Yang, An-Suei

YangAS 6x7Research Fellow
Deputy Director


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Telephone: +886-2-27871232
 

 

 

EDUCATION AND POSITIONS HELD:

  • Ph.D., Department of Chemistry The Johns Hopkins University, 1987
  • Postdoctoral Fellow, Department of Physics University of Virginia, 1987–1988
  • Postdoctoral Fellow, Department of Biochemistry Columbia University, 1988–1991
  • Associate Research Scientist - Research Scientist, Columbia University, 1991–2000
  • Assistant Professor of Pharmacology, Columbia University, 2000–2004
  • Associate Research Fellow, Genomics Research Center, Academia Sinica, 2004 - 2010
  • Research Fellow, Genomics Research Center, Academia Sinica, 2010 - present

HONORS:

  • Fellowship (2000-2002), William J. Matheson foundation at Columbia University.

RESEARCH INTERESTS:

YangAS-overviewOur lab has implemented phage-based protein display systems in connection with computational and bioinformatics methodologies harnessing the power of rapidly expanding computing capabilities and high throughput experimental technologies for antibody/protein engineering and antibody/protein design. The research directions are aiming at innovating antibody/protein design and engineering technologies and understanding the biological function of natural antibody repertoires with synthetic phage-displayed antibody libraries and bioinformatics; the goal is to develop antibody-based molecules for important biomedical applications. The works from our group can be found in [https://scholar.google.com.tw/citations?user=YBoSfnAAAAAJ&hl=en]

SELECTED PUBLICATIONS:

