Lab Publications
(#Co-first author, *Corresponding author. Research profile in Google Scholar, ResearcherID, and ResearchGate)
    2017
  1. Mary Ashley Rimmer, Owen W. Nadeau, Jianyi Yang, Antonio Artigues, Yang Zhang, Gerald M. Carlson
    The structure of the large regulatory alpha subunit of phosphorylase kinase examined by modeling and hydrogen-deuterium exchange
    Protein Science, in press (2017).
    [PDF]
  2. 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]
  3. 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]
  4. 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]
  5. 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
  6. 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]
  7. 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]
  8. 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]
  9. 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
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. 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
  16. 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]
  17. 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]
  18. 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]
  19. 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]
  20. 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
  21. 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]
  22. 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]
  23. 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]
  24. 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
  25. 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]
  26. 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
  27. 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]
  28. 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
  29. 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]
  30. 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]
  31. Xin Chen, Jianyi Yang
    Constructing consensus genetic maps in comparative analysis
    Journal of Computational Biology, 17: 1561-1573 (2010).
    [PDF] [Server]
    2009
  32. 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]
  33. 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
  34. 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]
  35. 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
  36. 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]