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2010
   
     
  An improved machine learning protocol for the identification ofcorrect Sequest search results  
[62]
Morten Kallberg and Hui Lu
PDF
  BMC Bioinformatics, 2010, 11:591  
     
  NAPS: a residue-level nucleic acid-binding prediction server  
[61]
Matthew Carson, Robert Langlois, Robert, Hui Lu
PDF
  NUCLEIC ACIDS RESEARCH,38: W431-W435 JUL 2010
   
     
  Probing static disorder in Arrhenius kinetics by single-molecule forcespectroscopy  
[60]
Kuo TL , Garcia-Manyes S , LiJY , Barel I , Lu H , Berne BJ , Urbakh M , Klafter J , Fernandez JM
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  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATESOF AMERICA, 107 : 25 : 11336-11340 : JUN 22 2010  
     
  Analysis of Combinatorial Regulation: Scaling of Partnerships betweenRegulators with the Number of Governed Targets  
[59]
Bhardwaj N , Carson MB , Abyzov A, Yan KK, Lu H, Gerstein MB
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  PLOS COMPUTATIONAL BIOLOGY, 6 : 5 : MAY 2010
   
     
  Boosting the prediction and understanding of DNA-binding domains from sequence  
[58]
Langlois RE , Lu H
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  NUCLEIC ACIDS RESEARCH , 38: 10 : 3149-3158 :JUN 2010  
     
  Genome-wide sequence-based prediction of peripheral proteins using anovel semi-supervised learning technique  
[57]
Bhardwaj N , Gerstein M , Lu H
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  BMC BIOINFORMATICS , 11 : S6 : Suppl. 1 : 2010
   
     
  Molecular Basis of the Potent Membrane-remodeling Activity of theEpsin 1 N-terminal Homology Domain  
[56]
Yoon Y, Tong JS , Lee PJ , Albanese A , Bhardwaj N , Kallberg M , Digman MA , Lu H , Gratton E , Shin YK , Cho W
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  JOURNAL OF BIOLOGICAL CHEMISTRY , 285 1 :531-540 JAN 1 2010  
     
  Visual Presentation as a Welcome Alternative to Textual Presentationof Gene Annotation Information  
[55]
Desai J , Flatow JM , Song J , Zhu LJ , Du P , Huang CC , Lu H , Lin SM , Kibbe WA
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  Advances in Experimental Medicine and Biology , 680 :709-715 2010
   
2009
   
     
  Structural Feature Extraction Protocol for Classifying Reversible Membrane Binding Protein Domains  
[54]
Morten Kallberg, Hui Lu
PDF
  Proceedings of the 31th Annual International Conference of the IEEE-EMBC 2009
   
     
  The PDZ2 domain of zonula occludens-1 and-2 is a phosphoinositidebinding domain  
[53]
Meerschaert K , Tun MP (3, Remue E2, De Ganck A 2 Boucherie C, Vanloo B , Degeest G , Vandekerckhove J , Zimmermann P, Bhardwaj N , Lu H , Cho W , Gettemans J
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  CELLULAR AND MOLECULAR LIFE SCIENCES, 66 24 :3951-3966 DEC 2009  
     
  Mechanical Signaling on the Single Protein Level Studied Using Steered Molecular Dynamics  
[52]
Genchev GZ, Kallberg M ,Gursoy G , Mittal A , Dubey L, Perisic O , Feng G ,Langlois R , Lu H
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  CELL BIOCHEMISTRY AND BIOPHYSICS , 55 3 141-152 DEC 2009
   
     
  Co-Expression among Constituents of a Motif in the Protein-Protein Interaction Network  
[51]
Nitin Bhardwaj and Hui Lu
PDF
  Journal of Bioinformatics and Computational Biology, V7, No1,page1-17, 2009.  
     
  Visual Annotation of the Gene Database  
[50]
Jing Wen, Xishu Wang, Warren Kibbe, Simon Lin, Hui Lu
PDF
  Proceedings of the 31th Annual International Conference of the IEEE-EMBC 2009
   
2008
   
     
  A Single-Molecule Perspective on the Role of Solvent Hydrogen Bonds in Protein Folding and Chemical Reactions  
[49]
Dougan L , Koti ASR ,Genchev G , Lu H , Fernandez JM
PDF
  CHEMPHYSCHEM, 9 18 2836-2847 DEC 22 2008  
     
  Machine Learning for Protein Structure and Function Prediction  
[48]
Robert E Langlois and Hui Lu
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  Annual Reports in Computational Chemistry, Vol. 4, 2008 In Press.
   