  • Chao-Ping Tung, Ing-Chien Chen, Chung-Ming Yu, Hung-Pin Peng, Jhih-Wei Jian, Shiou-Hwa Ma, Yu-Ching Lee, Jia-Tsrong Jan, An-Suei Yang*, submitted, “Discovering neutralizing antibodies targeting at the stem epitope of influenza hemagglutinin with synthetic phage-displayed antibody libraries”, Scientific Reports. (SCI)
  • Chen, H.-S., S.-C. Hou, J.-W. Jian, K.-S. Goh, S.-T. Shen, Y.-C. Lee, J.-J. You, H.-P. Peng, W.-C. Kuo, S.-T. Chen, M.-C. Peng, H.-J. Wang, C.-M. Yu, I.-C. Chen, C.-P. Tung, T.-H. Chen, K. P. Chiu, C. Ma, C. Y. Wu, S.-W. Lin and A.-S. Yang*, accepted, “Predominant structural configuration in natural antibody repertoires enables potent antibody responses against protein antigens”, Scientific Reports. (SCI)
  • Hung-Pin Peng, Kuo Hao Lee, Jhih-Wei Jian, An-Suei Yang*, 2014, “Origins of specificity and affinity in antibody-protein interactions”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111(26), E2656-E2665. (SCI)
  • Rajasekaran Mahalingama*, Hung-Pin Peng, An-Suei Yang*, 2014, “Prediction of fatty acid-binding residues on protein surfaces with three-dimensional probability distributions of interacting atoms”, BIOPHYSICAL CHEMISTRY, 192, 10-19. (SCI)
  • Rajasekaran Mahalingam*, Hung-Pin Peng, An-Suei Yang*, 2014, “Prediction of FMN-binding residues with three-dimensional probability distributions of interacting atoms on protein surfaces”, JOURNAL OF THEORETICAL BIOLOGY, 343, 154-161. (SCI)
  • Hsu, H.-J., K. H. Lee, J.-W. Jian, H.-J. Chang, C.-M. Yu, Y.-C. Lee, I.-C. Chen, H.-P. Peng, C. Y. Wu, Y.-F. Huang, C.-Y. Shao, K. P. Chiu and A.-S. Yang*, 2014, “Antibody variable domain interface and framework sequence requirements for stability and function by high throughput experiments.”, STRUCTURE, 22(1), 22-34. (SCI)
  • Chang, H.-J., J.-W. Jian, H.-J. Hsu, Y.-C. Lee, H.-S. Chen, J.-J. You, S.-C. Hou, C.-Y. Shao, Y.-J. Chen, K.-P. Chiu, H.-P. Peng, K. H. Lee and A.-S. Yang*, 2014, “Loop sequence features and stability determinants in antibody variable domains by high throughput experiments.”, STRUCTURE, 22(1), 9-21. (SCI)
  • Chang, H.-J. and A.-S. Yang*, 2014, “Design of Phage-Displayed Cystine-Stabilized Mini-Protein Libraries for Proteinaceous Binder Engineering”, Methods in Molecular Biology, 1088, 1-17.
  • Hsu, H.-J. and A.-S. Yang*, 2014, “Substrate Phage Display for Protease Substrate Sequence Characterization: Bovine Factor Xa as a Model System”, Methods in Molecular Biology, 1088, 107-124.
  • Keng-Chang Tsai, Ei-Wen Yang, Jhih-Wei Jian, Po-Chiang Hsu, Hung-Pin Peng, Ching-Tai Chen, Jun-Bo Chen, Jeng-Yih Chang, Wen-Lian Hsu. An-Suei Yang*, 2012, “Prediction of Carbohydrate Binding Sites on Protein Surfaces with 3-Dimensional Probability Density Distributions of Interacting Atoms”, PLoS One, 7(7), e40846. (SCI)
  • Ching-Tai Chen, Hung-Pin Peng, Jhih-Wei Jian, Keng-Chang Tsai, Jeng-Yih Chang, Ei-Wen Yang, Jun-Bo Chen, Wen-Lian Hsu, An-Suei Yang*, 2012, “Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces”, PLoS One, 7(6), e37706. (SCI)
  • Chung-Ming Yu, Hung-Pin Peng, Ing-Chien Chen, Yu-Ching Lee, Jun-Bo Chen, Keng-Chang Tsai, Ching-Tai Chen, Jeng-Yih Chang, Ei-Wen Yang, Po-Chiang Hsu, Jhih-Wei Jian, Hung-Ju Hsu, Hung-Ju Chang, Wen-Lian Hsu, Kai-Fa Huang, Alex Che Ma, An-Suei Yang*, 2012, “Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface”, PLoS One, 7(3), e33340. (SCI)
  • Yu-Ching Lee, Ing-Chien Chen, Chung-Ming Yu, Yi-Jen Huang, Hung-Ju Hsu, and An-Suei Yang*, 2011, “Effects of signal sequence on phage-displayed disulfide-stabilized single chain antibody variable fragment (sc-dsFv) libraries”, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 411(2), 348-353. (SCI)
  • Ing-Chien Chen, Chung-Ming Yu, Yu-Ching Lee, Yi-Jen Huang, Hung-Ju Hsu, and An-Suei Yang*, 2010, “Signal sequence as a determinant in expressing disulfide-stabilized single chain antibody variable fragments (sc-dsFv) against human VEGF”, MOLECULAR BIOSYSTEMS, 6(7), 1307-1315. (SCI)
  • Yi-Jen Huang, Ing-Chien Chen, Chung-Ming Yu, Yu-Ching Lee, Hung-Ju Hsu, Anna Ching-Ching Tung, Hung-Ju Chang, An-Suei Yang*, 2010, “Engineering Anti-vascular Endothelial Growth Factor Single Chain Disulfide-stabilized Antibody Variable Fragments (sc-dsFv) with Phage-displayed sc-dsFv Libraries”, Journal of Biological Chemistry, 285(11), 7880-7891. (SCI) (IF: 4.6; SCI ranking: 22.3%)
  • Hung-Ju Chang, Hung-Ju Hsu, Chi-Fon Chang, Hung-Pin Peng, Yi-Kun Sun, Hui-Ming Yu, Hsi-Chang Shih, Chun-Ying Song, Yi-Ting Lin, Chu-Chun Chen, Chia-Hung Wang, An-Suei Yang*., 2009, “Molecular Evolution of Cystine-Stabilized Miniproteins as Stable Proteinaceous Binders”, STRUCTURE, 17, 620-631. (SCI)
