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2005年博士毕业于南开大学,统计与数据科学学院教授,2014年3月-2014年7月, 2017年10月至2018年10月在美国宾夕法尼亚大学访问; 2007-2018年多次在加拿大阿尔伯塔大学访问。主要从事结构生物信息学、统计基因组学、单细胞多组学分析等方向的研究工作。主持国家自然科学基金2项、天津市自然科学基金1项。以主要作者在Circulation, Nature Communications, Bioinformatics等杂志发表SCI学术论文多篇。

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Hu G#, Katuwawala A#, Wang K#, Wu Z, Ghadermarzi S, Gao J., Kurgan L*, flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions. Nat Commun 12, 4438 (2021). Featured among the Editor's Highlights. Faculty Opinions Recommended. Hua X#, Hu G#, Hu Q#, Chang Y, Hu Y, Gao L, Chen X, Yang PC, Zhang Y*, Li M*, Song J*. Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis. Circulation. 2020 May 20. doi: 10.1161/CIRCULATIONAHA.119.043545. Li X, Wang K, Lyu Y, Pan H, Zhang J, Stambolian D, Susztak K, Reilly MP, Hu G*, Li M*. Deep learning enables accurate clustering with batch effect removal in single-cell RNA seq analysis. Nat Commun. 11, 2338 (2020). https://doi.org/10.1038/s41467-020-15851-3 Hu G, Wu Z, Oldfield C, Wang C, Kurgan L*. Quality Assessment for the Putative Intrinsic Disorder in Proteins. Bioinformatics. 2019 May 15;35(10):1692-1700. Hu G, Wang K, Groenendyk J, Barakat K, Mizianty MJ, Ruan J, Michalak M, Kurgan L. Human structural proteome-wide characterization of Cyclosporine A targets. Bioinformatics. 2014 Dec 15;30(24):3561-6. 【1】Gang Hu, Akila Katuwawala, Kui Wang, Zhonghua Wu, Sina Ghadermarzi, Jianzhao Gao & Lukasz Kurgan flDPnn: Accurate intrinsic disorder prediction with putative propensities of disorder functions Nature Communications volume 12, Article number: 4438 (2021) 【2】Marco Necci, Damiano Piovesan, CAID Predictors, DisProt Curators & Silvio C. E. Tosatto Critical assessment of protein intrinsic disorder prediction Nature Methods, (2021)18, 472–481. 【3】Akila Katuwawala, Sina Ghadermarzi, Gang Hu, Zhonghua Wu, Lukasz Kurgan. QUARTERplus: Accurate disorder predictions integrated with interpretable residue-level quality assessment scores Computational and structural biotechnology journal.(2021) 19, 2597-2606 【4】Justin Lakkis, David Wang, Yuanchao Zhang, Gang Hu, Kui Wang, Huize Pan, Lyle Ungar, Muredach Reilly, Xiangjie Li, Mingyao Li. A joint deep learning model enables simultaneous batch effect correction, denoising and clustering in single-cell transcriptomics Genome Research, 2021, gr. 271874.120 【5】Hong Su, Zhenling Peng*, Jianyi Yang* Recognition of small molecule-RNA binding sites using RNA sequence and structure Bioinformatics, in press (2021). 【6】Gao J, Wei H, Cano A, Kurgan L* PSIONplusm Server for Accurate Multi-Label Prediction of Ion Channels and Their Types Biomolecules, 10(6):876(2020) 【7】Saisai Sun, Wenkai Wang, Zhenling Peng, Jianyi Yang* RNA inter-nucleotide 3D closeness prediction by deep residual neural networks Bioinformatics, in press (2021). 【8】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, in press (2020). 【9】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). 【10】Aivi T Nguyen#,Kui Wang#,Gang Hu#,Xuran Wang,Zhen Miao,Joshua A Azevedo,EunRan Suh,Vivianna M Van Deerlin,David Choi,Kathryn Roeder,Mingyao Li*, Edward B Lee* APOE and TREM2 regulate amyloid-responsive microglia in Alzheimer's disease Acta Neuropathologica, 140:477-493(2020) 【11】Hua X#, Hu G#, Hu Q#, Chang Y, Hu Y, Gao L, Chen X, Yang PC, Zhang Y*, Li M*, Song J*. Single-Cell RNA Sequencing to Dissect the Immunological Network of Autoimmune Myocarditis Circulation. 142:384-400 (2020) 【12】Zongyang Du#, Shuo Pan#, Qi Wu, Zhenling Peng, Jianyi Yang* CATHER: a novel threading algorithm with predicted contacts Bioinformatics, 36: 2119-2125 (2020). 