Journal Articles:
  • Yang Zhang.
    Progress and challenges in protein structure prediction.
    Current Opinion in Structural Biology, vol 18, 342-348 (2008).
    [PDF].

  • Sitao Wu, Yang Zhang.
    A comprehensive assessment of sequence-based and template-based methods for protein contact prediction.
    Bioinformatics, vol 24, 924-931 (2008).
    [PDF] [Supporting Information].

  • Sitao Wu, Yang Zhang.
    ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction.
    PLoS One, vol 3, e3400 (2008).
    [PDF] [Server].

  • Sitao Wu, Yang Zhang.
    MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information.
    Proteins, vol 72, 547-556 (2008).
    [PDF] [Server].

  • Yang Zhang.
    I-TASSER server for protein 3D structure prediction.
    BMC Bioinformatics, vol 9, 40 (2008).
    [PDF] [Server].

  • Stephan Lorenzen, Yang Zhang.
    Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization.
    Protein Science, vol 16, 2716-2725 (2007).
    [PDF] .

  • Yang Zhang.
    Template-based modeling and free modeling by I-TASSER in CASP7.
    Proteins, Suppl vol 8, 108-117 (2007).
    [PDF].

  • Sitao Wu, Yang Zhang.
    LOMETS: A local meta-threading-server for protein structure prediction.
    Nucleic Acids Research, vol 35, 3375-3382 (2007).
    [PDF] [Supporting Information] [Server].

  • Sitao Wu, Jeffrey Skolnick, Yang Zhang.
    Ab initio modeling of small proteins by iterative TASSER simulations
    BMC Biology, vol 5, 17 (2007).
    [PDF].

  • Stephan Lorenzen, Yang Zhang.
    Identification of near-native structures by clustering protein docking conformations
    Proteins, vol 68, 187-194 (2007).
    [PDF].

  • Yang Zhang, Isaac A. Hubner, Adrian K. Arakaki, Eugene Shakhnovich, Jeffrey Skolnick.
    On the origin and highly likely completeness of single-domain protein structures.
    Proceedings of the National Academy of Sciences of USA, vol 103, 2605-2610 (2006).
    [PDF] [Supporting Information].

  • Yang Zhang, Mark E. DeVries, Jeffrey Skolnick.
    Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome.
    PLoS Computational Biology, vol 2, e13 (2006).
    [PDF].

  • Vera Grimm, Yang Zhang, Jeffrey Skolnick.
    Benchmarking of dimeric threading and structure refinement.
    Proteins, vol 63, 457-465 (2006).
    [PDF].

  • Seung Yup Lee, Yang Zhang, Jeffrey Skolnick.
    TASSER-based refinement of NMR structures.
    Proteins, vol 63, 451-456 (2006).
    [PDF].

  • Shashi Bhushan Pandit, Yang Zhang, Jeffrey Skolnick.
    TASSER-Lite: An Automated Tool for Protein Comparative Modeling.
    Biophysical Journal, vol 91, 4180-4190 (2006).
    [PDF].

  • Yang Zhang, Jeffrey Skolnick.
    TM-align: a protein structure alignment algorithm based on the TM-score.
    Nucleic Acids Research, vol 33, 2302 (2005).
    [PDF] [Server]

  • Yang Zhang, Jeffrey Skolnick.
    The protein structure prediction problem could be solved using the current PDB library.
    Proceedings of the National Academy of Sciences of USA, vol 102, 1029 (2005).
    [PDF].

  • Haijun Zhou, Yang Zhang.
    A Hierarchical Chain Model of Spider Capture Silk Elasticity.
    Physical Review Letters, vol 94, 028104 (2005).
    [PDF].

  • Yang Zhang, Adrian K. Arakaki, Jeffrey Skolnick.
    TASSER: An automated method for the prediction of protein tertiary structures in CASP6.
    Proteins, Suppl vol 7, 91-98 (2005).
    [PDF].

  • Yang Zhang, Jeffrey Skolnick.
    Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins.
    Biophysical Journal, vol 87, 2647 (2004).
    [PDF].

  • Wei Li, Yang Zhang, Jeffrey Skolnick.
    Application Of Sparse NMR Restraints To Large-Scale Protein Structure Prediction.
    Biophysical Journal, vol 87, 1241 (2004).
    [PDF].

  • Yang Zhang, Jeffrey Skolnick.
    A scoring function for the automated assessment of protein structure template quality.
    Proteins, vol 57, 702 (2004).
    [PDF] [Correction] [Server].

  • Yang Zhang, Jeffery Skolnick.
    SPICKER: Approach to clustering protein structures for near-native model selection.
    Journal of Computational Chemistry, vol 25, 865 (2004).
    [PDF].

  • Yang Zhang, Jeffrey Skolnick.
    Automated structure prediction of weakly homologous proteins on a genomic scale.
    Proceedings of the National Academy of Sciences of USA, vol 101, 7594 (2004).
    [PDF].

  • Jeffrey Skolnick, Daisuke Kihara, Yang Zhang.
    Development and testing of the PROSPECTOR 3.0 threading algorithm.
    Proteins, vol 56, 502 (2004).
    [PDF].

