hoosier oncology group randomized phase II study of docetaxel plus vinorelbine and docetaxel plus estramustine in combination for the treatment of hormone refractory prostate cancer with pharmacogenetic survival analysis. Clinical Cancer Research, 2006 12, 6094-6099.

29.  Chen Q., Yang Y., Li L., and Zhang J. T. The amino terminus of the human multidrug resistance transporter ABCC1 has a U-shaped folding with a gating function. Journal of Biological Chemistry, 2006, 281, 31152-31163.

28.  Fan M., Yan P. S., Hartman-Frey C., Chen L., Paik H., Abbosh P., Cheng A. S. L, Li L., Huang H. M. T., and Nephew K. Breast cancer cells with acquired resistance to 4-hydroxytamoxifen and fulvestrant display divergent gene expression and DNA methylation signatures. 2006, Cancer Research, 66, 11964-11966.

 2005 

27.  Jin Y, Desta Z, Stearns V., Ward B., Ho H., Lee J., Skaar T., Storniolo A. M., Li L., Araba A., Blanchard R., Nguyen A., Ullmer L., Hayden J, Lemler S., Weinshilboum R. M., Rae J. M., Hayes D. F., Flockhart D. A. Effects of CYP2D6 Genotype and Antidepressants on Tamoxifen Metabolism During Adjuvant Breast Cancer Treatment. Journal of National Cancer Institute. 2005, 97, 30-39.

26.  Ho H., Pinto A., Hall S. D., Flockhart D. A., Li L., Skaar, T., Cadman, P., O’Connor D. T., Wagner U, Fineberg N., and Weinberger M. H. The Association Between the CYP3A5 Genotype and Blood Pressure. Hypertension. 2005, 45, 294-298.

25.  Li L, Shi H, Yiannoutsos C, Huang Tim and Nephew K. Epigenetic hypothesis tests for methylation and acetylation in a triple microarray system. Journal of Computational Biology. 2005, 12, 370-390.

24.  Adigun A. Q., Pinto A. G., Flockhart D. A., Gorski J. C., Li L., Hall S. D., and Chalasani N. Effect of Cirrhosis and liver transplantation on the gender difference in QT interval. The American Journal of Cardiology, 2005, 95, 691- 694.

23.  Borges S., Li L., Hamman M. A., Jones D. R., Hall S. D., and Gorski C. Dextromethorphan to dextrorphan urinary metabolic ratio does not reflect dextromethorphan oral clearance. Drug Metabolism and Disposition, 2005, 33, 1052-1055.

22.  Rae J., Goetz M., Hayes D., Li L. Storniolo A., Stearns V., and Flockhart D. Letter to the Editor. Breast Cancer Research, 2005, 29, 7.

21.  Shen, C., Li L., and Chen J. Discover True Association Rates in Multi-protein Complex Proteomics Data Sets. Proceedings of the IEEE Computational Systems Biology Bioinformatics Conference, Stanford University, Stanford, CA, published by IEEE Computer Society Press, 2005, 1, 167-174.

20.  Li L. Statistical Methods in Bioinformatics – A review. Briefings in Bioinformatics, 2005, 6, 412.

 2004 

19.  Li L, Huang J, Sun S, Shen J, Unverzagt F, Gao S, Hendrie H, Hall K, and Hui S. Selecting Pre-Screening Items for EARLY INTERVENTION Trials of Dementia – A Case Study. Statistics in Medicine, 2004, 23, 271-283.

18.  Pan C., Kinch, M. S., Sweeney, C. J., Li L., Zhang S., Baldridge L .A., Koch M. O., Ulbright T. M., Eble J. N., Cheng K. PC cell-derived growth factor (PCDGF, epithelin/granulin precursor) Expression Correlates with Progression of Prostate Cancer. Clinical Cancer Research, 2004, 10, 1333-1337.

17.  Cheng L, Pan C, Zhang JT, Zhang S, Kinch MS, Li L, Baldridge LA, Wade C, Hu Z, Koch MO, Ulbright TM, Eble JN. Loss of 14-3-3s in Prostate Cancer and Its Precursors. Clinical Cancer Research, 2004, 10, 3064-3068.

16.  Li L, Lin X, Brown M, Gupta S. and Lee K. A population pharmacokinetic model with time-dependent covariates measured with errors. Biometrics, 2004, 60, 451-460.

15.  Li L, Desai M., Desta Z., and Flockhart D. QT analysis: a complex answer to a ‘simple’ problem. Statistics in Medicine, 2004, 23, 2625-2643.

14.  Arora R., Koch M. O., Eble J. N., Ulbright T. M., Li L. and Chen L. Heterogeneity of Gleason Grade in Multifocal Adenocarcinoma of the Prostate. Cancer 2004, 100, 2362-6.

13.  Hong H., Kao C., Jeng M. H., Eble J. N., Koch M. O., Gardner T. A., Zhang S., Li L., Pan C., Hu Z., MacLennan G. T., Cheng L. Aberrant Expression of CARM1, a Transcriptional Coactivator of Androgen Receptor, in the Development of Prostate Cancer and Androgen-Independent Status. Cancer, 2004, 101, 83-89.

12.  Sweeney C., Li L., Shanmugam R., Bhat-Nakshatri P., Jayaprakasan V., Baldridge L. A., Gardner T., Smith M., Nakshatri H., Cheng L. Nuclear Factor Kappa B is Constitutively Activated in Prostate Cancer In Vitro and is Over-expressed in Prostatic Intra-epithelial Neoplasia and Adenocarcinoma of the Prostate. Clinical Cancer Research, 2004, 10, 5501-5507.

11.  Chen J., Sivachenkoand A. and Li L. High-throughput Protein Interactome Data: Minable or Not?, Proceedings of the 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics at the International Conference on Knowledge Discovery and Data Mining, Seattle, WA, 2004, p18-23.

 2003 

10.  Desai M, Li L, Desta Z, Malik M, and Flockhart D. Variability of Heart Rate Correction Methods for the QT Interval: Potential for QTc Overestimation with a Low Dose of Haloperidol. 2002. British Journal of Clinical Pharmacology, 2003, 55, 511-517.

9.  Desai M., Tanus-Santos J., Li L., Gorski J. C., Arefayene M., Liu Y., Desta Z., and Flockhart D. Pharmacokinetics and QT interval pharmacodynamics of oral halporeridol in poor and extensive metabolizers of CYP2D6. The Pharmacogenomic Journal, 2003, 3, 105-113.

8.  Zeng G, Hu, Z, Kinch MS, Pan C, Flockhart, Kao C,Gardner TA, Zhang S, Li L, Baldridge LA, Koch MO, Ulbright TM, Eble JN, Cheng L. High level expression of EphA2 receptor tyrosine kinase in prostatic intraepithelial neoplasia. American Journal of Pathology, 2003, 163, 2271-6.

 2002 

7.  Song J, Tata D, Li L, Taylor J, Bao S, and Miller DL. Combined shockwave and immuno-gene therapy of mouse melanoma and renal carcinoma tumors. Ultrasound in Medicine and Biology, 2002, 28, 957-964.

6.  Li L, Brown M, Lee K. and Gupta S. Estimation and inference for a spline-enhanced nonlinear population pharmacokinetic model. Biometrics, 2002; 58, 601-611.

5.  Wang Z, Hall S D, Maya JF, Li L, Ashgar A, and Gorski CJ. Diabetes mellitus increases the in vivo activity of cytochrome P450 2e1 in human. British Journal of Clinical Pharmacology, 2002, 55, 77-85.

 2001 

4.  McKeever P. E., Junck L., Strawderman M., and Blaivas M, Tkaczyk A, Cates MA, Yan M and Li L. Proliferation Index is related to patient age in Glioblastoma. Neurology 2001, 56, 1216-1218.

3.  Chaib H., Rubin M.A., Mucci N.R., Li L., Taylor M.J., Day M.L., Rhim J., and Macoska J. Activated in Prostate Cancer: A PDZ Domain-Containing Protein Highly Expressed in Human Primary Prostate Tumors. Cancer Research 2001, 61, 2390-2394.

 1998 

2.  Vladmir K and Li L. A new symmetry test for multivariate distribution. Journal of Multivariate Analysis 1998, 65, 228-44.

1.  Smith D.C., Redman B.G., Flaherty L.E., Li L., Strawderman M., and Pienta K.J. A phase II trial of oral diethylstilbesterol as a second line hormonal agent in advanced prostate cancer. Urology 1998, 52, 257-260.

Yunlong Liu LabBack to Top
 In Press 

79.  Zhang X., Dangaiah D., Muson RS Jr., Spinola SM, and Liu Y., Correcting imbalanced reads coverage in a bacterial transcriptome sequencing with extreme deep coverage, in press

78.  Arindom C., Jiang G., Boustani M., Skaar T., Liu Y., and Li L., Simultaneous inferences based on empirical Bayes methods and false discovery rates in eQTL data analysis, in press

 2014 

77.  Radovich, M., Clare, SE., Atale, R., Pardo, I., Hancock, BA., Solzak, JP., Kassem, N., Mathieson, T., Storniolo, AM., Rufenbarger, C., Lillemoe, HA., Blosser, RJ., Choi, MR., Sauder, CA., Doxey, D., Henry, JE., Hilligoss, EE., Sakarya, O., Hyland, FC., Hickenbotham, M., Zhu, J., Glasscock, J., Badve, S., Ivan, M., Liu, Y., Sledge, GW., Schneider, BP. Characterizing the heterogeneity of triple-negative breast cancers using microdissected normal ductal epithelium and RNA-sequencing. Breast Cancer Res. Treat. 2014 Jan;143(1):57-68

76.  Gangaiah, D., Labandeira-Rey, M., Zhang, X., Fortney, KR., Ellinger, S., Zwickl, B., Baker, B., Liu, Y., Janowicz, DM., Katz, BP., Brautigam, CA., Munson, RS., Hansen, EJ., Spinola, SM. Haemophilus ducreyi Hfq contributes to virulence gene regulation as cells enter stationary phase. MBio 2014;5(1):e01081-13