【13】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, in press (2020). 【14】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). 【15】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) 【16】Li X, Wang K, Lyu Y, Pan H, Zhang J, Stambolian D, Susztak K, Reilly MP, Hu G*, Li M* Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis Nat Commun. 2020 May 11;11(1):2338. 【17】Zheng W, Wuyun Q, Cheng M, Hu G, Zhang Y Two-Level Protein Methylation Prediction using structure model-based features Sci Rep. 2020 Apr 7;10(1):6008. 【18】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). 【19】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). 【20】Mi P, Zhang QP, Zhang SH, Wang C, Zhang SZ, Fang YC, Gao JZ, Feng DF, Chen DY, Feng XZ The effects of fluorene-9-bisphenol on female zebrafish (Danio rerio) reproductive and exploratory behaviors Chemosphere, 2019 Apr 25;228:398-411. 【21】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). 【22】Wang J, Agarwal D, Huang M, Hu G, Zhou Z, Ye C, Zhang NR Data denoising with transfer learning in single-cell transcriptomics Nat Methods. 2019 Sep;16(9):875-878. 【23】Hu G, Wu Z, Oldfield CJ, Wang C, Kurgan L Quality assessment for the putative intrinsic disorder in proteins Bioinformatics. 2019 May 15;35(10):1692-1700. 【24】Hu G, Kurgan L Sequence Similarity Searching Curr Protoc Protein Sci. 2019 Feb;95(1):e71. 【25】Zheng W, Wuyun Q, Li Y, Mortuza SM, Zhang C, Pearce R, Ruan J, Zhang Y Detecting distant-homology protein structures by aligning deep neural-network based contact maps PLoS Comput Biol. 2019 Oct 17;15(10):e1007411. 【26】Wu Z, Liu W, Jin X, Ji H, Wang H, Glusman G, Robinson M, Liu L, Ruan J, Gao S NormExpression: An R Package to Normalize Gene Expression Data Using Evaluated Methods Front Genet. 2019 Apr 30;10:400. 【27】Xu X, Ji H, Jin X, Cheng Z, Yao X, Liu Y, Zhao Q, Zhang T, Ruan J, Bu W, Chen Z, Gao S Using Pan RNA-Seq Analysis to Reveal the Ubiquitous Existence of 5' and 3' End Small RNAs Front Genet.2019 Feb 14;10:105. 【28】Tan, C., Cui, W., Cui, X., Ning, K. Strain-GeMS: optimized subspecies identification from microbiome data based on accurate variant modeling Bioinformatics, 35(10), 1789-1791 (2019). 【29】Zhang Z, Ruan J, Gao J, Wu FX Predicting essential proteins from protein-protein interactions using order statistics J Theor Biol. , 480: 274-283 (2019) 【30】Gao J, Miao Z, Zhang Z, Wei H, Kurgan L Prediction of Ion Channels and their Types from Protein Sequences: Comprehensive Review and Comparative Assessment Curr Drug Targets. 2019;20(5):579-592. 【31】Gao J, Yang Y, Zhou Y Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures BMC Bioinformatics. 2018 Feb 1;19(1):29. 【32】Gao J, Wu Z, Hu G, Wang K, Song J, Joachimiak A, Kurgan L Survey of Predictors of Propensity for Protein Production and Crystallization with Application to Predict Resolution of Crystal Structures Curr Protein Pept Sci. 2018;19(2):200-210. 【33】Yang Y, Gao J, Wang J, Heffernan R, Hanson J, Paliwal K, Zhou Y. Sixty-five years of the long march in protein secondary structure prediction: the final stretch? Brief Bioinform. 2018 May 1;19(3):482-494. 【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). 【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). 【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). 【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). 【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). 【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). 【40】Gao S, Tian X, Chang H, Sun Y, Wu Z, Cheng Z, Dong P, Zhao Q, Ruan J, Bu W Two novel lncRNAs discovered in human mitochondrial DNA using PacBio full-length transcriptome data Mitochondrion. 2018 Jan;38:41-47. 