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Yang Zhang - Publications

Affiliations: 
computational biology University of Michigan, Ann Arbor, Ann Arbor, MI 
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Year Citation  Score
2024 Zulfiqar H, Guo Z, Ahmad RM, Ahmed Z, Cai P, Chen X, Zhang Y, Lin H, Shi Z. Deep-STP: a deep learning-based approach to predict snake toxin proteins by using word embeddings. Frontiers in Medicine. 10: 1291352. PMID 38298505 DOI: 10.3389/fmed.2023.1291352  0.344
2024 Liu Z, Zhang C, Zhang Q, Zhang Y, Yu DJ. TM-search: An Efficient and Effective Tool for Protein Structure Database Search. Journal of Chemical Information and Modeling. PMID 38270339 DOI: 10.1021/acs.jcim.3c01455  0.336
2024 Zheng W, Wuyun Q, Li Y, Zhang C, Freddolino PL, Zhang Y. Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data. Nature Methods. PMID 38167654 DOI: 10.1038/s41592-023-02130-4  0.355
2023 Zheng W, Wuyun Q, Freddolino PL, Zhang Y. Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15. Proteins. PMID 37650367 DOI: 10.1002/prot.26585  0.327
2023 Zhang C, Zhang X, Freddolino PL, Zhang Y. BioLiP2: an updated structure database for biologically relevant ligand-protein interactions. Nucleic Acids Research. PMID 37522378 DOI: 10.1093/nar/gkad630  0.406
2023 Pearce R, Huang X, Omenn GS, Zhang Y. De novo protein fold design through sequence-independent fragment assembly simulations. Proceedings of the National Academy of Sciences of the United States of America. 120: e2208275120. PMID 36656852 DOI: 10.1073/pnas.2208275120  0.366
2022 Zhu YH, Zhang C, Yu DJ, Zhang Y. Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. Plos Computational Biology. 18: e1010793. PMID 36548439 DOI: 10.1371/journal.pcbi.1010793  0.31
2022 LaLone CA, Blatz DJ, Jensen MA, Vliet SMF, Mayasich S, Mattingly KZ, Transue TR, Melendez W, Wilkinson A, Simmons CW, Ng C, Zhang C, Zhang Y. From Protein Sequence to Structure: The Next Frontier in Cross Species Extrapolation for Chemical Safety Evaluations. Environmental Toxicology and Chemistry. PMID 36524855 DOI: 10.1002/etc.5537  0.32
2022 Pearce R, Li Y, Omenn GS, Zhang Y. Fast and accurate Ab Initio Protein structure prediction using deep learning potentials. Plos Computational Biology. 18: e1010539. PMID 36112717 DOI: 10.1371/journal.pcbi.1010539  0.352
2022 Sun Y, Jiao Y, Shi C, Zhang Y. Deep learning-based molecular dynamics simulation for structure-based drug design against SARS-CoV-2. Computational and Structural Biotechnology Journal. PMID 36091720 DOI: 10.1016/j.csbj.2022.09.002  0.307
2022 Zhang C, Shine M, Pyle AM, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nature Methods. PMID 36038728 DOI: 10.1038/s41592-022-01585-1  0.357
2022 Bell EW, Schwartz JH, Freddolino PL, Zhang Y. PEPPI: Whole-proteome Protein-protein Interaction Prediction through Structure and Sequence Similarity, Functional Association, and Machine Learning. Journal of Molecular Biology. 434: 167530. PMID 35662463 DOI: 10.1016/j.jmb.2022.167530  0.346
2022 Zheng W, Wuyun Q, Zhou X, Li Y, Freddolino PL, Zhang Y. LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. Nucleic Acids Research. PMID 35420129 DOI: 10.1093/nar/gkac248  0.356
2022 MacCarthy EA, Zhang C, Zhang Y, Dukka KC. GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool. Bioinformatics (Oxford, England). PMID 34978562 DOI: 10.1093/bioinformatics/btab871  0.366
2021 Yang P, Zheng W, Ning K, Zhang Y. Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34873061 DOI: 10.1073/pnas.2110828118  0.341
2021 Mortuza SM, Zheng W, Zhang C, Li Y, Pearce R, Zhang Y. Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nature Communications. 12: 5011. PMID 34408149 DOI: 10.1038/s41467-021-25316-w  0.348
2021 Li Y, Zhang C, Zheng W, Zhou X, Bell EW, Yu DJ, Zhang Y. Protein inter-residue contact and distance prediction by coupling complementary coevolution features with deep residual networks in CASP14. Proteins. PMID 34382712 DOI: 10.1002/prot.26211  0.339
2021 Zheng W, Zhang C, Li Y, Pearce R, Bell EW, Zhang Y. Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods. 1. PMID 34355210 DOI: 10.1016/j.crmeth.2021.100014  0.34
2021 Zheng W, Li Y, Zhang C, Zhou X, Pearce R, Bell EW, Huang X, Zhang Y. Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14. Proteins. PMID 34331351 DOI: 10.1002/prot.26193  0.309
2021 Zhao KL, Liu J, Zhou XG, Su JZ, Zhang Y, Zhang GJ. MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction. Bioinformatics (Oxford, England). PMID 34185079 DOI: 10.1093/bioinformatics/btab484  0.326
2021 Pearce R, Zhang Y. Toward the solution of the protein structure prediction problem. The Journal of Biological Chemistry. 100870. PMID 34119522 DOI: 10.1016/j.jbc.2021.100870  0.414
2021 Li Y, Zhang C, Bell EW, Zheng W, Zhou X, Yu DJ, Zhang Y. Deducing high-accuracy protein contact-maps from a triplet of coevolutionary matrices through deep residual convolutional networks. Plos Computational Biology. 17: e1008865. PMID 33770072 DOI: 10.1371/journal.pcbi.1008865  0.309
2021 Gong W, Guerler A, Zhang C, Warner E, Li C, Zhang Y. Integrating multimeric threading with high-throughput experiments for structural interactome of Escherichia coli. Journal of Molecular Biology. 166944. PMID 33741411 DOI: 10.1016/j.jmb.2021.166944  0.34
2021 Pearce R, Zhang Y. Deep learning techniques have significantly impacted protein structure prediction and protein design. Current Opinion in Structural Biology. 68: 194-207. PMID 33639355 DOI: 10.1016/j.sbi.2021.01.007  0.311
2020 Zhou XG, Peng CX, Liu J, Zhang Y, Zhang GJ. Underestimation-Assisted Global-Local Cooperative Differential Evolution and the Application to Protein Structure Prediction. Ieee Transactions On Evolutionary Computation : a Publication of the Ieee Neural Networks Council. 24: 536-550. PMID 33603321 DOI: 10.1109/Tevc.2019.2938531  0.333
2020 Zhang W, Bell EW, Yin M, Zhang Y. EDock: blind protein-ligand docking by replica-exchange monte carlo simulation. Journal of Cheminformatics. 12: 37. PMID 33430966 DOI: 10.1186/S13321-020-00440-9  0.437
2020 Zhang B, Zhang X, Pearce R, Shen HB, Zhang Y. A New Protocol for Atomic-Level Protein Structure Modeling and Refinement Using Low-to-Medium Resolution Cryo-EM Density Maps. Journal of Molecular Biology. PMID 32771523 DOI: 10.1016/J.Jmb.2020.07.027  0.416
2020 Chan WKB, Zhang Y. Ligand-Profile Based Virtual Screening of Human GPCRs. Journal of Molecular Biology. PMID 32652079 DOI: 10.1016/J.Jmb.2020.07.003  0.709
2020 Wei X, Zhang C, Freddolino PL, Zhang Y. Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons. Bioinformatics (Oxford, England). PMID 32470107 DOI: 10.1093/bioinformatics/btaa548  0.317
2020 Zhu YH, Hu J, Ge F, Li F, Song J, Zhang Y, Yu DJ. Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. Briefings in Bioinformatics. PMID 32436937 DOI: 10.1093/Bib/Bbaa076  0.374
2020 Huang X, Pearce R, Zhang Y. FASPR: an open-source tool for fast and accurate protein side-chain packing. Bioinformatics (Oxford, England). PMID 32259206 DOI: 10.1093/Bioinformatics/Btaa234  0.455
2020 Zheng W, Zhou X, Wuyun Q, Pearce R, Li Y, Zhang Y. FUpred: Detecting protein domains through deep-learning based contact map prediction. Bioinformatics (Oxford, England). PMID 32227201 DOI: 10.1093/Bioinformatics/Btaa217  0.382
2020 Zhang C, Zheng W, Huang X, Bell EW, Zhou X, Zhang Y. Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. Journal of Proteome Research. PMID 32200634 DOI: 10.1021/Acs.Jproteome.0C00129  0.364
2019 Liu J, Zhou XG, Zhang Y, Zhang GJ. CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm. Bioinformatics (Oxford, England). PMID 31860059 DOI: 10.1093/Bioinformatics/Btz943  0.456
2019 Huang X, Pearce R, Zhang Y. Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries. Journal of Chemical Information and Modeling. PMID 31851497 DOI: 10.1021/Acs.Jcim.9B00812  0.462
2019 Huang X, Zheng W, Pearce R, Zhang Y. SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function. Bioinformatics (Oxford, England). PMID 31830252 DOI: 10.1093/Bioinformatics/Btz926  0.399
2019 Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, ... ... Zhang Y, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20: 244. PMID 31744546 DOI: 10.1186/S13059-019-1835-8  0.572
2019 Zhang C, Zheng W, Mortuza SM, Li Y, Zhang Y. DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinformatics (Oxford, England). PMID 31738385 DOI: 10.1093/Bioinformatics/Btz863  0.4
2019 Wang Y, Shi Q, Yang P, Zhang C, Mortuza SM, Xue Z, Ning K, Zhang Y. Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families. Genome Biology. 20: 229. PMID 31676016 DOI: 10.1186/S13059-019-1823-Z  0.423
2019 Soules KR, Dmitriev A, LaBrie SD, Dimond ZE, May BH, Johnson DK, Zhang Y, Battaile KP, Lovell S, Hefty PS. Structural and ligand binding analyses of the periplasmic sensor domain of RsbU in Chlamydia trachomatis supports role in TCA cycle regulation. Molecular Microbiology. PMID 31637787 DOI: 10.1111/Mmi.14401  0.342
2019 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 Computational Biology. 15: e1007411. PMID 31622328 DOI: 10.1371/Journal.Pcbi.1007411  0.493
2019 Huang X, Pearce R, Zhang Y. EvoEF2: Accurate and fast energy function for computational protein design. Bioinformatics (Oxford, England). PMID 31588495 DOI: 10.1093/Bioinformatics/Btz740  0.331
2019 Zhang C, Lane L, Omenn GS, Zhang Y. A Blinded Testing of Function Annotation for uPE1 Proteins by the I-TASSER/COFACTOR Pipeline Using the 2018-2019 Additions to neXtProt and the CAFA3 Challenge. Journal of Proteome Research. PMID 31581775 DOI: 10.1021/Acs.Jproteome.9B00537  0.457
2019 Wu J, Liu B, Chan WKB, Wu W, Pang T, Hu H, Yan S, Ke X, Zhang Y. Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors. Bioinformatics (Oxford, England). 35: i324-i332. PMID 31510691 DOI: 10.1093/Bioinformatics/Btz336  0.696
2019 Hong J, Luo Y, Zhang Y, Ying J, Xue W, Xie T, Tao L, Zhu F. Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning. Briefings in Bioinformatics. PMID 31504150 DOI: 10.1093/bib/bbz081  0.308
2019 Wu J, Yin Q, Zhang C, Geng J, Wu H, Hu H, Ke X, Zhang Y. Function Prediction for G Protein-Coupled Receptors through Text Mining and Induction Matrix Completion. Acs Omega. 4: 3045-3054. PMID 31459527 DOI: 10.1021/acsomega.8b02454  0.309
2019 Zheng W, Zhang C, Bell EW, Zhang Y. I-TASSER gateway: A protein structure and function prediction server powered by XSEDE. Future Generations Computer Systems : Fgcs. 99: 73-85. PMID 31427836 DOI: 10.1016/J.Future.2019.04.011  0.487
2019 Li Y, Zhang C, Bell EW, Yu DJ, Zhang Y. Ensembling multiple raw coevolutionary features with deep residual neural networks for contact-map prediction in CASP13. Proteins. PMID 31407406 DOI: 10.1002/Prot.25798  0.349
2019 Vangaveti S, Vreven T, Zhang Y, Weng Z. Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. Bioinformatics (Oxford, England). PMID 31393558 DOI: 10.1093/Bioinformatics/Btz623  0.478
2019 Zheng W, Li Y, Zhang C, Pearce R, Mortuza SM, Zhang Y. Deep-learning contact-map guided protein structure prediction in CASP13. Proteins. PMID 31365149 DOI: 10.1002/Prot.25792  0.375