 2013 

75.  Todd, AG., Lin, H., Ebert, AD., Liu, Y., Androphy, EJ. COPI transport complexes bind to specific RNAs in neuronal cells. Hum. Mol. Genet. 2013 Feb 15;22(4):729-36

74.  Wang, G., Qi, K., Zhao, Y., Li, Y., Juan, L., Teng, M., Li, L., Liu, Y., Wang, Y. Identification of regulatory regions of bidirectional genes in cervical cancer. BMC Med Genomics 2013;6 Suppl 1:S5

73.  Juan, L., Wang, G., Radovich, M., Schneider, BP., Clare, SE., Wang, Y., Liu, Y. Potential roles of microRNAs in regulating long intergenic noncoding RNAs. BMC Med Genomics 2013;6 Suppl 1:S7

72.  Breese, MR., Liu, Y. NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. Bioinformatics 2013 Feb 15;29(4):494-6

71.  Zhao, H., Yang, Y., Lin, H., Zhang, X., Mort, M., Cooper, DN., Liu, Y., Zhou, Y. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Genome Biol. 2013 Mar 13;14(3):R23

70.  Kelly, KJ., Liu, Y., Zhang, J., Goswami, C., Lin, H., Dominguez, JH. Comprehensive genomic profiling in diabetic nephropathy reveals the predominance of proinflammatory pathways. Physiol. Genomics 2013 Aug 15;45(16):710-9

69.  Gangaiah, D., Zhang, X., Fortney, KR., Baker, B., Liu, Y., Munson, RS., Spinola, SM. Activation of CpxRA in Haemophilus ducreyi primarily inhibits the expression of its targets, including major virulence determinants. J. Bacteriol. 2013 Aug;195(15):3486-502

68.  Jiang, G., Chakraborty, A., Wang, Z., Boustani, M., Liu, Y., Skaar, T., Li, L. New aQTL SNPs for the CYP2D6 identified by a novel mediation analysis of genome-wide SNP arrays, gene expression arrays, and CYP2D6 activity. Biomed Res Int 2013;2013:493019

67.  Hsu, PY., Hsu, HK., Lan, X., Juan, L., Yan, PS., Labanowska, J., Heerema, N., Hsiao, TH., Chiu, YC., Chen, Y., Liu, Y., Li, L., Li, R., Thompson, IM., Nephew, KP., Sharp, ZD., Kirma, NB., Jin, VX., Huang, TH. Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. Cancer Cell 2013 Aug 12;24(2):197-212

66.  Ramamoorthy, A., Liu, Y., Philips, S., Desta, Z., Lin, H., Goswami, C., Gaedigk, A., Li, L., Flockhart, DA., Skaar, TC. Regulation of microRNA expression by rifampin in human hepatocytes. Drug Metab. Dispos. 2013 Oct;41(10):1763-8

65.  Lin, J., Welker, NC., Zhao, Z., Li, Y., Zhang, J., Reuss, SA., Zhang, X., Lee, H., Liu, Y., Bronner, MP. Novel specific microRNA biomarkers in idiopathic inflammatory bowel disease unrelated to disease activity. Mod. Pathol. 2013 Sep 20:

64.  Lin, J., Welker, NC., Zhao, Z., Li, Y., Zhang, J., Reuss, SA., Zhang, X., Lee, H., Liu, Y., Bronner, MP. Novel specific microRNA biomarkers in idiopathic inflammatory bowel disease unrelated to disease activity. Mod. Pathol. 2013 Sep 20:

 2012 

63.  Teng M., Ichikawa S., Padgett L.R., Wang Y., Mort M., Cooper D.N., Koller D.L., Foroud T., Edenberg H.J., Econs M.J., and Liu Y., regSNPs: A tool for prioritizing regulatory single nucleotide substitutions, Bioinformatics, 2012 Jul 15;28(14):1879-86. Epub 2012 May 18.

62.  Direnzo, D., Hess, DA., Damsz, B., Hallet, JE., Marshall, B., Goswami, C., Liu, Y., Deering, T., Macdonald, RJ., Konieczny, SF. Induced Mist1 Expression Promotes Remodeling of Mouse Pancreatic Acinar Cells. Gastroenterology 2012 Apr 14:

61.  Teng, M., Balch, C., Liu, Y., Li, M., Huang, TH., Wang, Y., Nephew, KP., Li, L. The influence of cis-regulatory elements on DNA methylation fidelity. PLoS ONE 2012;7(3):e32928

60.  Mantila Roosa, SM., Turner, CH., Liu, Y. Regulatory mechanisms in bone following mechanical loading. Gene Regul Syst Bio 2012;6:43-53

59.  Zhang, P., Mourad, R., Xiang, Y., Huang, K., Huang, T., Nephew, K., Liu, Y., Li, L. A dynamic time order network for time-series gene expression data analysis. BMC Syst Biol 2012;6 Suppl 3:S9

58.  Teng M., Balch C., Liu Y., Li M., Huang T.H., Wang Y., Nephew K.P., Li L., The Influence of cis-Regulatory Elements on DNA Methylation Fidelity, PLoS One. 2012;7(3):e32928. Epub 2012 Mar 6. PMID: 22412954

57.  Zhou, A., Breese, MR., Hao, Y., Edenberg, HJ., Li, L., Skaar, TC., Liu, Y. Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data. BMC Genomics 2012;13 Suppl 8:S10

56.  Wu, HY., Zheng, P., Jiang, G., Liu, Y., Nephew, KP., Huang, TH., Li, L. A modulator based regulatory network for ERα signaling pathway. BMC Genomics 2012;13 Suppl 6:S6

 2011 

55.  Wang, X., Juan, L., Lv, J., Wang, K., Sanford, JR., Liu, Y. Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1. BMC Genomics 2011 Dec 23;12 Suppl 5:S8

54.  Hu, Y., Liu, Y., Jung, J., Dunker, AK., Wang, Y. Changes in predicted protein disorder tendency may contribute to disease risk. BMC Genomics 2011 Dec 23;12 Suppl 5:S2

53.  Teng, M., Wang, Y., Wang, G., Jung, J., Edenberg, HJ., Sanford, JR., Liu, Y. Prioritizing single-nucleotide variations that potentially regulate alternative splicing. BMC proceedings 2011 Nov 29;5 Suppl 9:S40

52.  Jung, J., Dantzer, J., Liu, Y. Identification of multiple rare variants associated with a disease. BMC proceedings 2011 Nov 29;5 Suppl 9:S103

51.  Namkung, J., Raska, P., Kang, J., Liu, Y., Lu, Q., Zhu, X. Analysis of exome sequences with and without incorporating prior biological knowledge. Genet. Epidemiol. 2011;35 Suppl 1:S48-55

50.  Appaiah, HN., Goswami, CP., Mina, LA., Badve, S., Sledge, GW., Liu, Y., Nakshatri, H. Persistent upregulation of U6:SNORD44 small RNA ratio in the serum of breast cancer patients. Breast Cancer Res. 2011;13(5):R86

49.  Shen, C., Huang, Y., Liu, Y., Wang, G., Zhao, Y., Wang, Z., Teng, M., Wang, Y., Flockhart, DA., Skaar, TC., Yan, P., Nephew, KP., Huang, TH., Li, L. A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer. BMC Syst Biol 2011;5:67

48.  Zhou, FC., Zhao, Q., Liu, Y., Goodlett, CR., Liang, T., McClintick, JN., Edenberg, HJ., Li, L. Alteration of gene expression by alcohol exposure at early neurulation. BMC Genomics 2011;12:124

47.  Zhou, FC., Balaraman, Y., Teng, M., Liu, Y., Singh, RP., Nephew, KP. Alcohol alters DNA methylation patterns and inhibits neural stem cell differentiation. Alcohol. Clin. Exp. Res. 2011 Apr;35(4):735-46

 2010 

46.  Jiang, Q., Hao, Y., Wang, G., Juan, L., Zhang, T., Teng, M., Liu, Y., Wang, Y. Prioritization of disease microRNAs through a human phenome-microRNAome network. BMC Syst Biol 2010;4 Suppl 1:S2

45.  Alam, I., Carr, LG., Liang, T., Liu, Y., Edenberg, HJ., Econs, MJ., Turner, CH. Identification of genes influencing skeletal phenotypes in congenic P/NP rats. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2010 Jan 8:

44.  Di Leva, G., Gasparini, P., Piovan, C., Ngankeu, A., Garofalo, M., Taccioli, C., Iorio, MV., Li, M., Volinia, S., Alder, H., Nakamura, T., Nuovo, G., Liu, Y., Nephew, KP., Croce, CM. MicroRNA Cluster 221-222 and Estrogen Receptor {alpha} Interactions in Breast Cancer. Journal of the National Cancer Institute 2010 Apr 13:

43.  Cheng, BH., Liu, Y., Xuei, X., Liao, CP., Lu, D., Lasbury, ME., Durant, PJ., Lee, CH. Microarray studies on effects of Pneumocystis carinii infection on global gene expression in alveolar macrophages. BMC microbiology 2010 Apr 8;10(1):103

42.  Wang, G., Wang, Y., Teng, M., Zhang, D., Li, L., Liu, Y. Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon gamma-stimulated HeLa cells. PLoS ONE 2010;5(7):e11794

41.  Yang, JY., Niemierko, A., Bajcsy, R., Xu, D., Athey, BD., Zhang, A., Ersoy, OK., Li, GZ., Borodovsky, M., Zhang, JC., Arabnia, HR., Deng, Y., Dunker, AK., Liu, Y., Ghafoor, A. 2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research. BMC Genomics 2010;11 Suppl 3:I1

40.  Mantila Roosa, SM., Liu, Y., Turner, CH. Gene expression patterns in bone following mechanical loading. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2010 Jul 23:

39.  Jeong, J., Li, L., Liu, Y., Nephew, KP., Huang, TH., Shen, C. An empirical Bayes model for gene expression and methylation profiles in antiestrogen resistant breast cancer. BMC Med Genomics 2010;3:55

38.  Wang, G., Wang, Y., Shen, C., Huang, YW., Huang, K., Huang, TH., Nephew, KP., Li, L., Liu, Y. RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation. PLoS ONE 2010;5(11):e13798