【41】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). 【42】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). 【43】Hu G, Wang K, Song J, Uversky VN, Kurgan L Taxonomic Landscape of the Dark Proteomes: Whole-Proteome Scale Interplay Between Structural Darkness, Intrinsic Disorder, and Crystallization Propensity Proteomics. 2018 Nov;18(21-22):e1800243. 【44】Hu Y, Lin J, Hu J, Hu G, Wang K, Zhang H, Reilly MP, Li M PennDiff: detecting differential alternative splicing and transcription by RNA sequencing Bioinformatics. 2018 Jul 15;34(14):2384-2391. 【45】Groenendyk J, Paskevicius T, Urra H, Viricel C, Wang K, Barakat K, Hetz C, Kurgan L, Agellon LB, Michalak M Cyclosporine A binding to COX-2 reveals a novel signaling pathway that activates the IRE1α unfolded protein response sensor Sci Rep. 2018 Nov 12;8(1):16678. 【46】Liu C, Chen Z, Hu Y, Ji H, Yu D, Shen W, Li S, Ruan J, Bu W, Gao S Complemented Palindromic Small RNAs First Discovered from SARS Coronavirus Genes (Basel). 2018 Sep 5;9(9). pii: E442. 【47】Li Y, Zheng W, Qiqige W, Cao S, Ruan J, Zhang Y. A Novel Method for Drug Screen to Regulate G Protein-Coupled Receptors in the Metabolic Network of Alzheimer's Disease Biomed Res Int. 2018 Feb 20;2018:5486403. 【48】Cheng Z, Sun Y, Niu X, Shang Y, Ruan J, Chen Z, Gao S, Zhang T Gene expression profiling reveals U1 snRNA regulates cancer gene expression Oncotarget. 2017 Dec 1;8(68):112867-112874. 【49】Wang X, Hou Y, Mao J, Zhang Y, Li Z, Zhao Y, Niu T, Yuan R, Wang Y, Cui J, Shi L, Jia X, Fan R, Lin Q, Shang H, Wang B, Wang H, Zhang B, Cui X, Soh S, Ruan J Western medication plus Traditional Chinese Medicine preparations in patients with chronic heart failure: a prospective, single-blind, randomized, controlled, and multicenter clinical trial J Tradit Chin Med. 2017 Dec;37(6):756-766 【50】Ferreira L, Wu Z, Kurgan LA, Uversky VN, Zaslavsky How to manipulate partition behavior of proteins in aqueous two-phase systems: Effect of trimethylamine N-oxide (TMAO) Fluid Phase Equilibria, 449:217-224, 2017 【51】Qi Wu, Zuguo Yu*, Jianyi Yang* DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method Bioinformatics,33: 2214-2215. (2017). 【52】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). 【53】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). 【54】Hu G, Wu Z, Uversky VN, Kurgan L Functional Analysis of Human Hub Proteins and Their Interactors Involved in the Intrinsic Disorder-Enriched Interactions Int J Mol Sci. 2017 Dec 19;18(12). pii: E2761. 【55】Wu Z, Hu G, Wang K, Zaslavsky BY, Kurgan L, Uversky VN What are the structural features that drive partitioning of proteins in aqueous two-phase systems? Biochim Biophys Acta Proteins Proteom. 2017 Jan;1865(1):113-120. 【56】Wu Z, Hu G, Wang K, Kurgan Exploratory Analysis of Quality Assessment of Putative Intrinsic Disorder in Proteins 16th International Conference on Artificial Intelligence and Soft Computing (ICAISC 2017), pp 722-732 【57】Niu X, Sun Y, Chen Z, Li R, Padmanabhan C, Ruan J, Kreuze JF, Ling K, Fei Z, Gao S Using Small RNA-seq Data to Detect siRNA Duplexes Induced by Plant Viruses Genes (Basel). 2017 Jun 16;8(6). pii: E163. 【58】Chen Z, Sun Y, Yang X, Wu Z, Guo K, Niu X, Wang Q, Ruan J, Bu W, Gao S Two featured series of rRNA-derived RNA fragments (rRFs) constitute a novel class of small RNAs PLoS One. 2017 Apr 25;12(4):e0176458. 【59】Gao J, Tao XW, Zhao J, Feng YM, Cai YD, Zhang N Computational Prediction of Protein Epsilon Lysine Acetylation Sites Based on a Feature Selection Method Comb Chem High Throughput Screen. 2017;20(7):629-637. 【60】Wang T, Zheng W, Wuyun Q, Wu Z, Ruan J, Hu G, Gao J. PrAS: Prediction of amidation sites using multiple feature extraction Comput Biol Chem. 2017 Feb;66:57-62. 