Selected Publications in Biological Physics
- Network Class Superposition Analyses, Carl Pearson, Chen Zeng, Rahul Simha, PLoS ONE 8, e59046 (2013)
- Effect of Mimetic CDK9 Inhibitors on HIV1-Activated Transcription, Van Duyne R, Guendel I, Jaworski E, Sampey G, Klase Z, Chen H, Chen Zeng, Kovalskyy D, El Kouni MH, Lepene B, Patanarut A, Nekhai S, Price DH, Kashanchi F, Journal of Molecular Biology 425(4), 812-829 (2013)
- Process-Driven Inference of Biological Network Structure: Feasibility, Minimality, and Multiplicity, Guanyu Wang, Yongwu Rong, Hao Chen, Carl Pearson, Chenghang Du, Rahul Simha, Chen Zeng, PLoS ONE 7(7), e40330 (2012)
- Process-Based Network Decomposition Reveals Backbone Motif Structure, Guanyu Wang, Chenghang Du, Hao Chen, Rahul Simha, Yongwu Rong, Yi Xiao, and Chen Zeng, Proceedings of the National Academy of Sciences 107, 10478 (2010)
- Topology and dynamics of Boolean networks with strong inhibition, Yongwu Rong, Chen Zeng, Christina Evans, Hao Chen, and Guanyu Wang, Journal Discrete and Continuous Dynamical Systems 4, 1565-1575 (2010)
- A Clustering Approach For Identification Of Enriched Domains From Histone Modification Chip-Seq Data, Chongzhi Zang, Dustin E. Schones, Chen Zeng, Kairong Cui, Keji Zhao, and Weiqun Peng, Bioinformatics 25, 1952-1958 (2009)
- De Novo Design Of A Monomeric Protein With Beta-Alpha-Beta Fold, Huanhuan Liang, Hao Chen, Keqiang Fan, Ping Wei, Xianrong Guo, Changwen Jin, Chen Zeng, Chao Tang, Luhua Lai, Angew Chem Int Ed Engl. 48(18), 3301-3 (2009)
- A Novel Binding Pocket of Cyclin-Dependent Kinase 2, Hao Chen, Rachel Va Duyne, Naigong Zhang, Fatah Kashanchi, and Chen Zeng, Proteins: Structure, Function and Bioinformatics 74, 122-132 (2008)
- Effect of Transcription Peptide Inhibitors on HIV-1 Replication, Rachel Van Duye, Jessica Cardenas, Weilin Wu, Kylene Kehn-Hall, Zak Klase, Susana Mendez, Chen Zeng, Hao Chen, Mohammed Saifuddin, and Fatah Kashanchi, Virology 376(2), 308-22 (2008)
- Reference Energy Extremal Optimization as a Stochastic Search Algorithm Applied to Computational Protein Design, Naigong Zhang and Chen Zeng, Journal of Computational Chemistry 29(11):1762-71 (2008)
- An Improved Pairwise Decomposable Finite Difference Poisson-Boltzmann Method for Computational Protein Design, C.L. Vizcarra, N.G. Zhang, S.A. Marshall, N.S. Wingreen, Chen Zeng, and S.L. Mayo, Journal of Computational Chemistry 29 (7), 1153-1162 (2008)
- Pathway Switching Explains the Sharp Response Characteristic of Hypoxia Response Network, Yihai Yu, Guanyu Wang, Rahul Simha, Weiqun Peng, Frank Turano, and Chen Zeng, PLoS Computational Biology 3(8), 1657-1668 (2007)
- Inhibition of HIV-1 Virus Replication Using Small Soluble Tat Peptides, E.Agbottah, N.G. Zhang, S. Dadgar, A. Pumfery, J.D. Wade, Chen Zeng, and F. Kashanchi, Virology 345(2), 373-389 (2006)
- Fast Accurate Evaluation of Protein Surface Exposure, N.G. Zhang, Chen Zeng, and N. Wingreen, Proteins: Structure, Function, and Bioinformatics 57, 565 (2004)
- Identifying Proteins of High Designability via Surface-Exposure Patterns, E. Emberly, J. Miller, Chen Zeng, N. Wingreen, C. Tang, Proteins: Structure, Function and Genetics 47, 295 (2002)
- Emergence Of Highly-Designable Protein-Backbone Conformations In An Off-Lattice Model, J. Miller, Chen Zeng, N.S. Wingreen, C. Tang, Proteins: Structure, Function and Genetics 47, 506 (2002)
- The Designability of Protein Structure, R. Helling, H. Li, R. Mullin, J. Miller, N. Wingreen, Chen Zeng, and C. Tang, Journal of Molecular Graphics and Modeling 19, 157 (2001)
Selected Publications in Condensed Matter Physics
- Test of Replica Theory: Thermodynamics of Two-dimensional Model with Quenched Disorder, S. Bogner, T. Emig, A. Taha, and C. Zeng, Phys. Rev. B 69, 104420 (2004)
- Thermodynamics of Mesoscopic Vortex Systems in 1+1 Dimensions, C. Zeng, P.L. Leath, and Terence Hwa, Phys. Rev. Letts. 83, 4860 (1999)
- Absence of Two-Dimensional Bragg Glass, C. Zeng, P.L. Leath, and D.S. Fisher, Phys. Rev. Letts. 82, 1935 (1999)
- Statistical Topography of Glassy Interfaces, C. Zeng, J. Kondev, D. McNamara, and A.A. Middleton, Phys. Rev. Letts. 80, 109 (1998)
- An Efficient Implementation of High-order Coupled-Cluster Methods Applied to Quantum Magnets, C. Zeng, D.J.J. Farnell, and R.F. Bishop, J. Stat. Phys. 90, 327 (1998)
- Zero-Temperature Transitions of Antiferromagnetic Ising Model of Spin-S on a Triangular Lattice, C. Zeng and C. Henley, Phys. Rev. B. 55, 14935 (1997)
- Ground-State Roughness of the Disordered Substrate and Flux Lines in two dimensions, C. Zeng, A.A. Middleton, and Y. Shapir, Phys. Rev. Letts. 77, 3204 (1996)
- Quantum Dimer Calculations on Spin-1/2 Kagome Antiferromagnets, C. Zeng and V. Elser, Phys. Rev. B 51, 8313 (1995)
- Spin-Peierls and Spin-Liquid Phases of Kagome Quantum Antiferromagnets, B. Marston and C. Zeng, J. Appl. Phys. 62, 5962 (1991)
- Numerical Studies of Antiferromagnetism on a Kagome Net, C. Zeng and V. Elser, Phys. Rev. B 42, 8436 (1990)