37.  Herbert, BS., Chanoux, RA., Liu, Y., Baenziger, PH., Goswami, CP., McClintick, JN., Edenberg, HJ., Pennington, RE., Lipkin, SM., Kopelovich, L. A molecular signature of normal breast epithelial and stromal cells from Li-Fraumeni syndrome mutation carriers. Oncotarget 2010 Oct;1(6):405-22

 2009 

36.  Jiang, Q., Wang, Y., Hao, Y., Juan, L., Teng, M., Zhang, X., Li, M., Wang, G., Liu, Y. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 2009 Jan;37(Database issue):D98-104

35.  Sanford, JR., Wang, X., Mort, M., Vanduyn, N., Cooper, DN., Mooney, SD., Edenberg, HJ., Liu, Y. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res. 2009 Mar;19(3):381-94

34.  Xin, F., Li, M., Balch, C., Thomson, M., Fan, M., Liu, Y., Hammond, SM., Kim, S., Nephew, KP. Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance. Bioinformatics 2009 Feb 15;25(4):430-4

33.  Wang X., Teng M., Wang G., Zhao Y., Feng W., Li L., Sanford J.R., and Liu Y., xIP-seq platform: an integrative framework for high-throughput sequencing data analysis, the Ohio Collaborative Conference on Bioinformatics (OCCBIO), Cleveland, OH, 2009, June 15

32.  Bhat-Nakshatri, P., Wang, G., Collins, NR., Thomson, MJ., Geistlinger, TR., Carroll, JS., Brown, M., Hammond, S., Srour, EF., Liu, Y., Nakshatri, H. Estradiol-regulated microRNAs control estradiol response in breast cancer cells. Nucleic Acids Res. 2009 Aug;37(14):4850-61

31.  He, B., Wang, K., Liu, Y., Xue, B., Uversky, VN., Dunker, AK. Predicting intrinsic disorder in proteins: an overview. Cell Res. 2009 Aug;19(8):929-49

30.  Wang, X., Wang, K., Radovich, M., Wang, Y., Wang, G., Feng, W., Sanford, JR., Liu, Y. Genome-wide prediction of cis-acting RNA elements regulating tissue-specific pre-mRNA alternative splicing. BMC Genomics 2009;10 Suppl 1:S4

29.  Wang, Y., Wang, G., Yang, B., Tao, H., Yang, JY., Deng, Y., Liu, Y. Reconstruct gene regulatory network using slice pattern model. BMC Genomics 2009;10 Suppl 1:S2

28.  Edenberg H.J. and Liu Y., Methods for high throughput analysis, Genetics of Complex Human Diseases, Editors: Ammar Al-Chalabi and Laura Almasy, Publisher: Cold Spring Harbor Press (book chapter)

27.  Camerlengo T., Ozer H.G., Teng M., Perez F., Yang P., Li L., Parvin J., Huang T., Kurc T., Liu Y., Huang K., Enabling Data Analysis on High-throughput Data in Large Data Depository Using Web-based Analysis Platform – A Case Study on Integrating QUEST with GenePattern in Epigenetics Research. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (BIBM'09), Washington DC, Nov. 2009.

26.  Alam, I., Sun, Q., Koller, DL., Liu, L., Liu, Y., Edenberg, HJ., Foroud, T., Turner, CH. Genes influencing spinal bone mineral density in inbred F344, LEW, COP, and DA rats. Functional & integrative genomics 2009 Oct 15:

25.  Edenberg, HJ., Liu, Y. Laboratory methods for high-throughput genotyping. CSH Protoc 2009 Nov;2009(11):pdb.top62

24.  Liu, Y., Balaraman, Y., Wang, G., Nephew, KP., Zhou, FC. Alcohol exposure alters DNA methylation profiles in mouse embryos at early neurulation. Epigenetics 2009 Oct;4(7):500-11

 2008 

23.  Wang, X., Wang, G., Shen, C., Li, L., Edenberg, H.J., Sanford, J., Liu, Y., Refining Detection of Protein Binding Regions Using Pyrosequencing-derived RNA Fragments, BMC Genomics, 9 (S1):S17 (2008)

22.  Wang, G., Wang, X., Li, L., Nephew, N.P., Edenberg, H.J., Zhou, F.C., Liu, Y. Identification of Transcription Factor and microRNA Binding Sites from Array-derived Gene Expression Data, BMC Genomics, 9 (S1):S19 (2008)

21.  Hamamura K., Liu Y., and Yokota H. Microarray Analysis of Thapsigargin-Induced Stress to Endoplasmic Reticulum of Mouse Osteoblasts, Journal of Bone and Mineral Metabolism, 2008;26(3):231-40. Epub 2008 May 11.

20.  Feng, W.*, Liu, Y.*, Wu, J., Nephew, K.P., Huang, T.H., and Li, L., A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology, BMC Genomics 2008, 9(S2):S23. * co-first author

19.  Wang, G., Wang, Y., Feng, W., Wang, X., Yang, J.Y., Zhao, Y, Wang, Y., Liu, Y., Transcription factor and microRNA regulation in androgen-dependent and -independent prostate cancer cells, BMC Genomics 2008, 9(S2):S22

18.  Wang X., Wang K., Wang G., Sanford, J.R., Liu Y., Model-based prediction of cis-acting RNA elements regulating tissue-specifc alternative splicing, 8th IEEE International Conference on BioInformatics and BioEngineering, Athens, Greece, October 2008.

17.  Alam I, Sun Q, Liu L, Koller DL, Liu Y, Edenberg HJ, Econs MJ, Foroud T, Turner CH., Genomic expression analysis of rat chromosome 4 for skeletal traits at femoral neck, Physiol Genomics. 2008 Aug 26.

16.  Bhat-Nakshatri, P., Wang, G., Appaiah, H., Luktuke, N., Carroll, JS., Geistlinger, TR., Brown, M., Badve, S., Liu, Y., Nakshatri, H. AKT alters genome-wide estrogen receptor alpha binding and impacts estrogen signaling in breast cancer. Mol. Cell. Biol. 2008 Dec;28(24):7487-503

 2007 

15.  Zhang, P., Su, M., Liu, Y., Hsu, A. and Yokota, H. Knee Loading Dynamically Alters Intramedullary Pressure in Mouse Femora. Bone 40(2):538-43 (2007).

14.  Liu, Y., Computational Genome Analysis: an Introduction (book review), Briefings in Bioinformatics, doi:10.1093/bib/bbm020

13.  Chen, A., Hamamura, K., Wang, G., Xing, W., Mohan, S., Yokota, H, and Liu, Y., Model-Based Comparative Prediction of Transcription-Factor Binding Motifs in Anabolic Responses in Bone, Genomics, Proteomics and Bioinformatics, Aug-Nov 5 (3-4), 158-65 (2007).

12.  McClintick, J.N.*, Liu, Y.*, Edenberg, H.J., Mapping of trans-acting regulatory factors from microarray data, BMC Genetics, BMC Proceedings 2007, 1 (Suppl 1):S155 (18 December 2007). *co-first author.

 2006 

11.  Liu, Y. & Yokota, H. Artificial Ants Deposit Pheromone to Search for Regulatory DNA Elements. BMC Genomics, Aug 30;7:221 (2006)

10.  Su, M., Jiang, H., Zhang, P., Liu, Y., Tanaka, S., and Yokota, H. Load-Driven Molecular Transport Using FRAP, Annals of Biomedical Engineering, Oct;34(10):1600-1606. (2006).

9.  Liu, Y. & Edenberg, H. Identification and Evaluation of Transcription Factor Binding Sites Responsive to PEG-IFN-alpha in PBMC in vitro. Genomics 2006, 88: 452-461.

 2005 

8.  Liu, Y., Vincenti, M. P. & Yokota, H. Principal Component Analysis for Predicting Transcription-Factor Binding Motifs from Array-Derived Data. BMC Bioinformatics 2005, 6:276.

7.  Liu, Y. and Yokota, H. Modeling Transcriptional Regulation in Chondrogenesis Using Particle Swarm Optimization. 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 311-317, San Diego, CA (2005).

 2004 

6.  Liu, Y. & Yokota, H. Modeling of Dynamic Transcriptional Regulation in Human Chondrogenesis. Systems Biology 1, 85-92 (2004).

5.  Sun, I., Liu, Y., Tanaka, S., Sun, H. & Yokota, H. Biochemical Aspects of High-Impact Exercises in Joint Degradation. Journal of Sports Sci. and Med 3, 37-43 (2004).

 2003 

4.  Liu, Y., Sun, H. B. & Yokota, H. Regulating Gene Expression Using Optimal Control Theory. Third IEEE Symposium Bioinformatics and Bioengineering 313 -318, Bethesda, MD (2003).

3.  Sun, H. B., Liu, Y., Qian, L. & Yokota, H. Model-based analysis of matrix metalloproteinase expression under mechanical shear. Ann Biomed Eng 31, 171-80 (2003).

 2002 

2.  Qian, L., Liu, Y., Sun, H. B. & Yokota, H. Systems analysis of matrix metalloproteinase mRNA expression in skeletal tissues. Front Biosci 7, a126-34 (2002).