  • Hung-Ju Hsu, Keng-Chang Tsai, Yi-Kun Sun, Hung-Ju Chang, Yi-Jen Huang, Hui-Ming Yu, Chun-Hung Lin, Shi-Shan Mao and An-Suei Yang, 2008, “Factor-XaActive Site Substrate Specificity with Substrate Phage Display and Computational Molecular Modeling”, J. Biol. Chem, 283, 12343-12353. (SCI) (IF: 4.6; SCI ranking: 22.3%)
  • Chen CT, Yang EW, Hsu HJ, Sun YK, Hsu WL, Yang AS, 2008, “Protease substrate site predictors derived from machine learning on multilevel substrate phage display data.”, BIOINFORMATICS, 24(23), 2691-7. (SCI)
  • H. P. Peng and A. S. Yang, 2007, “Modeling protein loops with knowledge-based prediction of sequence-structure alignment”, Bioinformatics, 23(21), 2836-2842. (SCI)
  • Y. M. Shao, W. B. Yang, H. P. Peng, M. F. Hsu, K. C. Tsai, T. H. Kuo, A. H. Wang, P. H. Liang, C. H. Lin, A. S. Yang and C. H. Wong, 2007, “Structure-Based Design and Synthesis of Highly Potent SARS-CoV 3CL Protease Inhibitors”, ChemBioChem, 8, 1654-1657. (SCI)
  • H. Hsu, H. Cheng, H-P. Peng, S-S. Huang, M-Y. Lin and A. S. Yang, 2006, “Assessing Computational Amino Acid beta-turn Propensities with Phage-displayed Combinatorial Library and Directed Evolution”, Structure, 14, 1499-1510. (SCI)
  • R. Kuang, C. S. Leslie and A. S. Yang, 2004, “Protein backbone angle prediction with machine learning approaches”, Bioinformatics, 20, 1612-1621. (SCI)
  • A. S. Yang, L. Y. Wang, 2003, “Local structure prediction with local structure-based sequence profiles”, Bioinformatics, 19, 1267-1274. (SCI)
  • A. S. Yang, L. Y. Wang, 2002, “Local structure-based sequence profile database for local and global protein structure predictions”, Bioinformatics, 18, 1650-1657. (SCI)
  • A. S. Yang, 2002, “Structure-dependent sequence alignment for remotely related proteins”, Bioinformatics, 18, 1658-1665. (SCI)
  • A. S. Yang, B. Honig, 2000, “An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance”, J Mol Biol, 301, 665-678. (SCI)
  • A. S. Yang, B. Honig, 2000, “An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence”, J Mol Biol, 301, 679-689. (SCI)
  • A. S. Yang, B. Honig, 2000, “An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments”, J Mol Biol, 201, 691-711. (SCI)
  • A. S. Yang, B. Honig, 1999, “Sequence to structure alignment in comparative modeling using PrISM”, Proteins, Suppl 3, 66-72. (SCI)
  • V. K. Misra, J. L. Hecht, A. S. Yang and B. Honig, 1998, “Electrostatic Contributions to the Binding Free Energy of the cI Repressor to DNA”, Biophys J, 75, 2262-2273. (SCI)
  • A. S. Yang, B. Hitz, B. Honig, 1996, “Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding”, J Mol Biol, 259, 873-882. (SCI)
  • A. S. Yang, A. S. Brill, 1996, “Thermal access to amplified chemical potential and the determination of equilibrium constants in protein solutions at subfreezing temperatures”, Biophys Chem, 58, 341-354. (SCI)
  • A. S. Yang, B. Honig, 1995, “Free energy determinants of secondary structure formation: I. alpha-Helices”, J Mol Biol, 252, 351-365. (SCI)
  • A. S. Yang, B. Honig, 1995, “Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets”, J Mol Biol, 252, 366-376. (SCI)
  • B. Honig, A. S. Yang, 1995, “The free energy balance in protein folding”, Adv Protein Chem, 46, 27-58.
  • A. S. Yang, B. Honig, 1994, “Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin”, J Mol Biol, 237, 602-614. (SCI)
  • A. S. Yang, M. R. Gunner, R. Sampogna, K. Sharp and B. Honig, 1993, “On the calculation of pKas in proteins”, Proteins, 15, 252-265. (SCI)
  • A. S. Yang, B. Honig, 1993, “On the pH Dependence of Protein Stability”, J Mol Biol, 231, 459-474. (SCI)
  • A. S. Yang, K. A. Sharp and B. Honig, 1992, “Analysis of the heat capacity dependence of protein folding”, J Mol Biol, 227, 889-900. (SCI)
  • A. S. Yang, B. Honig, 1992, “Electrostatic effects on protein stability”, Curr Opin Struct Biol, 2, 40-45.
  • A. S. Yang, A. S. Brill, 1991, “Influence of the freezing process upon fluoride binding to hemeproteins”, Biophys J, 59, 1050-1063. (SCI)
  • A. S. Yang, B. J. Gaffney, 1990, “EPR Detection of Kinetic Responses to Photochemically Generated Protein Cofactors”, J Magn Reson, 90, 580-583. (SCI)
  • A. S. Yang, B. J. Gaffney, 1987, “Determination of relative spin concentration in some high-spin ferric proteins using E/D-distribution in electron paramagnetic resonance simulations”, Biophys J, 51, 55-67. (SCI)