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| 2009 | |
| 1 |
Ambrish Roy, Alper Kucukural, Yang Zhang
I-TASSER: a unified platform for automated protein structure and function prediction.
Nature Protocols, In press (2009).
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| 2 |
Yang Zhang
Protein structure prediction: when is it useful?.
Current Opinion in Structural Biology, vol 19, 145-155 (2009).
[PDF]
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| 3 |
Srayanta Mukherjee, Yang Zhang
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming.
Nucleic Acids Research, vol 37, e83 (2009).
[PDF] [Support Information] [Server]
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| 4 |
Dong Xu, Yang Zhang
Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform.
PLoS One, vol 4, e8140 (2009).
[PDF] [Server]
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| 5 |
Jooyoung Lee, Sitao Wu, Yang Zhang
Ab initio protein structure prediction.
From Protein Structure to Function with Bioinformatics, Chapter 1, Edited by D. J. Rigden, (Springer-London, 2009), P. 1-26.
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| 6 |
Yunqi Li, Yang Zhang
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks.
Proteins, vol 76, 665-676 (2009).
[PDF] [Server]
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| 7 |
Yang Zhang
I-TASSER: Fully automated protein structure prediction by I-TASSER in CASP8.
Proteins, vol S9, 100-113 (2009).
[PDF] [Support Information]
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| 8 |
Yunqi Li, Ambrish Roy, Yang Zhang
HAAD: An accurate algorithm for quickly predicting hydrogen positions in protein structures.
PLoS One, vol 4, e6701 (2009).
[PDF] [Server]
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| 9 |
Sitao Wu, Yang Zhang
Protein structure prediction.
Bioinformatics: Tools and Applications, Chapter 11, Edited by D. Edwards, D. Hansen and J. Stajich, (Springer-London, 2009), P. 225-242.
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| 10 |
Ambrish Roy, Sitao Wu, Yang Zhang
Composite approaches to protein tertiary structure prediction: A case-study by I-TASSER.
Protein Structure Prediction: Method and Algorithms, Chapter 12, Edited by H. Rangwala and G. Karypis, (Wiley, 2009), In press.
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| 11 |
Emanuele Bultrini, Kevin Brick, Srayanta Mukherjee, Yang Zhang, Francesco Silvestrini, Pietro Alano, Elisabetta Pizzi
Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction.
BMC Genomics, vol 10, 445 (2009).
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| 12 |
Alper Kucukural, Andras Szilagyi, Ugur Sezerman, Yang Zhang
Protein Homology Analysis for Function Prediction with Parallel Sub-Graph Isomorphism.
Chemoinformatics: Advances in Chemoinformatics and Computational Methods, Edited by H. Lodhi and Y. Yamanishi, (IGI global, 2009), In press.
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| 2008 | |
| 13 |
Yang Zhang
Progress and challenges in protein structure prediction..
Current Opinion in Structural Biology, vol 18, 342-348 (2008).
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| 14 |
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] [Support Information]
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| 15 |
Sitao Wu, Yang Zhang
ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction.
PLoS One, vol 3, e3400 (2008).
[PDF] [Server]
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| 16 |
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]
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| 17 |
Yang Zhang
I-TASSER server for protein 3D structure prediction.
BMC Bioinformatics, vol 9, 40 (2008).
[PDF] [Server]
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| 2007 | |
| 18 |
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).
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| 19 |
Yang Zhang
Template-based modeling and free modeling by I-TASSER in CASP7.
Proteins, vol S8, 108-117 (2007).
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| 20 |
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.
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| 21 |
Sitao Wu, Yang Zhang
LOMETS: A local meta-threading-server for protein structure prediction.
Nucleic Acids Research, vol 35, 3375-3382 (2007).
[PDF] [Support Information]
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| 22 |
Sitao Wu, Jeffrey Skolnick, Yang Zhang
Ab initio modeling of small proteins by iterative TASSER simulations.
BMC Biology, vol 5, 17 (2007).