 1999 

1.  Du, X. & Liu, Y. Network Management for Enterprise Intranet, Journal of Automation (1999).

Samy Meroueh LabBack to Top
 In Press 

76.  Liu, D., Zhou, D., Wang, B., Knabe, W. E., and Meroueh, S. O. (2015) A New Class of Orthosteric uPAR•uPA Small-Molecule Inhibitors Are Allosteric Modulators of the uPAR•Vitronectin Interaction. ACS Chem. Biol. In Press

75.  Xu, D., Wang, B., and Meroueh, S. O. (2015) Structure-Based Computational Approaches for Small Molecules Targeting Protein-Protein Interactions. Protein-Protein Interactions: Methods and Applications. In Press

 2014 

74.  Peng, X., Wang, F., Li, L., Bum-Erdene, K., Xu, D., Wang, B., Sinn, A. A., Pollok, K. E., Sandusky, G. E., Li, L., Turchi, J. J., Jalal, S. I., and Meroueh, S. O. (2014) Exploring a structural protein-drug interactome for new therapeutics in lung cancer. Mol Biosyst DOI: 10.1039/C3MB70503J

73.  Wang, B., Buckman, C., Li, L., Hurley, T., and Meroueh, S. O. (2014) Enrichment of Chemical Libraries Docked to Protein Conformational Ensembles and Application to Aldehyde Dehydrogenase 2. J. Chem. Inf. Model In press

72.  Yan, C., Li, L., Liu, D., Wempe, M., Reigan, P., Hoffman, B., Guin, S., Helfrich, B., Schwartz, M., Ross, D., Meroueh, S. O., and Theodorescu, D. (2014) Discovery and Characterization of Small Molecules targeting Ral GTPase. Nature 515:443-447

 2013 

71.  Mani, T., Wang, F., Knabe, W. E., Sinn, A. L., Khanna, M., Jo, I., Sandusky, G. E., Sledge, G. W., Jr., Jones, D. R., Khanna, R., Pollok, K. E., and Meroueh, S. O. (2013) Small-molecule inhibition of the uPAR.uPA interaction: synthesis, biochemical, cellular, in vivo pharmacokinetics and efficacy studies in breast cancer metastasis, Bioorg. Med. Chem. 21, 2145-2155.

70.  Mani, T., Liu, D., Li, L., Zhou, D., Knabe, W. E., Wang, F., Oh, K., and Meroueh, S. O. (2013) Probing Binding and Cellular Activity of Small Molecules Targeting the Urokinase Receptor, ChemMedChem 8, 1963-1977.

69.  Wang, B., Li, L., Jo, I., Hurley, T., and Meroueh, S. O. (2013) Molecular Recognition in a Diverse Set of Protein-Ligand Interactions Studied with Molecular Dynamics Simulations and End-Point Free Energy Calculations, J. Chem. Inf. Model, 53, 2659-70

68.  Liu, D., Zhou, D., Mani, T., Knabe, W. E., Wang, F., Wang, B., Li, L., and Meroueh, S. O. (2013) A New Class of Small Molecule Orthosteric Inhibitors of the uPAR-uPA Interaction are Allosteric Inhibitors of the uPAR-Vitronectin Interaction, ACS Chem Biol Submitted.

 2012 

67.  Peng, X., Wang, F., Li, L., Bumerdene, K., Wang, B., Sinn, T., Pollok, K., Jalal, S., Hanna, N., Turchi, J. J., Lang, L., SIu, H., and Meroueh, S. O. (2012) Exploring Polypharmacology for Drug Repurposing: Docking of Approved Drugs to the Human Structural Genome, Patient Records Mining, Cellular and In Vivo Studies in Lung Cancer Mol. Syst. Biol. Submitted.

66.  Mani, T., Wang, F., Knabe, W. E., Sinn, A. L., Khanna, A., Jo, I., Li, J., Silver, J. M., Sandusky, G., Sledge, C. B., Jones, D. R., Khanna, R., Pollock, K. E., and Meroueh, S. O. (2012) A Small Molecule Inhibitor of Protein-Protein Interactions of the Urokinase Receptor Impairs Breast Tumor Metastasis, J. Med. Chem. submitted.

65.  Zhang, Q., Zeng, S. X., Zhang, Y., Ding, D., Ye, Q., Meroueh, S. O., and Lu, H. (2012) A small molecule Inauhzin inhibits SIRT1 activity and suppresses tumour growth through activation of p53, EMBO molecular medicine 4, 298-312.

64.  Wang, F., Eric Knabe, W., Li, L., Jo, I., Mani, T., Roehm, H., Oh, K., Li, J., Khanna, M., and Meroueh, S. O. (2012) Design, synthesis, biochemical studies, cellular characterization, and structure-based computational studies of small molecules targeting the urokinase receptor, Bioorg Med Chem 20, 4760-4773.

63.  Piekarz, A. D., Due, M. R., Khanna, M., Wang, B., Ripsch, M. S., Wang, R., Meroueh, S. O., Vasko, M. R., White, F. A., and Khanna, R. (2012) CRMP-2 peptide mediated decrease of high and low voltage-activated calcium channels, attenuation of nociceptor excitability, and anti-nociception in a model of AIDS therapy-induced painful peripheral neuropathy, Molecular pain 8, 54.

 2011 

62.  Li, L., Khanna, M., Jo, I., Wang, F., Ashpole, N., Hudmon, A., and Meroueh, S. O. (2011) Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation, Journal of Chemical Information and Molecular Modeling 51, 755-759. PMID: 21438548 PDF

61.  Khanna, M., Chelladurai, B., Gavini, A., Li, L., Shao, M., Courtney, D., Turchi,J. J., Matei, D., and Meroueh, S. O. (2011) Targeting Ovarian Tumor Cell Adhesion Mediated by Tissue Transglutaminase, Mol. Cancer Ther., 10(4):626-36. PMID: 21330459 PDF

60.  Khanna, M., Wang, F., Jo, I., Knabe, W. E., Wilson, S. M., Li, L., Bum-Erdene, K., Li, J., G, W. S., Khanna, R., and Meroueh, S. O. (2011) Targeting multiple conformations leads to small molecule inhibitors of the uPAR.uPA protein-protein interaction that block cancer cell invasion, ACS Chem. Biol.,6, 1232-1243. PDF

59.  Li.L., Wang. B., and Meroueh, S. O. (2011) Support Vector Machine Scoring of Receptor-Ligand Complexes for Virtual Screening of Chemical Libraries, J Chem Inf Model, 51, 2132-2138. PMID: 21728360. PDF

58.  Shi, Q., Meroueh, S. O., Fisher, J. F., and Mobashery, S. (2011) A computational evaluation of the mechanism of penicillin-binding protein-catalyzed cross-linking of the bacterial cell wall, Journal of the American Chemical Society 133, 5274-5283. PMID: 21417389 PDF

57.  Wang, F., Li. J., Sinn, A. L., Knabe, W. C., Khanna, May, Jo, I., Silver, J. M., Oh, K., Li, L., Sandusky, G. E., Sledge, G. W., Nakshatri, H., Jones, D. R., Pollok, K. E., Meroueh, S. O. (2011) Virtual screening targeting the urokinase receptor, biochemical and cell-based studies, synthesis, pharmacokinetic characterization, and effect on breast tumor metastasis, Journal of medicinal chemistry 54, 7193-7205. PMID: 21851064. PDF

56.  Brittain, JM., Duarte, DB., Wilson, SM., Zhu, W., Ballard, C., Johnson, PL., Liu, N., Xiong, W., Ripsch, MS., Wang, Y., Fehrenbacher, JC., Fitz, SD., Khanna, M., Park, CK., Schmutzler, BS., Cheon, BM., Due, MR., Brustovetsky, T., Ashpole, NM., Hudmon, A., Meroueh, SO., Hingtgen, CM., Brustovetsky, N., Ji, RR., Hurley, JH., Jin, X., Shekhar, A., Xu, XM., Oxford, GS., Vasko, MR., White, FA., Khanna, R. (2011) Suppression of inflammatory and neuropathic pain by uncoupling CRMP-2 from the presynaptic Ca²⁺ channel complex. Nat. Med. 2011 Jul;17(7):822-9. PMID: 21642979. PDF

55.  Parajuli, B., Kimble-Hill, A. C., Khanna, M., Ivanova, Y., Meroueh, S., and Hurley, T. D. (2011) Discovery of novel regulators of aldehyde dehydrogenase isoenzymes, Chem Biol Interact 191, 153-158.

 2010 

54.  Li, L.; Bumerdene, K.; Baenziger, P. H.; Hemmert, J. R.; Rosen, J.; Nellis, J.; Pierce, M. ; Meroueh, S. O. (2010) BioDrugScreen: A Computational Drug Design Resource for Ranking Molecules Docked to the Human Proteome, Nucleic Acid Research, 38, D765-73. PDF

53.  Li, L., J. Li, M. Khanna, I. Jo, J.P. Baird, and Meroueh, S. O. (2010) Docking to Erlotinib Off-Targets Leads to Inhibitors of Lung Cancer Cell Proliferation with Suitable in Vitro Pharmacokinetics. ACS Med. Chem. Lett. 1, 229-233. PDF

52.  Wang, Y., Brittain, J. M., Jarecki, B. W., Park, K. D., Wilson, S. M., Wang, B., Hale, R., Meroueh, S. O., Cummins, T. R., and Khanna, R., (2010) In silico docking and electrophysiological characterization of lacosamide binding sites on collapsin response mediator protein 2 (CRMP-2) identifies a pocket important in modulating sodium channel slow inactivation. Journal of Biological Chemistry, 285, 25296-307. PMID: 20538611. PDF

 2009 

51.  Liang, S. D., Li, L. W., Hsu, W. L., Pilcher, M. N., Uversky, V., Zhou, Y. Q., Dunker, A. K., and Meroueh, S. O. (2009) Exploring the Molecular Design of Protein Interaction Sites with Molecular Dynamics Simulations and Free Energy Calculations, Biochemistry 48, 399-414. PDF

50.  Liang, S. D., Meroueh, S. O., Wang, G. C., Qiu, C., and Zhou, Y. Q. (2009) Consensus scoring for enriching near-native structures from protein-protein docking decoys, Proteins-Structure Function and Bioinformatics 75, 397-403. PDF

49.  Xue, B., Oldfield, C., Li, L., Meroueh, S. O., Dunker, A. K., and Uversky, V. Analysis of structured and intrinsically disordered regions of integral transmembrane proteins, Molecular Biosystems, 5,1688-1702. PDF

48.  Matute, J. D., Arias, A. A., Wright, N., Wrobel, I., Waterhouse, C. C. M., Li, X. J., Marchal, M. S., Stull, N. D., Lewis, D. B., Steele, M., Kellner, J. D., Yu, M., Meroueh, S. O., Nauseef, W. M., and Dinauer, M. C. (2009) A new genetic subgroup of chronic granulomatous disease with defects in p40phox in a box who presented with colitis, Blood, 114, 3309. PDF