2019 Zhou X, Hu J, Zhang C, Zhang G, Zhang Y. Assembling multidomain protein structures through analogous global structural alignments. Proceedings of the National Academy of Sciences of the United States of America. PMID 31341084 DOI: 10.1073/Pnas.1905068116  0.448
2019 Wang D, Geng L, Zhao YJ, Yang Y, Huang Y, Zhang Y, Shen HB. Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. Bioinformatics (Oxford, England). PMID 31274151 DOI: 10.1093/Bioinformatics/Btz544  0.457
2019 Bell EW, Zhang Y. DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. Journal of Cheminformatics. 11: 40. PMID 31175455 DOI: 10.1186/S13321-019-0362-7  0.333
2019 Zheng W, Zhang C, Wuyun Q, Pearce R, Li Y, Zhang Y. LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins. Nucleic Acids Research. PMID 31081035 DOI: 10.1093/Nar/Gkz384  0.438
2019 Li Y, Hu J, Zhang C, Yu DJ, Zhang Y. ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks. Bioinformatics (Oxford, England). PMID 31070716 DOI: 10.1093/Bioinformatics/Btz291  0.448
2019 Han Z, Shao Q, Gong W, Wang S, Su J, Li C, Zhang Y. Interpreting the Dynamics of Binding Interactions of snRNA and U1A Using a Coarse-Grained Model. Biophysical Journal. PMID 30975455 DOI: 10.1016/J.Bpj.2019.03.008  0.323
2019 Pearce R, Huang X, Setiawan D, Zhang Y. EvoDesign: Designing Protein-Protein Binding Interactions Using Evolutionary Interface Profiles in Conjunction with an Optimized Physical Energy Function. Journal of Molecular Biology. PMID 30851277 DOI: 10.1016/J.Jmb.2019.02.028  0.459
2019 Li F, Zhang Y, Purcell AW, Webb GI, Chou KC, Lithgow T, Li C, Song J. Positive-unlabelled learning of glycosylation sites in the human proteome. Bmc Bioinformatics. 20: 112. PMID 30841845 DOI: 10.1186/S12859-019-2700-1  0.357
2019 Quan L, Wu H, Lyu Q, Zhang Y. DAMpred: Recognizing Disease-Associated nsSNPs through Bayes-Guided Neural-Network Model Built on Low-Resolution Structure Prediction of Proteins and Protein-Protein Interactions. Journal of Molecular Biology. PMID 30796987 DOI: 10.1016/J.Jmb.2019.02.017  0.418
2019 Shultis D, Mitra P, Huang X, Johnson J, Khattak NA, Gray F, Piper C, Czajka J, Hansen L, Wan B, Chinnaswamy K, Liu L, Wang M, Pan J, Stuckey J, ... ... Zhang Y, et al. Changing the Apoptosis Pathway through Evolutionary Protein Design. Journal of Molecular Biology. PMID 30625288 DOI: 10.1016/J.Jmb.2018.12.016  0.413
2019 Fan YX, Pan X, Zhang Y, Shen HB. LabCaS for Ranking Potential Calpain Substrate Cleavage Sites from Amino Acid Sequence. Methods in Molecular Biology (Clifton, N.J.). 1915: 111-120. PMID 30617800 DOI: 10.1007/978-1-4939-8988-1_10  0.37
2019 Xu D, Li H, Zhang Y. Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 7821: 304-316. PMID 25035865 DOI: 10.1007/978-3-642-37195-0_30  0.313
2018 Deng H, Jia Y, Zhang Y. Protein structure prediction. International Journal of Modern Physics. B. 32. PMID 30853739 DOI: 10.1007/978-0-387-92738-1_11  0.455
2018 Hu R, Xiao J, Gu T, Yu X, Zhang Y, Chang J, Yang G, He G. Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.). Bmc Genomics. 19: 803. PMID 30400808 DOI: 10.1186/S12864-018-5157-0  0.38
2018 Zhang C, Wei X, Omenn GS, Zhang Y. Structure and Protein Interaction-based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17. Journal of Proteome Research. PMID 30265558 DOI: 10.1021/Acs.Jproteome.8B00453  0.485
2018 Diamond JS, Zhang Y. THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes. Database : the Journal of Biological Databases and Curation. 2018. PMID 30239678 DOI: 10.1093/Database/Bay090  0.479
2018 Virtanen JJ, Zhang Y. MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models. Acta Crystallographica. Section D, Structural Biology. 74: 606-620. PMID 29968671 DOI: 10.1107/S2059798318005612  0.406
2018 Wu Q, Peng Z, Zhang Y, Yang J. COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking. Nucleic Acids Research. PMID 29846643 DOI: 10.1093/Nar/Gky439  0.398
2018 Dong R, Pan S, Peng Z, Zhang Y, Yang J. mTM-align: a server for fast protein structure database search and multiple protein structure alignment. Nucleic Acids Research. PMID 29788129 DOI: 10.1093/Nar/Gky430  0.421
2018 Setiawan D, Brender J, Zhang Y. Recent advances in automated protein design and its future challenges. Expert Opinion On Drug Discovery. 1-18. PMID 29695210 DOI: 10.1080/17460441.2018.1465922  0.703
2018 Zhang C, Zheng W, Freddolino PL, Zhang Y. MetaGO: Predicting Gene Ontology of non-homologous proteins through low-resolution protein structure prediction and protein-protein network mapping. Journal of Molecular Biology. PMID 29534977 DOI: 10.1016/J.Jmb.2018.03.004  0.467
2018 Hu J, Liu Z, Yu DJ, Zhang Y. LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening. Bioinformatics (Oxford, England). PMID 29462237 DOI: 10.1093/Bioinformatics/Bty081  0.373
2018 Wu J, Zhang Q, Wu W, Pang T, Hu H, Chan WKB, Ke X, Zhang Y, Wren J. WDL-RF: Predicting Bioactivities of Ligand Molecules Acting with G Protein-coupled Receptors by Combining Weighted Deep Learning and Random Forest. Bioinformatics (Oxford, England). PMID 29432522 DOI: 10.1093/Bioinformatics/Bty070  0.706
2018 Hu J, Li Y, Zhang Y, Yu DJ. ATPbind: accurate protein-ATP binding site prediction by combining sequence-profiling and structure-based comparisons. Journal of Chemical Information and Modeling. PMID 29361215 DOI: 10.1021/Acs.Jcim.7B00397  0.371
2017 Dong R, Peng Z, Zhang Y, Yang J. mTM-align: an algorithm for fast and accurate multiple protein structure alignment. Bioinformatics (Oxford, England). PMID 29281009 DOI: 10.1093/Bioinformatics/Btx828  0.457
2017 Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, ... ... Zhang Y, et al. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Medicine. 9: 113. PMID 29254494 DOI: 10.1186/S13073-017-0509-Y  0.389
2017 Thomas JMH, Simkovic F, Keegan R, Mayans O, Zhang C, Zhang Y, Rigden DJ. Approaches to ab initio molecular replacement of α-helical transmembrane proteins. Acta Crystallographica. Section D, Structural Biology. 73: 985-996. PMID 29199978 DOI: 10.1107/S2059798317016436  0.416
2017 Wang J, Yang B, An Y, Marquez-Lago T, Leier A, Wilksch J, Hong Q, Zhang Y, Hayashida M, Akutsu T, Webb GI, Strugnell RA, Song J, Lithgow T. Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. Briefings in Bioinformatics. PMID 29186295 DOI: 10.1093/Bib/Bbx164  0.326
2017 Zhang C, Mortuza SM, He B, Wang Y, Zhang Y. Template-based and free modeling of I-TASSER and QUARK pipelines using predicted contact maps in CASP12. Proteins. PMID 29082551 DOI: 10.1002/Prot.25414  0.389
2017 Wang Y, Wang J, Li R, Shi Q, Xue Z, Zhang Y. ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly. Nucleic Acids Research. PMID 28498994 DOI: 10.1093/Nar/Gkx410  0.34
2017 Wang Y, Virtanen J, Xue Z, Zhang Y. I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation. Nucleic Acids Research. PMID 28472524 DOI: 10.1093/Nar/Gkx349  0.355
2017 Zhang C, Freddolino PL, Zhang Y. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research. PMID 28472402 DOI: 10.1093/Nar/Gkx366  0.489
2017 He B, Mortuza SM, Wang Y, Shen HB, Zhang Y. NeBcon: Protein contact map prediction using neural network training coupled with naïve Bayes classifiers. Bioinformatics (Oxford, England). PMID 28369334 DOI: 10.1093/Bioinformatics/Btx164  0.434
2017 Li H, Zhang Y, Guan Y, Menon R, Omenn GS. Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks. Methods in Molecular Biology (Clifton, N.J.). 1558: 415-436. PMID 28150250 DOI: 10.1007/978-1-4939-6783-4_20  0.432
2017 Brender JR, Shultis D, Khattak NA, Zhang Y. An Evolution-Based Approach to De Novo Protein Design. Methods in Molecular Biology (Clifton, N.J.). 1529: 243-264. PMID 27914055 DOI: 10.1007/978-1-4939-6637-0_12  0.723
2017 Zhang Y, Yang R, Zhang W, Hu Z, Zhao W. Structural characterization and physicochemical properties of protein extracted from soybean meal assisted by steam flash-explosion with dilute acid soaking Food Chemistry. 219: 48-53. DOI: 10.1016/j.foodchem.2016.09.079  0.312
2016 Xiong P, Zhang C, Zheng W, Zhang Y. BindProfX: Assessing mutation-induced binding affinity change by protein interface profiles with pseudo counts. Journal of Molecular Biology. PMID 27899282 DOI: 10.1016/J.Jmb.2016.11.022  0.36
2016 An Y, Wang J, Li C, Leier A, Marquez-Lago T, Wilksch J, Zhang Y, Webb GI, Song J, Lithgow T. Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI. Briefings in Bioinformatics. PMID 27777222 DOI: 10.1093/bib/bbw100  0.306
2016 Li C, Lv D, Zhang L, Yang F, Wang C, Su J, Zhang Y. Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model. The Journal of Chemical Physics. 145: 014104. PMID 27394096 DOI: 10.1063/1.4954992  0.314
2016 Quan L, Lv Q, Zhang Y. STRUM: Structure-based prediction of protein stability changes upon single-point mutation. Bioinformatics (Oxford, England). PMID 27318206 DOI: 10.1093/Bioinformatics/Btw361  0.397
2016 Wang Y, Virtanen J, Xue Z, Tesmer JJ, Zhang Y. Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. Acta Crystallographica. Section D, Structural Biology. 72: 616-628. PMID 27139625 DOI: 10.1107/S2059798316003016  0.542
2016 Li HD, Menon R, Eksi R, Guerler A, Zhang Y, Omenn GS, Guan Y. A Network of Splice Isoforms for the Mouse. Scientific Reports. 6: 24507. PMID 27079421 DOI: 10.1038/Srep24507  0.323
2015 Yang J, Zhang Y. Protein Structure and Function Prediction Using I-TASSER. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 52: 5.8.1-5.8.15. PMID 26678386 DOI: 10.1002/0471250953.Bi0508S52  0.484
2015 Brender JR, Zhang Y. Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles. Plos Computational Biology. 11: e1004494. PMID 26506533 DOI: 10.1371/Journal.Pcbi.1004494  0.697
2015 Deng H, Jia Y, Zhang Y. 3DRobot: Automated Generation of Diverse and Well-packed Protein Structure Decoys. Bioinformatics (Oxford, England). PMID 26471454 DOI: 10.1093/Bioinformatics/Btv601  0.432
2015 Yang J, Wang Y, Zhang Y. ResQ: An approach to unified estimation of B-factor and residue-specific error in protein structure prediction. Journal of Molecular Biology. PMID 26437129 DOI: 10.1016/J.Jmb.2015.09.024  0.427
2015 Bai C, Zhang Y, Zhao X, Hu Y, Xiang S, Miao J, Lou C, Zhang L. Exploiting a precise design of universal synthetic modular regulatory elements to unlock the microbial natural products in Streptomyces. Proceedings of the National Academy of Sciences of the United States of America. PMID 26374838 DOI: 10.1073/Pnas.1511027112  0.309
2015 Zhang W, Yang J, He B, Walker SE, Zhang H, Govindarajoo B, Virtanen J, Xue Z, Shen HB, Zhang Y. Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11. Proteins. PMID 26370505 DOI: 10.1002/Prot.24930  0.458
2015 Yang J, Zhang W, He B, Walker SE, Zhang H, Govindarajoo B, Virtanen J, Xue Z, Shen HB, Zhang Y. Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade. Proteins. PMID 26343917 DOI: 10.1002/Prot.24918  0.414
2015 Yang J, He BJ, Jang R, Zhang Y, Shen HB. Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins. Bioinformatics (Oxford, England). PMID 26254435 DOI: 10.1093/Bioinformatics/Btv459  0.439
