2024:

  • A partition function estimator. Y.-C. Chiang, F. Otto, J. W. Essex. J. Chem. Phys. Recently accepted.
  • DeepKlapred: A deep learning framework for identifying protein lysine lactylation sites via multi-view feature fusion. J. Guan, P. Xie, D. Dong, Q. Liu, Z. Zhao, Y. Guo, Y. Zhang, T.-Y. Lee, L. Yao, Y.-C. Chiang. Int. J. Biol. Macromol. 283(3): 137668 (2024).
  • dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era. L. Yao, J. Guan, P. Xie, C.-R. Chung, Z. Zhao, D. Dong, Y. Guo, W. Zhang, J. Deng, Y. Pang, Y. Liu, Y. Peng, J.-T. Horng, Y.-C. Chiang, T.-Y. Lee. Nucleic Acids Res. gkae1019 (2024).
  • dbPTM 2025 update: comprehensive integration of PTMs and proteomic data for advanced insights into cancer research. C.-R. Chung, Y. Tang, Y.-P. Chiu, S. Li, W.-K. Hsieh, L. Yao, Y.-C. Chiang, Y. Pang, G.-T. Chen, K.-C. Chou, Y. S. Paik, P. Lam Tran, C.-P. Lin, Y.-M. Kao, Y.-J. Chen, W.-C. Chang, J. B.-K. Hsu, J.-T. Horng, T.-Y. Lee. Nucleic Acids Res. gkae1005 (2024).
  • ACP-CapsPred: an explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network. L. Yao, P. Xie, J. Guan, C.-R. Chung, W. Zhang, J. Deng, Y. Huang, Y.-C. Chiang, T.-Y. Lee. Brief. Bioinform. 25(5): bbae460 (2024).
  • Enhanced Recognition of a Herbal Compound Epiberberine by a DNA Quadruplex-Duplex Structure. X. Zhan, L. Deng, Y. Lian, Z. Shu, Y. Xu, X. Mai, M. S Krishna, R. Lu, A. Wang, S. Bai, F. Zhou, C. Xiong, Y. Xu, J. Ni, J. J. Vandana, Z. Wang, Y. Li, D. Sun, S. Huang, J. Liu, G.-J. Cheng, S. Wu, Y.-C. Chiang, G. Stjepanovic, C. Jiang, Y. Shao, G. Chen. Anal. Chem. 96(32): 13174-13184 (2024).
  • CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network. L. Yao, P. Xie, J. Guan, C.-R. Chung, Y. Huang, Y. Pang, H. Wu, Y.-C. Chiang, and T.-Y. Lee. J. Chem. Inf. Model. 64(14): 5725–5736 (2024).
  • Discovery and substrate specificity engineering of nucleotide halogenases. J. Ni, J. Zhuang, Y. Shi, Y.-C. Chiang, and G.-J. Cheng. Nat. Commun. 15(1): 5254 (2024).
  • AMPActiPred: A three‐stage framework for predicting antibacterial peptides and activity levels with deep forest. L. Yao, J. Guan, P. Xie, C.‐R. Chung, J. Deng, Y. Huang, Y.-C. Chiang, and Tzong‐Yi Lee. Prot. Sci. 33(6): e5006 (2024).
  • A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy. J. Guan, L. Yao, P. Xie, C.-R. Chung, Y. Huang, Y.-C. Chiang, and T.-Y. Lee. Brief. Bioinform. 25(3): bbae208 (2024).
  • Identifying Residues for Substrate Recognition in Human GPAT4 by Molecular Dynamics Simulations. Y. Liu, Y. Xu, Y. Xu, Z. Zhao, G.-J. Cheng, R. Ren, and Y.-C. Chiang. Int. J. Mol. Sci. 25(7): 3729 (2024).
  • Identifying Antitubercular Peptides via Deep Forest Architecture with Effective Feature Representation. L. Yao, J. Guan, W. Li, C.-R. Chung, J. Deng, Y.-C. Chiang, and T.-Y. Lee. Anal. Chem. 96(4): 1538-1546 (2024).
  • Structural insights into the activation and inhibition of CXC chemokine receptor 3. H. Jiao, B. Pang, A. Liu, Q. Chen, Q. Pan, X. Wang, Y. Xu, Y.-C. Chiang, R. Ren and H. Hu. Nat. Struct. Mol. Biol. 31: 610-620 (2024).

