Publications

Lee-Wei Yang (楊立威),

Professor and Director, Institute of Bioinformatics and Structural Biology, and Director of PhD Program in Biomedical Artificial IntelligenceNational Tsing-Hua University

Program Coordinator, National Center of Theoretical Sciences (Physics Division); Honorary Professor, University of Liverpool, UK;  Visiting Professor, University of Osaka (2018)

Faculty member in TIGP Bioinformatics & CBMB PhD program,  Academia Sinica, Taiwan

101, Sec 2, Kuang-Fu Rd., Hsinchu, Taiwan, R.O.C.
Voice: +886-3-5742467
lwyang@life.nthu.edu.tw

PhD, School of Medicine, Univ of Pittsburgh, 2005                                                                 M.S., 國立清華大學, 1999                                                                                                                 B.S., 國立台灣大學, 1997

Positions:

Division Director of International Students, Office of Global Affairs (2016-2019)
Visiting Professor, Osaka University (Aug, 2018 – Oct, 2018)
Associate Professor, NTHU (2015-2018)
Assistant Professor, NTHU (2011-2015)

Awards:

Awarded 48,000 node-hours computation resources by High Performance Computing Infrastructure (HPCI), Japan, for the year 2019-2020 (2019)                                                    108年第1梯次中研院短期訪問學人 (fund:150,000 NTD)(2019)
Ta-You Wu Memorial Award 吳大猷先生紀念獎 (cash prize: 300,000 NTD) (2017) International Collaboration Research of IPR, Osaka University (funding : 400,000 JP Yen (2017-2018)

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Past and Current Collaborators :

Prof. Eugene Shakhnovich, Harvard University, USA
Prof. Ivet Bahar, University of Pittsburgh, USA
Prof. Chakra Chennubhotla, University of Pittsburgh, USA
Prof. Akio Kitao (北尾 彰朗), University of Tokyo, Japan
Dr Kazuhiro Takemura (竹村 和浩), University of Tokyo, Japan
Dr Sakuraba Shun (桜庭 俊), Kyoto University, Japan
Prof. Nobuhiro Gō (郷 信広), Spring 8, Japan
Prof. Yasumasa Joti (城地 保昌), Spring 8, Japan
Prof. Qing Zhang, University of North Carolina, Chapel Hill, USA
Dr Choon-Ping Chng, A* Institute of High Performance Computing, Singapore
Prof. Carmay Lim (林小喬), Academia Sinica, Taiwan
Prof. Kong-Yao Chang (張功耀), National Chung Hsing University, Taiwan
Prof. Jin-Der Wen (溫進德), National Taiwan University, Taiwan
Prof. Danny Shang-Te Hsu (徐尚德), Academia Sinica, Taiwan

Selected Publications:

Justin Chan, Hong-Rui Lin, Kazuhiro Takemura, Kai-Chun Chang, Yuan-Yu Chang, Yasumasa Joti, Akio Kitao* and Lee-Wei Yang* (2020) An efficient timer and sizer of biomacromolecular motions. Structure, 28, 259-269

Justin Chan, Jinhao Zou, Chi-Hong Chang Chien, Rong-Long Pan, Lee-Wei Yang* (2020) DR-SIP: Protocols for Higher Order Structure Modeling with Distance Restraints- and Cyclic Symmetry-Imposed Packing. Bioinformatics, 36, 449–461 (accepted)

 Kai-Chun Chang , Emmanuel Oluwatobi Salawu, Yuan-Yu Chang, Jin-Der Wen and Lee-Wei Yang* (2019) Resolution-exchanged structural modeling and simulations jointly unravel that subunit rolling underlies the mechanism of programmed ribosomal frameshifting. Bioinformatics 35, 945-952. doi:10.1093/bioinformatics/bty762.

Pei-Feng Liu†; Kun-Lin Tsai†; Chien-Jen Hsu; Wei-Lun Tsai; Jin-Shiung Cheng; Hsueh-Wei Chang; Chung-Wai Shiau; Yih-Gang Goan; Ho-Hsing Tseng; Chih-Hsuan Wu; John C. Reed; Lee-Wei Yang*; Chih-Wen Shu*(2018) Drug Repurposing Screening Identifies Tc as an ATG4B Inhibitor that Suppresses Autophagy and Sensitizes Cancer Cells to Chemotherapy, Theranostics 8, 830-845 http://www.thno.org/v08p0830.htm

Hongchun Li†, Yuan-Yu Chang†, Ji Young Lee, Ivet Bahar* and Lee-Wei Yang* (2017). DynOmics: Dynamics of Structural Proteome and Beyond. Nucleic Acids Research, 45, W374–W380. doi: 10.1093/nar/gkx385.