2015 Dong Q, Menon R, Omenn GS, Zhang Y. Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome. Journal of Proteome Research. 14: 3750-61. PMID 26193931 DOI: 10.1021/Acs.Jproteome.5B00516  0.411
2015 Zhang J, Yang J, Jang R, Zhang Y. GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome. Structure (London, England : 1993). 23: 1538-1549. PMID 26190572 DOI: 10.1016/j.str.2015.06.007  0.343
2015 Shultis D, Dodge G, Zhang Y. Crystal structure of designed PX domain from cytokine-independent survival kinase and implications on evolution-based protein engineering. Journal of Structural Biology. PMID 26073968 DOI: 10.1016/J.Jsb.2015.06.009  0.416
2015 Chan WK, Zhang H, Yang J, Brender JR, Hur J, Özgür A, Zhang Y. GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. Bioinformatics (Oxford, England). PMID 25971743 DOI: 10.1093/Bioinformatics/Btv302  0.734
2015 Yang J, Zhang Y. I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Research. 43: W174-81. PMID 25883148 DOI: 10.1093/Nar/Gkv342  0.432
2015 Jang R, Wang Y, Xue Z, Zhang Y. NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment. Journal of Biomolecular Nmr. PMID 25737244 DOI: 10.1007/S10858-015-9914-Y  0.389
2015 Keegan RM, Bibby J, Thomas J, Xu D, Zhang Y, Mayans O, Winn MD, Rigden DJ. Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models. Acta Crystallographica. Section D, Biological Crystallography. 71: 338-43. PMID 25664744 DOI: 10.1107/S1399004714025784  0.382
2015 Cheng S, Zhang Y, Brooks CL. PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. Bmc Bioinformatics. 16: 33. PMID 25638036 DOI: 10.1186/S12859-015-0471-X  0.439
2015 Li F, Li C, Wang M, Webb GI, Zhang Y, Whisstock JC, Song J. GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome. Bioinformatics (Oxford, England). 31: 1411-9. PMID 25568279 DOI: 10.1093/Bioinformatics/Btu852  0.364
2015 Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nature Methods. 12: 7-8. PMID 25549265 DOI: 10.1038/Nmeth.3213  0.434
2015 Sun HP, Huang Y, Wang XF, Zhang Y, Shen HB. Improving accuracy of protein contact prediction using balanced network deconvolution. Proteins. 83: 485-96. PMID 25524593 DOI: 10.1002/Prot.24744  0.411
2015 Xu YY, Yang F, Zhang Y, Shen HB. Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning. Bioinformatics (Oxford, England). 31: 1111-9. PMID 25414362 DOI: 10.1093/Bioinformatics/Btu772  0.36
2015 Du H, Brender JR, Zhang J, Zhang Y. Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening. Methods (San Diego, Calif.). 71: 77-84. PMID 25220914 DOI: 10.1016/J.Ymeth.2014.08.017  0.723
2015 Zhang J, Yang J, Jang R, Zhang Y. GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome Structure. 23: 1538-1549. DOI: 10.1016/J.Str.2015.06.007  0.42
2014 Szilagyi A, Zhang Y. Template-based structure modeling of protein-protein interactions. Current Opinion in Structural Biology. 24: 10-23. PMID 24721449 DOI: 10.1016/J.Sbi.2013.11.005  0.426
2014 Quan S, Wang L, Petrotchenko EV, Makepeace KA, Horowitz S, Yang J, Zhang Y, Borchers CH, Bardwell JC. Super Spy variants implicate flexibility in chaperone action. Elife. 3: e01584. PMID 24497545 DOI: 10.7554/Elife.01584  0.346
2014 Zhang Y. Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10 Proteins. 82: 175-187. PMID 23760925 DOI: 10.1002/Prot.24341  0.448
2013 Mitra P, Shultis D, Brender JR, Czajka J, Marsh D, Gray F, Cierpicki T, Zhang Y. An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis. Plos Computational Biology. 9: e1003298. PMID 24204234 DOI: 10.1371/Journal.Pcbi.1003298  0.741
2013 Yan R, Xu D, Yang J, Walker S, Zhang Y. A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction. Scientific Reports. 3: 2619. PMID 24018415 DOI: 10.1038/Srep02619  0.436
2013 Xu D, Li H, Zhang Y. Protein depth calculation and the use for improving accuracy of protein fold recognition. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 805-16. PMID 23992298 DOI: 10.1089/cmb.2013.0071  0.357
2013 Yang J, Roy A, Zhang Y. Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Bioinformatics (Oxford, England). 29: 2588-95. PMID 23975762 DOI: 10.1093/Bioinformatics/Btt447  0.377
2013 Yang J, Jang R, Zhang Y, Shen HB. High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling Bioinformatics. 29: 2579-2587. PMID 23946502 DOI: 10.1093/Bioinformatics/Btt440  0.438
2013 Xue Z, Xu D, Wang Y, Zhang Y. ThreaDom: extracting protein domain boundary information from multiple threading alignments. Bioinformatics (Oxford, England). 29: i247-56. PMID 23812990 DOI: 10.1093/Bioinformatics/Btt209  0.359
2013 Xu YY, Yang F, Zhang Y, Shen HB. An image-based multi-label human protein subcellular localization predictor (iLocator) reveals protein mislocalizations in cancer tissues. Bioinformatics (Oxford, England). 29: 2032-40. PMID 23740749 DOI: 10.1093/Bioinformatics/Btt320  0.342
2013 Xu D, Zhang Y. Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment. Scientific Reports. 3: 1895-1895. PMID 23719418 DOI: 10.1038/Srep01895  0.432
2013 Mitra P, Shultis D, Zhang Y. EvoDesign: De novo protein design based on structural and evolutionary profiles. Nucleic Acids Research. 41: W273-280. PMID 23671331 DOI: 10.1093/Nar/Gkt384  0.438
2013 Omenn GS, Menon R, Zhang Y. Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. Journal of Proteomics. 90: 28-37. PMID 23603631 DOI: 10.1016/J.Jprot.2013.04.007  0.358
2013 Zhang Y, Skolnick J. Segment assembly, structure alignment and iterative simulation in protein structure prediction. Bmc Biology. 11: 44. PMID 23587325 DOI: 10.1186/1741-7007-11-44  0.685
2013 Abrusán G, Zhang Y, Szilágyi A. Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins. The Journal of Biological Chemistry. 288: 16127-38. PMID 23530042 DOI: 10.1074/Jbc.M113.451500  0.421
2013 Guerler A, Govindarajoo B, Zhang Y. Mapping monomeric threading to protein-protein structure prediction. Journal of Chemical Information and Modeling. 53: 717-25. PMID 23413988 DOI: 10.1021/Ci300579R  0.485
2013 Abrusán G, Szilágyi A, Zhang Y, Papp B. Turning gold into ‘junk’: transposable elements utilize central proteins of cellular networks Nucleic Acids Research. 41: 3190-3200. PMID 23341038 DOI: 10.1093/Nar/Gkt011  0.342
2013 Wu S, Li N, Ma J, Shen H, Jiang D, Chang C, Zhang C, Li L, Zhang H, Jiang J, Xu Z, Ping L, Chen T, Zhang W, Zhang T, ... ... Zhang Y, et al. First proteomic exploration of protein-encoding genes on chromosome 1 in human liver, stomach, and colon. Journal of Proteome Research. 12: 67-80. PMID 23256928 DOI: 10.1021/Pr3008286  0.31
2013 Fan YX, Zhang Y, Shen HB. LabCaS: labeling calpain substrate cleavage sites from amino acid sequence using conditional random fields. Proteins. 81: 622-634. PMID 23180633 DOI: 10.1002/Prot.24217  0.345
2013 Yang J, Roy A, Zhang Y. BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Research. 41: D1096-103. PMID 23087378 DOI: 10.1093/Nar/Gks966  0.427
2013 Xu D, Zhang Y. Toward optimal fragment generations for ab initio protein structure assembly Proteins: Structure, Function and Bioinformatics. 81: 229-239. PMID 22972754 DOI: 10.1002/Prot.24179  0.41
2013 Mitra P, Shultis D, Brender JR, Czajka J, Marsh D, Gray F, Cierpicki T, Zhang Y. Illustrative examples of the EBM design on M. tuberculosis proteins. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1003298.G006  0.606
2013 Mukherjee S, Lee KI, Zhang Y, Fisher M, Im W. Modeling, Ion Conductance, and Electrostatic Properties of the Protective Antigen Pore Structure of Anthrax Toxin Biophysical Journal. 104: 63a. DOI: 10.1016/J.Bpj.2012.11.386  0.365
2012 Garma L, Mukherjee S, Mitra P, Zhang Y. How many protein-protein interactions types exist in nature? Plos One. 7: e38913. PMID 22719985 DOI: 10.1371/Journal.Pone.0038913  0.434
2012 Deng H, Jia Y, Wei Y, Zhang Y. What is the best reference state for designing statistical atomic potentials in protein structure prediction? Proteins. 80: 2311-22. PMID 22623012 DOI: 10.1002/Prot.24121  0.367
2012 Roy A, Yang J, Zhang Y. COFACTOR: an accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Research. 40: W471-7. PMID 22570420 DOI: 10.1093/Nar/Gks372  0.446
2012 Roy A, Zhang Y. Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement. Structure (London, England : 1993). 20: 987-97. PMID 22560732 DOI: 10.1016/J.Str.2012.03.009  0.46
2012 Xu D, Zhang Y. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field Proteins: Structure, Function and Bioinformatics. 80: 1715-1735. PMID 22411565 DOI: 10.1002/Prot.24065  0.462
2012 Qi X, Hong L, Zhang Y. A variational model for oligomer-formation process of GNNQQNY peptide from yeast prion protein Sup35. Biophysical Journal. 102: 597-605. PMID 22325283 DOI: 10.1016/J.Bpj.2011.12.036  0.301
2012 Dror I, Shazman S, Mukherjee S, Zhang Y, Glaser F, Mandel-Gutfreund Y. Predicting nucleic acid binding interfaces from structural models of proteins. Proteins. 80: 482-9. PMID 22086767 DOI: 10.1002/Prot.23214  0.442
2012 Szilágyi A, Zhang Y, Závodszky P. Intra-chain 3D segment swapping spawns the evolution of new multidomain protein architectures. Journal of Molecular Biology. 415: 221-35. PMID 22079367 DOI: 10.1016/J.Jmb.2011.10.045  0.395
2012 Li Y, Zhang J, Tai D, Middaugh CR, Zhang Y, Fang J. PROTS: a fragment based protein thermo-stability potential. Proteins. 80: 81-92. PMID 21976375 DOI: 10.1002/Prot.23163  0.407
2012 Lee HS, Zhang Y. BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures. Proteins. 80: 93-110. PMID 21971880 DOI: 10.1002/Prot.23165  0.444
2011 dos Reis MA, Aparicio R, Zhang Y. Improving protein template recognition by using small-angle x-ray scattering profiles. Biophysical Journal. 101: 2770-81. PMID 22261066 DOI: 10.1016/J.Bpj.2011.10.046  0.469
2011 Zhang J, Liang Y, Zhang Y. Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling Structure. 19: 1784-1795. PMID 22153501 DOI: 10.1016/J.Str.2011.09.022  0.406
2011 Xu D, Zhang Y. Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical Journal. 101: 2525-34. PMID 22098752 DOI: 10.1016/J.Bpj.2011.10.024  0.379
2011 Roy A, Xu D, Poisson J, Zhang Y. A protocol for computer-based protein structure and function prediction. Journal of Visualized Experiments : Jove. e3259. PMID 22082966 DOI: 10.3791/3259  0.48
2011 Xu D, Zhang J, Roy A, Zhang Y. Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement. Proteins. 79: 147-60. PMID 22069036 DOI: 10.1002/Prot.23111  0.453
2011 Menon R, Roy A, Mukherjee S, Belkin S, Zhang Y, Omenn GS. Functional implications of structural predictions for alternative splice proteins expressed in Her2/neu-induced breast cancers. Journal of Proteome Research. 10: 5503-11. PMID 22003824 DOI: 10.1021/Pr200772W  0.437
2011 Kemege KE, Hickey JM, Lovell S, Battaile KP, Zhang Y, Hefty PS. Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes. Journal of Bacteriology. 193: 6517-28. PMID 21965559 DOI: 10.1128/Jb.05488-11  0.408
2011 Wu S, Szilagyi A, Zhang Y. Improving Protein Structure Prediction Using Multiple Sequence-Based Contact Predictions Structure. 19: 1182-1191. PMID 21827953 DOI: 10.1016/J.Str.2011.05.004  0.416
