| [1] | Hongyi Zhou and Yu-Ping Kuang , ``Coupled-channel effects in hadronic transitions in heavy quarkonium systems'', Phys. Rev. D 44, 756-769 (1991). |
| [2] | Hongyi Zhou and Yu-Ping Kuang , ``Difficulties of detecting the intermediate-mass Higgs boson in the associate production channel Phys. Rev. D 47, R3680-3684 (1993). |
| [3] | Hongyi Zhou and Yu-Ping Kuang , ``Detecting the intermediate-mass Higgs boson through the associate production channel Phys. Rev. D 53, 4095-4098 (1996). |
| [4] | Hua Wang, Chong-Sheng Li, Hongyi Zhou and Yu-Ping Kuang, ``Supersymmetric QCD corrections to top quark pair production in photon-photon collision'', Phys. Rev. D 54, 4374-4379 (1996). |
| [5] | Chong-Sheng Li, Hongyi Zhou , Yun-Lun Zhu and Jin-Min Yang , ``Strong supersymmetric quantum effects on top quark production at the Fermilab Tevatron'', Phys. Lett. B 379 , 135-140 (1996). |
| [6] | Chong-Sheng Li, Jin-Min Yang, Yun-Lun Zhu and Hongyi Zhou, ``Yukawa corrections to top pair production in photon-photon collision'', Phys.Rev. D 54, 4662-4676 (1996). |
| [7] | Hongyi Zhou , Chong-Sheng Li and Yu-Ping Kuang , ``Yukawa corrections to top quark production at LHC in Two-Higgs-Doublet models'', Phys. Rev. D 55, 4412-4420 (1997). |
| [8] | Chong-Xing Yue, Hongyi Zhou, Yu-Ping Kuang, and Gong-Ru Lu, production rates at the Tevatron and the LHC in topcolor-assisted multiscale Technicolor models'', Phys. Rev. D 55, 5541-5548 (1997). |
| [9] | Hongyi Zhou and Chong-Sheng Li, ``Supersymmetric QCD corrections to top quark pair production at LHC'', Phys. Rev. D 55, 4421-4429 (1997). |
| [10] | Chong-Sheng Li, Robert J. Oakes, Jin-Min Yang, Hongyi Zhou, `` Supersymmetric QCD corrections to single top quark production at the Fermilab Tevatron'' , Phys. Rev. D 57, 2009-2012 (1998). |
| [11] | Hongyi Zhou, Yu-Ping Kuang, Chong-Xing Yue, Hua Wang, Gong-Ru Lu, ``Testing Technicolor models in top quark pair production at high energy photon colliders'', Phys. Rev. D 57, 4205-4218 (1998). |
| [12] | Chong-Sheng Li, C.P. Yuan, Hongyi Zhou, ``Supersymmetric QCD parity nonconservation in top quark pairs at the Fermilab Tevatron'', Phys. Lett. 424, 76-84 (1998). |
| [13] | Chong-Sheng Li, P. Nadolsky, C.P. Yuan, Hongyi Zhou, ``Signatures of the light gluino in the top quark production'', Phys. Rev. D 58, 095004 (1998). |
| [14] | Hongyi Zhou, ``CP violation in top quark pair production at hadron colliders'', Phys. Rev. D 58, 114002 (1998). |
| [15] | Hongyi Zhou and Chong-Sheng Li, ``Supersymmetric electroweak corrections to top quark'' Commun. Theor. Phys. 30, 465 (1998). |
| [16] | Hongyi Zhou, ``Determining top quark CP violating couplings from'', Phys. Lett. B 439, 393-397 (1998). |
| [17] | Xue-Lei Wang, Yu-Ping Kuang, Hongyi Zhou, Hua Wang,Ling Zhang, ``Single top quark production in γ collisions and testing Technicolor models'', Phys. Rev. D 60, 014002 (1999). |
| [18] | Hongyi Zhou, Yu-Ping Kuang , Chong-Xing Yue , Hua Wang , Gong-Ru Lu, `` Testing Technicolor models via top quark pair production in high-energy photon collisions'', Nucl. Phys. Proc. Suppl. 75 B, 302-304 (1999). |
| [19] | Ling Zhang, Xue-Lei Wang, Yu-Ping Kuang, Hongyi Zhou, ``Pseudogoldstone boson effects in top - anti -top productions at high-energy hadron colliders and testing Technicolor models'', Phys. Rev. D 61, 115007 (2000). |
| [20] | Hongyi Zhou, Emad Tajkhorshid, Thomas Frauenheim, and Sàndor Suhai, Marcus Elstner, ``Performance of the AM1, PM3, and SCC-DFTB methods in the study of conjugated Schiff base molecules'', Chem. Phys. 277, 91-103 (2002). |
