Lab Publications
(#Co-first author, *Corresponding author. Research profile in Google Scholar and Web of Science)
    2024
    		2. Hong Wei, Wenkai Wang, Zhenling Peng*, Jianyi Yang*
    Q-BioLiP: a comprehensive resource for quaternary structure-based protein-ligand interactions
    Genomics, Proteomics & Bioinformatics, in press (2024).
    [PDF] [Supporting Information] [Server]
    		3. Zongyang Du, Zhenling Peng, Jianyi Yang*
    RNA threading with secondary structure and sequence profile
    Bioinformatics, 40: btae080 (2024).
    [PDF] [Supporting Information] [Server]
    		4. Xiaochen Bai*, Tamir Gonen*, Angela Gronenborn*, Anastassis Perrakis*, Andrea Thorn*, Jianyi Yang*
    Challenges and opportunities in macromolecular structure determination
    Nature Reviews Molecular Cell Biology, 25: 7-12 (2024).
    [PDF] [Invited Viewpoint]
    		5. Wei Liu, Ziye Wang, Ronghui You, Chenghan Xie, Hong Wei, Yi Xiong, Jianyi Yang*, Shanfeng Zhu*
    PLMSearch: Protein language model powers accurate and fast sequence search for remote homology
    Nature Communications, 15: 2775 (2024).
    [PDF] [Supporting Information]
    		6. Bintao He, Fa Zhang, Chenjie Feng, Jianyi Yang, Xin Gao*, Renmin Han*
    Accurate global and local 3D alignment of cryo-EM density maps using local spatial structural features
    Nature Communications, 15: 1593 (2024).
    [PDF] [Supporting Information]
    		7. Junhai Qi, Chenjie Feng, Yulin Shi, Jianyi Yang, Fa Zhang, Guojun Li*, Renmin Han*
    FP-Zernike: an open-source structural database construction toolkit for fast structure retrieval
    Genomics, Proteomics & Bioinformatics, in press (2024).
    [PDF] [Supporting Information]
    2023
    		8. Wenkai Wang#, Chenjie Feng#, Renmin Han#, Ziyi Wang, Lisha Ye, Zongyang Du, Hong Wei, Fa Zhang*, Zhenling Peng*, Jianyi Yang*
    trRosettaRNA: automated prediction of RNA 3D structure with transformer network
    Nature Communications, 14: 7266 (2023).
    [PDF] [Supporting Information] [Server]
    		9. Zhenling Peng#, Wenkai Wang#, Hong Wei#, Xiaoge Li, Jianyi Yang*
    Improved protein structure prediction with trRosettaX2, AlphaFold2, and optimized MSAs in CASP15
    Proteins: Structure, Function, and Bioinformatics, 91: 1704-1711 (2023).
    [PDF] [Invited CASP15 article]
    		10. Kun Zhu#, Hong Su#, Zhenling Peng, Jianyi Yang*
    A unified approach to protein domain parsing with inter-residue distance matrix
    Bioinformatics, 39: btad070 (2023).
    [PDF] [Supporting Information] [Server]
    2022
    		11. Wenkai Wang, Zhenling Peng, Jianyi Yang*
    Single-sequence protein structure prediction using supervised transformer protein language models
    Nature Computational Science, 2: 804-814 (2022).
    [PDF] [Supporting Information] [Server] [Nature CS Featured Article] [ Nature CS News & Views ] [ Nature Methods Research Highlight ] [ Nature Methods Editorial ]
    		12. Zhenling Peng#, Wenkai Wang#, Renmin Han#, Fa Zhang*, Jianyi Yang*
    Protein structure prediction in the deep learning era
    Current Opinion in Structural Biology, 77: 102495 (2022).
    [PDF] [Invited review]
    		13. Zongyang Du, Zhenling Peng, Jianyi Yang*
    Toward the assessment of predicted inter-residue distance
    Bioinformatics, 38: 962-969 (2022).
    [PDF] [Supporting Information] [Server]
    		14. Xingjian Chen, Zifan Zhu, Weitong Zhang, Yuchen Wang, Fuzhou Wang, Jianyi Yang, Ka-Chun Wong*
    Human disease prediction from microbiome data by multiple feature fusion and deep learning
    iScience, 25: 104081 (2022).
    [PDF]
    		15. Syed Nabeel-Shah, Hyunmin Lee, Nujhat Ahmed, Giovanni L. Burke, Shaghayegh Farhangmehr, Kanwal Ashraf, Shuye Pu, Ulrich Braunschweig, Guoqing Zhong, Hong Wei, Hua Tang, Jianyi Yang, Edyta Marcon, Benjamin J. Blencowe, Zhaolei Zhang, Jack F. Greenblatt*
    SARS-CoV-2 Nucleocapsid protein attenuates stress granules and interacts with mRNAs to impair host stress response
    iScience, 25: 103562 (2022).