2011 Du H, Hu Z, Bazzoli A, Zhang Y. Prediction of inhibitory activity of epidermal growth factor receptor inhibitors using grid search-projection pursuit regression method. Plos One. 6: e22367. PMID 21811593 DOI: 10.1371/Journal.Pone.0022367  0.314
2011 Mukherjee S, Zhang Y. Protein-protein complex structure predictions by multimeric threading and template recombination. Structure (London, England : 1993). 19: 955-66. PMID 21742262 DOI: 10.1016/J.Str.2011.04.006  0.462
2011 Rankin CA, Roy A, Zhang Y, Richter M. Parkin, A Top Level Manager in the Cell's Sanitation Department. The Open Biochemistry Journal. 5: 9-26. PMID 21633666 DOI: 10.2174/1874091X01105010009  0.314
2011 Bazzoli A, Tettamanzi AGB, Zhang Y. Computational Protein Design and Large-Scale Assessment by I-TASSER Structure Assembly Simulations Journal of Molecular Biology. 407: 764-776. PMID 21329699 DOI: 10.1016/J.Jmb.2011.02.017  0.395
2010 Zhang J, Zhang Y. A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction Plos One. 5. PMID 21060880 DOI: 10.1371/Journal.Pone.0015386  0.422
2010 Zhang J, Zhang Y. GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation. Bioinformatics (Oxford, England). 26: 3004-5. PMID 20926423 DOI: 10.1093/Bioinformatics/Btq563  0.409
2010 Wu S, Zhang Y. Recognizing Protein Substructure Similarity Using Segmental Threading Structure. 18: 858-867. PMID 20637422 DOI: 10.1016/J.Str.2010.04.007  0.46
2010 Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols. 5: 725-38. PMID 20360767 DOI: 10.1038/Nprot.2010.5  0.469
2010 Xu J, Zhang Y. How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics (Oxford, England). 26: 889-95. PMID 20164152 DOI: 10.1093/Bioinformatics/Btq066  0.382
2010 SOMARELLI JA, MESA A, ROY A, ZHANG Y, HERRERA RJ. A three-dimensional model of the U1 small nuclear ribonucleoprotein particle Entomological Research. 40: 104-112. DOI: 10.1111/J.1748-5967.2010.00266.X  0.381
2009 Xu D, Zhang Y. Generating triangulated macromolecular surfaces by Euclidean Distance Transform. Plos One. 4: e8140. PMID 19956577 DOI: 10.1371/Journal.Pone.0008140  0.312
2009 Bultrini E, Brick K, Mukherjee S, Zhang Y, Silvestrini F, Alano P, Pizzi E. Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction. Bmc Genomics. 10: 445. PMID 19769795 DOI: 10.1186/1471-2164-10-445  0.406
2009 Zhang Y. I-TASSER: fully automated protein structure prediction in CASP8. Proteins. 77: 100-113. PMID 19768687 DOI: 10.1002/Prot.22588  0.409
2009 Li Y, Roy A, Zhang Y. HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures. Plos One. 4: e6701. PMID 19693270 DOI: 10.1371/Journal.Pone.0006701  0.341
2009 Mukherjee S, Zhang Y. MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming. Nucleic Acids Research. 37: e83. PMID 19443443 DOI: 10.1093/Nar/Gkp318  0.361
2009 Zhang Y. Protein structure prediction: when is it useful? Current Opinion in Structural Biology. 19: 145-155. PMID 19327982 DOI: 10.1016/J.Sbi.2009.02.005  0.449
2009 Li Y, Zhang Y. REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins. 76: 665-676. PMID 19274737 DOI: 10.1002/Prot.22380  0.378
2008 Wu S, Zhang Y. ANGLOR: a composite machine-learning algorithm for protein backbone torsion angle prediction. Plos One. 3. PMID 18923703 DOI: 10.1371/Journal.Pone.0003400  0.389
2008 Zhang Y. Progress and challenges in protein structure prediction. Current Opinion in Structural Biology. 18: 342-348. PMID 18436442 DOI: 10.1016/J.Sbi.2008.02.004  0.458
2008 Wu S, Zhang Y. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics (Oxford, England). 24: 924-31. PMID 18296462 DOI: 10.1093/Bioinformatics/Btn069  0.363
2008 Wu S, Zhang Y. MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins. 72: 547-556. PMID 18247410 DOI: 10.1002/Prot.21945  0.422
2008 Zhang Y. I-TASSER server for protein 3D structure prediction. Bmc Bioinformatics. 9: 40. PMID 18215316 DOI: 10.1186/1471-2105-9-40  0.41
2007 Lorenzen S, Zhang Y. Monte Carlo refinement of rigid‐body protein docking structures with backbone displacement and side‐chain optimization Protein Science. 16: 2716-2725. PMID 17965193 DOI: 10.1110/Ps.072847207  0.429
2007 Zhang Y. Template‐based modeling and free modeling by I‐TASSER in CASP7 Proteins. 69: 108-117. PMID 17894355 DOI: 10.1002/Prot.21702  0.426
2007 Wu S, Skolnick J, Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. Bmc Biology. 5: 17. PMID 17488521 DOI: 10.1186/1741-7007-5-17  0.669
2007 Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Research. 35: 3375-3382. PMID 17478507 DOI: 10.1093/Nar/Gkm251  0.421
2007 Lorenzen S, Zhang Y. Identification of near-native structures by clustering protein docking conformations. Proteins. 68: 187-194. PMID 17397057 DOI: 10.1002/Prot.21442  0.385
2007 Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality Proteins: Structure, Function, and Bioinformatics. 68: 1020-1020. DOI: 10.1002/Prot.21643  0.597
2006 Pandit SB, Zhang Y, Skolnick J. TASSER-Lite: an automated tool for protein comparative modeling. Biophysical Journal. 91: 4180-90. PMID 16963505 DOI: 10.1529/Biophysj.106.084293  0.665
2006 Zhang Y, Devries ME, Skolnick J. Structure modeling of all identified G protein-coupled receptors in the human genome. Plos Computational Biology. 2: e13. PMID 16485037 DOI: 10.1371/Journal.Pcbi.0020013  0.663
2006 Zhang Y, Hubner IA, Arakaki AK, Shakhnovich E, Skolnick J. On the origin and highly likely completeness of single-domain protein structures. Proceedings of the National Academy of Sciences of the United States of America. 103: 2605-10. PMID 16478803 DOI: 10.1073/Pnas.0509379103  0.669
2006 Grimm V, Zhang Y, Skolnick J. Benchmarking of dimeric threading and structure refinement. Proteins. 63: 457-65. PMID 16463265 DOI: 10.1002/Prot.20878  0.655
2006 Lee SY, Zhang Y, Skolnick J. TASSER-based refinement of NMR structures. Proteins. 63: 451-6. PMID 16456861 DOI: 10.1002/Prot.20902  0.544
2006 Zhang Y, DeVries ME, Skolnick J. Correction: Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome Plos Computational Biology. 2. DOI: 10.1371/Journal.Pcbi.0020029  0.521
2005 Zhang Y, Arakaki AK, Skolnick J. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins. 61: 91-8. PMID 16187349 DOI: 10.1002/Prot.20724  0.596
2005 Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Research. 33: 2302-9. PMID 15849316 DOI: 10.1093/Nar/Gki524  0.681
2005 Zhou H, Zhang Y. Hierarchical chain model of spider capture silk elasticity. Physical Review Letters. 94: 28104-28104. PMID 15698235 DOI: 10.1103/Physrevlett.94.028104  0.344
2005 Zhang Y, Skolnick J. The protein structure prediction problem could be solved using the current PDB library. Proceedings of the National Academy of Sciences of the United States of America. 102: 1029-34. PMID 15653774 DOI: 10.1073/Pnas.0407152101  0.682
2004 Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality Proteins: Structure, Function and Genetics. 57: 702-710. PMID 15476259 DOI: 10.1002/Prot.20264  0.629
2004 Zhang Y, Skolnick J. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins Biophysical Journal. 87: 2647-2655. PMID 15454459 DOI: 10.1529/Biophysj.104.045385  0.703
2004 Li W, Zhang Y, Skolnick J. Application of sparse NMR restraints to large-scale protein structure prediction Biophysical Journal. 87: 1241-1248. PMID 15298926 DOI: 10.1529/Biophysj.104.044750  0.67
2004 Skolnick J, Kihara D, Zhang Y. Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm Proteins: Structure, Function and Genetics. 56: 502-518. PMID 15229883 DOI: 10.1002/Prot.20106  0.639
2004 Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale Proceedings of the National Academy of Sciences of the United States of America. 101: 7594-7599. PMID 15126668 DOI: 10.1073/Pnas.0305695101  0.694
2004 Zhang Y, Skolnick J. SPICKER: A clustering approach to identify near-native protein folds Journal of Computational Chemistry. 25: 865-871. PMID 15011258 DOI: 10.1002/Jcc.20011  0.634
2004 Arakaki AK, Zhang Y, Skolnick J. Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinformatics (Oxford, England). 20: 1087-96. PMID 14764543 DOI: 10.1093/Bioinformatics/Bth044  0.627
2003 Skolnick J, Zhang Y, Arakaki AK, Kolinski A, Boniecki M, Szilágyi A, Kihara D. TOUCHSTONE: a unified approach to protein structure prediction. Proteins. 53: 469-79. PMID 14579335 DOI: 10.1002/Prot.10551  0.599
2003 Li W, Zhang Y, Kihara D, Huang YJ, Zheng D, Montelione GT, Kolinski A, Skolnick J. TOUCHSTONEX: Protein structure prediction with sparse NMR data Proteins: Structure, Function and Genetics. 53: 290-306. PMID 14517980 DOI: 10.1002/Prot.10499  0.641
2003 Zhang Y, Kolinski A, Skolnick J. TOUCHSTONE II: A new approach to ab initio protein structure prediction Biophysical Journal. 85: 1145-1164. PMID 12885659 DOI: 10.1016/S0006-3495(03)74551-2  0.649
2002 Zhang Y, Kihara D, Skolnick J. Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding Proteins: Structure, Function and Genetics. 48: 192-201. PMID 12112688 DOI: 10.1002/Prot.10141  0.598
2002 Kihara D, Zhang Y, Lu H, Kolinski A, Skolnick J. Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genome Proceedings of the National Academy of Sciences of the United States of America. 99: 5993-5998. PMID 11959918 DOI: 10.1073/Pnas.092135699  0.689
2001 Zhang Y, Zhou H, Ou-Yang ZC. Stretching Single-Stranded DNA: Interplay of Electrostatic, Base-Pairing, and Base-Pair Stacking Interactions Biophysical Journal. 81: 1133-1143. PMID 11463654 DOI: 10.1016/S0006-3495(01)75770-0  0.316
2001 Zhou H, Zhang Y, Ou-Yang ZC. Stretch-Induced Hairpin-Coil Transitions in Designed Polynucleotide Chains Physical Review Letters. 86: 356-359. PMID 11177830 DOI: 10.1103/Physrevlett.86.356  0.347
2001 Zhang Y, Skolnick J. Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures Journal of Chemical Physics. 115: 5027-5032. DOI: 10.1063/1.1396672  0.523
Low-probability matches (unlikely to be authored by this person)
2018 Zhu Y, Lei Q, Li D, Zhang Y, Jiang X, Hu Z, Xu G. Proteomic and Biochemical Analyses Reveal a Novel Mechanism for Promoting Protein Ubiquitination and Degradation by UFBP1, a Key Component of Ufmylation. Journal of Proteome Research. PMID 29533670 DOI: 10.1021/acs.jproteome.7b00843  0.299
2017 An Y, Wang J, Li C, Revote J, Zhang Y, Naderer T, Hayashida M, Akutsu T, Webb GI, Lithgow T, Song J. SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems. Scientific Reports. 7: 41031. PMID 28112271 DOI: 10.1038/Srep41031  0.299
2020 Liu X, Zhang W, Liu J, Pearce R, Zhang Y, Zhang K, Ruan Q, Yu Y, Liu B. Mg2+ inhibits heat-induced aggregation of BSA: The mechanism and its binding site Food Hydrocolloids. 101: 105450. DOI: 10.1016/J.Foodhyd.2019.105450  0.299
2019 Khalid RR, Maryam A, Fadouloglou VE, Siddiqi AR, Zhang Y. Cryo-EM density map fitting driven in-silico structure of human soluble guanylate cyclase (hsGC) reveals functional aspects of inter-domain cross talk upon NO binding. Journal of Molecular Graphics & Modelling. 90: 109-119. PMID 31055154 DOI: 10.1016/j.jmgm.2019.04.009  0.299
2001 Zhou H, Zhang Y. Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter? Journal of Chemical Physics. 114: 8694-8700. DOI: 10.1063/1.1368401  0.297