  • Adrian K. Arakaki, Yang Zhang, Jeffrey Skolnick.
    Large-scale assessment of the utility of low resolution protein structures for biochemical assignment.
    Bioinformatics, vol 20, 511 (2004).
    [PDF].

  • Wei Li, Yang Zhang, Daisuke Kihara, Yuanpeng Janet Huang, Deyou Zheng, Gaetano T. Montelione, Andrzej Kolinski, Jeffrey Skolnick.
    TOUCHSTONEX: Protein Structure Prediction Using Sparse NMR Data.
    Proteins, vol 53, 290 (2003).
    [PDF].

  • Yang Zhang, Andrzej Kolinski, Jeffrey Skolnick.
    Touchstone II: A new approach to ab initio protein Structure Prediction.
    Biophysical Journal, vol 85, 1145 (2003).
    [PDF].

  • Jeffrey Skolnick, Yang Zhang, Adrian K. Arakaki, Andrzej Kolinski, Michal Boniecki, Andras Szilaqyi, and Daisuke Kihara.
    Touchstone: A Unified Approach to Protein Structure Prediction.
    Proteins, Suppl vol 53, 469-479 (2003).
    [PDF].

  • M. Dessinges, B. Maier, Yang Zhang, M. Peliti, D. Bensimon, V. Croquette.
    Stretching ssDNA, a model polyelectrolyte.
    Physical Review Letter, vol 89, 248102 (2002).
    [PDF].

  • Yang Zhang, Daisuke Kihara, Jeffrey Skolnick.
    Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding.
    Proteins, vol 48, 192 (2002).
    [PDF].

  • Haijun Zhou, Yang Zhang, Zhongcan Ouyang.
    Elastic theories of single DNA molecules
    Physica, vol A 306, 359 (2002).
    [PDF].

  • Daisuke Kihara, Yang Zhang, Hui Lu, Andrzej Kolinski, Jeffrey Skolnick.
    Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma Genitalium Genome.
    Proceedings of the National Academy of Sciences of USA, vol 99, 5993 (2002).
    [PDF].

  • Yang Zhang, Jeffrey Skolnick.
    Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures.
    Journal of Chemical Physics, vol 115, 5027(2001).
    [PDF].

  • Yang Zhang, Haijun Zhou, Zhongcan Ouyang.
    Stretching single-stranded DNA: Interplay of electrostatic, base-pairing, and basepair stacking interactions.
    Biophysical Journal, vol 81, 1133(2001).
    [PDF].

  • Haijun Zhou, Yang Zhang.
    Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?
    Journal of Chemical Physics, vol 114, 8694 (2001).
    [PDF].

  • Haijun Zhou, Yang Zhang, Zhongcan Ouyang, Xi Z. Feng, Stuart M. Lindsay, Pichumani Balagurumoorthy, Rodney E. Harrington.
    Conformation and Rigidity of DNA Microcircles Containing waf1 Response Element for p53 Regulatory Protein.
    Journal of Molecular Biology, vol 306, 227 (2001).
    [PDF].

  • Haijun Zhou, Yang Zhang, Zhongcan Ouyang.
    Stretch-induced hairpin-coil transitions in designed polynucleotide chains,
    Physical Review Letters, vol 86, 356 (2001).
    [PDF].

  • Yang Zhang, Haijun Zhou, Zhongcan Ouyang.
    Monte Carlo implementation of supercoiled double-stranded DNA.
    Biophysical Journal, vol 78, 1979 (2000).
    [PDF].

  • Haijun Zhou, Yang Zhang, Zhongcan Ouyang.
    Elastic property of single double-stranded DNA molecules: Theoretical study and comparison with experiments.
    Physical Review, vol E 62, 1045 (2000).
    [PDF].

  • Yang Zhang, Haijun Zhou, Zhongcan Ouyang.
    Theory of Stretching Individual Polynucleotide Molecule.
    Proceedings of Biological Physics 2000, edited by V. Sa-yakanit, L. Matsson, and H. Frauenfelder, 294-326 (2000).

  • Yang Zhang.
    New approach to Monte Carlo calculation of the buckling of supercoiled DNA loops.
    Physical Review, vol E 62, RAPID COMMUNICATIONS, 5923 (2000).
    [PDF].

  • C. Boros, T. C. Meng, R. Rittel, K. Tabelow, Yang Zhang.
    Formation of color-singlet gluon cluster and inelastic diffractive scattering.
    Physical Review, vol D 61, 094010 (2000).
    [PDF].

  • Haijun Zhou, Yang Zhang, Zhongcan Ouyang.
    Bending and base-stacking interactions in double-stranded semiflexible polymers.
    Physical Review Letter, vol. 82, 4560 (1999).
    [PDF].

  • T. C. Meng, R. Rittel, Yang Zhang.
    Diffraction and colorless gluon-clusters in high-energy hadron-hadron and lepton-hadron collisions.
    Physical Review Letter, vol. 82, 2044(1999).
    [PDF].

  • Yang Zhang.
    Intermittency in diffractive deep-inelastic ep scattering.
    Nuclear Physics, vol B 70, 243c (1999).
    [PDF].