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| 23 |
Stephan Lorenzen, Yang Zhang
Identification of near-native structures by clustering protein docking conformations.
Proteins, vol 68, 187-194 (2007).
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| 2006 | |
| 24 |
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] [Support Information]
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| 25 |
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).
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| 26 |
Vera Grimm, Yang Zhang, Jeffrey Skolnick
Benchmarking of dimeric threading and structure refinement.
Proteins, vol 63, 457-465 (2006).
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| 27 |
Seung Yup Lee, Yang Zhang, Jeffrey Skolnick
TASSER-based refinement of NMR structures.
Proteins, vol 63, 451-456 (2006).
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| 28 |
Haijun Zhou, Yang Zhang, Zhong-can Ou-Yang
Theoretical and computational treatment of DNA and RNA molecules.
Handbook of Theoretical and Computational Nanotechnology, Edited by M. Rieth and W. Schommers, (American Scientific Publishers, 2006), P. 419-487.
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| 29 |
Shashi Bhushan Pandit, Yang Zhang, Jeffrey Skolnick
TASSER-Lite: An Automated Tool for Protein Comparative Modeling.
Biophysical Journal, vol 91, 4180-4190 (2006).
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| 30 |
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.
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| 2005 | |
| 31 |
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]
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| 32 |
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).
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| 33 |
Haijun Zhou, Yang Zhang
A Hierarchical Chain Model of Spider Capture Silk Elasticity.
Physical Review Letters, vol 94, 028104 (2005).
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| 34 |
Yang Zhang, Adrian K. Arakaki, Jeffrey Skolnick
TASSER: An automated method for the prediction of protein tertiary structures in CASP6.
Proteins, vol S7, 91-98 (2005).
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| 2004 | |
| 35 |
Yang Zhang, Jeffrey Skolnick
Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins.
Biophysical Journal, vol 87, 2647 (2004).
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| 36 |
Wei Li, Yang Zhang, Jeffrey Skolnick
Application Of Sparse NMR Restraints To Large-Scale Protein Structure Prediction.
Biophysical Journal, vol 87, 1241 (2004).
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| 37 |
Yang Zhang, Jeffrey Skolnick
A scoring function for the automated assessment of protein structure template quality.
Proteins, vol 57, 702 (2004).
[PDF] [Correction] [Server]
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| 38 |
Yang Zhang, Jeffery Skolnick
SPICKER: Approach to clustering protein structures for near-native model selection.
Journal of Computational Chemistry, vol 25, 865 (2004).
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| 39 |
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).
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| 40 |
Jeffrey Skolnick, Daisuke Kihara, Yang Zhang
Development and testing of the PROSPECTOR 3.0 threading algorithm.
Proteins, vol 56, 502 (2004).
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| 41 |
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).
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| 2003 | |
| 42 |
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).
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| 43 |
Yang Zhang, Andrzej Kolinski, Jeffrey Skolnick
Touchstone II: A new approach to ab initio protein Structure Prediction.
Biophysical Journal, vol 85, 1145 (2003).
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| 44 |
Jeffrey Skolnick, Yang Zhang, Adrian K. Arakaki, Andrzej Kolinski, Michal Boniecki, Andras Szilaqyi, Daisuke Kihara
Touchstone: A Unified Approach to Protein Structure Prediction.
Proteins, vol S53, 469-479 (2003).
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| 2002 | |
| 45 |
Haijun Zhou, Yang Zhang, Zhongcan Ouyang
Elastic theories of single DNA molecules.
Physica, vol A306, 359 (2002).
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| 46 |
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).
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| 47 |
M. Dessinges, B. Maier, Yang Zhang, M. Peliti, D. Bensimon, V. Croquette
Stretching ssDNA, a model polyelectrolyte.
Physical Review Letter, vol 89, 248102 (2002).
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| 48 |
Yang Zhang, Daisuke Kihara, Jeffrey Skolnick
Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding.
Proteins, vol 48, 192 (2002).
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| 2001 | |
| 49 |
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).