2015 Li HD, Menon R, Govindarajoo B, Panwar B, Zhang Y, Omenn GS, Guan Y. Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project. Journal of Proteome Research. PMID 26216192 DOI: 10.1021/Acs.Jproteome.5B00494  0.297
2011 Jin GZ, Li Y, Cong WM, Yu H, Dong H, Shu H, Liu XH, Yan GQ, Zhang L, Zhang Y, Kang XN, Guo K, Wang ZD, Yang PY, Liu YK. iTRAQ-2DLC-ESI-MS/MS based identification of a new set of immunohistochemical biomarkers for classification of dysplastic nodules and small hepatocellular carcinoma. Journal of Proteome Research. 10: 3418-28. PMID 21631109 DOI: 10.1021/Pr200482T  0.294
2014 Lu W, Zhang Y, Shen C, Yin X, Liu X, Yang P. [A method using spectrum alignment to improve analysis efficiency of liquid chromatography combined with mass spectrometry]. SE Pu = Chinese Journal of Chromatography / Zhongguo Hua Xue Hui. 32: 349-54. PMID 25069322 DOI: 10.3724/Sp.J.1123.2013.10030  0.292
2021 Verba K, Gupta M, Azumaya C, Moritz M, Pourmal S, Diallo A, Merz G, Jang G, Bouhaddou M, Fossati A, Brilot A, Diwanji D, Hernandez E, Herrera N, Kratochvil H, ... ... Zhang Y, et al. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. Research Square. PMID 34031651 DOI: 10.21203/rs.3.rs-515215/v1  0.291
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2016 Hu X, Dong Q, Yang J, Zhang Y. Recognizing metal and acid radical ion binding sites by integrating ab initio modeling with template-based transferals. Bioinformatics (Oxford, England). PMID 27378301 DOI: 10.1093/Bioinformatics/Btw396  0.29
2008 Gao M, Deng C, Yu W, Zhang Y, Yang P, Zhang X. Large scale depletion of the high-abundance proteins and analysis of middle- and low-abundance proteins in human liver proteome by multidimensional liquid chromatography. Proteomics. 8: 939-47. PMID 18324721 DOI: 10.1002/Pmic.200600099  0.289
2011 Hong L, Qi X, Zhang Y. A lattice-gas model for amyloid fibril aggregation. Epl. 94: 68006. PMID 23275684 DOI: 10.1209/0295-5075/94/68006  0.288
2018 Hu R, Xiao J, Gu T, Yu X, Zhang Y, Chang J, Yang G, He G. Correction to: Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.). Bmc Genomics. 19: 852. PMID 30497365 DOI: 10.1186/S12864-018-5252-2  0.288
2022 Wang J, Zhang Y, Shi H, Yang Y, Wang S, Wang F. Construction of Mitochondrial Protection and Monitoring Model of Lon Protease Based on Machine Learning under Myocardial Ischemia Environment. Journal of Environmental and Public Health. 2022: 4805009. PMID 36254306 DOI: 10.1155/2022/4805009  0.287
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2022 Zhang X, Zhang B, Freddolino PL, Zhang Y. CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks. Nature Methods. 19: 195-204. PMID 35132244 DOI: 10.1038/s41592-021-01389-9  0.285
2012 Nadeau OW, Lane LA, Xu D, Sage J, Priddy TS, Artigues A, Villar MT, Yang Q, Robinson CV, Zhang Y, Carlson GM. Structure and location of the regulatory β subunits in the (αβγδ)4 phosphorylase kinase complex. The Journal of Biological Chemistry. 287: 36651-61. PMID 22969083 DOI: 10.1074/Jbc.M112.412874  0.284
2017 Rimmer MA, Nadeau OW, Yang J, Artigues A, Zhang Y, Carlson GM. The Structure of the Large Regulatory α Subunit of Phosphorylase Kinase Examined by Modeling and Hydrogen-Deuterium Exchange. Protein Science : a Publication of the Protein Society. PMID 29098725 DOI: 10.1002/Pro.3339  0.282
2003 Zhou H, Zhang Y, Ou-Yang ZC. The elastic theory of a single DNA molecule Pramana. 61: 353-360. DOI: 10.1007/Bf02708315  0.282
2017 Yang Y, Fan X, Mao M, Song X, Wu P, Zhang Y, Jin Y, Yang Y, Chen L, Wang Y, Wong CC, Xiao X, Wang Z. Extensive translation of circular RNAs driven by N(6)-methyladenosine. Cell Research. PMID 28281539 DOI: 10.1038/Cr.2017.31  0.281
2015 Liu YR, Huang T, Gai YB, Zhang Y, Feng YJ, Huang W. Three-Dimensional Assignment of the Structures of Atomic Clusters: an Example of Au8M (M=Si, Ge, Sn) Anion Clusters. Scientific Reports. 5: 17738. PMID 26631620 DOI: 10.1038/Srep17738  0.279
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2011 Guild K, Zhang Y, Stacy R, Mundt E, Benbow S, Green A, Myler PJ. Wheat germ cell-free expression system as a pathway to improve protein yield and solubility for the SSGCID pipeline. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 67: 1027-31. PMID 21904045 DOI: 10.1107/S1744309111032143  0.278
2019 Gong S, Zhang C, Zhang Y. RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA. Bioinformatics (Oxford, England). PMID 31161212 DOI: 10.1093/Bioinformatics/Btz282  0.277
2012 Zhang Y, Zhao AC, Sima YH, Lu C, Xiang ZH, Nakagaki M. The molecular structures of major ampullate silk proteins of the wasp spider, Argiope bruennichi: a second blueprint for synthesizing de novo silk. Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology. 164: 151-8. PMID 23262065 DOI: 10.1016/j.cbpb.2012.12.002  0.277
2017 Luo Q, Wei Q, Wang R, Zhang Y, Zhang F, He Y, Zhou S, Feng J, Yang G, He G. BdCIPK31, a Calcineurin B-Like Protein-Interacting Protein Kinase, Regulates Plant Response to Drought and Salt Stress. Frontiers in Plant Science. 8: 1184. PMID 28736568 DOI: 10.3389/Fpls.2017.01184  0.276
2013 Bai Q, Zhang Y, Ban Y, Liu H, Yao X. Computational study on the different ligands induced conformation change of β2 adrenergic receptor-Gs protein complex. Plos One. 8: e68138. PMID 23922653 DOI: 10.1371/journal.pone.0068138  0.275
2014 Borgwardt DS, Martin AD, Van Hemert JR, Yang J, Fischer CL, Recker EN, Nair PR, Vidva R, Chandrashekaraiah S, Progulske-Fox A, Drake D, Cavanaugh JE, Vali S, Zhang Y, Brogden KA. Histatin 5 binds to Porphyromonas gingivalis hemagglutinin B (HagB) and alters HagB-induced chemokine responses. Scientific Reports. 4: 3904. PMID 24473528 DOI: 10.1038/Srep03904  0.274
2024 Pan X, Ren L, Yang Y, Xu Y, Ning L, Zhang Y, Luo H, Zou Q, Zhang Y. MCSdb, a database of proteins residing in membrane contact sites. Scientific Data. 11: 281. PMID 38459036 DOI: 10.1038/s41597-024-03104-7  0.273
2017 Zhang F, Wei Q, Shi J, Jin X, He Y, Zhang Y, Luo Q, Wang Y, Chang J, Yang G, He G. Brachypodium distachyon BdPP2CA6 Interacts with BdPYLs and BdSnRK2 and Positively Regulates Salt Tolerance in Transgenic Arabidopsis. Frontiers in Plant Science. 8: 264. PMID 28293246 DOI: 10.3389/Fpls.2017.00264  0.272
2015 Xu K, Jiang S, Zhu Y, Huang T, Liu Y, Zhang Y, Lv Y, Huang W. On the properties of Au2P3z (z = −1, 0, +1): analysis of geometry, interaction, and electron density Rsc Advances. 5: 26071-26080. DOI: 10.1039/C5Ra00131E  0.271
2001 Zhou H, Zhang Y, Ou-Yang Z, Lindsay SM, Feng XZ, Balagurumoorthy P, Harrington RE. Conformation and rigidity of DNA microcircles containing waf1 response element for p53 regulatory protein. Journal of Molecular Biology. 306: 227-38. PMID 11237596 DOI: 10.1006/Jmbi.2000.4370  0.271
2021 Zhang C, Zheng W, Cheng M, Omenn GS, Freddolino PL, Zhang Y. Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome. Journal of Proteome Research. PMID 33393786 DOI: 10.1021/acs.jproteome.0c00359  0.27
2018 Luo J, Guan M, Zhang Y, Chen L, Zeng Y. The influence of MBE and device structure on the electrical properties of GaAs HEMT biosensors Journal of Semiconductors. 39: 124007. DOI: 10.1088/1674-4926/39/12/124007  0.269
2015 Sun J, Liu W, Hu Y, Li M, Yang X, Zhang Y, Xu M. Structurally Improved, Core-in-Shell, CaO-Based Sorbent Pellets for CO2 Capture Energy & Fuels. 29: 6636-6644. DOI: 10.1021/Acs.Energyfuels.5B01419  0.269
2019 Lin H, Wang M, Zhang YW, Tong S, Leal RA, Shetty R, Vaddi K, Luengo JI. Discovery of Potent and Selective Covalent Protein Arginine Methyltransferase 5 (PRMT5) Inhibitors. Acs Medicinal Chemistry Letters. 10: 1033-1038. PMID 31312404 DOI: 10.1021/acsmedchemlett.9b00074  0.269
2014 Chang C, Li L, Zhang C, Wu S, Guo K, Zi J, Chen Z, Jiang J, Ma J, Yu Q, Fan F, Qin P, Han M, Su N, Chen T, ... ... Zhang Y, et al. Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP. Journal of Proteome Research. 13: 38-49. PMID 24256510 DOI: 10.1021/Pr4009018  0.268
2012 Yang Y, Dib-Hajj SD, Zhang J, Zhang Y, Tyrrell L, Estacion M, Waxman SG. Structural modelling and mutant cycle analysis predict pharmacoresponsiveness of a Na(V)1.7 mutant channel. Nature Communications. 3: 1186. PMID 23149731 DOI: 10.1038/Ncomms2184  0.268
2020 Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US. Publisher Correction: Cryo-EM structure of the human MLL1 core complex bound to the nucleosome. Nature Communications. 11: 1165. PMID 32109228 DOI: 10.1038/S41467-020-14973-Y  0.267
2018 Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, ... ... Zhang Y, et al. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports. 8: 9939. PMID 29967418 DOI: 10.1038/s41598-018-26812-8  0.266
2018 Chen S, Yang J, Zhang Y, Duan C, Liu Q, Huang Z, Xu Y, Zhou L, Xu G. Ubiquitin-conjugating enzyme UBE2O regulates cellular clock function by promoting the degradation of the transcription factor BMAL1. The Journal of Biological Chemistry. PMID 29871923 DOI: 10.1074/Jbc.Ra117.001432  0.266
2024 Miao Y, Li L, Wang Y, Wang J, Zhou Y, Guo L, Zhao Y, Nie D, Zhang Y, Zhang X, Gan Y. Regulating protein corona on nanovesicles by glycosylated polyhydroxy polymer modification for efficient drug delivery. Nature Communications. 15: 1159. PMID 38326312 DOI: 10.1038/s41467-024-45254-7  0.264
2016 Wang C, Liu Y, Chang C, Wu S, Gao J, Zhang Y, Chen Y, Zhong F, Deng G. Human Fallopian Tube Proteome Shows High Coverage of Mesenchymal Stem Cells Associated Proteins. Bioscience Reports. PMID 26759384 DOI: 10.1042/BSR20150220  0.264
2020 Tseng-Rogenski SS, Munakata K, Choi DY, Martin PK, Mehta S, Koi M, Zheng W, Zhang Y, Carethers JM. The human DNA mismatch repair protein MSH3 contains nuclear localization and export signals that enable nuclear-cytosolic shuttling in response to inflammation. Molecular and Cellular Biology. PMID 32284349 DOI: 10.1128/Mcb.00029-20  0.263
2020 Pan X, Thompson MC, Zhang Y, Liu L, Fraser JS, Kelly MJS, Kortemme T. Expanding the space of protein geometries by computational design of de novo fold families. Science (New York, N.Y.). 369: 1132-1136. PMID 32855341 DOI: 10.1126/Science.Abc0881  0.262
2015 Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D, Dieterich SH, Staker BL, Gardberg AS, Choi R, ... ... Zhang Y, et al. Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinburgh, Scotland). 95: 142-8. PMID 25613812 DOI: 10.1016/J.Tube.2014.12.003  0.261
2018 Zhang Y, Gong X, Chen X, Yin L, Zhang J, Liu W. Performance of synthetic CaO-based sorbent pellets for CO2 capture and kinetic analysis Fuel. 232: 205-214. DOI: 10.1016/J.Fuel.2018.05.143  0.26
2018 Tang J, Zhang Y, Fu J, Wang Y, Li Y, Yang Q, Yao L, Xue W, Zhu F. Computational Advances in the Label-free Quantification of Cancer Proteomics Data. Current Pharmaceutical Design. PMID 30387388 DOI: 10.2174/1381612824666181102125638  0.259
2020 Ong E, Huang X, Pearce R, Zhang Y, He Y. Rational Design of SARS-CoV-2 Spike Glycoproteins To Increase Immunogenicity By T Cell Epitope Engineering. Biorxiv : the Preprint Server For Biology. PMID 32817949 DOI: 10.1101/2020.08.14.251496  0.258