| [21] | Hongyi Zhou and Yaoqi Zhou, ``Folding rate prediction using total contact distance.'', Biophys. J. 82, 458--463 (2002). |
| [22] | Hongyi Zhou and Yaoqi Zhou, ``Stability scale and atomic solvation parameters extracted from 1023 mutation experiments'', Proteins, 49, 483-492 (2002). |
| [23] | Apichart Linhananta§, Hongyi Zhou§ and Yaoqi Zhou, ``The dual role of a loop with low loop contact distance in folding and domain swapping'', Protein Science, 11, 1695-1701 (2002). [§ equal contribution] |
| [24] | Hongyi Zhou and Yaoqi Zhou, ``Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction'', Protein Science 11, 2714-2726 (2002). |
| [25] | Yaoqi Zhou, Hongyi Zhou and Martin Karplus, ``Cooperativity in {\it Scapharca} dimeric hemoglobin: simulation of binding intermediates and elucidation of the role of interfacial water'', J. Mol. Biol., 326, 593-606 (2003) . |
| [26] | Hongyi Zhou and Yaoqi Zhou, ``Predicting the topology of transmembrane helical proteins using mean burial propensity and a Hidden-Markov-Model-based method'', Protein Science 12, 1547-1555 (2003) |
| [27] | Hongyi Zhou and Yaoqi Zhou, ``Quantifying the effect of burial of amino acid residues on protein stability'', Proteins 54, 315-322 (2004). |
| [28] | Hongyi Zhou and Yaoqi Zhou, `` Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition'', Proteins 55, 1005-1013 (2004) . |
| [29] | S. Liu, C. Zhang, H. Zhou, and Y. Zhou, ``A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.'', Proteins 56, 93-101 (2004). |
| [30] | C. Zhang, S. Liu, H. Zhou, and Y. Zhou, ``An accurate residue-level pair potential of mean force for folding and binding based on the distance-scaled ideal-gas reference state.'', Protein Science 13, 400-411 (2004). |
| [31] | C. Zhang, S. Liu, H. Zhou, and Y. Zhou, ``The dependence of all-atom statistical potentials on training structural database.'', Biophys. J. 86, 3349-3358 (2004). |
| [32] | Y. Bai, H. Zhou, and Y. Zhou, ``Critical nucleation size in the folding of small apparently two-state proteins.'', Protein Science 13, 1173-1181 (2004). |
| [33] | Hongyi Zhou and Yaoqi Zhou, ``Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments'', Proteins. 58, 321-328 (2005). |
| [34] | Hongyi Zhou, C. Zhang, S. Liu, and Y. Zhou, ``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). |
| [35] | Hongyi Zhou and Yaoqi Zhou, ``SPARKS 2 and SP3 servers in CASP 6.'', Proteins (Supplement CASP issue), Suppl 7 152--156 (2005). |
| [36] | Hongyi Zhou and Yaoqi Zhou, ``SPEM: Sequence, secondary structure profiles enhanced multiple sequence alignment'', Bioinformatics 21, 3615--3621 ( 2005). |
| [37] | Z. Zhou, H. Feng, H. Zhou, Y. Zhou and Y. Bai, ``Design and folding of a multi-domain protein'', Biochemistry 44, 12107--12112 (2005). |
| [38] | Y. Zhou, H. Zhou,
C. Zhang and S. Liu, ``What is a desirable statistical energy function for
proteins and how can it be obtained?'', Cell Biochem. Biophys. in press
(2006) [Review]. |
| [39] | H. Zhou, S. B. Pandit, S. Lee, J. Borreguerro, H. Chen, L. Wroblewska and J. Skolnick. Analysis of TASSER based CASP7 protein structure prediction results. Proteins (in press). |
| [40] | H. Zhou and J. Skolnick. Ab initio protein structure prediction using chunk-TASSER. Biophysical Journal (in press). |
| [41] | H. Zhou and J. Skolnick. Protein model quality assessment prediction by combining fragment comparisons and a consensus Cα contact potential. Proteins (submitted). |