  • Yang Zhang.
    Characteristic plot of pomeron-exchange processes in diffractive DIS.
    Journal of Physics, LETTERS TO THE EDITOR, vol G 25, L63 (1999).
    [PDF].

  • Yang Zhang.
    Factorial moment analyses in diffractive lepton-nucleon scattering,
    Physical Review, vol D 57, RAPID COMMUNICATIONS, 1327 (1998).
    [PDF].

  • Yang Zhang.
    Fractality of pomeron-exchange processes in diffractive DIS.
    Proceeding of 28th Int. Symp. on Multiparticle Dynamics, edited by N. G. Antoniou et al., 271-280 (1998).

  • Lianshou Liu, Yang Zhang, Yue Deng.
    On the Influence of Momentum Conservation Upon the Scaling Behaviour of Factorial Moments in High Energy Multiparticle Productions.
    Zeitschrift fur Physik, vol C 73, 535 (1997).

  • Yang Zhang, Yue Deng, Lianshou Liu.
    On the restriction of transverse momentum conservation to the dynamic fluctuation in high energy collision.
    High Energy Physics and Nuclear Physics, vol 21, 130 (1997).

  • Yang Zhang.
    Nonlinear dynamical fluctuations in diffractive DIS processes.
    Proceeding of 27th Int. Symp. on Multiparticle Dynamics, edited by G. Pancheri et al., 322-331 (1997).

  • Yang Zhang, Lianshou Liu, Yuanfang Wu.
    On the Levy stability of the anisotropic dynamical fluctuation in high energy multiparticle production.
    Zeitschrift fur Physik, vol C 71, 499 (1996).

  • Yang Zhang, Lianshou Liu.
    A quantitative criterion for anisotropic dynamic fluctuation in high energy collision.
    Scientia Sinica vol A 26, 343 (1996).

  • Yang Zhang, Yuanfang Wu and Lianshou Liu.
    The randomly cascading model and its scaling.
    High Energy Physics and Nuclear Physics, vol 20, 715 (1996).

  • Yang Zhang, Hai Lin, Lianshou Liu.
    The analytical study of two-dimensional self-affine fractal in high energy collision.
    High Energy Physics and Nuclear Physics, vol 20, 65 (1996).

  • Yang Zhang, Lianshou Liu, Yuanfang Wu.
    On the random cascading model study of anomalous scaling in multiparticle production with continuously diminishing scale.
    Zeitschrift fur Physik, vol C 69 323 (1996).

  • Yang Zhang, Hai Lin, Lianshou Liu.
    Levy stability analysis of random cascade model,
    Communication of Theoretical Physics, vol 24, 85 (1995).

  • Yang Zhang, Lianshou Liu.
    On the bin-wise and strip integrals of density function in high energy multiparticle production.
    Zeitschrift fur Physik, vol C 68, 463 (1995).

  • Yuanfang Wu, Yang Zhang, Lianshou Liu.
    Is there anomalous scaling in multiparticle final states of high energy collision?
    Physical Review, vol D 51, 6576 (1995).

  • Hai Lin, Yang Zhang, Lianshou Liu.
    The refinement of Alpha-model and the analytical calculation of the Levy index.
    High Energy Physics and Nuclear Physics, vol 18, 275 (1994).

  • Yang Zhang, Yuan Hu, Yuanfang Wu, Lianshou Liu, Yonghe Zhang.
    On the intermittency and correlation integral of multiparticle final states in high energy collision.
    High Energy Physics and Nuclear Physics, vol 18, 175 (1994).

  • Yang Zhang, Xu Cai.
    The cluster effect of the semi-inclusive single-particle rapidity distribution.
    High Energy Physics and Nuclear Physics, vol 17, 822 (1994).

  • Yang Zhang, Lianshou Liu.
    The clustered production of final particles and forward-backward correlation in high energy p-p collision.
    High Energy Physics and Nuclear Physics, vol 18, 69 (1994).


Books and Book Chapters:
  • Jooyoung Lee, Sitao Wu, Yang Zhang.
    Ab Initio Protein Structure Prediction.
    From Protein Structure to Function with Bioinformatics, Chapter 1, Edited by Daniel John Rigden (Springer, 2008). P 1-26.

  • Jeffrey Skolnick, Yang Zhang.
    Protein Structure Prediction.
    Systems Biology, Volume I: Genomics, Edited by I. Rigoutsos and G. Stephanopoulos (Oxford University Press, 2007). P 187-218.

  • Jeffrey Skolnick, Yang Zhang, Andrzej Kolinski.
    Ab Initio Modelling.
    Structural Genomics and High Throughput Structural Biology, Chapter 8, Edited by M. Sundstrom, M. Norin, and A. Edwards (Taylor and Francis, 2006). P 137-162.

  • Haijun Zhou, Yang Zhang, Zhong-can Ou-Yang
    Theoretical and Computational Treatment of DNA Molecules.
    Handbook of Theoretical and Computational Nanotechnology, Edited by M. Rieth and W. Schommers, (American Scientific Publishers, 2003).

 


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