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2019 Lee H, Li C, Zhang Y, Zhang D, Otterbein LE, Jin Y. Caveolin-1 selectively regulates microRNA sorting into microvesicles after noxious stimuli. The Journal of Experimental Medicine. PMID 31235510 DOI: 10.1084/Jem.20182313  0.256
2009 He X, Zhang Y, Yu Z. In silico cloning, expression of Rieske-like apoprotein gene and protein subcellular localization in the Pacific oyster, Crassostrea gigas. Molecular Biology Reports. 37: 3259-64. PMID 19876765 DOI: 10.1007/s11033-009-9910-y  0.256
2022 Zhou X, Peng C, Zheng W, Li Y, Zhang G, Zhang Y. DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. Nucleic Acids Research. PMID 35536281 DOI: 10.1093/nar/gkac340  0.256
2012 Hong L, Qi X, Zhang Y. Dissecting the kinetic process of amyloid fiber formation through asymptotic analysis. Journal of Physical Chemistry B. 116: 6611-6617. PMID 22126094 DOI: 10.1021/Jp205702U  0.255
2022 Zhu YH, Zhang C, Liu Y, Omenn GS, Freddolino PL, Yu DJ, Zhang Y. Integrating transcript expression profiles with protein homology inferences for gene function prediction. Genomics, Proteomics & Bioinformatics. PMID 35568117 DOI: 10.1016/j.gpb.2022.03.001  0.255
2018 Zhang Y, Zhang J, Guo J, Zhou F, Singh S, Xu X, Xie Q, Yang Z, Huang CF. F-box protein RAE1 regulates the stability of the aluminum-resistance transcription factor STOP1 in . Proceedings of the National Academy of Sciences of the United States of America. PMID 30559192 DOI: 10.1073/Pnas.1814426116  0.254
2016 Hu Y, Liu W, Sun J, Yang X, Zhou Z, Zhang Y, Xu M. High Temperature CO2 Capture on Novel Yb2O3-Supported CaO-Based Sorbents Energy & Fuels. 30: 6606-6613. DOI: 10.1021/Acs.Energyfuels.6B01185  0.253
2019 Zhuang Y, Wang C, Zhang Y, Chen S, Wang D, Liu Q, Zhou G, Chai G. Overexpression of Confers Tolerance to Drought Stress Depending on Its CCCH Domain in . Frontiers in Plant Science. 10: 1748. PMID 32063912 DOI: 10.3389/Fpls.2019.01748  0.253
2017 Xu T, Park SS, Giaimo BD, Hall D, Ferrante F, Ho DM, Hori K, Anhezini L, Ertl I, Bartkuhn M, Zhang H, Milon E, Ha K, Conlon KP, Kuick R, ... ... Zhang Y, et al. RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1. The Embo Journal. PMID 29030483 DOI: 10.15252/Embj.201796525  0.253
2006 Zhang Y, Lin H, Zhang B, Mi C. Performance Modeling and Optimization of a Novel Multi-mode Hybrid Powertrain Journal of Mechanical Design. 128: 79-89. DOI: 10.1115/1.2114892  0.252
2014 Holdren GO, Rosenthal DJ, Yang J, Bates AM, Fischer CL, Zhang Y, Brogden NK, Brogden KA. Antimicrobial Activity of Chemokine CXCL10 for Dermal and Oral Microorganisms. Antibiotics (Basel, Switzerland). 3: 527-539. PMID 25859394 DOI: 10.3390/Antibiotics3040527  0.252
2012 Chen L, Hu W, Tan S, Wang M, Ma Z, Zhou S, Deng X, Zhang Y, Huang C, Yang G, He G. Genome-wide identification and analysis of MAPK and MAPKK gene families in Brachypodium distachyon. Plos One. 7: e46744. PMID 23082129 DOI: 10.1371/Journal.Pone.0046744  0.252
2020 Mao F, Mu H, Wong NK, Liu K, Song J, Qiu J, Lin Y, Zhang X, Xu D, Xiang Z, Li J, Zhang Y, Yu Z. Hemocyte phagosomal proteome is dynamically shaped by cytoskeleton remodeling and interorganellar communication with endoplasmic reticulum during phagocytosis in a marine invertebrate, Crassostrea gigas. Scientific Reports. 10: 6577. PMID 32313134 DOI: 10.1038/S41598-020-63676-3  0.251
2022 Zhou X, Zheng W, Li Y, Pearce R, Zhang C, Bell EW, Zhang G, Zhang Y. I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction. Nature Protocols. PMID 35931779 DOI: 10.1038/s41596-022-00728-0  0.251
2020 Zhou X, Li Y, Zhang C, Zheng W, Zhang G, Zhang Y. Progressive and accurate assembly of multi-domain protein structures from cryo-EM density maps. Biorxiv : the Preprint Server For Biology. PMID 33083802 DOI: 10.1101/2020.10.15.340455  0.251
2019 Li Z, Zhang Y, Zou D, Zhao Y, Wang HL, Zhang Y, Xia X, Luo J, Guo H, Zhang Z. LSD 3.0: a comprehensive resource for the leaf senescence research community. Nucleic Acids Research. PMID 31599330 DOI: 10.1093/Nar/Gkz898  0.251
2018 Xu X, Hao L, Zhu J, Tang B, Zhou Q, Song F, Chen T, Zhang S, Dong L, Lan L, Wang Y, Sang J, Liang F, Cao J, Liu F, ... ... Zhang Y, ... ... Zhang Y, et al. Database Resources of the BIG Data Center in 2018 Nucleic Acids Research. 46. PMID 29036542 DOI: 10.1093/Nar/Gkx897  0.25
2023 Yao J, Wang ZN, Liu H, Jin H, Zhang Y. Survey of Acetylation for Thermoanaerobacter tengcongensis. Applied Biochemistry and Biotechnology. PMID 36809429 DOI: 10.1007/s12010-023-04361-9  0.25
2002 Dessinges M-, Maier B, Zhang Y, Peliti M, Bensimon D, Croquette V. Stretching single stranded DNA, a model polyelectrolyte. Physical Review Letters. 89: 248102. PMID 12484983 DOI: 10.1103/Physrevlett.89.248102  0.249
2019 Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US. Cryo-EM structure of the human MLL1 core complex bound to the nucleosome. Nature Communications. 10: 5540. PMID 31804488 DOI: 10.1038/S41467-019-13550-2  0.249
2019 Hong J, Luo Y, Mou M, Fu J, Zhang Y, Xue W, Xie T, Tao L, Lou Y, Zhu F. Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery. Briefings in Bioinformatics. PMID 31860715 DOI: 10.1093/bib/bbz120  0.249
2017 Luo Q, Wei Q, Wang R, Zhang Y, Zhang F, He Y, Yang G, He G. Ectopic expression of BdCIPK31 confers enhanced low-temperature tolerance in transgenic tobacco plants. Acta Biochimica Et Biophysica Sinica. PMID 29309501 DOI: 10.1093/Abbs/Gmx140  0.248
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2017 Xia CQ, Han K, Qi Y, Zhang Y, Yu DJ. A Self-Training Subspace Clustering Algorithm under Low-Rank Representation for Cancer Classification on Gene Expression Data. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 28600258 DOI: 10.1109/Tcbb.2017.2712607  0.246
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2017 Zhang Y, Chen X, Huang Y, Zhang C, Li F, Shu H. The Role of Intrinsic Defects in Electrocatalytic Activity of Monolayer VS2 Basal Planes for the Hydrogen Evolution Reaction The Journal of Physical Chemistry C. 121: 1530-1536. DOI: 10.1021/Acs.Jpcc.6B11987  0.246
2020 Zhang Y, Gong X, Peng Y, Leng E, Li Y, Li X. Experimental and Kinetic Study on CaO-based CO2 Sorbent Pellets with Different Binders Energy & Fuels. 34: 2028-2034. DOI: 10.1021/Acs.Energyfuels.9B03438  0.246
2017 Sang J, Wang Z, Li M, Cao J, Niu G, Xia L, Zou D, Wang F, Xu X, Han X, Fan J, Yang Y, Zuo W, Zhang Y, Zhao W, et al. ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization. Nucleic Acids Research. PMID 29036693 DOI: 10.1093/Nar/Gkx875  0.245
2021 Fu T, Li F, Zhang Y, Yin J, Qiu W, Li X, Liu X, Xin W, Wang C, Yu L, Gao J, Zheng Q, Zeng S, Zhu F. VARIDT 2.0: structural variability of drug transporter. Nucleic Acids Research. PMID 34747471 DOI: 10.1093/nar/gkab1013  0.244
2018 Li J, Zhang Y, Zhang Y, Mao F, Xiao S, Xiang Z, Ma H, Yu Z. A Lysin motif (LysM)-containing protein from Hong Kong oyster, Crassostrea hongkongensis functions as a pattern recognition protein and an antibacterial agent. Gene. PMID 29960066 DOI: 10.1016/j.gene.2018.06.091  0.244
2013 Fu J, Ling S, Liu Y, Yang J, Naveh S, Hannah M, Gilon C, Zhang Y, Holoshitz J. A small shared epitope-mimetic compound potently accelerates osteoclast-mediated bone damage in autoimmune arthritis. Journal of Immunology (Baltimore, Md. : 1950). 191: 2096-103. PMID 23885107 DOI: 10.4049/Jimmunol.1203231  0.244
2018 Zhang Y, Zou J, Zhao X, Yuan Z, Yi Z. Hepatitis C virus NS5A inhibitor daclatasvir allosterically impairs NS4B-involved protein-protein interactions within the viral replicase and disrupts the replicase quaternary structure in a replicase assembly surrogate system. The Journal of General Virology. PMID 30516462 DOI: 10.1099/jgv.0.001180  0.243
2016 Sun G, Cao C, Chen W, Zhang Y, Dai Y. Differential proteomic analysis of respiratory failure in peripheral blood mononuclear cells using iTRAQ technology. Biomedical Reports. 4: 573-577. PMID 27123249 DOI: 10.3892/br.2016.633  0.243
2021 Woodard J, Zheng W, Zhang Y. Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders. Plos Computational Biology. 17: e1009370. PMID 34529671 DOI: 10.1371/journal.pcbi.1009370  0.243
2020 Zhang Y, Meng J, Chen K, Wu Q, Wu X, Li C. Behind the Candelabra: A Facile Flame Vapor Deposition Method for Interfacial Engineering of Garnet Electrolyte to Enable Ultralong Cycling Solid-State Li-FeF3 Conversion Batteries. Acs Applied Materials & Interfaces. PMID 32602697 DOI: 10.1021/Acsami.0C08203  0.242
2017 Zhang B, Leng E, Wang Y, Gong X, Zhang Y, Xu M. Characterization of Water-Soluble Intermediates and Solid Residues from Fast Pyrolysis of Cellulose in a Wire-Mesh Reactor Bioresources. 12: 2731-2747. DOI: 10.15376/Biores.12.2.2731-2747  0.242
2017 Li X, Liu CX, Xue W, Zhang Y, Jiang S, Yin QF, Wei J, Yao RW, Yang L, Chen LL. Coordinated circRNA Biogenesis and Function with NF90/NF110 in Viral Infection. Molecular Cell. PMID 28625552 DOI: 10.1016/J.Molcel.2017.05.023  0.242
2011 Ma F, Zhang H, Zhai Y, Huang W, Zhao C, Ou S, Zhou H, Yuan W, Wang Z, Wang H, Yue W, Yu L, Li P, Xia X, Cai M, ... Zhang Y, et al. Functional polymorphism -31C/G in the promoter of BIRC5 gene and risk of nasopharyngeal carcinoma among chinese. Plos One. 6: e16748. PMID 21304814 DOI: 10.1371/Journal.Pone.0016748  0.242
2017 Wang JL, Saha TT, Zhang Y, Zhang C, Raikhel AS. Juvenile hormone and its receptor methoprene-tolerant promote ribosomal biogenesis and vitellogenesis in the Aedes aegypti mosquito. The Journal of Biological Chemistry. PMID 28446607 DOI: 10.1074/Jbc.M116.761387  0.241
2018 Leng E, Costa M, Peng Y, Zhang Y, Gong X, Zheng A, Huang Y, Xu M. Role of different chain end types in pyrolysis of glucose-based anhydro-sugars and oligosaccharides Fuel. 234: 738-745. DOI: 10.1016/J.Fuel.2018.07.075  0.241
2020 Xu M, Li S, Guan M, Zhang Y, Zeng Y. Extended-gate AlGaAs/GaAs HEMT for accurate cardiac troponin I antigen detection in clinical human serum Applied Physics Express. 13: 21003. DOI: 10.35848/1882-0786/Ab6A00  0.241
2016 Li F, Li C, Revote J, Zhang Y, Webb GI, Li J, Song J, Lithgow T. GlycoMine(struct): a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features. Scientific Reports. 6: 34595. PMID 27708373 DOI: 10.1038/srep34595  0.241
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2021 Zhang B, Zhang W, Pearce R, Zhang Y, Shen HB. Fitting Low-Resolution Protein Structures into Cryo-EM Density Maps by Multiobjective Optimization of Global and Local Correlations. The Journal of Physical Chemistry. B. PMID 33397114 DOI: 10.1021/acs.jpcb.0c09903  0.241
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2018 Zhang Y, Zhao H, Zhou S, He Y, Luo Q, Zhang F, Qiu D, Feng J, Wei Q, Chen L, Chen M, Chang J, Yang G, He G. Expression of TaGF14b, a 14-3-3 adaptor protein gene from wheat, enhances drought and salt tolerance in transgenic tobacco. Planta. PMID 29616395 DOI: 10.1007/S00425-018-2887-9  0.238
2016 Zhang Y, Liu W, Yang X, Sun J, Hu Y, Xu M. Incorporation of CaO in inert solid matrix by spray drying sol mixture of precursors Rsc Advances. 6: 57658-57666. DOI: 10.1039/C6Ra10958F  0.237
