Lab Publications
(#Co-first author, *Corresponding author. Research profile in Google Scholar, ResearcherID, and ResearchGate)
    2017
  1. Yang Li, Jianyi Yang*
    Structural and sequence similarity makes a significant impact on machine learning-based scoring functions for protein-ligand interactions
    Journal of Chemical Information and Modeling, 57: 1007-1012 (2017).
    [PDF] [Supporting Information] [Datasets]
  2. Qi Wu, Zuguo Yu*, Jianyi Yang*
    DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method
    Bioinformatics, 33: 2214-2215. (2017).
    [PDF] [Supporting Information] [Server]
  3. Qiqige Wuyun#, Wei Zheng#, Zhenling Peng, Jianyi Yang*
    A large-scale comparative assessment of methods for residue-residue contact prediction
    Briefings in Bioinformatics, in press (2017).
    [PDF] [Supporting Information] [Datasets]
  4. Jiaqi Xia, Zhenling Peng, Dawei Qi, Hongbo Mu*, Jianyi Yang*
    An ensemble approach to protein fold classification by integration of template-based assignment and support vector machine classifier
    Bioinformatics, 33: 863-887 (2017).
    [PDF] [Supporting Information] [Server]
    2016
  5. Xiuzhen Hu, Qiwen Dong, Jianyi Yang, Yang Zhang
    Recognizing metal and acid radical ion binding sites by integrating ab initio modeling with template-based transferals
    Bioinformatics, 32: 3260-3269 (2016).
    [PDF] [Server]
  6. Jianyi Yang, Yan Wang, Yang Zhang
    ResQ: An approach to unified estimation of B-factor and residue-specific error in protein structure prediction
    Journal of Molecular Biology, 428: 693-701 (2016).
    [PDF] [Supporting Information] [Server]
  7. Jianyi Yang, Wenxuan Zhang, Haoji He, Sara Elizabeth Walker, Hongjiu Zhang, Brandon Govindarajoo, Jouko Virtanen, Zhidong Xue, Hongbin Shen, Yang Zhang
    Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade
    Proteins: Structure, Function, and Bioinformatics, 84: 233-246 (2016).
    [PDF]
  8. Wenxuan Zhang, Jianyi Yang, Haoji He, Sara Elizabeth Walker, Hongjiu Zhang, Brandon Govindarajoo, Jouko Virtanen, Zhidong Xue, Hongbin Shen, Yang Zhang
    Integration of QUARK and I-TASSER for ab initio protein structure prediction in CASP11
    Proteins: Structure, Function, and Bioinformatics, 84: 76-86 (2016).
    [PDF] [Supporting Information]
    2015
  9. Zhonghua Wu, Gang Hu, Jianyi Yang, Zhenling Peng, Vladimir N. Uversky, Lukasz Kurgan
    In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces
    FEBS Letters, 589: 2561-2569 (2015).
    [PDF]
  10. Jianyi Yang*, Yang Zhang*
    Protein structure and function prediction using I-TASSER protocol
    Current Protocols in Bioinformatics, 52: 5.8.1-5.8.15 (2015).
    [PDF] [Server]
  11. Wallace Chan, Hongjiu Zhang, Jianyi Yang, Jeffrey Brender, Junguk Hur, Arzucan Ozgur, Yang Zhang
    GLASS: a comprehensive database for experimentally-validated GPCR-ligand associations
    Bioinformatics, 31: 3035-3042 (2015).
    [PDF] [Supporting Information] [Database]
  12. Jian Zhang#, Jianyi Yang#, Richard Jang, Yang Zhang
    GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome
    Structure, 23: 1538-1549 (2015).
    [PDF] [Supporting Information] [Server] [Database]
  13. Jianyi Yang*, Yang Zhang*
    I-TASSER server: new development for protein structure and function predictions
    Nucleic Acids Research, 43: W174-W181 (2015).
    [PDF] [Supporting Information] [Server] [This paper was a "Highly Cited Paper" in Web of Science]
  14. Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang
    The I-TASSER Suite: Protein structure and function prediction
    Nature Methods, 12: 7-8 (2015).
    [PDF] [Supporting Information] [Server]
    2014
  15. Shu Quan, Lili Wang, Evgeniy V Petrotchenko, Karl AT Makepeace, Scott Horowitz, Jianyi Yang, Yang Zhang, Christoph H Borchers, James CA Bardwell
    Super Spy variants implicate flexibility in chaperone action
    eLife, 3: e01584 (2014).
    [PDF]
  16. Irina Kufareva, Vsevolod Katritch, Participants of GPCR Dock 2013 (include Jianyi Yang), Raymond C Stevens, Ruben Abagyan
    Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges
    Structure, 22: 1120-1139 (2014).