2023:

  • Structure basis for the modulation of CXC chemokine receptor 3 by antagonist AMG487. H. Jiao, B. Pang, Y.-C. Chiang, Q. Chen, Q. Pan, R. Ren and H. Hu. Cell Discov. 9: 119 (2023).
  • Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning.J. Guan, L. Yao, C.-R. Chung, P. Xie, Y. Zhang, J. Deng, Y.-C. Chiang, and T.-Y. Lee. J. Chem. Inf. Model. 63(24): 7886-7898 (2023).
  • DeepAFP: an effective computational framework for identifying antifungal peptides based on deep learning. L. Yao, Y. Zhang, W. Li, C.-R. Chung, J. Guan, W. Zhang, Y.-C. Chiang, and T.-Y. Lee. Protein Sci. 32(10): e4758 (2023).
  • StackTHPred: Identifying Tumor-Homing Peptides through GBDT-Based Feature Selection with Stacking Ensemble Architecture. J. Guan, L. Yao, C.-R. Chung, Y.-C. Chiang, and T.-Y. Lee. Int. J. Mol. Sci. 24(12): 10348 (2023).
  • ABPCaps: A Novel Capsule Network-Based Method for the Prediction of Antibacterial Peptides. L. Yao, Y. Pang, J. Wan, C.-R. Chung, J. Yu, J. Guan, C. Leung, Y.-C. Chiang, and T.-Y. Lee. Appl. Sci. 13(12): 6965 (2023).
  • Accelerating the discovery of anticancer peptides through deep forest architecture with deep graphical representation. L. Yao, W. Li, Y. Zhang, J. Deng, Y. Pang, Y. Huang, C.-R. Chung, J. Yu, Y.-C. Chiang, and T.-Y. Lee. Int. J. Mol. Sci. 24(5): 4328 (2023).
  • Exploring the chemical space of CYP17A1 inhibitors using cheminformatics and machine learning. T. Yu, T. Huang, L. Yu, C. Nantasenama, N. Anuwongcharoen, T. Piacham, R. Ren, and Y.-C. Chiang. Molecules 28(4): 1679 (2023).

2022:

  • Identification of neurotoxic compounds in cyanobacteria exudate mixtures. Y. Zi, J. R. Barker, H. J. MacIsaac, R. Zhang, R. Gras, Y-C. Chiang, Y. Zhou, F. Lu, W. Cai, C. Sun, and X. Chang. Sci. Total Environ. 857: 159257 (2022).
  • On the force field optimisation of β-lactam cores using the force field Toolkit. Q. Wu, T. Huang, S. Xia, F. Otto, T.-Y. Li, H.-D. Huang, Y.-C. Chiang. J. Comput. Aided Mol. Des. 36, 537-547 (2022).
  • dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data. J.-H. Jhong, L. Yao, Y. Pang, Z. Li, C.-R. Chung, R. Wang, S. Li, W. Li, M. Luo, R. Ma, Y. Huang, X. Zhu, J. Zhang, H. Feng, Q. Cheng, C. Wang, K. Xi, L.-C. Wu, T.-H. Chang, J.-T. Horng, L. Zhu, Y.-C. Chiang, Z. Wang, T.-Y. Lee. Nucleic Acids Res. 50(D1), D460-D470 (2022).

2021:

  • Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism. Y. Han, Q. Zhuang, B. Sun, W. Lv, S. Wang, Q. Xiao, B. Pang, Y. Zhou, F. Wang, P. Chi, Q. Wang, Z. Li, L. Zhu, F. Li, D. Deng, Y.-C. Chiang, Z. Li, and R. Ren. Nat. Commun. 12, 449 (2021).

2020:

  • Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins. M. P. Torrens-Spence, Y.-C. Chiang, T. Smith, M. A. Vicent, Y. Wang and J.-K. Weng. Proc. Natl. Acad. Sci. U.S.A. 117, 10806 (2020).
  • Molecular Dynamics Simulations of Antibiotic Ceftaroline at the Allosteric Site of Penicillin-Binding Protein 2a (PBP2a). Y.-C. Chiang, Mabel T. Y. Wong and J. W. Essex. Isr. J. Chem. 60, 1-11 (2020).

2019:

  • Molecular bond-breaking induced by Interatomic Coulombic Decay. Y.-C. Chiang, S. Engin, P. Bao, F. Otto, P. Kolorenc, P. Votavova, T. Miteva, J. Gao, and N. Sisourat. Phys. Rev. A 100, 052701 (2019).

2018:

  • Structural and dynamic basis of substrate permissiveness in hydroxy-cinnamoyl-transferase (HCT). Y.-C. Chiang, O. Levsh, C. K. Lam, J.-K. Weng and Y. Wang. PLOS Comput. Biol. 14, e1006511 (2018).
  • Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants. G. Liou, Y.-C. Chiang, Y. Wang and J.-K. Weng. J. Biol. Chem. 293, 18601-18612 (2018).
  • Accuracy of Potfit-based potential representations and its impact on the performance of (ML-)MCTDH. F. Otto, Y.-C. Chiang, and D. Peláez. Chem. Phys. 509, 116-130 (2018).

2017:

  • Strong field control of the interatomic Coulombic decay process in quantum dots. A. Haller, Y.-C. Chiang, M. Menger, E. F. Aziz, and A. Bande. Chem. Phys. 482, 135-145 (2017).

2016:

  • Dynamic conformational states dictate selectivity toward native substrate in a substrate-permissive acyltransferase. O. Levsh, Y.-C. Chiang, C. F. Tung, J. P. Noel, Y. Wang, and J.-K. Weng. Biochemistry. 55, 6314-6326 (2016).
  • The role of intramolecular nonbonded interaction and angle sampling in single-step free energy perturbation. Y.-C. Chiang, Y. T. Pang, and Y. Wang. J. Chem. Phys. 145, 234109 (2016).
  • Virtual substitution scan via single-step free energy perturbation. Y.-C. Chiang and Y. Wang. Biopolymers. 105, 324-336 (2016).