     
  Differential Roles of Phosphatidylserine, PtdIns(4,5)P2 and PtdIns(3,4,5)P3 in Plasma Membrane Targeting of C2 Domains: Molecular Dynamics Simulation, Membrane Binding, and Cell Translocation Studies of the PKCa C2 Domain  
[47]
Debasis Manna, Nitin Bhardwaj, Mohsin S. Vora, Robert V. Stahelin, Hui Lu* and Wonhwa Cho*
PDF
  Journal of Biological Chemistry In Press. 2008. (* co-corresponding authors)  
     
     
  Stabilization provided by neighboring strands is critical for the mechanical stability of proteins  
[46]
Deepak Sharma, Gang Feng, Dingyue Khor, Georgi Genchev, Hui Lu* and Hongbin Li*
PDF
  Biophysical Journal 2008 In Press. (* co-corresponding authors)
   
     
  Intelligible machine learning with malibu  
[45]
Robert Langlois and Hui Lu
  Proceedings of the 30th Annual International Conference of the IEEE, EMBC. Vancouver, British Columbia, Canada: IEEE, August 20-24 2008 LINK
     
     
  Mining Knowledge for the Methylation Status of CpG Islands Using Alternating Decision Trees  
[44]
Matthew B. Carson, Robert Langlois, and Hui Lu
  Proceedings of the 30th Annual International Conference of the IEEE, EMBC. Vancouver, British Columbia, Canada: IEEE, August 20-24 2008.
   
     
   
   
     
2007
   
     
  MeTaDoR: A comprehensive resource for membrane targeting domains and their host proteins  
[42]
Nitin Bhardwaj, Robert V. Stahelin, Guijun Zhao, Wonhwa Cho and Hui Lu
  Bioinformatics (2007) Vol 23, No. 22, pp 3110-3112
   
   
  Prediction of Specific Protein-DNA Recognition by Knowledge-based Two-body and Three-body Interaction Potentials
[40]
Guijun Zhao , Matthew B Carson and Hui Lu
  Proceedings of the 29th Annual International Conference of the IEEE EMBC, Lyon, France, 2007
   
   
  Finding new structural and sequence attributes to predict disease-association of single amino acid polymorphisms (SAPs)  
[39]
Zhi-Qiang Ye, Shu-Qi Zhao, Ge Gao, Xiao-Qiao Liu, Robert E. Langlois, Hui Lu, and Liping Wei
Bioinformatics. 2007. v23, No 12, p1444-1450  
     
     
  Learning to Translate Sequence and Structure to Function: Identifying DNA Binding and Membrane Binding Proteins  
[38]
Robert E Langlois, Matthew B Carson, Nitin Bhardwaj and Hui Lu
  Annals of Biomedical Engineering. (2007) v25, No 6, p1043-1052.  
     
     
  Single-molecule force spectroscopy reveals a mechanically stable protein fold and the rational tuning of its mechanical stability  
[37]
Deepak Sharma, Ognjen Perisic, Qing Peng, Yi Cao, Canaan Lam, Hui Lu, and Hongbin Li
  Proceedings of National Academy of Sciences, (2007) v104, no.22, p9278-9283.  
     
     
  Residue-Level Prediction of DNA-Binding Sites and its Application on DNA-Binding Protein Predictions  
[36]
Nitin Bhardwaj and Hui Lu
  FEBS Letters 581(5), 1058-1066.  
     
     
  Contour Length and Refolding Rate of a Small Protein Controlled byEngineered Disulfide Bonds
[35]
Sri Rama Koti Ainavarapu, Jasna Brujic, Hector H. Huang, Arun P. Wiita, Hui Lu, Lewyn Li, Kirstin A. Walther, Mariano Carrion-Vazquez, Hongbin Li, and Julio M. Fernandez
  Biophysical Journal Volume 92, January 2007, 225-233
     
     
  Physical and Chemical Basis for Structural Bioinformatics
[34]
Hui Lu, Ognjen Perisic and Dong Xu
PDF
  Book Chapter, “Computational Methods for Protein Structure Prediction and Modeling”
  edited by Ying Xu, Dong Xu, and Jie Liang. Springer-Verlag.  
     