【61】Gao J, Yang Y, Zhou Y Predicting the errors of predicted local backbone angles and non-local solvent-accessibilities of proteins by deep neural networks Bioinformatics. 2016 Dec 15;32(24):3768-3773. 【62】Gao J, Cui W, Sheng Y, Ruan J, Kurgan L. PSIONplus: Accurate Sequence-Based Predictor of Ion Channels and Their Types PLoS One. 2016 Apr 4;11(4):e0152964. 【63】Gao S, Ren Y, Sun Y, Wu Z, Ruan J, He B, Zhang T, Yu X, Tian X, Bu W PacBio full-length transcriptome profiling of insect mitochondrial gene expression RNA Biol. 2016 Sep;13(9):820-5. 【64】Wuyun Q, Zheng W, Zhang Y, Ruan J, Hu G Improved Species-Specific Lysine Acetylation Site Prediction Based on a Large Variety of Features Set PLoS One. 2016 May 16;11(5):e0155370. 【65】Wang F, Sun Y, Ruan J, Chen R, Chen X, Chen C, Kreuze JF, Fei Z, Zhu X, Gao S Using Small RNA Deep Sequencing Data to Detect Human Viruses Biomed Res Int. 2016;2016:2596782 【66】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). 【67】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). 【68】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). 【69】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). 【70】Murillo, G. H., You, N., Su, X., Cui, W., Reilly, M. P., Li, M., ... & Cui, X MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data Bioinformatics. 2016 May 15;32(10):1486-92. 【71】Wang C, Hu G, Wang K, Brylinski M, Xie L, Kurgan L PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. Bioinformatics. 2016 Feb 15;32(4):579-86. 【72】Gang Hu, Zhonghua Wu, Kui Wang, Vladimir N Uversky*, Lukasz Kurgan* Untapped Potential of Disordered Proteins in Current Druggable Human Proteome Curr Drug Targets. 2016;17(10):1198-205. 【73】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). 【74】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). 【75】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). 【76】Jianyi Yang*, Yang Zhang* I-TASSER server: new development for protein structure and function predictions Nucleic Acids Research, 43: W174-W181 (2015). 【77】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). 【78】Wu Z, Hu G, Yang J, Peng Z, Uversky VN, Kurgan L In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces FEBS Lett. 2015 Sep 14;589(19 Pt A):2561-9. 【79】Zhenling Peng, Jing Yan, Xiao Fan, Marcin J Mizianty, Bin Xue, Kui Wang, Gang Hu, Vladimir N Uversky, Lukasz Kurgan* Exceptionally abundant exceptions: comprehensive characterization of intrinsic disorder in all domains of life Cell Mol Life Sci. 2015 Jan;72(1):137-51 【80】Cao S, Yu L, Mao J, Wang Q, Ruan J Uncovering the Molecular Mechanism of Actions between Pharmaceuticals and Proteins on the AD Network PLoS One. 2015 Dec 9;10(12):e0144387. 【81】Wu FX, Li M, Ruan J, Luo F Systems Biology Approaches to Mining High Throughput Biological Data Biomed Res Int. 2015;2015:504362. 【82】Zheng W, Ruan J, Hu G, Wang K, Hanlon M, Gao J Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull PLoS One. 2015 Aug 5;10(8):e0134835. 【83】Gao J, Kurgan L Computational prediction of B cell epitopes from antigen sequences Methods Mol Biol. 2014;1184:197-215. 【84】Zheng W, Zhang C, Hanlon M, Ruan J, Gao J An ensemble method for prediction of conformational B-cell epitopes from antigen sequences. Comput Biol Chem. 2014 Apr; 49:51-8. 【85】Zhang Y, Xu J, Zheng W, Zhang C, Qiu X, Chen K, Ruan J newDNA-Prot: Prediction of DNA-binding proteins by employing support vector machine and a comprehensive sequence representation Comput Biol Chem. 2014 Oct;52:51-9. 【86】Hu G, Wang K, Groenendyk J, Barakat K, Mizianty MJ, Ruan J, Michalak M, Kurgan L Human structural proteome-wide characterization of Cyclosporine A targets Bioinformatics. 