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| 50 |
Haijun Zhou, Yang Zhang
Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?.
Journal of Chemical Physics, vol 114, 8694 (2001).
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| 51 |
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).
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| 52 |
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).
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| 53 |
Haijun Zhou, Yang Zhang, Zhongcan Ouyang
Stretch-induced hairpin-coil transitions in designed polynucleotide chains.
Physical Review Letters, vol 86, 356 (2001).
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| | 2000 and earlier |
| 54 |
Yang Zhang, Haijun Zhou, Zhongcan Ouyang
Monte Carlo implementation of supercoiled double-stranded DNA.
Biophysical Journal, vol 78, 1979 (2000).
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| 55 |
Haijun Zhou, Yang Zhang, Zhongcan Ouyang
Elastic property of single double-stranded DNA molecules: Theoretical study and comparison with experiments.
Physical Review, vol E62, 1045 (2000).
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| 56 |
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, (World Scientific, Singapore, 2000), P. 294-326.
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| 57 |
Yang Zhang
New approach to Monte Carlo calculation of the buckling of supercoiled DNA loops.
Physical Review, vol E62, 5923 (2000).
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| 58 |
C. Boros, T. C. Meng, R. Rittel, K. Tabelow, Yang Zhang
Formation of color-singlet gluon cluster and inelastic diffractive scattering.
Physical Review, vol D61, 094010 (2000).
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| 59 |
Haijun Zhou, Yang Zhang, Zhongcan Ouyang
Bending and base-stacking interactions in double-stranded semiflexible polymers.
Physical Review Letter, vol 82, 4560 (1999).
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| 60 |
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).
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| 61 |
Yang Zhang
Intermittency in diffractive deep-inelastic ep scattering.
Nuclear Physics, vol D70, 243c (1999).
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| 62 |
Yang Zhang
Characteristic plot of pomeron-exchange processes in diffractive DIS.
Journal of Physics, vol G25, L63 (1999).
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| 63 |
Yang Zhang
Factorial moment analyses in diffractive lepton-nucleon scattering.
Physical Review, vol D57, RAPID COMMUNICATIONS, 1327 (1998).
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| 64 |
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., (World Scientific, Singapore, 1998), P. 271-280.
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| 65 |
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 C73, 535 (1997).
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| 66 |
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).
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| 67 |
Yang Zhang
Nonlinear dynamical fluctuations in diffractive DIS processes.
Proceeding of 27th Int. Symp. on Multiparticle Dynamics, Edited by G. Pancheri et al., (World Scientific, Singapore, 1997), P. 322-331.
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| 68 |
Yang Zhang, Lianshou Liu, Yuanfang Wu
On the Levy stability of the anisotropic dynamical fluctuation in high energy multiparticle production.
Zeitschrift fur Physik, vol C71, 499 (1996).
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| 69 |
Yang Zhang, Lianshou Liu
A quantitative criterion for anisotropic dynamic fluctuation in high energy collision.
Scientia Sinica, vol A26, 343 (1996).
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| 70 |
Yang Zhang, Yuanfang Wu and Lianshou Liu
The randomly cascading model and its scaling.
High Energy Physics and Nuclear Physics, vol 20, 715 (1996).
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| 71 |
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).
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| 72 |
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 C69, 323 (1996).
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| 73 |
Yang Zhang, Hai Lin, Lianshou Liu
Levy stability analysis of random cascade model.
Communication of Theoretical Physics, vol 24, 85 (1995).
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| 74 |
Yang Zhang, Lianshou Liu
On the bin-wise and strip integrals of density function in high energy multiparticle production.
Zeitschrift fur Physik, vol C68, 463 (1995).
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| 75 |
Yuanfang Wu, Yang Zhang, Lianshou Liu
Is there anomalous scaling in multiparticle final states of high energy collision?.
Physical Review, vol D51, 6576 (1995).
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| 76 |
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).
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| 77 |
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).
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| 78 |
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).
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| 79 |
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).
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