47.  Li, L., Liang, S., Pilcher, M. M., and Meroueh, S. O. Incorporating receptor flexibility in the molecular design of protein interfaces, Protein Engineering Design and Selection, 22, 575-86. PDF

 2008 

46.  Li, Liwei; O’Callaghan, B. J.; Dantzer, J. J. and Meroueh S. O. PDBcal: A Comprehensive Dataset for Receptor-Ligand Interactions with Three-Dimensional structures and Binding Thermodynamics from Isothermal Titration Calorimetry. Chem. Biol. & Drug Design. 71:529-32. (2008) PDF

45.  Li, L., and Meroueh, S. O. Receptor-Ligand Interactions in Biological Systems. In: Encyclopedia for the Life Sciences, p 19, John Wiley and Sons, London. (2008)

44.  Jewell, J. L., Oh, E., Bennett, S. M., Meroueh, S. O., and Thurmond, D. C. The Tyrosine Phosphorylation of Munc18c Induces a Switch in Binding Specificity from Syntaxin 4 to Doc2{beta}, The Journal of biological chemistry 283, 21734-21746. (2008) PDF

43.  Shi, Q., Meroueh, S. O., Fisher, J. F., and Mobashery, S. Investigation of the mechanism of the cell wall DD-carboxypeptidase reaction of penicillin-binding protein 5 of Escherichia coli by quantum mechanics/molecular mechanics calculations, Journal of the American Chemical Society 130, 9293-9303. (2008) PDF

 2007 

42.  Meroueh, S. O.; Cha, J.; Mobashery, S. Inhibition of Class A ß-Lactamases, In Enzyme-Mediated Resistance to Antibiotics: Mechanisms, Dissemination, and Prospects for Inhibition, Bonomo, R. A.; Tolmasky, M. E., Eds.; ASM Press, 2007, pp101-114, Washington D.C.

41.  Meroueh, S. O. and Mobashery, S., Conformational Transition in the Aminoacyl t-RNA Site of the Bacterial Ribosome both in the Presence and Absence of an Aminoglycoside Antibiotic. Chemical Biology and Drug Design 2007, 69, (5), 291-297. PDF

40.  Rosenblum, G.*; Meroueh, S.*; Toth, M.; Fisher, J. F.; Fridman, R.; Mobashery, S.; Sagi, I. Molecular Structures and Dynamics of the Stepwise Activation Mechanism of a Matrix Metalloproteinase Zymogen: Challenging the Cysteine Switch Dogma, J. Am. Chem. Soc. 2007 129(44),13566-74. (Authors contributed equally) PDF

39.  Zhang, W.; Shi, Q.; Meroueh, S. O.; Vakulenko, S. B.; Mobashery, S., Catalytic Mechanism of Penicillin-Binding Protein 5 of Escherichia coli. J. Biol. Chem. 2007, 46, 10113-10121. PDF

38.  Li, Liwei; Uversky N. V.; Dunker, K. A.; Meroueh, S. O. A Computational Investigation of Allostery in the Catabolite Activator Protein. J. Am. Chem. Soc. (2007) 129(50), 15668-76 PDF

37.  Samy Meroueh: Normal Mode Analysis Theoretical and Applications to Biological and Chemical Systems. Briefings in Bioinformatics 8(5): 378-379 (2007) PDF

 2006 

36.  Rekharsky, M.; Hesek, D.; Lee, M.; Meroueh, S. O.; Inoue, Y.; Mobashery, S., Thermodynamics of interactions of vancomycin and synthetic surrogates of bacterial cell wall. J. Am. Chem. Soc. 2006, 128, (24), 7736-7737.

35.  Fisher, J. F.; Meroueh, S. O.; Mobashery, S., Nanomolecular and Supramolecular Paths toward the Bacterial Peptidoglycan Structure. Microbe 2006, 1, 420-427. PDF

34.  Meroueh, S. O.; Bencze, K. Z.; Hesek, D.; Lee, M.; Fisher, J. F.; Stemmler, T. L.; Mobashery, S., Three-Dimensional Structure of the Bacterial Cell Wall Peptidoglycan. Proc. Natl. Acad. Sci. USA 2006, 103, (12), 4404-4409. PDF

33.  Hesek, D.; Toth, M.; Meroueh, O.; Brown, S.; Zhao, H.; Sakr, W.; Fridman, R.; Mobashery, S., Design and Characterization of a Metalloproteinase Inhibitor-Tethered Resin for the Detection of Active MMPs in Biological Samples. Chem. Biol. 2006, 13, 379-386. PDF

32.  Murray, J. B.; Meroueh, S. O.; Russell, R. J.; Lentzen, G.; Haddad, J.; Mobashery, S., Interactions of Designer Antibiotics and the Bacterial Ribosomal Aminoacyl-tRNA Site. Chem. Biol. 2006, 13, (2), 129-38. PDF

31.  Rahaman, A., Song, H., Wang, A. X., Meroueh, S. O., and Hase, W. L. Chemical Dynamics Simulations of Energy Transfer and Unimolecular Decomposition in Collision-Induced Dissociation (CID) and Surface-Induced Dissociation (SID). Principles of Mass Spectrometry Applied to Biomolecules (Litschitz, C., and Laskin, J., Eds.), pp 379-432, Wiley, New York.

 2005 

30.   Toth, M.; Osenkowski, P.; Hesek, D.; Brown, S.; Meroueh, S. O. ; Sakr, W.; Mobashery, S.; Fridman, R., Cleavage at the Stem Region Releases an Active Ectodomain of the Membrane Type 1 Matrix Metalloproteinase. Biochem. J. 2005, 387, 497-506.

29.   Osenkowski, P.; Meroueh, S. O. ; Pavel, D.; Mobashery, S.; Fridman, R., Mutational and Structural Analyses of the Hinge Region of Membrane Type 1-Matrix Metalloproteinase and Enzyme Processing. J. Biol. Chem. 2005, 280, (28), 26160-26168. PDF

28.  Meroueh, S. O. ; Fisher, J. F.; Schlegel, H. B.; Mobashery, S., Ab initio QM/MM Study of Class A Beta-Lactamase Acylation: Dual Participation of Glu166 and Lys73 in a Concerted Base Promotion of Ser70. J. Am. Chem. Soc. 2005, 127, (44), 15397-15407.

27.  Li, J.; Cross, J. B.; Vreven, T.; Meroueh, S. O. ; Mobashery, S.; Schlegel, H. B., Lysine Carboxylation in Proteins: OXA-10 Beta-Lactamase. Proteins 2005, 61, (2), 246-257. PDF

26.  Lee, M.; Bernardo, M. M.; Meroueh, S. O. ; Brown, S.; Fridman, R.; Mobashery, S., Synthesis of Chiral 2-(4-Phenoxyphenylsulfonylmethyl)-Thiiranes as Selective Gelatinase Inhibitors. Org. Lett. 2005, 7, (20), 4463-4465.

25.   Ikejiri, M.; Bernardo, M. M.; Meroueh, S. O. ; Brown, S.; Chang, M.; Fridman, R.; Mobashery, S., Design, Synthesis, and Evaluation of a Mechanism-Based Inhibitor for Gelatinase A. J. Org. Chem. 2005, 70, (14), 5709-5712.

24.  Fisher, J. F.; Meroueh, S. O.; Mobashery, S., Bacterial Resistance to Beta-Lactam Antibiotics: Compelling Opportunism, Compelling Opportunity. Chem. Rev. 2005, 105, (2), 395-424.

23.  Cross, J. B.; Vreven, T.; Meroueh, S. O.; Mobashery, S.; Schlegel, H. B., Computational Investigation of Irreversible Inactivation of the Zinc-Dependent Protease Carboxypeptidase A. J. Phys. Chem. B 2005, 109, (10), 4761-4769.

 2004 

22.  Kim, C.; Haddad, J.; Vakulenko, S. B.; Meroueh, S. O.; Wu, Y.; Yan, H.; Mobashery, S., Fluorinated Aminoglycosides and their Mechanistic Implication for Aminoglycoside 3 '-Phosphotransferases from Gram-Negative Bacteria. Biochemistry 2004, 43, (9), 2373-2383.

21.  Golemi-Kotra, D.; Meroueh, S. O.; Kim, C.; Vakulenko, S. B.; Bulychev, A.; Stemmler, A. J.; Stemmler, T. L.; Mobashery, S., The Importance of a Critical Protonation State and the Fate of the Catalytic Steps in Class A Beta-Lactamases and Penicillin-Binding Proteins. J. Biol. Chem. 2004, 279, (33), 34665-34673.

20.  Brown, S.; Meroueh, S. O.; Fridman, R.; Mobashery, S., Quest for Selectivity in Inhibition of Matrix Metalloproteinases. Curr. Top. Med. Chem. 2004, 4, (12), 1227-1238.

19.  Birck, C.; Cha, J. Y.; Cross, J.; Schulze-Briese, C.; Meroueh, S. O.; Schlegel, H. B.; Mobashery, S.; Samama, J. P., X-ray Crystal Structure of the Acylated Beta-Lactam Sensor Domain of BlaR1 from Staphylococcus aureus and the Mechanism of Receptor Activation for Signal Transduction. J. Am. Chem. Soc. 2004, 126, (43), 13945-13947.

18.  T. Lim, S. O. Meroueh, M. Lee, M. J. Heeg, S. Mobashery "Strategy in Inhibition of Cathepsin B, A Target in Tumor Invasion and Metastasis" J. Am. Chem. Soc. 2004, 126, 10271-10277.

 2003 

17.  Wilkinson, A. S.; Bryant, P. K.; Meroueh, S. O.; Page, M. G. P.; Mobashery, S.; Wharton, C. W., A Dynamic Structure for the Acyl-Enzyme Species of the Antibiotic Aztreonam with the Citrobacter freundii Beta-Lactamase Revealed by Infrared Spectroscopy and Molecular Dynamics Simulations. Biochemistry 2003, 42, (7), 1950-1957.

16.  Wang, J. P.; Meroueh, S. O.; Wang, Y. F.; Hase, W. L., Efficiency of Energy Transfer in Protonated Diglycine and Dialanine SID - Effects of Collision Angle, Peptide Ion Size, and Intramolecular Potential. Int. J. Mass. Spectrom. 2003, 230, (1), 57-64.