2014 Dec 15;30(24):3561-6 【87】Backues SK, Chen D, Ruan J, Xie Z, Klionsky DJ Estimating the size and number of autophagic bodies by electron microscopy Autophagy. 2014 Jan;10(1):155-64 【88】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). 【89】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). 【90】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 B Histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and alters HagB-induced chemokine responses Scientific Reports, 4: 3904 (2014). 【91】Gao J, Hu G, Wu Z, Ruan J, Shen S, Hanlon M, Wang K* Improved Prediction of Protein Crystallization, Purification and Production Propensity Using Hybrid Sequence Representation Current Bioinformatics 9(1):57-64 · January 2014 【92】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). 【93】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). 【94】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). 【95】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). 【96】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). 【97】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). 【98】Sheng Y, Zhang C, Qiu X, Zheng W, Ruan J, Shao Y Exploring the molecular mechanism of action between drug and RNA polymerase based on partially-resolved spatial structures Curr Comput Aided Drug Des. 2013 Dec;9(4):547-55 【99】Wang K, Gao J, Shen S, Tuszynski JA, Ruan J, Hu G. An accurate method for prediction of protein-ligand binding site on protein surface using SVM and statistical depth function. Biomed Res Int. 2013;2013:409658. 【100】Gao J, Zhang N, Ruan J Prediction of protein modification sites of gamma-carboxylation using position specific scoring matrices based evolutionary information Comput Biol Chem. 2013 Dec;47:215-20. 【101】Hu G, Gao J, Wang K, Mizianty MJ, Ruan J, Kurgan L Finding protein targets for small biologically relevant ligands across fold space using inverse ligand binding predictions. Structure. 2012 Nov 7;20(11):1815-22. 【102】Gao J, Faraggi E, Zhou Y, Ruan J, Kurgan L BEST: improved prediction of B-cell epitopes from antigen sequences PLoS One. 2012;7(6):e40104. 【103】Wang K, Cui W, Hu G, Gao J, Wu Z, Qiu X, Ruan J, Feng Y, Qi Z, Shao Y, Tuszynski JA Computable features required to evaluate the efficacy of drugs and a universal algorithm to find optimally effective drug in a drug complex. PLoS One. 2012;7(3):e33709 【104】Cui W, Wang K, Ruan J, Qi Z, Feng Y, Shao Y, Tuszynski JA The molecular mechanism of action of the CR6261-Azichromycin combination found through computational analysis PLoS One. 2012;7(5):e37790. 【105】Zhang N, Feng Y, Gao S, Ruan J, Zhang T New insights regarding protein folding as learned from beta-sheets EXCLI J. 2012 Aug 27;11:543-55. eCollection 2012. 【106】Ambrish Roy, Jianyi Yang, Yang Zhang COFACTOR: An accurate comparative algorithm for structure-based protein function annotation Nucleic Acids Research, 40: W471-W477 (2012). 【107】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). 【108】Zhang S, Du J, Zhang L, Zeng C, Liu Q, Zhang T, Hu G Circular Cone: a novel approach for protein ligand shape matching using modified PCA Comput Methods Programs Biomed. 2012 Oct;108(1):168-75. 【109】Zhang H, Zhang T, Gao J, Ruan J, Shen S, Kurgan L* Determination of protein folding kinetic types using sequence and predicted secondary structure and solvent accessibility Amino Acids,2012; 42(1):271-83 【110】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). 【111】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). 【112】Hu G, Shen S, Wang K On the evolution rate in mammalian mitochondrial genomes Comput Biol Chem. 2011 Jun;35(3):137-42. 