2024 Shendy NAM, Bikowitz M, Sigua LH, Zhang Y, Mercier A, Khashana Y, Nance S, Liu Q, Delahunty IM, Robinson S, Goel V, Rees MG, Ronan MA, Wang T, Kocak M, et al. Group 3 medulloblastoma transcriptional networks collapse under domain specific EP300/CBP inhibition. Nature Communications. 15: 3483. PMID 38664416 DOI: 10.1038/s41467-024-47102-0  0.236
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2023 Song L, Weng K, Bao Q, Wu J, Zhang Y, Xu Q, Zhang Y. TMT-based quantitative proteomic analysis unveils uterine fluid difference in hens producing normal and pimpled eggs. Poultry Science. 102: 103081. PMID 37774518 DOI: 10.1016/j.psj.2023.103081  0.236
2019 Liu TY, Zhang YC, Lin YQ, Hu YF, Zhang Y, Wang D, Wang Y, Ning L. Exploration of invasive mechanisms via global ncRNA-associated virus-host crosstalk. Genomics. PMID 31626899 DOI: 10.1016/j.ygeno.2019.10.002  0.236
2020 Guo J, Zhang Y, Gao H, Li S, Wang ZY, Huang CF. Mutation of HPR1 encoding a component of the THO/TREX complex reduces STOP1 accumulation and aluminum resistance in Arabidopsis thaliana. The New Phytologist. PMID 32406528 DOI: 10.1111/Nph.16658  0.236
2012 Li J, Zhang Y, Yang Y. Characterization of the diatomite binding domain in the ribosomal protein L2 from E. coli and functions as an affinity tag. Applied Microbiology and Biotechnology. 97: 2541-9. PMID 22926644 DOI: 10.1007/s00253-012-4367-7  0.236
2022 He S, Almalki AA, Rafeeq MM, Sain ZM, Alqosaibi AI, Alnamshan MM, Al-Dhuayan IS, Rahaman A, Zhang Y, Banjer HJ, Anjum F, Alzghaibi HAM, Alharbi AH, Jamal QMS. Targeting Cytotoxin-Associated Antigen A, a Virulent Factor of -Associated Gastric Cancer: Structure-Based In Silico Screening of Natural Compounds. Molecules (Basel, Switzerland). 27. PMID 35164000 DOI: 10.3390/molecules27030732  0.235
2017 Chen J, Jiang S, Liu Y, Huang T, Wang C, Miao S, Wang Z, Zhang Y, Huang W. Interaction of oxalic acid with dimethylamine and its atmospheric implications Rsc Advances. 7: 6374-6388. DOI: 10.1039/C6Ra27945G  0.235
2013 Guan M, Cao G, Chu X, Zhang Y, Liu X, Zeng Y. Effect of MoO3 doped PTCDA as buffer layer on the performance of CuPc C60 solar cells Physica Status Solidi (a). 210: 1178-1182. DOI: 10.1002/Pssa.201228597  0.235
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2018 Feng J, Wang L, Wu Y, Luo Q, Zhang Y, Qiu D, Han J, Su P, Xiong Z, Chang J, Yang G, He G. , a Sucrose Non-fermenting 1-Related Protein Kinase Gene, Positively Regulates Plant Response to Drought and Salt Stress in Transgenic Tobacco. Frontiers in Plant Science. 9: 2003. PMID 30693013 DOI: 10.3389/Fpls.2018.02003  0.234
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2016 Hu Y, Liu W, Sun J, Li M, Yang X, Zhang Y, Liu X, Xu M. Structurally improved CaO-based sorbent by organic acids for high temperature CO2 capture Fuel. 167: 17-24. DOI: 10.1016/J.Fuel.2015.11.048  0.23
2014 Lin XX, Liu YR, Huang T, Xu KM, Zhang Y, Jiang S, Gai YB, Zhang WJ, Huang W. Theoretical studies of the hydration reactions of stabilized Criegee intermediates from the ozonolysis of β-pinene Rsc Advances. 4: 28490-28498. DOI: 10.1039/C4Ra04172K  0.23
2014 Ding K, Wang C, Zhang B, Zhang Y, Guan M, Cui L, Zhang Y, Zeng Y, Lin Z, Huang F. Specific Detection of Alpha-Fetoprotein Using AlGaAs/GaAs High Electron Mobility Transistors Ieee Electron Device Letters. 35: 333-335. DOI: 10.1109/Led.2014.2298397  0.23
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2022 Liu W, Liu B, Zhang G, Yao G, Zhang Y, Cen X, He M. Giant Triton Snail Macrophage-Expressed Gene 1 Protein Ct-Mpeg1: Molecular Identification, Expression Analysis, and Antimicrobial Activity. International Journal of Molecular Sciences. 23. PMID 36362196 DOI: 10.3390/ijms232113415  0.229
2018 Niu G, Zou D, Li M, Zhang Y, Sang J, Xia L, Li M, Liu L, Cao J, Zhang Y, Wang P, Hu S, Hao L, Zhang Z. Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human. Nucleic Acids Research. PMID 30357418 DOI: 10.1093/Nar/Gky958  0.229
2019 Tseng-Rogenski S, Zheng W, Koi M, Zhang Y, Carethers JM. 455 – Differential Post-Translational Modification of Polymorphic Msh3 and Novel Binding Partner Nemo is Associated with Its Nuclear-To-Cytosol Shuttling Gastroenterology. 156: S-96. DOI: 10.1016/S0016-5085(19)37028-3  0.229
2015 Qu F, Xiang Z, Wang F, Zhang Y, Li J, Zhang Y, Xiao S, Yu Z. Identification and function of an evolutionarily conserved signaling intermediate in Toll pathways (ECSIT) from Crassostrea hongkongensis. Developmental and Comparative Immunology. PMID 26204814 DOI: 10.1016/j.dci.2015.07.015  0.228
2013 Zhang Y, Zhang Y, Wang C, Zeng Y. Transport properties in AlInSb/InAsSb heterostructures Journal of Applied Physics. 114: 243710. DOI: 10.1063/1.4858399  0.228
2015 Zhang P, Guo Z, Zhang Y, Gao Z, Ji N, Wang D, Zou L, Sun W, Zhang L. A preliminary quantitative proteomic analysis of glioblastoma pseudoprogression. Proteome Science. 13: 12. PMID 25866482 DOI: 10.1186/s12953-015-0066-5  0.228
2019 Mao F, Liu K, Bao Y, Lin Y, Zhang X, Xu D, Xiang Z, Li J, Zhang Y, Yu Z. Opsonic character of the plasma proteins in phagocytosis-dependent host response to bacterial infection in a marine invertebrate, Crassostrea gigas. Developmental and Comparative Immunology. 103596. PMID 31877328 DOI: 10.1016/j.dci.2019.103596  0.228
2018 Xiong L, Yan W, Zubia E, Zhou Y, Zhang Y, Duan Q, Narayan M, Xu G. Quantitative proteomics and biochemical analyses reveal the role of endoplasmin in the regulation of the expression and secretion of A Disintegrin And Metalloproteinase 12. Journal of Proteomics. PMID 29729432 DOI: 10.1016/J.Jprot.2018.04.033  0.228
2016 Yang X, Liu W, Sun J, Hu Y, Wang W, Chen H, Zhang Y, Li X, Xu M. Preparation of Novel Li4 SiO4 Sorbents with Superior Performance at Low CO2 Concentration. Chemsuschem. PMID 27312486 DOI: 10.1002/Cssc.201501699  0.227
2023 Peng N, Zhang Y, Zhang X, Wu HY, Nakamura F. NAP1L1 is a novel microtubule-associated protein. Cytoskeleton (Hoboken, N.J.). PMID 37098731 DOI: 10.1002/cm.21761  0.227
2020 Mu H, Ke S, Zhang D, Zhang Y, Song X, Yu Z, Zhang Y, Qiu JW. The Sperm Proteome of the Oyster Crassostrea hongkongensis. Proteomics. e2000167. PMID 32865869 DOI: 10.1002/pmic.202000167  0.227
2015 Lei L, Xue YB, Liu Z, Peng SS, He Y, Zhang Y, Fang R, Wang JP, Luo ZW, Yao GM, Zhang JW, Zhang G, Song HP, Zhang YH. Coumarin derivatives from Ainsliaea fragrans and their anticoagulant activity. Scientific Reports. 5: 13544. PMID 26315062 DOI: 10.1038/Srep13544  0.226
2016 Song W, Xu Q, Zhang Y, Zhan Y, Zheng W, Song L. Fully integrated reflection-mode photoacoustic, two-photon, and second harmonic generation microscopy in vivo. Scientific Reports. 6: 32240. PMID 27576922 DOI: 10.1038/Srep32240  0.226
2021 Yan XM, Geng J, Ma Z, Gao L, Du W, Li HB, Yuan LX, Zhou ZY, Zhang JS, Zhang Y, Chen L. Genome-wide identification and analysis of TMT-based proteomes in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle. Animal Biotechnology. 1-12. PMID 34965845 DOI: 10.1080/10495398.2021.2019756  0.225
2022 Zhang Y, Wang G, Huang P, Sun E, Kweon J, Li Q, Zhe J, Ying LL, Zhang HF. Minimizing Molecular Misidentification in Imaging Low-Abundance Protein Interactions Using Spectroscopic Single-Molecule Localization Microscopy. Analytical Chemistry. PMID 36165784 DOI: 10.1021/acs.analchem.2c02417  0.225
2017 Xing YH, Yao RW, Zhang Y, Guo CJ, Jiang S, Xu G, Dong R, Yang L, Chen LL. SLERT Regulates DDX21 Rings Associated with Pol I Transcription. Cell. 169: 664-678.e16. PMID 28475895 DOI: 10.1016/J.Cell.2017.04.011  0.225
2020 Meng J, Zhang Y, Zhou X, Lei M, Li C. LiCO-affiliative mechanism for air-accessible interface engineering of garnet electrolyte via facile liquid metal painting. Nature Communications. 11: 3716. PMID 32709915 DOI: 10.1038/S41467-020-17493-X  0.224
2020 Wu B, Feng D, Tong W, Liu J, Wang C, Zhao W, Zhang Y. A Low Power Reconfigurable Memory Architecture for Complementary Resistive Switches Ieee Transactions On Computer-Aided Design of Integrated Circuits and Systems. 39: 1806-1819. DOI: 10.1109/Tcad.2019.2927520  0.223
2022 Liu W, Liu B, Zhang G, Jia H, Zhang Y, Cen X, Yao G, He M. Molecular and Functional Characterization of a Short-Type Peptidoglycan Recognition Protein, Ct-PGRP-S1 in the Giant Triton Snail . International Journal of Molecular Sciences. 23. PMID 36232364 DOI: 10.3390/ijms231911062  0.223
2014 Pei X, Sun Q, Zhang Y, Wang P, Peng X, Guo C, Xu E, Zheng Y, Mo X, Ma J, Chen D, Zhang Y, Zhang Y, Song Q, Guo S, et al. PC3-secreted microprotein is a novel chemoattractant protein and functions as a high-affinity ligand for CC chemokine receptor 2. Journal of Immunology (Baltimore, Md. : 1950). 192: 1878-86. PMID 24442440 DOI: 10.4049/jimmunol.1300758  0.223
2013 Chu X, Guan M, Zhang Y, Li Y, Liu X, Zhu Z, Wang B, Zeng Y. Influences of organic–inorganic interfacial properties on the performance of a hybrid near-infrared optical upconverter Rsc Advances. 3: 23503-23507. DOI: 10.1039/C3Ra43143F  0.222
2016 Zhou Y, Xiong L, Zhang Y, Yu R, Jiang X, Xu G. Quantitative proteomics identifies myoferlin as a novel regulator of A Disintegrin and Metalloproteinase 12 in HeLa cells. Journal of Proteomics. PMID 27432471 DOI: 10.1016/J.Jprot.2016.07.015  0.222
2015 Yin X, Zhang Y, Guo S, Jin H, Wang W, Yang P. Large scale systematic proteomic quantification from non-metastatic to metastatic colorectal cancer. Scientific Reports. 5: 12120. PMID 26175278 DOI: 10.1038/Srep12120  0.222
2018 Zhang Y, Duan C, Yang J, Chen S, Liu Q, Zhou L, Huang Z, Xu Y, Xu G. Deubiquitinating enzyme USP9X regulates cellular clock function by modulating the ubiquitination and degradation of a core circadian protein BMAL1. The Biochemical Journal. PMID 29626158 DOI: 10.1042/Bcj20180005  0.221
2019 Xu J, Zhang Y, Shi Y, Yin D, Dai P, Zhao W, Zhang T. Identification of Predictive Proteins and Biological Pathways for the Tumorigenicity of Vestibular Schwannoma by Proteomic Profiling. Proteomics. Clinical Applications. e1800175. PMID 31120176 DOI: 10.1002/prca.201800175  0.221
2020 Dong H, Zhang Y, Cui L, Guan M, Li Y, Zhu Z, Wang B, Zeng Y. Electrical properties of Si and Be doped InSb and InAlSb/InSb superlattice applied to improve the doping efficiency Journal of Crystal Growth. 535: 125377. DOI: 10.1016/J.Jcrysgro.2019.125377  0.22
2018 Li M, Xia L, Zhang Y, Niu G, Li M, Wang P, Zhang Y, Sang J, Zou D, Hu S, Hao L, Zhang Z. Plant editosome database: a curated database of RNA editosome in plants. Nucleic Acids Research. PMID 30364952 DOI: 10.1093/Nar/Gky1026  0.22
2015 Zhang Y, Guo Z, Zou L, Yang Y, Zhang L, Ji N, Shao C, Wang Y, Sun W. Data for a comprehensive map and functional annotation of the human cerebrospinal fluid proteome. Data in Brief. 3: 103-7. PMID 26217727 DOI: 10.1016/j.dib.2015.02.004  0.22
2018 Liu X, Zhang Y, Hu Z, Li Q, Yang L, Xu G. The Catalytically Inactive Mutation of the Ubiquitin-Conjugating Enzyme CDC34 Affects its Stability and Cell Proliferation. The Protein Journal. PMID 29564676 DOI: 10.1007/s10930-018-9766-x  0.22
2017 Peng Y, Deng A, Gong X, Li X, Zhang Y. Coupling process study of lipid production and mercury bioremediation by biomimetic mineralized microalgae. Bioresource Technology. 243: 628-633. PMID 28709067 DOI: 10.1016/J.Biortech.2017.06.165  0.22