    [PDF]
  17. Derek S Borgwardt, Aaron D. Martin, Jonathan R Van Hemert, Jianyi Yang, Carol L Fischer, Erica N Recker, Prashant R Nair, Robinson Vidva, Shwetha Chandrashekaraiah, Ann Progulske-Fox, David Drake, Joseph E Cavanaugh, Shireen Vali, Yang Zhang, Kim A Brogden
    Histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and alters HagB-induced chemokine responses
    Scientific Reports, 4: 3904 (2014).
    [PDF]
  18. Grant Holdren#, David Rosenthal#, Jianyi Yang#, Amber Bates, Carol Fischer, Yang Zhang, Nicole Brogden, Kim Brogden
    Antimicrobial activity of chemokine CXCL10 for dermal and oral microorganisms
    Antibiotics, 3: 527-539 (2014).
    [PDF]
  19. Zuguo Yu, Vo Anh, Jianyi Yang, Shaoming Zhu
    Fractal related methods for predicting protein structure classes and functions
    Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics, Chapter16: 317-337 (2014).
    [PDF]
    2013
  20. Jianyi Yang, Ambrish Roy, Yang Zhang
    BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions
    Nucleic Acids Research, 41: D1096-D1103 (2013).
    [PDF] [Database]
  21. Jianyi Yang, Ambrish Roy, Yang Zhang
    Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment
    Bioinformatics, 29: 2588-2595 (2013).
    [PDF] [Supporting Information] [Server] [This paper was a "Highly Cited Paper" in Web of Science]
  22. Renxiang Yan, Dong Xu, Jianyi Yang, Sara Walker, Yang Zhang
    A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction
    Scientific Reports, 3: 2619 (2013).
    [PDF] [Supporting Information]
  23. Jiaqi Fu, Song Ling, Ying Liu, Jianyi Yang, Shirly Naveh, Margaret Hannah, Chaim Gilon, Yang Zhang, Joseph Holoshitz
    A small shared epitope-mimetic compound potently accelerates osteoclast-mediated bone damage in autoimmune arthritis
    The Journal of Immunology, 191: 2096-2103 (2013).
    [PDF]
    2012
  24. Ambrish Roy, Jianyi Yang, Yang Zhang
    COFACTOR: An accurate comparative algorithm for structure-based protein function annotation
    Nucleic Acids Research, 40: W471-W477 (2012).
    [PDF] [Supporting Information] [Server] [This paper was a "Highly Cited Paper" in Web of Science]
  25. Heng Lian, Xin Chen, Jianyi Yang
    Identification of partially linear structure in additive models with an application to gene expression prediction from sequences
    Biometrics, 68: 437-445 (2012).
    [PDF]
    2011
  26. Jianyi Yang*, Xin Chen
    Improving taxonomy-based protein fold recognition by using global and local features
    Proteins: Structure, Function, and Bioinformatics, 79: 2053-2064 (2011).
    [PDF] [Supporting Information] [Server]
  27. Jianyi Yang*, Xin Chen
    A consensus approach to predicting protein contact map via logistic regression
    Lecture Notes in Bioinformatics, Springer Verlag, 6674: 136-147 (2011).
    [PDF] [Supporting Information]
    2010
  28. Zhenling Peng#, Jianyi Yang*#, Xin Chen
    An improved classification of G-protein-coupled receptors using sequence-derived features
    BMC Bioinformatics, 11: 420 (2010).
    [PDF] [Server] [This paper was "highly accessed" in BMC Bioinformatics]
  29. Jianyi Yang*, Zhenling Peng, Xin Chen
    Prediction of protein structural classes for low-homology sequences based on predicted secondary structure
    BMC Bioinformatics, 11: S9 (2010).
    [PDF] [Server]
  30. Xin Chen, Jianyi Yang
    Constructing consensus genetic maps in comparative analysis
    Journal of Computational Biology, 17: 1561-1573 (2010).
    [PDF] [Server]
    2009
  31. Jianyi Yang*#, Zhenling Peng#, Zuguo Yu, Ruijie Zhang, Vo Anh, Desheng Wang
    Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation
    Journal of Theoretical Biology, 257: 618-626 (2009).
    [PDF] [This paper was one of the most cited JTB papers published since 2009]
  32. Jianyi Yang, Zuguo Yu, Vo Anh
    Clustering structures of large proteins using multifractal analyses based on 6-letters model and hydrophobicity scale of amino acids
    Chaos, Solitons & Fractals, 40: 607-620 (2009).
    [PDF]
    2008
  33. Jianyi Yang, Yu Zhou, Zuguo Yu, Vo Anh, Liqian Zhou
    Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides
    BMC Bioinformatics, 9: 113 (2008).
    [PDF]
  34. Jianyi Yang, Zuguo Yu, Vo Anh
    Protein structure classification based on chaos game representation and multifractal analysis
    Proceedings of the 2008 Fourth International Conference on Natural Computation (ICNC'08), 665-669 (2008).
    [PDF]
    2007
  35. Jianyi Yang, Zuguo Yu, Vo Anh
    Correlations between designability and various structural characteristics of protein lattice models
    Journal of Chemical Physics, 126: 195101 (2007).
    [PDF]