15.  Song, K. Y.; Meroueh, O.; Hase, W. L., Dynamics of Cr(CO)(6)(+) Collisions with Hydrogenated Surfaces. J. Chem. Phys. 2003, 118, (6), 2893-2902.

14.  Rosenblum, G.; Meroueh, S. O.; Kleifeld, O.; Brown, S.; Singson, S. P.; Fridman, R.; Mobashery, S.; Sagi, I., Structural Basis for Potent Slow Binding Inhibition of Human Matrix Metalloproteinase-2 (MMP-2). J. Biol. Chem. 2003, 278, (29), 27009-27015.

13.  Meroueh, S. O.; Minasov, G.; Lee, W.; Shoichet, B. K.; Mobashery, S., Structural Aspects for Evolution of Beta-Lactamases from Penicillin-Binding Proteins. J. Am. Chem. Soc. 2003, 125, (32), 9612-9618.

12.  Golemi-Kotra, D.; Cha, J. Y.; Meroueh, S. O.; Vakulenko, S. B.; Mobashery, S., Resistance to Beta-Lactam Antibiotics and its Mediation by the Sensor Domain of the Transmembrane BlaR Signaling Pathway in Staphylococcus aureus. J. Biol. Chem. 2003, 278, (20), 18419-18425.

11.  Fridman, R.; Toth, M.; Chvyrkova, I.; Meroueh, S. O.; Mobashery, S., Cell Surface Association of Matrix Metalloproteinase-9 (Gelatinase B). Cancer and Metastasis Rev 2003, 22, (2-3), 153-166.

 2002 

10.  Toth, M.; Hernandez-Barrantes, S.; Osenkowski, P.; Bernardo, M. M.; Gervasi, D. C.; Shimura, Y.; Meroueh, O.; Kotra, L. P.; Galvez, B. G.; Arroyo, A. G.; Mobashery, S.; Fridman, R., Complex Pattern of Membrane type 1 Matrix Metalloproteinase Shedding - Regulation by Autocatalytic Cell Surface Inactivation of Active Enzyme. J. Biol. Chem. 2002, 277, (29), 26340-26350.

9.  Meroueh, S. O.; Wang, Y. F.; Hase, W. L., Direct Dynamics Simulations of Collision- and Surface-Induced Dissociation of N-Protonated Glycine. Shattering Fragmentation. J. Phys. Chem. A 2002, 106, (42), 9983-9992.

8.  Meroueh, S. O.; Roblin, P.; Golemi, D.; Maveyraud, L.; Vakulenko, S. B.; Zhang, Y.; Samama, J. P.; Mobashery, S., Molecular Dynamics at the Root of Expansion of Function in the M69L Inhibitor-Resistant TEM Beta-Lactamase from Escherichia coli. J. Am. Chem. Soc. 2002, 124, (32), 9422-9430.

7.  Meroueh, O.; Hase, W. L., Dynamics of Energy Transfer in Peptide-Surface Collisions. J. Am. Chem. Soc. 2002, 124, (7), 1524-1531.

6.  Maveyraud, L.; Golemi-Kotra, D.; Ishiwata, A.; Meroueh, O.; Mobashery, S.; Samama, J. P., High-Resolution X-ray Structure of an Acyl-Enzyme Species for the Class D OXA-10 Beta-Lactamase. J. Am. Chem. Soc. 2002, 124, (11), 2461-2465.

 2001 

5.  Sun, L. P.; Claire, P. D.; Meroueh, O.; Hase, W. L., Dynamics of Ar+CH4/Ni{111} Collision-Induced Desorption. J. Chem. Phys. 2001, 114, (1), 535-544.

4.  Meroueh, O.; Hase, W. L., Effect of Surface Stiffness on the Efficiency of Surface-Induced Dissociation. Phys. Chem. Chem. Phys. 2001, 3, (12), 2306-2314.

 2000 

3.  Sawilowsky, E. F.; Meroueh, O.; Schlegel, H. B.; Hase, W. L., Structures, Energies, and Electrostatics for Methane Complexed with Alumina clusters. J. Phys. Chem. A 2000, 104, (21), 4920-4927.

2.  Meroueh, O.; Hase, W. L., Energy Transfer Pathways in the Collisional Activation of Peptides. Int. J. Mass. Spectrom. 2000, 201, (1-3), 233-244.

 1999 

1.  Meroueh, O.; Hase, W. L., Collisional Activation of Small Peptides. J. Phys. Chem. A 1999, 103, (20), 3981-3990.

Li Shen LabBack to Top
 Submitted 

88.  Kim S, Shen L, Saykin AJ, and West JD. Visual exploration of genetic association with voxel-based imaging phenotypes in an MCI/AD study. EMBC'09: the 31st Annual Int. Conf. of the IEEE Engineering in Medicine and Biology Society, September 2-6, 2009, Minneapolis, Minnesota.

87.  Wan J, Shen L, Sheehan KE, Kim S, Roth RM, Ford J, Fang S, Saykin AJ, and Wishart HA. Shape analysis of thalamic atrophy in multiple sclerosis. MIAMS 2009: MICCAI Workshop on "Medical Image Analysis on Multiple Sclerosis", September 20, 2009, Imperial College London, UK.

 2009 

86.  Risacher SL, Saykin AJ, Shen L, West JD, Kim S, McDonald BC, and the ADNI. Volumetric, cortical thickness, and grey matter density changes on MRI over 12 months: Relationship to conversion status in the ADNI cohort. International Conference on Alzheimer's Disease (ICAD), July 11-16, 2009, Vienna, Austria.

85.  Saykin AJ, Shen L, Risacher SL, Kim S, Nho K, West JD, Forond TM, and the ADNI. Genetic predictors of 12 month change in MRI hippocampal volume in the Alzheimer’s Disease Neuroimaging Initiative cohort: Analysis of leading candidates from the AlzGene database. International Conference on Alzheimer's Disease (ICAD), selected for oral presentation, July 11-16, 2009, Vienna, Austria.

84.  Shen L, Kim S, West JD, Saykin AJ. Building an imaging genomic browsing system for examining genetic effects on brain. OHBM’09: 15th Annual Meeting of Organization for Human Brain Mapping, selected for oral presentation, Neuroimage, 7(Sup. 1):S32, June 18 - 23, 2009, San Francisco, CA.

83.  Kim S, Shen L, Saykin AJ, and West JD. Data synthesis and tool development for exploring imaging genomic patterns. CIBCB'09: IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pages 298-305, 3/30-4/2, 2009, Nashville, TN.

82.  Li H, Yan M, Henschel R, Shen L. Implementing 3D SPHARM surfaces registration on cell processor. SAAHPC'09: Symposium on Application Accelerators in High Performance Computing. July 28-30, 2009 Urbana, Illinois.

81.  McPeek MA, Shen L, and Farid H. The correlated evolution of 3-dimensional reproductive structures between male and female damselflies. Evolution, 63(1):73-83, 2009.

80.  Shen L, Farid H, and McPeek MA.< a href="http://www3.interscience.wiley.com/journal/121460196/abstract">Modeling 3-dimensional morphological structures using spherical harmonics. Evolution, 63(4):1003-1016, 2009.

79.  Risacher SL, Saykin AJ, West JD, Shen L, Firpi HA, McDonald BC, and ADNI. Baseline MRI predictors of conversion from MCI to probable AD in the ADNI cohort. Current Alzheimer Research, 6(4): 347-361, 2009.

78.  Shen L, Firpi HA, Saykin AJ, West JD. Parametric surface modeling and registration for comparison of manual and automated segmentation of the hippocampus. Hippocampus (Special Issue on Computational Anatomy and Physiology of the Hippocampus), 19(6):588-95, 2009.

77.  Shen L, Kim S, Saykin AJ. Fourier method for large scale surface modeling and registration. Computers and Graphics (Special Issue on Shape Modeling International 2009), 33(3):299-311.

 2008 

76.  Saykin AJ, West JD, Shen L, Firpi HA, Wessels AM, Cannon A, Risacher S, McDonald BC, and the Alzheimer's Disease Neuroimaging Initiative. Hippocampal and Distributed Gray Matter Abnormalities in MCI and Early AD in the ADNI Baseline 1.5T MRI Scans: Cross-Sectional Analysis and Relation to Verbal Learning. Alzheimer's & Dementia, Vol. 4, Iss. 4, Suppl 2:T59, 2008.

75.  Shen L, Saykin AJ, Firpi HA, West JD, McHugh TL, Wishart HA, Flashman LA, Wessels AM, McDonald BC, Cannon A. Comparison of manual and automated determination of hippocampal volumes in MCI and older adults with cognitive complaints. Alzheimer's & Dementia, Vol. 4, Iss. 4, Suppl 2:T29-30, 2008.

74.  Huang H, Shen L, Ford JC, Wang Y, and Xu Y. Computational issues in biomedical nanometrics and nano-materials. Journal of Nano Research, Inaugural Issue, Vol. 1:50-58, 2008.

73.  McPeek MA, Shen L, Torrey JZ, and Farid H. The tempo and mode of 3-dimensional morphological evolution in male reproductive structures. American Naturalist, 171(5):E158-E178, 2008.

72.  Shen L and Makedon FS. Mining 3D shape data for morphometric pattern discovery. Book chapter in Encyclopedia of Data Warehousing and Mining, 2nd Edition, John Wang eds., Idea Group Inc (IGI), 2008.

71.  Shen L, Firpi HA, Saykin AJ, West JW. Parametric surface modeling and registration for comparison of manual and automated segmentation of the hippocampus. MICCAI 2008 Workshop on the Computational Anatomy and Physiology of the Hippocampus, NYC, Sep 6, 2008.

 2007 

70.  Xu Y, Ford JC, Makedon FS, Popa D, Huang H, Shen L. In-home localization for home care of Alzheimer's disease patients using wireless sensor networks. International workshop on Pervasive Technologies for the support of Alzheimer's Disease and Related Disorders Sufferers, Thessaloniki, February 24, 2007.