2006
   
     
    Structural Bioinformatics Prediction of Membrane-Binding Proteins
 
[33]
Nitin Bhardwaj, Robert V Stahelin, Robert E Langlois, Wonhwa Cho*, and Hui Lu*
    Journal of Molecular Biology (2006) 359, 486-495. (* co-corresponding authors)
     
2005
   
     
    Improved protein fold assignment using support vector machines
 
[32]
Robert E. Langlois, Alice Diec, Ognjen Perisic, Yang Dai and Hui Lu
    International Journal of Bioinformatics Research and Applications, 1(3):319, 2005
     
     
  Kernel-based machine learning protocol for recognizing DNA-binding proteins  
[31]
Nitin Bhardwaj, Robert E. Langlois, Guijun Zhao and Hui Lu
  Nucleic Acid Research, 33(20):6486-6493  
     
     
    Development of a Grid-based Statistical Potential for Protein Structure Prediction
 
[30]
Guijun Zhao and Hui Lu
PDF
    Proceedings of the 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference, 2465
     
     
    Structure Based Prediction of Binding Residues on DNA-binding Proteins
 
[29]
Nitin Bhardwaj, Robert E. Langlois, Guijun Zhao and Hui Lu
    Proceedings of the 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference, 2347
     
     
    Correlation between gene expression profiles and protein-protein interactions within/across genomes
 
[28]
Nitin Bhardwaj and Hui Lu
    Bioinformatics, 21:2730, 2005
     
2004
   
     
    Chemistry on a single protein, vascular cell adhesion molecule-1, during forced unfolding
 
[27]
Nishant Bhasin, Philippe Carl, Sandy Harper, Gang Feng, Hui Lu, David W. Speicher, Dennis E. Discher
    Journal of Biological Chemistry, 279:45865, 2004
 
     
    Kernel based approach for protein fold prediction from sequence
 
[26]
Robert Ezra Langlois, Alice Diec, Yang Dai, Hui Lu
    26th Annual International Conference of the Engineering in Medicine and Biology Society, 2:2885, 2004
   
 
2003
   
    The mechanical stability of ubiquitin is linkage dependent
 
[25]
Mariano Carrion-Vazquez, Hongbin Li, Hui Lu, Andres Oberhauser, Piotr Marslazek, and Julio Fernandez
    Nature Struct Biology, 10:738-743, 2003.
   
   
    Statistical potential guided protein structure refinement from ab initio prediction
 
[24]
Hui Lu and Jeffery Skolnick
    Biopolymers, 70:575-584, 2003.
   
   
    Development of unified statistical potentials describing protein-protein interactions
 
[23]
Hui Lu, Long Lu, and Jeffery Skolnick
    Biophysical Journal, 84:1895-1901, 2003
   
   
    Multimeric Threading Based Prediction of Protein Interactions on a Genomic Scale: Application to the Saccharomyces Cerevisiae Proteome.
 
[22]
Long Lu, Andre Arakaki, Hui Lu and Jeffery Skolnick
    Genome Research, 13:1146-1154, 2003
   
 
2002
 
     
    Unfolding of titin domains studied by molecular dynamics simulations  
 
[21]
Mu Gao, Hui Lu, Klaus Schulten
    Journal of muscle research and cell motility, 23:513-521, 2002  
     
     
    Reverse engineering of the giant muscle protein titin
 
[20]
Hongbin Li, Wolfgang Linke, Andres Oberhauser, Mariano Carrion-Vazquez, Jason Kerkvliet, Hui Lu, Piotr Marslazek, and Julio Fernandez
    Nature, 418:998-1002, August 2002
   
   
    MULTIPROSPECTOR: An algorithm for the prediction of protein-protein interaction by multimeric threading
 
[19]
Long Lu, Hui Lu, and Jeffery Skolnick
    PROTEINS: Structure, Function, Genetics, 49:350-364, 2002
   
   
    Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma Genitalium Genome
 
[18]
Daisuke Kihara, Yang Zhang, Hui Lu, Andrzej Kolinski, and Jeffrey Skolnick
    Proceedings of National Academy of Sciences (USA), 99:5993-5998, April 2002  
     
 
2001
 
     
    Simulated refolding of stretched titin immunoglobulin domain
 
[17]
Mu Gao, Hui Lu, and Klaus Schulten
    Biophysical Journal, 81:2268-2277, Oct 2001
   
   
    TOUCHSTONE: An ab initio Protein Structure Prediction Method that Uses Threading-Based Tertiary Restraints
 
[16]
Daisuke Kihara, Hui Lu, Andrzej Kolinski and Jeffery Skolnick
    Proceedings of National Academy of Sciences (USA), 98:10125-10130, Aug 2001
   