Jui-Chieh Yin, Chun-Hsien Fei, Yen-Chen Lo, Yu-Yuan Hsiao, Jyun-Cyuan Chang, Jay C Nix, Yuan-Yu Chang, Lee-Wei Yang*, I-Hsiu Huang*, Shuying Wang* (2016) Structural insights into substrate recognition by Clostridium difficile sortase. Frontiers in Cellular and Infection Microbiology. 6, article 160. doi: 10.3389/fcimb.2016.00160

Chandrasekaran, Aravind, Chan, Justin, Lim, Carmay*, Yang, Lee-Wei* (2016) Protein dynamics and contact topology reveal protein-DNA binding orientation. Journal of Chemical Theory and Computation 12, 5269–5277. DOI: 10.1021/acs.jctc.6b00688

Chin-Chi Chang, Md Imran  Khan, Kun-Lin Tsai, Hongchun Li, Lee-Wei Yang* Ruey-Hwang Chou* and Chin Yu* (2016) Blocking the interaction between S100A9 and RAGE V domain using CHAPS molecule: A novel route to drug development against cell proliferation. BBA – Proteins and Proteomics doi: 10.1016/j.bbapap.2016.08.008

Wen-Ting Chen, Wen-Yang Huang, Ting Wen, Emmanuel Oluwatobi Salawu, Dongli Wang, Yi-Zong Lee, Yuan-Yu Chang, Lee-Wei Yang, Shih-Che Sue, Xinquan Wang, and Hsien-Sheng Yin (2016) Structure and function of chicken interleukin-1 beta mutants: uncoupling of receptor binding and in vivo biological activity. Scientific Reports

Hongchun Li, Yuan-Yu Chang, Lee-Wei Yang* and Ivet Bahar* (2016) iGNM 2.0: The Gaussian Network Model Database for Biomolecular Structural Dynamics. Nucleic Acids Research, 44, D415-D422

Hongchun Li, Shun Sakuraba, Aravind Chandrasekaran and Yang, L-W.* (2014) Molecular binding sites are located near theinterface of intrinsic dynamics domains (IDDs) J.Chem. Inf. Model. 54 (8), 2275–2285.

Yang, L.-W.*, Akio Kitao, Bang-Chieh Huang and Nobuhiro Gō (2014) Ligand-induced Protein Responses and Mechanical Signal Propagationdescribed by Linear Response Theories. Biophys J. 107, 1415-1425.

Yang, L.-W.* (2011) Models with energy penalty on Inter-residue rotation address insufficiencies of conventional elastic network models. Biophys J, 100(7), 1784-1793.

Bahar, I., Lezon, T.R., Yang, L.-W. and Eyal. E. (2010) Global Dynamics of Proteins: Bridging Between Structure and Function. Annual Review of Biophysics, 39, 23-42.

Yang, L.-W.*, Eyal, E., Bahar, I. and Kitao, A. (2009) Principal Component Analysis of Native Ensembles of Biomolecular Structures (PCA_NEST): Insights into Functional Dynamics. Bioinformatics, 25, 606-614 http://ignm.ccbb.pitt.edu/oPCA_Online.htm

Yang, L.-W., Eyal, E., Chennubhotla, C., Jee, J., Gronenborn, AM., Bahar, I. (2007) Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-ray Data with Computational Predictions. Structure, 15, 741-749

Eyal, E., Yang, L.-W., Bahar, I. (2006) Anisotropic Network Model: a new web interface. http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi Bioinformatics, 22, 2619-2627.

Yang, L.-W., Rader, A.J., Liu, X., Jursa, C.J., Chen S.C., Karimi, H. and Bahar, I. (2006) oGNM: A protein dynamics online calculation engine using the Gaussian Network Model http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm Nucleic Acids Res, 34, W24-31

Yang, L.-W. and Bahar, I. (2005) Coupling between catalytic site and collective dynamics: A requirement for mechanochemical activity of enzymes. Structure, 13, 893-904 An interview regarding this article Preview and comments by Dmitry A. Kondrashov and George N. Phillips, Jr. “Molecular Mastication Mechanics” (2005) Structure, 13, 836-837

Yang, L.-W.*, Liu, X., Jursa, C.J., Holliman, M., Rader, A.J., Karimi, H.A., Bahar, I. (2005) iGNM: a database of protein functional motions based on Gaussian Network Model. http://ignm.ccbb.pitt.edu/ Bioinformatics, 21, 2978-2987.

Seki, M., Masutani, C., Yang, L.-W., Schuffert, A., Iwai, S., Bahar, I. and Wood, R.D. (2004) High efficiency bypass of DNA damage by a single human DNA polymerase. EMBO J. 23, 4484-4494.

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