    [PDF] [Supporting Information]
    		16. Saisai Sun, Jianyi Yang, Zhaolei Zhang*
    RNALigands: a database and web server for RNA-ligand interactions
    RNA, 28: 115-122 (2022).
    [PDF] [Faculty Opinions ]
    		17. Yajun Dai, Yang Li, Liping Wang, Zhenling Peng, Jianyi Yang*
    On monomeric and multimeric structures-based protein-ligand interactions
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19: 569-574 (2022).
    [PDF] [Supporting Information]
    2021
    		18. Hong Su#, Wenkai Wang#, Zongyang Du, Zhenling Peng, Shang-Hua Gao, Ming-Ming Cheng, Jianyi Yang*
    Improved protein structure prediction using a new multi-scale network and homologous templates
    Advanced Science, 8, 2102592 (2021).
    [PDF] [Supporting Information] [Server]
    		19. Zongyang Du#, Hong Su#, Wenkai Wang, Lisha Ye, Hong Wei, Zhenling Peng, Ivan Anishchenko, David Baker, Jianyi Yang*
    The trRosetta server for fast and accurate protein structure prediction
    Nature Protocols, 16: 5634-5651 (2021).
    [PDF] [Supporting Information] [Server] [ Nature Protocols Featured Protocol] [ Hot Paper ]
    		20. Andriy Kryshtafovych*, John Moult, Wendy M. Billings, Dennis Della Corte, Krzysztof Fidelis, Sohee Kwon, Kliment Olechnovi, Chaok Seok, Ceslovas Venclovas, Jonghun Won, CASP-COVID participants (including Zongyang Du, Lisha Ye, Jianyi Yang)
    Modeling SARS-CoV-2 proteins in the CASP-commons experiment
    Proteins: Structure, Function, and Bioinformatics, 89: 1987-1996 (2021).
    [PDF]
    		21. Xingjian Chen, Lingjing Liu, Weitong Zhang, Jianyi Yang, Ka-Chun Wong*
    Human host status inference from temporal microbiome changes via recurrent neural networks
    Briefings in Bioinformatics, 22: bbab223 (2021).
    [PDF] [Supporting Information]
    		22. Ruiyang Song#, Baixin Cao#, Zhenling Peng, Christopher J. Oldfield, Lukasz Kurgan*, Ka-Chun Wong, Jianyi Yang*
    Accurate sequence-based prediction of deleterious nsSNPs with multiple sequence profiles and putative binding residues
    Biomolecules, 11:1337 (2021).
    [PDF] [Supporting Information] [Server]
    		23. Hong Wei, Boling Wang, Jianyi Yang, Jianzhao Gao*
    RNA flexibility prediction with sequence profile and predicted solvent accessibility
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18: 2017-2019 (2021).
    [PDF] [Server]
    		24. Lisha Ye, Peikun Wu, Zhenling Peng, Jianzhao Gao, Jian Liu, Jianyi Yang*
    Improved estimation of model quality using predicted inter-residue distance
    Bioinformatics, 37: 3752-3759 (2021).
    [PDF] [Supporting Information] [Server]
    		25. Hong Su, Zhenling Peng*, Jianyi Yang*
    Recognition of small molecule-RNA binding sites using RNA sequence and structure
    Bioinformatics, 37: 36-42 (2021).
    [PDF] [Supporting Information] [Server]
    		26. Saisai Sun, Wenkai Wang, Zhenling Peng, Jianyi Yang*
    RNA inter-nucleotide 3D closeness prediction by deep residual neural networks
    Bioinformatics, 37: 1093-1098 (2021).
    [PDF] [Supporting Information] [Server]
    2020
    		27. Jianyi Yang#, Ivan Anishchenko#, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker*
    Improved protein structure prediction using predicted interresidue orientations
    PNAS, 117: 1496-1503 (2020).
    [PDF] [Supporting Information] [Server] [ Hot Paper] [ Nature Methods Research Highlight] [ Faculty Opinions ]
    		28. Kui Wang, Gang Hu, Zhonghua Wu, Hong Su, Jianyi Yang, Lukasz Kurgan*
    Comprehensive survey and comparative assessment of RNA-binding residue predictions with analysis by RNA type
    International Journal of Molecular Sciences, 21: 6879 (2020).
    [PDF]
    		29. Zongyang Du#, Shuo Pan#, Qi Wu, Zhenling Peng, Jianyi Yang*
    CATHER: a novel threading algorithm with predicted contacts
    Bioinformatics, 36: 2119-2125 (2020).
