dr. L. (Li) Xue
Gegenereerd op 2017-09-25 00:56:24

Curriculum vitae Download PDF

Dr. L. Xue Studied at Pattern Recognition (artificial intelligence) and Image Processing for her Master's degree at Shanghai Jiao Tong University (China). She gained her PhD degree in Bioinformatics at Iowa State University (USA). At the sametime, Understanding The Importance of statistics in her research in machine learning, she obtained a minor in statistics from the prestigious statistics program at Iowa State University. in 2014, Dr. Xue was Awarded by a prestigious Veni award from the Dutch Research Council, and joined Prof. Alexandre Bonvin's lab at Utrecht University (NL), a world-leading group in biomolecular docking. Dr. Xue is dedicated to bridging structural biology and artificial intelligence to better understand the molecular basis of diseases and to rationalize drug design. 

Gegenereerd op 2017-09-25 00:56:25

Peer-reviewed JOURNAL PAPERS

(* Corresponding author)

  1. Vangone A., Rodrigues J.P.G.L.M., Xue L., et al., Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI, accepted.
  2. Xue, L. C., et al., (2016). PRODIGY: a web server for predicting the binding affinity of protein-protein complexes, Bioinformatics, btw514.
  3. Lensink, M. F., Velankar, S., Kryshtafovych, A., … L. C. Xue, ... & Grudinin, S. (2016). Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins: Structure, Function, and Bioinformatics.
  4. Xue, L. C.*, Rodrigues, J. P., Dobbs, D., Honavar, V., & Bonvin, A. M. (2016). Template-based protein–protein docking exploiting pairwise interfacial residue restraints. Briefings in Bioinformatics, bbw027.
  5. Jung, S., Fischer, J., Spudy, B., Kerkow, T., Sönnichsen, F. D., Xue, L., ... & Grötzinger, J. (2016). The solution structure of the kallikrein-related peptidases inhibitor SPINK6. Biochemical and biophysical research communications, 471(1), 103-108.
  6. Xue, L. C.*, Dobbs, D., Bonvin, A. M., & Honavar, V. (2015). Computational prediction of protein interfaces: A review of data driven methods. FEBS letters, 589(23), 3516-3526.
  7. Walia, R., Xue, L. C., Wilkins, K., El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2014), RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins. PloS One 9.5: e97725.
  8. Xue, L. C., Jordan, R. A., El-Manzalawy, Y., Dobbs, D., & Honavar, V. (2013). DockRank: ranking docked conformations using partner-specific sequence homology based protein interface prediction. Proteins: Structure, Function, and Bioinformatics, doi: 10.1002/prot.24370. A figure selected for the back cover of the Feburary Issue of Proteins.
  9. Xue, L. C.*, Dobbs, D., and Honavar, V. (2011), HomPPI:  A class of sequence homology based protein-protein interface prediction methods. BMC Bioinformatics, 12: 244.
  10. Zhang, G. L., Ansari, H. R., Bradley, P., Cawley, G. C., Hertz, T., Hu, X., Jojic, N., Kim, Y., Kohlbacher, O., Lund, O., Lundegaard, C., Magaret, C. A., Nielsen, M., Papadopoulos, H., Raghava, G. P., Tal, V. S., Xue, L. C., Yanover, C., Zhu, S., Rock, M. T., Crowe, J. E., Panayiotou, C., Polycarpou, M. M., Duch, W., and Brusic, V. (2011), Machine learning competition in immunology - Prediction of HLA class I binding peptides. J Immunol Methods, 374 (1-2): 1-4.
  11. 11.  Xue, L., Petersen, L., Broderick, S., Narasimhan, B., and Rajan, K. (2011), Identifying factors controlling protein release from combinatorial biomaterial libraries via hybrid data mining methods. ACS Combinatorial Science, 13: 50-58.
  12. Petersen, L. K., Xue, L., Wannemuehler, M. J., Rajan, K., and Narasimhan, B. (2009), The simultaneous effect of polymer chemistry and device geometry on the in vitro activation of murine dendritic cells. Biomaterials, 30: 5131-5142.
  13. Lee, J. H., Hamilton, M., Gleeson, C., Caragea, C., Zaback, P., Sander, J. D., Xue, L., Wu, F., Terribilini, M., Honavar, V., and Dobbs, D. (2008), Striking similarities in diverse telomerase proteins revealed by combining structure prediction and machine learning approaches. Pac Symp Biocomput, 501-12.
  14. Liu, H., Yang, J., Wang, M., Xue, L., and Chou, K. C. (2005), Using Fourier spectrum analysis and pseudo amino acid composition for prediction of membrane protein types. The Protein Journal, 24: 385-389.


  1. Xue, L. C., Jordan, R., El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2011), Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: A preliminary study. In:  Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM, 441–445. Best Poster Award
  2. Xue, L. C., Walia, R., EL-Manzalawy, Y., Dobbs, D., and Honavar, V. (2011), Improved prediction of protein-RNA interfaces using combined sequence homology and machine learning methods: A preliminary study. In Proceedings of the 2nd ACM International Conference On Bioinformatics and Computational Biology (ACM-BCB), 556-558. (ACM – Association for Computing Machinery)
  3. Yao, L., Xue, L., and Liu, H. (2007), A novel approach predicting the signal peptides and their cleavage sites. In: Proceedings of International Conference on Bioinformatics & Biomedical Engineering, 8: 391-393.
  4. Li, G. Z., Yang, J., Liu, G.P., and Xue, L. (2004), Feature selection for multi-class problems using support vector machines. Lecture Notes In Artificial Intelligence, 3157, 292-300.