69.  Shen L, Huang H, Makedon FS, and Saykin AJ. Efficient registration of 3D SPHARM surfaces. CRV 2007: Fourth Canadian Conference on Computer and Robot Vision, Montreal, QC, pages 81-88, May 28-30, 2007.

68.  Huang H, and Shen L. Surface harmonics for shape modeling. ICIP 2007: 14th IEEE International Conference on Image Processing, Volume 2:553-556, San Antonio, Texas, September 16-19, 2007.

67.  Shen L, Saykin AJ, Chung MK, and Huang H. Morphometric analysis of hippocampal shape in mild cognitive impairment: an imaging genetics study. IEEE 7th International Symposium on Bioinformatics and BioEngineering, pages 211-217, Boston, MA, October 14-17, 2007.

66.  McHugh TL, Saykin AJ, Wishart HA, Flashman LA, Cleavinger HB, Rabin LA, Mamourian AC, and Shen L. Hippocampal volume and shape analysis in an older adult population. The Clinical Neuropsychologist (special technology issue), 21(1): 131-146, 2007.

65.  Chung MK, Dalton KM, Shen L, Robbins SM, Evans AC, and Davidson RJ. Weighted fourier series representation and its application to quantifying amount of gray matter. IEEE Transactions on Medical Imaging, Special Issue on Computational Neuroanatomy (invited paper), 26(4): 566-581, 2007.

64.  Huang H, Shen L, Zhang R, Makedon FS, Saykin AJ, and Pearlman JD. A novel surface registration algorithm in medical modeling applications. IEEE Transactions on Information Technology in Biomedicine, 11(4): 474-482, 2007.

63.  Huang H, and Shen L. Three dimensional model for cardiac bioelectricity simulation: cell to organ. Simulation: Transactions of the Society for Modeling and Simulation International, 83(4): 321-327, 2007.

 2006 

62.  Zheng W, Wang Z, Shen L, Makedon FS, and Pearlman JD. Measuring blood delivery to solitary pulmonary nodule by perfusion magnetic resonance imaging.  SPIE Medical Imaging 2006: Physiology, Function, and Structure from Medical Images, Proc. of SPIE Vol 6143, 614332 (9 pages), San Diego, CA, February 2006.

61.  Huang H, Shen L, Zhang R, Makedon FS, Hettleman B, Pearlman JD. Fast surface alignment for cardiac spatiotemporal modeling. SPIE Medical Imaging 2006: Image Processing, Proc. of SPIE Vol 6144:1002-1009, San Diego, California, February 2006.

60.  Shen L, Huang H, Ford JC, Lu C, Gao L, Zheng W, Makedon FS, and Pearlman JD. Spatio-temporal analysis tool for modeling pulmonary nodules in MR images.  SPIE Medical Imaging 2006: Visualization, Image-Guided Procedures, and Display, Proc. of SPIE Vol 6141:740-749, San Diego, CA, February 2006.

59.  Moolani V, Balasubramanian R, Shen L, and Tandon A. Shape analysis and spatio-temporal tracking of mesoscale eddies in Miami isopycnic coordinate ocean model. IEEE 3DPVT 2006: Third International Symposium on 3D Data Processing, Visualization and Transmission, UNC, Chapel Hill, USA, June 14-16, 2006.

58.  Huang H, Shen L, Makedon FS, and Pearlman JD. A Spatio-temporal modeling method for shape representation. IEEE 3DPVT 2006: Third International Symposium on 3D Data Processing, Visualization and Transmission, UNC, Chapel Hill, USA, June 14-16, 2006.

57.  Huang H, Zhang L, Samaras D, Shen L, Makedon FS, and Pearlman JD. Hemispherical harmonic surface description and applications to medical image analysis. IEEE 3DPVT 2006: Third International Symposium on 3D Data Processing, Visualization and Transmission, UNC, Chapel Hill, USA, June 14-16, 2006.

56.  Shen L and Chung MK. Large-scale modeling of parametric surfaces using spherical harmonics. IEEE 3DPVT 2006: Third International Symposium on 3D Data Processing, Visualization and Transmission, UNC, Chapel Hill, USA, June 14-16, 2006.

55.  Chung MK, Shen L, Dalton KM, and Davidson RJ. Multi-scale voxel-based morphometry via weighted spherical harmonic representation. MIAR 2006: International Workshop on Medical Imaging and Augmented Reality, LNCS 4091, pages 36-43, Shanghai, China, August 17-18, 2006.

54.  Shen L, Saykin AJ, Chung MK, Huang H, Ford JC, Makedon FS, McHugh TL, and Rhodes CH. Morphometric analysis of genetic variation in hippocampal shape in mild cognitive impairment: Role of an IL-6 promoter polymorphism. CSB 2006: LSS Computational Systems Bioinformatics Conference, Stanford University, CA, August 14-18, 2006.

53.  Huang H, Shen L, Ford JC, Gao L, and Pearlman JD. Early lung cancer detection based on registered perfusion MRI. Oncology Reports, Special Issue on Computational Analysis and Decision Support Systems in Oncology, 15:1081-1084, 2006.

52.  Shen L, Zheng W, Gao L, Huang H, Makedon FS, and Pearlman JD. Spatio-temporal modeling of lung images for cancer detection.  Oncology Reports, Special Issue on Computational Analysis and Decision Support Systems in Oncology, 15:1085-1090, 2006.

51.  Shen L, and Makedon FS. Spherical mapping for processing of 3-D closed surfaces. Image and Vision Computing, 24(7): 743-761, 2006.

50.  Huang H, Shen L, Zhang R, Makedon FS, Hettleman B, and Pearlman JD. Cardiac motion analysis to improve pacing site selection in CRT. Journal of Academic Radiology, Elsevier Science, 13(9):1124-1134, September 2006.

 2005 

49.  Huang H, Shen L, Ford JC, Makedon FS, Zhang R, Gao L, and Pearlman JD. Functional analysis of cardiac MR images using SPHARM modeling. SPIE Medical Imaging 2005, Proc. of SPIE Vol 5747:1384-1391, San Diego, CA, 12-17 February 2005.

48.  Shen L, Gao L, Zhuang Z, DeMuinck E, Huang H, Makedon FS, and Pearlman JD. An interactive 3D visualization and manipulation tool for effective assessment of angiogenesis and arteriogenesis using computed tomographic angiography. SPIE Medical Imaging 2005, Proc. of SPIE Vol 5744: 848-858, San Diego, CA, 12-17 February 2005.

47.  Huang H, Shen L, Makedon FS, Sheng Zhang, Greenberg M, Gao L, and Pearlman JD. A clustering-based approach for prediction of cardiac resynchronization therapy. 20th ACM Symposium on Applied Computing, pages 260-266, Santa Fe, NM, March 13-17, 2005.

46.  Shen L, Saykin AJ, McHugh TL, West JD, Rabin LA, Wishart HA, Chung MK, Makedon FS. Morphometric MRI study of hippocampal shape in MCI using spherical harmonics. Alzheimer's Association International Conference on Prevention of Dementia: Early diagnosis and intervention, P-120, Washington, D.C., June 18-21, 2005.

45.  Shen L, Saykin AJ, McHugh TL, West JD, Rabin LA, Wishart HA, Chung MK, Makedon FS. Morphometric analysis of 3D surfaces: Application to hippocampal shape in mild cognitive impairment. CVPRIP 2005: 6th Int. Conf. on Computer Vision, Pattern Recognition and Image Processing, pages 699-702, Salt Lake City, Utah, July 21-26, 2005.

44.  Huang H, Zhang R, Fei Xiong, Makedon FS, Shen L, Hettleman B, Pearlman JD. K-means+ method for improving gene selection for classification of microarray Data. Poster at CSB 2005: IEEE Computational Systems Bioinformatics Conference, pages 110-111, Stanford, California, Aug 8-11, 2005.

43.  Shen L, Zheng W, Gao L, Huang H, Makedon FS, and Pearlman JD. Modeling time-intensity profiles for pulmonary nodules in MR images.  EMBS 2005: The 27th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pages 1359-1362, Shanghai, China, September 1-4, 2005.

42.  Huang H, Shen L, Zhang R, Makedon FS, Hettleman B, Pearlman JD. Clustering based cardiac resynchronization therapy prediction using open source toolkit PRTools. ISC/NA-MIC Open-Source Workshop at MICCAI 2005: 8th Int. Conf. on Medical Image Computing and Computer Assisted Intervention, Palm Springs, California, USA, Oct 26-29, 2005.

41.  Huang H, Shen L, Zhang R, Makedon FS, Pearlman JD. A prediction framework for cardiac resynchronization therapy via 4D cardiac motion analysis. MICCAI 2005: 8th International Conference on Medical Image Computing and Computer Assisted Intervention, LNCS 3749, pages 704-711, Palm Springs, California, USA, Oct 26-29, 2005.

40.  Huang H, Shen L, Zhang R, Makedon FS, Hettleman B, Pearlman JD. Surface alignment of 3D spherical harmonic models: Application to cardiac MRI analysis. MICCAI 2005: 8th International Conference on Medical Image Computing and Computer Assisted Intervention, LNCS 3749, pages 67-74, Palm Springs, California, USA, Oct 26-29, 2005.

 2004 

39.  Shen L, Makedon FS, and Saykin AJ. Shape-based discriminative analysis of combined bilateral hippocampi using multiple object alignment. Medical Imaging 2004: Image Processing, SPIE Proceedings 5370, pages 274-282, San Diego, California, 14-19 February 2004.

38.  Huang H, Shen L, Makedon FS, Gao L, and Pearlman JD. Three-dimensional analysis of cardiac magnetic resonance imaging using spherical harmonics model. ACC'04: Annual Scientific Session of the American College of Cardiology, New Orleans, March 7-10, 2004.

37.  Makedon FS, Ye S, Sheng Zhang, Ford JC, Shen L, Kapidakis S. Data brokers: Building collections through automated negotiation. SETN'04: The 3rd Hellenic Conference on Artificial Intelligence, LNCS 3025, pages 13-22, Samos, Greece, 5-8 May 2004

36.  Shen L and Makedon FS. Spherical parameterization for 3D surface analysis in volumetric images. IEEE Conference on ITCC'04: International Conference on Information Technology, pages 643-649, Las Vegas, NV, April 5-7, 2004.