2009 - 2015:

  • A Single Atom Antenna. F. Trinter, J. B. Williams, M. Weller, M. Waitz, M. Pitzer, J. Voigtsberger, C. Schober, G. Kastirke, C. Müller, C. Goihl, P. Burzynski, F. Wiegandt, R. Wallauer, A. Kalinin, L. Ph. H. Schmidt, M. S. Schöffler, Y.-C. Chiang, K. Gokhberg, T. Jahnke and, R. Dörner. J. Phys. Conf. Ser. 635, 112099 (2015).
  • Ab initio calculation of ICD widths in photoexcited HeNe. G. Jabbari, S. Klaiman, Y.-C. Chiang, F. Trinter, T. Jahnke and K. Gokhberg. J. Chem. Phys. 140, 224305 (2014).
  • The effect of the partner atom on the spectra of interatomic Coulombic decay triggered by resonant Auger processes. T. Miteva, Y.-C. Chiang, P. Kolorenc, A. I. Kuleff, L. S. Cederbaum and K. Gokhberg. J. Chem. Phys. 141, 164303 (2014).
  • Interatomic Coulombic decay following resonant core excitation of Ar in argon dimer. T. Miteva, Y.-C. Chiang, P. Kolorenc, A. I. Kuleff, K. Gokhberg and L. S. Cederbaum. J. Chem. Phys. 141, 064307 (2014).
  • The exact wavefunction factorization of a vibronic coupling system. Y.-C. Chiang, S. Klaiman, F. Otto and L. S. Cederbaum. J. Chem. Phys. 140, 054104 (2014).
  • Vibrationally resolved decay width of Interatomic Coulombic Decay in HeNe. F. Trinter, J. B. Williams, M. Weller, M. Waitz, M. Pitzer, J. Voigtsberger, C. Schober, G. Kastirke, C. Müller, C. Goihl, P. Burzynski, F. Wiegandt, R. Wallauer, A. Kalinin, L. Ph. H. Schmidt, M. S. Schöffler, Y.-C. Chiang, K. Gokhberg, T. Jahnke, and R. Dörner. Phys. Rev. Lett. 111, 233004 (2013).
  • Quenching molecular photodissociation by intermolecular Coulombic decay. S. Kopelke, Y.-C. Chiang, K. Gokhberg and L. S. Cederbaum. J. Chem. Phys. 137, 034302 (2012).
  • Kinetic energy release in fragmentation processes following electron emission: A time-dependent approach. Y.-C. Chiang, F. Otto, H.-D. Meyer and L. S. Cederbaum. J. Chem. Phys. 136, 114111 (2012).
  • Interatomic Coulombic decay following Ne 1s Auger decay in NeAr. T. Ouchi, K. Sakai, H. Fukuzawa, I. Higuchi, Ph. V. Demekhin, Y.-C. Chiang, S. D. Stoychev, A. I. Kuleff, T. Mazza, M. Schöffler, K. Nagaya, M. Yao, Y. Tamenori, N. Saito and K. Ueda. Phys. Rev. A 83, 053415 (2011).
  • Resonant Auger decay of the core-excited C*O molecule in intense X-ray laser fields. Ph. V. Demekhin, Y.-C. Chiang and L. S. Cederbaum. Phys. Rev. A 84, 033417 (2011).
  • Interrelation between the distributions of kinetic energy release and emitted electron energy following the decay of electronic states. Y.-C. Chiang, F. Otto, H.-D. Meyer and L. S. Cederbaum. Phys. Rev. Lett. 107, 173001 (2011).
  • Resonant Auger decay of molecules in intense X-ray laser fields: Light-induced strong nonadiabatic effects. L. S. Cederbaum, Y.-C. Chiang, Ph. V. Demekhin and N. Moiseyev. Phys. Rev. Lett. 106, 123001 (2011).
  • Interatomic electronic decay processes in singly and multiply ionized clusters. V. Averbukh, Ph. V. Demekhin, P. Kolorenč, S. Scheit, S. D. Stoychev, A. I. Kuleff, Y.-C. Chiang, K. Gokhberg, S. Kopelke, N. Sisourat, and L. S. Cederbaum. J. Electron. Spectrosc. Relat. Phenom. 183, 36-47 (2011).
  • Linewidth and lifetime of atomic levels and the time evolution of spectra and coincidence spectra. Y.-C. Chiang, P. V. Demekhin, A. I. Kuleff, S. Scheit and L. S. Cederbaum. Phys. Rev. A 81, 032511 (2010).
  • Interatomic Coulombic decay and its dynamics in NeAr following K-LL Auger transition in the Ne atom. Ph. V. Demekhin, Y.-C. Chiang, S. D. Stoychev, P. Kolorenc, S. Scheit, A. I. Kuleff, F. Tarantelli and L. S. Cederbaum. J. Chem. Phys. 131, 104303 (2009).