All publications
  2017 - Scholarly publications
Vangone, A, Garcia Lopes Maia Rodrigues, João, Xue, L C, van Zundert, G C P, Geng, C, Kurkcuoglu Soner, Zeynep, Nellen, M, Narasimhan, S, Karaca, E, van Dijk, M, Melquiond, A S J, Visscher, K M, Trellet, M, Kastritis, P L & Bonvin, A M J J (2017). Sense and simplicity in HADDOCK scoring - Lessons from CASP-CAPRI round 1. Proteins: Structure, Function and Genetics, 85 (3), (pp. 417–423). © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc..
  2016 - Scholarly publications
Lensink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen You, Schneidman-Duhovny, Dina, Sali, Andrej, Segura, Joan, Fernandez-Fuentes, Narcis, Viswanath, Shruthi, Elber, Ron, Grudinin, Sergei, Popov, Petr, Neveu, Emilie, Lee, Hasup, Baek, Minkyung, Park, Sangwoo, Heo, Lim, Rie Lee, Gyu, Seok, Chaok, Qin, Sanbo, Zhou, Huan Xiang, Ritchie, David W., Maigret, Bernard, Devignes, Marie Dominique, Ghoorah, Anisah, Torchala, Mieczyslaw, Chaleil, Raphaël A G, Bates, Paul A., Ben-Zeev, Efrat, Eisenstein, Miriam, Negi, Surendra S., Weng, Zhiping, Vreven, Thom, Pierce, Brian G., Borrman, Tyler M., Yu, Jinchao, Ochsenbein, Françoise, Guerois, Raphaël, Vangone, Anna, Garcia Lopes Maia Rodrigues, João, van Zundert, Gydo, Nellen, Mehdi, Xue, Li, Karaca, Ezgi, Melquiond, Adrien S J, Visscher, Koen, Kastritis, Panagiotis L., Bonvin, Alexandre M J J, Xu, Xianjin, Qiu, Liming, Yan, Chengfei, Li, Jilong, Ma, Zhiwei, Cheng, Jianlin, Zou, Xiaoqin, Shen, Yang, Peterson, Lenna X., Kim, Hyung Rae, Roy, Amit, Han, Xusi, Esquivel-Rodriguez, Juan, Kihara, Daisuke, Yu, Xiaofeng, Bruce, Neil J., Fuller, Jonathan C., Wade, Rebecca C., Anishchenko, Ivan, Kundrotas, Petras J., Vakser, Ilya A., Imai, Kenichiro, Yamada, Kazunori, Oda, Toshiyuki, Nakamura, Tsukasa, Tomii, Kentaro, Pallara, Chiara, Romero-Durana, Miguel, Jiménez-García, Brian, Moal, Iain H., Férnandez-Recio, Juan, Joung, Jong Young, Kim, Jong Yun, Joo, Keehyoung, Lee, Jooyoung, Kozakov, Dima, Vajda, Sandor, Mottarella, Scott, Hall, David R., Beglov, Dmitri, Mamonov, Artem, Xia, Bing, Bohnuud, Tanggis, Del Carpio, Carlos A., Ichiishi, Eichiro, Marze, Nicholas, Kuroda, Daisuke, Roy Burman, Shourya S., Gray, Jeffrey J., Chermak, Edrisse, Cavallo, Luigi, Oliva, Romina, Tovchigrechko, Andrey & Wodak, Shoshana J. (2016). Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling - A CASP-CAPRI experiment. Proteins: Structure, Function and Genetics, 84 (S1), (pp. 323-348) (26 p.).
Xue, Li, Garcia Lopes Maia Rodrigues, João, Kastritis, Panagiotis L, Bonvin, Alexandre Mjj & Vangone, Anna (01.12.2016). PRODIGY - a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics, 32 (23), (pp. 3676-3678) (3 p.). © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com..
Xue, Li C, Garcia Lopes Maia Rodrigues, João, Dobbs, Drena, Honavar, Vasant & Bonvin, Alexandre M J J (2016). Template-based protein-protein docking exploiting pairwise interfacial residue restraints. Briefings in Bioinformatics, (pp. 1-9) (10 p.). © The Author 2016. Published by Oxford University Press..
Jung, Sascha, Fischer, Jan, Spudy, Björn, Kerkow, Tim, Sönnichsen, Frank D, Xue, Li, Bonvin, Alexandre M J J, Goettig, Peter, Magdolen, Viktor, Meyer-Hoffert, Ulf & Grötzinger, Joachim (29.01.2016). The solution structure of the kallikrein-related peptidases inhibitor SPINK6. Biochemical and Biophysical Research Communications, 471 (1), (pp. 103-108) (6 p.). Copyright © 2016. Published by Elsevier Inc..
  2015 - Scholarly publications
Xue, Li, Dobbs, Drena, Bonvin, Alexandre M J J & Honavar, Vasant (30.11.2015). Computational prediction of protein interfaces - A review of data driven methods. FEBS Letters, 589 (23), (pp. 3516-26) (11 p.). Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved..
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Gegenereerd op 2017-09-25 00:56:25
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Gegenereerd op 2017-09-25 00:56:25
Full name
dr. L. Xue Contact details
Hugo R. Kruytgebouw

Padualaan 8
Room -
The Netherlands


Visiting address:
Nicolaas Bloembergengebouw, room 1.18
Padualaan 8, 3584 CH Utrecht
Accessible via Kruyt Building -> first floor -> bridge to Sjoerd Groenman Building
See http://www.nmr.chem.uu.nl/Main/contact.php

Postal address:
Utrecht University, NMR
Padualaan 8, 3584 CH Utrecht, The Netherlands

Phone: +31 30 253 3641


Gegenereerd op 2017-09-25 00:56:25
Last updated 14.08.2017