35.  Steinberg T, Ford JC, Ouyang Y, Shen L, Wang Y, Zheng W, and Makedon FS. Tracking resource usage using heterogeneous feature spaces with local exceptions. EDBT'04 Workshop: Clustering Information over the Web, Heraklion-Crete, Greece, March 14th, 2004.

34.  Wang Y, Makedon FS, Ford JC, Shen L, and Goldin D. Generating fuzzy semantic metadata describing spatial relations from images using the R-histogram. The 4th ACM/IEEE-CS Joint Conference on Digital Libraries, pages 202-211, Tucson, Arizona, June 7-11, 2004.

33.  Huang H, Makedon FS, Pearlman JD, Ford JC, Shen L, Wang Y, and Gao L. Efficient similarity retrieval framework for temporal shape sequences: A case study in cardiac MR images. Proc. 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pages 3250-3253, San Francisco, California, September 1, 2004.

32.  Shen L, Ford JC, Makedon FS, and Saykin AJ. A surface-based approach for classification of 3D neuroanatomic structures. Intelligent Data Analysis, An International Journal, 8(6):519-542, 2004.

 2003 

31.  Shen L, Ford JC, Makedon FS, and Saykin AJ. Hippocampal shape analysis: Surface-based representation and classification. Medical Imaging 2003: Image Processing, SPIE Proceedings 5032, pages 253-264, San Diego, CA, February 15-20, 2003.

30.  Makedon FS, Wang Y, Steinberg T, Wishart HA, Saykin AJ, Ford JC, Ye S, and Shen L. A system framework for the integration and analysis of multi-modal spatio-temporal data streams: A case study in MS lesion analysis. The First International IEEE EMBS Neural Engineering Conference, pages 495-498, Capri Island, Italy, March 20-22, 2003.

29.  Saykin AJ, Flashman LA, T. McHugh, C. Pietras, McAllister TW, A. C. Mamourian, R. Vidaver, Shen L, Ford JC, Wang L, and Makedon FS. Principal components analysis of hippocampal shape in schizophrenia. Schizophrenia Research, 60(1):206, March 29 - April 2, 2003.

28.  Ye S, Makedon FS, Steinberg T, Shen L, Wang Y, Zhao Y, and Ford JC. SCENS: a system for the mediated sharing of sensitive data. JCDL'03: The 3rd ACM/IEEE-CS Joint Conference on Digital Libraries, pages 263-265, Houston, TX, May 27-31, 2003.

27.  Shen L, Ford JC, Makedon FS, Flashman LA, and Saykin AJ. Surface-based morphometric analysis for hippocampal shape in schizophrenia. Neuroimage, 19(2):e1966-e1970, Human Brain Mapping 2003, New York, USA, June 18-22, 2003.

26.  Steinberg T, Wang Y, Makedon FS, Shen L, Saykin AJ, and Wishart HA. A spatio-temporal multi-modal data management and analysis environment for tracking MS lesions. SSDBM'03: the 15th Int. Conference on Scientific and Statistical Database Management, pages 245-246, Cambridge, MA, July 9-11, 2003.

25.  Shen L, Ford JC, Makedon FS, and Saykin AJ. Effective classification of 3D closed sur-faces: Application to modeling neuroanatomical structures. CVPRIP’03: International Conference on Computer Vision, Pattern Recognition and Image Processing, pages 708-711, Cary, NC, September 26-30, 2003.

24.  Makedon FS, Tzika AA, Astrakas L, Pearlman JD, Wang Y, Steinberg T, Shen L, Chambers K, and Ford JC. Fusing information for tracking tumors. The 8th World Congress on Advances in Oncology and 6th International Symposium on Molecular Medicine, Hersonissos, Crete, Greece, October 16-18, 2003.

23.  Shen L, Ford JC, Makedon FS, Wang Y, Steinberg T, Ye S, and Saykin AJ. Morphometric analysis of brain structures for improved discrimination. MICCAI'03: Medical Image Computing and Computer Assisted Intervention, LNCS 2879, pages 513-520, Montreal, Quebec, Canada, November 15-18, 2003.

 2002 

22.  Ford JC, Makedon FS, Shen L, Steinberg T, Saykin AJ, and Wishart HA. Evaluation metrics for user-centered ranking of content in metaDLs. The 4th DELOS Workshop on Evaluation of Digital Libraries: Testbeds, Measurements, and Metrics, Budapest, Hungary, May 6-7, 2002.

21.  Saykin AJ, Wishart HA, Flashman LA, McAllister TW, T. McHugh, Ford JC, Shen L, Steinberg T, and Makedon FS. Structure/function relationships in brain disorders: Strategies for mining volume, shape, lesion and bold fMRI activation data. Society for Biological Psychiatry Meeting, Philadelphia, PA, May 16-18, 2002.

20.  Makedon FS, Ford JC, Shen L, Steinberg T, Saykin AJ, Wishart HA, and Kapidakis S. MetaDL: A digital library of metadata for sensitive or complex research data. ECDL'02: European Conference on Digital Libraries, LNCS 2458, pages 374-389, Rome, Italy, September 16-18, 2002.

19.  Ford JC, Shen L, Makedon FS, Flashman LA, and Saykin AJ. A combined structural-functional classification of schizophrenia using hippocampal volume plus fMRI activation. EMBS-BMES'02: The 2nd Joint Meeting of the IEEE Engineering in Medicine and Biology Society and the Biomedical Engineering Society, volume 1, pages 48-49, Houston, Texas, October 23-26, 2002.

 2001 

18.  Saykin AJ, Flashman LA, Shen L, Ashburner J, Sparling M, Donnelly AM, Makedon FS, Isecke D, Ford JC, Megalooikonomou V, and McAllister TW. Hippocampal shape in schizophrenia: A deformation-based morphometric analysis. Neuroimage, 13(6):s1096, Human Brain Mapping, Brighton, UK, June  2001.

17.  Cheng L, Shen L, Makedon FS, Donnelly AM, Flashman LA, and Saykin AJ. TROI: a training and research system for tracing regions of interest in brain images. Neuroimage, 13(6):s1298, Human Brain Mapping 2001, Brighton, UK, June 10-14, 2001.

16.  Ford JC, Makedon FS, Megalooikonomou V, Shen L, Steinberg T, and Saykin AJ. Spatial comparison of fMRI activation maps for data mining. Neuroimage, 13(6):s1302, Human Brain Mapping, Brighton, UK, June 10-14, 2001.

15.  Cheng L, Shen L, Makedon FS, Donnelly AM, Flashman LA, and Saykin AJ. On the development of a training and research system for tracing human brain structures. SCI'01: The 5th World Multi-Conference on Systemics, Cybernetics and Informatics, Volumn VIII, pages 151-155, Orlando, FL, July 22-25, 2001.

14.  Shen L, Cheng L, Teng F, Makedon FS, Ford JC, Steinberg T, and Saykin AJ. A multimedia system for tracing and studying regions-of-interest in brain images. MTAC'01: IEEE Multimedia Technology and Application Conference, pages 238-245, Irvine, CA, November 7-9, 2001.

 2000 

13.  Steinberg T, Shen L, Cheng L, and Makedon FS. Tracking human expression actions in lectures. ED-MEDIA'00: World Conference on Educational Multimedia, Hypermedia & Telecommunication, pages 1090-1095, Montreal, Quebec, Canada, June 26 - July 1, 2000.

12.  Shen L, Cheng L, Ford JC, Makedon FS, Megalooikonomou V, and Steinberg T. Mining the most interesting web access associations. WebNet'00: World Conference on the WWW and Internet, pages 489-494, San Antonio, TX, Oct. 30 - Nov. 4, 2000.

11.  Shen L, Shen H, Cheng L, and Pritchard P. Fast association discovery in derivative transaction collections. Knowledge and Information Systems, An International Journal, 2(2):147-160, May 2000.

10.  Megalooikonomou V, Ford JC, Shen L, Makedon FS, and Saykin AJ. Data mining in brain imaging. Statistical Methods in Medical Research, 9(4):359-394, 2000.

 1999 

9.  Shen L, Shen H, and Cheng L. New algorithms for efficient mining of association rules. IEEE Frontiers'99: The 7th Symposium on the Frontiers of Massively Parallel Computation, pages 234-241, Annapolis, Maryland, February 21-25, 1999.

8.  Steinberg T, Cheng L, Shen L, Makedon FS, Owen C, and Ottmann T. A model for authoring for retrieval (AFR): Retrieval on parallel data streams of recorded lecture information. Multimedia Storage and Archiving Systems IV, SPIE Photonics EAST, pages 423-430, Boston, MA, September 19-22, 1999.

7.  Shen L, Shen H, and Cheng L. New algorithms for efficient mining of association rules. Information Sciences, 118(1-4):251-268, September, 1999.

 1998 

6.  Shen L and Shen H. Mining flexible multiple-level association rules in all concept hierarchies. DEXA'98: The 9th International Conference on Database and Expert Systems Applications, LNCS 1460, pages 786-795, Vienna, Austria, August 24-28, 1998.

5.  Shen L, Shen H, Pritchard P, and Topor R. Finding the N largest itemsets. ICDM'98: International Conference on Data Mining, pages 211-222, Rio de Janeiro, RJ, Brazil, September 2-4, 1998.

 1997 

4.  Shen L, and Sun Y. Needed parallel-outermost reduction strategy. Journal of Software (in Chinese), 8(10):760-767, October 1997.

3.  Sun Y, Lin K, and Shen L. The design and implementation of a program development system based on rewriting methods. ACM SIGPLAN Notices, 32(2):27-34, February 1997.

 1996 

2.  Lin K, Shen L, Lu C, and Sun Y. The design and implementation of function-specification mixed programming language. Journal of Shanghai Jiaotong University (in Chinese), 30(6):100-106, 1996.

1.  Shen L, Lin K, and Sun Y. Parallel-outermost pattern matching. Journal of Software (in Chinese), 7(Supplement):329-337, 1996.