Lab Publications
(#Co-first author, *Corresponding author. Research profile in Google Scholar
and Web of Science)
2024 | |
Zhenling Peng, Peilong Lu*, Jianyi Yang* AI accurately predicting the structure of biomolecular interactions Cell Research, 34: 601-602(2024). [PDF] [Invited Research Highlight] |
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Hong Wei, Wenkai Wang, Zhenling Peng*, Jianyi Yang* Q-BioLiP: a comprehensive resource for quaternary structure-based protein-ligand interactions Genomics, Proteomics & Bioinformatics, 22, qzae001, (2024). [PDF] [Supporting Information] [Server] |
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Zongyang Du, Zhenling Peng, Jianyi Yang* RNA threading with secondary structure and sequence profile Bioinformatics, 40: btae080 (2024). [PDF] [Supporting Information] [Server] |
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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] |
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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] |
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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] |
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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,22: qzae007 (2024). [PDF] |
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2023 | |
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] |
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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] |
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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] |
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2022 | |
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 ] |
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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] |
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Zongyang Du, Zhenling Peng, Jianyi Yang* Toward the assessment of predicted inter-residue distance Bioinformatics, 38: 962-969 (2022). [PDF] [Supporting Information] [Server] |
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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] |
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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] |
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Saisai Sun, Jianyi Yang, Zhaolei Zhang* RNALigands: a database and web server for RNA-ligand interactions RNA, 28: 115-122 (2022). [PDF] [Faculty Opinions ] |
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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] |
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2021 | |
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] |
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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 ] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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2020 | |
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 ] |
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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] |
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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] |
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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] |
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2019 | |
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] |
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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] |
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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] |
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2018 | |
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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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2017 | |
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] |
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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] |
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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] |
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2016 | |
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] |
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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] |
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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] |
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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] |
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2015 | |
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] |
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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] |
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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] |
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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] |
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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] |
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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] |
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2014 | |
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] |
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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] |
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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] |
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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] |
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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] |
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2013 | |
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] |
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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] |
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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] |
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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] |
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2012 | |
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] |
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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] |
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2011 | |
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] |
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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] |
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2010 | |
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] |
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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] |
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Xin Chen*, Jianyi Yang Constructing consensus genetic maps in comparative analysis Journal of Computational Biology, 17: 1561-1573 (2010). [PDF] [Server] |
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2009 | |
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] |
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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] |
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2008 | |
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] |
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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] |
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2007 | |
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] |