   
    A Distance-Dependent Atomic Knowledge-based Potential for Improved Protein Structure Selection
 
[15]
Hui Lu and Jeffery Skolnick
    PROTEINS: Structure, Function, Genetics, 44:223-232, August 15, 2001
   
 
2000
   
    The key event in force-induced unfolding of titin's immunoglobulin domains
 
[14]
Hui Lu and Klaus Schulten
    Biophysical Journal, 79(1):51-65, July 2000
   
   
    Computer Modeling of Force-induced Titin Domain Unfolding
 
[13]
Hui Lu, Andre Krammer, Barry Isralewitz, Viola Vogel, and Klaus Schulten
PDF
    Adv Exp Med Biol. 481:143-60, 2000  
     
 
1999
 
 
 
 
Mechanical Unfolding Intermediates in Titin Modules
 
[12]
Piotr Marszalek, Hui Lu, Hongbin Li, Mariano Carrion-Vazquez, Andres Oberhauser, Klaus Schulten, and Julio Fernandez
 
Nature, 402:100-103, 1999
 
 
 
Steered Molecular Dynamics Simulation of Conformational Changes of Immunoglobulin Domain I27 Interprete Atomic Force Microscopy Observations
 
[11]
Hui Lu and Klaus Schulten
 
Chemical Physics, 247(1):141-153, 1999
 
 
 
Steered Molecular Dynamics Simulations of Force-Induced protein Domain Unfolding
 
[10]
Hui Lu and Klaus Schulten
 
PROTEINS: Structure, Function, Genetics, 35:453-463, June 1999
 
 
 
Forced Unfolding of the Fibronectin Type III Module Reveals a Tensile Molecular Recognition Switch
 
[09]
Andre Krammer, Hui Lu, Barry Isralewitz, Klaus Schulten, and Viola Vogel
 
Proceedings of National Academy of Sciences (USA), 96:1351-1356, Feb 16, 1999
 
 
 
Steered Molecular Dynamics
 
[08]
Sergei Izrailev, Sergey Stepaniants, Barry Isralewitz, Dorina Kosztin, Hui Lu, Ferenc Molnar, Willy Wriggers, and Klaus Schulten
PDF
 
Computational Molecular Dynamics: Challenges, Methods, Ideas., Edited by P. Deuflhard et. al., p36-63, Springer-Verlag, Berlin, Heidelberg, 1999
 
 
1998
 
 
 
Three Electronic State Model of the Primary Photoisomerization of Bacteriorhodopsin
 
[07]
William Humphrey, Hui Lu, Ilya Logunov, Hans Werner, and Klaus Schulten
PDF
 
Biophysical Journal, 75(4):1689-1699, Oct 1998
 
 
 
 
Unfolding of Titin Immunoglobulin Domains by Steered Molecular Dynamics
 
[06]
Hui Lu, Barry Isralewitz, Andre Krammer, Viola Vogel, and Klaus Schulten
 
Biophysical Journal, 75(2):662-671, Aug 1998
 
 
 
Quantum Dynamics of Retinal's Femtosecond Photoisomerization in Bacteriorhodopsin
 
[05]
M. Ben-Nun, Ferenc Molnar, Hui Lu, James Phillips, Todd Martinez, and Klaus Schulten
 
Faraday Discussion, 110:447-462, 1998
 
 
1997
and before  
 
 
Probing Protein Motion Through Temperature Echoes
 
[04]
Klaus Schulten, Hui Lu, and Linsen Bai
PDF
 
Physics of Biological Systems, Edited by H. Flyvbjerg et. al., Springer, 1997
 
 
 
Geometrization of Electrodynamics in a Finsler Space-time with Gauge Symmetry
 
[03]
Hui Lu, Pey-Schuan Jian, and Jong-Ping Hsu
PDF
 
JingShin Physics Symposium in Memory of Professor Wolfgang Kroll, Edited by J.P. Hsu et. al., World Scientific, 1997
 
 
 
Transverse Conductivity in Non-ideal Fiber Composite Geometries
 
[02]
Ke-da Bao, Hui Lu, and G. Grimvall
PDF
 
International Journal of Heat and Mass Transfer, 36(16):4033-4038, Nov 1993
 
 
 
Effective Conductivity in a Checkerboard Geometry at High Conductance Ratio and High Concentration
 
[01]
Hui Lu and Ke-da Bao
PDF
 
Physical Review B, 46(14):9209-9213, Oct 1992