    [PDF] [Supporting Information] [Server]
    		30. Qi Wu, Zhenling Peng*, Ivan Anishchenko, Qian Cong, David Baker, Jianyi Yang*
    Protein contact prediction using metagenome sequence data and residual neural networks
    Bioinformatics, 36: 41-48 (2020).
    [PDF] [Supporting Information] [Server]
    2019
    		31. Hong Su, Mengchen Liu, Saisai Sun, Zhenling Peng*, Jianyi Yang*
    Improving the prediction of protein-nucleic acids binding residues via multiple sequence profiles and the consensus of complementary algorithms
    Bioinformatics, 35:930-936 (2019).
    [PDF] [Supporting Information] [Server]
    		32. Saisai Sun, Qi Wu, Zhenling Peng*, Jianyi Yang*
    Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles
    Bioinformatics, 35:1686-1691 (2019).
    [PDF] [Supporting Information] [Server]
    		33. Akila Katuwawala, Zhenling Peng, Jianyi Yang, Lukasz Kurgan*
    Computational prediction of MoRFs, short disorder-to-order transitioning protein binding regions
    Computational and Structural Biotechnology Journal, 17: 454-462 (2019).
    [PDF]
    2018
    		34. Evan N. Feinberg*, Debnil Sur, Zhenqin Wu, Brooke E. Husic, Huanghao Mai, Yang Li, Saisai Sun, Jianyi Yang, Bharath Ramsundar, Vijay S. Pande*
    PotentialNet for molecular property prediction
    ACS Central Science, 4: 1520-1530 (2018).
    [PDF]
    		35. Zijuan Zhao, Zhenling Peng*, Jianyi Yang*
    Improving sequence-based prediction of protein-peptide binding residues by introducing intrinsic disorder and a consensus method
    Journal of Chemical Information and Modeling, 58: 1459-1468 (2018).
    [PDF] [Supporting Information] [Server]
    		36. Qi Wu, Zhenling Peng*, Yang Zhang, Jianyi Yang*
    COACH-D: improved protein-ligand binding site prediction with refined ligand-binding poses through molecular docking
    Nucleic Acids Research, 46: W438-W442 (2018).
    [PDF] [Supporting Information] [Server]
    		37. Runze Dong#, Shuo Pan#, Zhenling Peng*, Yang Zhang, Jianyi Yang*
    mTM-align: a server for fast protein structure database search and multiple protein structure alignment
    Nucleic Acids Research, 46: W380-W386 (2018).
    [PDF] [Supporting Information] [Server]
    		38. Qiaozhen Meng, Zhenling Peng*, Jianyi Yang*
    CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction
    Bioinformatics, 34: 2598-2604 (2018).
    [PDF] [Supporting Information] [Server]
    		39. Runze Dong, Zhenling Peng, Yang Zhang*, Jianyi Yang*
    mTM-align: an algorithm for fast and accurate multiple protein structure alignment
    Bioinformatics, 34: 1719-1725 (2018).
    [PDF] [Supporting Information] [Server]
    		40. Qiqige Wuyun#, Wei Zheng#, Zhenling Peng, Jianyi Yang*
    A large-scale comparative assessment of methods for residue-residue contact prediction
    Briefings in Bioinformatics, 19: 219-230 (2018).
    [PDF] [Supporting Information] [Datasets]
    		41. 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, 27: 472-484 (2018).
    [PDF]
    2017
    		42. 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]
    		43. 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]
    		44. 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
    		45. 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]
    		46. 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]
    		47. 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]
    		48. 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
    		49. 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]
    		50. Jianyi Yang*, Yang Zhang*
    Protein structure and function prediction using I-TASSER
    Current Protocols in Bioinformatics, 52: 5.8.1-5.8.15 (2015).
    [PDF] [Server] [This paper was a "Most Cited Articles" in Current Protocols in Bioinformatics]
    		51. 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]
    		52. 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]
    		53. 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]
    		54. 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
    		55.  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]
    		56. 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]
    		57. 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]
    		58. 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]
    		59. 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
    		60.  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] [This paper was a "Highly Cited Paper" in Web of Science]
    		61. 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]
    		62. 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]
    		63. 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
    		64.  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]
    		65. 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
    		66.  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]
    		67. 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
    		68.  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]
    		69. 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]
    		70. Xin Chen*, Jianyi Yang
    Constructing consensus genetic maps in comparative analysis
    Journal of Computational Biology, 17: 1561-1573 (2010).
    [PDF] [Server]
    2009
    		71.  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]
    		72. 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
    		73.  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]
    		74. 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
    		75.  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]