【113】Chen K, Mizianty M, Gao J, Kurgan L* A critical comparative assessment of predictions of protein binding sites for small organic compounds Structure. 2011 May 11;19(5):613-21. 【114】Zhenling Peng#, Jianyi Yang*#, Xin Chen An improved classification of G-protein-coupled receptors using sequence-derived features BMC Bioinformatics, 11: 420 (2010). 【115】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). 【116】Xin Chen, Jianyi Yang Constructing consensus genetic maps in comparative analysis Journal of Computational Biology, 17: 1561-1573 (2010). 【117】Zhang T, Zhang H, Chen K, Ruan J, Shen S, Kurgan L Analysis and prediction of RNA-binding residues using sequence, evolutionary conservation, and predicted secondary structure and solvent accessibility Curr Protein Pept Sci. 2010 Nov;11(7):609-28. 【118】Zhang N, Duan G, Gao S, Ruan J, Zhang T Prediction of the parallel/antiparallel orientation of beta-strands using amino acid pairing preferences and support vector machines J Theor Biol. 2010 Apr 7;263(3):360-8. 【119】Gao J, Zhang T, Zhang H, Shen S, Ruan J, Kurgan L Accurate prediction of protein folding rates from sequence and sequence-derived residue flexibility and solvent accessibility Proteins. 2010 Jul;78(9):2114-30. 【120】Zhang N, Ruan J, Duan G, Gao S, Zhang T The interstrand amino acid pairs play a significant role in determining the parallel or antiparallel orientation of beta-strands Biochem Biophys Res Commun. 2009 Aug 28;386(3):537-43. 【121】Zhang H, Zhang T, Chen K, Shen S, Ruan J, Kurgan L On the relation between residue flexibility and local solvent accessibility in proteins Proteins. 2009 Aug 15;76(3):617-36. 【122】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). 【123】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). 【124】Zhang H, Zhang T, Chen K, Shen S, Ruan J, Kurgan L Sequence based residue depth prediction using evolutionary information and predicted secondary structure BMC Bioinformatics. 2008 Sep 20;9:388. 【125】Zhang T, Zhang H, Chen K, Shen S, Ruan J, Kurgan L Accurate sequence-based prediction of catalytic residues Bioinformatics. 2008 Oct 15;24(20):2329-38. 【126】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). 【127】 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). 【128】Hu G, Shen S, Ruan J. SGA: a grammar-based alignment algorithm Comput Methods Programs Biomed. 2007 Apr;86(1):17-20. 【129】Shen S, Hu G, Tuszynski JA Analysis of protein three-dimension structure using amino acids depths Protein J. 2007 Apr;26(3):183-92. 【130】Jianyi Yang, Zuguo Yu, Vo Anh Correlations between designability and various structural characteristics of protein lattice models Journal of Chemical Physics, 126: 195101 (2007). 【131】Shen S, Kai B, Ruan J, Torin Huzil J, Carpenter E, Tuszynski JA Probabilistic analysis of the frequencies of amino acid pairs within characterized protein sequences Physica A. 2006 Oct 15;370(2):651-662. 【132】Ruan J, Chen K, Tuszynski JA, Kurgan LA Quantitative analysis of the conservation of the tertiary structure of protein segments Protein J. 2006 Jul;25(5):301-15. 【133】Chen K, Ruan J, Kurgan LA Prediction of three dimensional structure of calmodulin Protein J. 2006 Jan;25(1):57-70. 【134】Shen SY, Wang K, Hu G, Chen LS, Zhang H, Xia ST On the alignment space Conf Proc IEEE Eng Med Biol Soc. 2005;2006:244-7. 【135】Shen S, Dong L, Wang K, Hu G SMA: An Efficient Tool for Large-Scale Multiple Alignment Conf Proc IEEE Eng Med Biol Soc. 2005;2005:2836-8. 【136】Ruan J, Wang K, Yang J, Kurgan LA, Cios K Highly accurate and consistent method for prediction of helix and strand content from primary protein sequences Artif Intell Med. 2005 Sep-Oct;35(1-2):19-35

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