2018 Peng Y, Liu X, Gong X, Li X, Liu Y, Leng E, Zhang Y. Enhanced Hg(II) Adsorption by Monocarboxylic-Acid-Modified Microalgae Residuals in Simulated and Practical Industrial Wastewater Energy & Fuels. 32: 4461-4468. DOI: 10.1021/Acs.Energyfuels.7B03094  0.219
2012 Chu X, Guan M, Li L, Zhang Y, Zhang F, Li Y, Zhu Z, Wang B, Zeng Y. Improved efficiency of organic/inorganic hybrid near-infrared light upconverter by device optimization. Acs Applied Materials & Interfaces. 4: 4976-80. PMID 22931090 DOI: 10.1021/Am301340P  0.219
2017 Dong K, Huang L, Wang C, Xu P, Zhang Y, Feng C, Chen T, Wang Q, Zhang Y. Metal/TiO2 hierarchical nanocomposite arrays for the remarkable enhancement of photocatalytic activity Rsc Advances. 7: 16535-16541. DOI: 10.1039/C7Ra00312A  0.218
2014 Zhang C, Li N, Zhai L, Xu S, Liu X, Cui Y, Ma J, Han M, Jiang J, Yang C, Fan F, Li L, Qin P, Yu Q, Chang C, ... ... Zhang Y, et al. Systematic analysis of missing proteins provides clues to help define all of the protein-coding genes on human chromosome 1. Journal of Proteome Research. 13: 114-25. PMID 24256544 DOI: 10.1021/Pr400900J  0.218
2013 Li L, Gong H, Yu H, Liu X, Liu Q, Yan G, Zhang Y, Lu H, Zou Y, Yang P. Knockdown of nucleosome assembly protein 1-like 1 promotes dimethyl sulfoxide-induced differentiation of P19CL6 cells into cardiomyocytes. Journal of Cellular Biochemistry. 113: 3788-96. PMID 22807403 DOI: 10.1002/Jcb.24254  0.218
2013 Zhang Y, Zhang Y, Guan M, Cui L, Wang C, Zeng Y. Theoretical study of transport property in InAsSb quantum well heterostructures Journal of Applied Physics. 114: 153707. DOI: 10.1063/1.4826071  0.218
2018 Chen S, Yang J, Yang L, Zhang Y, Zhou L, Liu Q, Duan C, Mieres CA, Zhou G, Xu G. Ubiquitin ligase TRAF2 attenuates the transcriptional activity of the core clock protein BMAL1 and affects the maximal Per1 mRNA level of the circadian clock in cells. The Febs Journal. PMID 29935055 DOI: 10.1111/Febs.14595  0.218
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2014 Chu X, Guan M, Niu L, Zeng Y, Li Y, Zhang Y, Zhu Z, Wang B. Fast responsive and highly efficient optical upconverter based on phosphorescent OLED. Acs Applied Materials & Interfaces. 6: 19011-6. PMID 25310022 DOI: 10.1021/Am504721G  0.217
2021 Perica T, Mathy CJP, Xu J, Jang GΜ, Zhang Y, Kaake R, Ollikainen N, Braberg H, Swaney DL, Lambright DG, Kelly MJS, Krogan NJ, Kortemme T. Systems-level effects of allosteric perturbations to a model molecular switch. Nature. PMID 34646016 DOI: 10.1038/s41586-021-03982-6  0.217
2017 Nurain IO, Bewaji CO, Johnson JS, Davenport RD, Zhang Y. Potential of Three Ethnomedicinal Plants as Antisickling Agents. Molecular Pharmaceutics. 14: 172-182. PMID 28043127 DOI: 10.1021/Acs.Molpharmaceut.6B00767  0.217
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2015 Zhang Y, Guo Z, Zou L, Yang Y, Zhang L, Ji N, Shao C, Sun W, Wang Y. A comprehensive map and functional annotation of the normal human cerebrospinal fluid proteome. Journal of Proteomics. 119: 90-9. PMID 25661039 DOI: 10.1016/j.jprot.2015.01.017  0.216
2020 Zhang Y, Meng J, Chen K, Wu H, Hu J, Li C. Garnet-Based Solid-State Lithium Fluoride Conversion Batteries Benefiting from Eutectic Interlayer of Superior Wettability Acs Energy Letters. 5: 1167-1176. DOI: 10.1021/Acsenergylett.0C00383  0.216
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2011 Li Y, Zhang Y, Zeng Y. Electron mobility in modulation-doped AlSb/InAs quantum wells Journal of Applied Physics. 109: 73703. DOI: 10.1063/1.3552417  0.215
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2018 Leng E, Zhang Y, Peng Y, Gong X, Mao M, Li X, Yu Y. In situ structural changes of crystalline and amorphous cellulose during slow pyrolysis at low temperatures Fuel. 216: 313-321. DOI: 10.1016/J.Fuel.2017.11.083  0.215
2014 Wang L, Chen X, Yu A, Zhang Y, Ding J, Lu W. Highly sensitive and wide-band tunable terahertz response of plasma waves based on graphene field effect transistors. Scientific Reports. 4: 5470. PMID 24969065 DOI: 10.1038/Srep05470  0.214
2016 Zhang Y, Yang L, Chen LL. Characterization of Circular RNAs. Methods in Molecular Biology (Clifton, N.J.). 1402: 215-27. PMID 26721494 DOI: 10.1007/978-1-4939-3378-5_17  0.214
2018 Yin L, Leng E, Gong X, Zhang Y, Li X. Pyrolysis mechanism of β-O-4 type lignin model polymers with different oxygen functional groups on Cα Journal of Analytical and Applied Pyrolysis. 136: 169-177. DOI: 10.1016/J.Jaap.2018.10.008  0.214
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2013 Dai Z, Chen Y, Qi W, Huang L, Zhang Y, Zhou T, Yang X, Gao G. Codon optimization increases human kallistatin expression in Escherichia coli. Preparative Biochemistry & Biotechnology. 43: 123-36. PMID 23215659 DOI: 10.1080/10826068.2012.712079  0.213
2018 Liu S, Guan M, Zhang Y, Li Y, Liu X, Sun W, Liu C, Zeng Y. The charge confinement effect of quantum-well Alq3-based OLEDs by dual-pulsed transient electroluminescence Optics Communications. 419: 13-17. DOI: 10.1016/J.Optcom.2018.02.049  0.213
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2013 Chen SR, Zheng QS, Zhang Y, Gao F, Liu YX. Disruption of genital ridge development causes aberrant primordial germ cell proliferation but does not affect their directional migration. Bmc Biology. 11: 22. PMID 23497137 DOI: 10.1186/1741-7007-11-22  0.213
2019 Zhang Y, Bai R, Zhao Z, Liao Q, Chen P, Guo W, Cai C, Yang F. Highly selective and sensitive probes for the detection of Cr(VI) in aqueous solutions using diglycolic acid-functionalized Au nanoparticles Rsc Advances. 9: 10958-10965. DOI: 10.1039/C9Ra00010K  0.213
2015 Zhang B, Leng E, Wang P, Gong X, Zhang J, Zhang Y, Xu M. Effect of reducing ends on the pyrolysis characteristics and product distribution of cellulose Journal of Analytical and Applied Pyrolysis. 114: 119-126. DOI: 10.1016/J.Jaap.2015.05.007  0.213
2022 Deng Y, Wang X, Zhang Y, Zhang C, Xie P, Huang L. Inhibitory effect of Ginkgo biloba seeds peptides on methylglyoxal-induced glycations. Food and Chemical Toxicology : An International Journal Published For the British Industrial Biological Research Association. 113587. PMID 36596446 DOI: 10.1016/j.fct.2022.113587  0.212
2020 Li Q, Zhang Y, Huang J, Wu Z, Tang L, Huang L, Zhang X. Basic Strong Cation Exchange Chromatography, BaSCX, a Highly Efficient Approach for C-Terminomic Studies Using LysargiNase Digestion. Analytical Chemistry. PMID 32097557 DOI: 10.1021/acs.analchem.9b05280  0.212
2014 Shen F, Zhang Y, Yao Y, Hua W, Zhang HS, Wu JS, Zhong P, Zhou LF. Proteomic analysis of cerebrospinal fluid: toward the identification of biomarkers for gliomas. Neurosurgical Review. 37: 367-80; discussion 3. PMID 24781189 DOI: 10.1007/s10143-014-0539-5  0.212
2019 Yuan Y, Miao Y, Qian L, Zhang Y, Liu C, Liu J, Zuo Y, Feng Q, Guo T, Zhang L, Chen X, Jin L, Huang F, Zhang H, Zhang W, et al. Targeting UBE4A Revives Viperin Protein in Epithelium to Enhance Host Antiviral Defense. Molecular Cell. PMID 31812350 DOI: 10.1016/j.molcel.2019.11.003  0.212
2014 Zhang Y, Zhao Q, Shao B, Lü W, Dong X, You H. Facile hydrothermal synthesis and luminescent properties of Eu-doped CaF2–YF3alkaline-earth ternary fluoride microspheres Rsc Advances. 4: 35750. DOI: 10.1039/C4Ra04185B  0.212
2020 Liu Y, Tian H, Chen X, Liu W, Xia K, Huang J, de la Chapelle ML, Huang G, Zhang Y, Fu W. Indirect surface-enhanced Raman scattering assay of insulin-like growth factor 2 receptor protein by combining the aptamer modified gold substrate and silver nanoprobes. Mikrochimica Acta. 187: 160. PMID 32040773 DOI: 10.1007/s00604-020-4126-x  0.212
2017 Zhao X, Zhang Y, Cui L, Guan M, Wang B, Zhu Z, Zeng Y. Growth and Characterization of InSb Thin Films on GaAs (001) without Any Buffer Layers by MBE Chinese Physics Letters. 34: 76105. DOI: 10.1088/0256-307X/34/7/076105  0.212
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2011 He X, Zhang Y, Yu Z. An Mpeg (macrophage expressed gene) from the Pacific oyster Crassostrea gigas: molecular characterization and gene expression. Fish & Shellfish Immunology. 30: 870-6. PMID 21272653 DOI: 10.1016/j.fsi.2011.01.009  0.195
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2016 Liu Y, Li J, Zhang Y, Zhang Y, Mao F, Wang F, Yu Z. The first molluscan TRIM9 is involved in the negative regulation of NF-κB activity in the Hong Kong oyster Crassostrea hongkongensis. Fish & Shellfish Immunology. PMID 27393236 DOI: 10.1016/j.fsi.2016.06.057  0.19
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2021 Lv H, Zhang Y, Wang JS, Yuan SS, Sun ZJ, Dao FY, Guan ZX, Lin H, Deng KJ. iRice-MS: An integrated XGBoost model for detecting multitype post-translational modification sites in rice. Briefings in Bioinformatics. PMID 34864888 DOI: 10.1093/bib/bbab486  0.189
2020 Kieft R, Zhang Y, Marand AP, Moran JD, Bridger R, Wells L, Schmitz RJ, Sabatini R. Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes. Plos Genetics. 16: e1008390. PMID 32084124 DOI: 10.1371/Journal.Pgen.1008390  0.188
2018 Zhang R, Wang Y, Yang Y, Zhang Y, Ma J. Predicting CTCF-mediated chromatin loops using CTCF-MP. Bioinformatics (Oxford, England). 34: i133-i141. PMID 29949986 DOI: 10.1093/bioinformatics/bty248  0.188
2017 Huang J, Wang J, Li Q, Zhang Y, Zhang X. Enzyme and Chemical Assisted N-Terminal Blocked Peptides Analysis, ENCHANT, as a Selective Proteomics Approach Complementary to Conventional Shotgun Approach. Journal of Proteome Research. PMID 29172542 DOI: 10.1021/acs.jproteome.7b00521  0.187
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2010 Kang YN, Zhang Y, Allan PW, Parker WB, Ting JW, Chang CY, Ealick SE. Structure of grouper iridovirus purine nucleoside phosphorylase. Acta Crystallographica. Section D, Biological Crystallography. 66: 155-62. PMID 20124695 DOI: 10.1107/S0907444909048276  0.182
2022 Zhang Y, Xing YY, Wang C, Pang R, Ren WW, Wang S, Li ZM, Yang L, Tong WC, Wang QY, Zang SQ. Programming a Metal-Organic Framework toward Excellent Hypergolicity. Acs Applied Materials & Interfaces. PMID 35576940 DOI: 10.1021/acsami.2c05252  0.182
2015 Zhang Y, Sun J, Mu H, Li J, Zhang Y, Xu F, Xiang Z, Qian PY, Qiu JW, Yu Z. Proteomic basis of stress responses in the gills of the pacific oyster Crassostrea gigas. Journal of Proteome Research. 14: 304-17. PMID 25389644 DOI: 10.1021/Pr500940S  0.181
2022 Xiao H, Bozi LHM, Sun Y, Riley CL, Philip VM, Chen M, Li J, Zhang T, Mills EL, Emont MP, Sun W, Reddy A, Garrity R, Long J, Becher T, ... ... Zhang Y, et al. Architecture of the outbred brown fat proteome defines regulators of metabolic physiology. Cell. PMID 36334589 DOI: 10.1016/j.cell.2022.10.003  0.181
2014 Liu M, Zhang Y, Chen Y, Yan G, Shen C, Cao J, Zhou X, Liu X, Zhang L, Shen H, Lu H, He F, Yang P. Efficient and accurate glycopeptide identification pipeline for high-throughput site-specific N-glycosylation analysis. Journal of Proteome Research. 13: 3121-9. PMID 24766575 DOI: 10.1021/Pr500238V  0.181
2015 Duan W, Chen S, Zhang Y, Li D, Wang R, Chen S, Li J, Qiu X, Xu G. Protein C-terminal enzymatic labeling identifies novel caspase cleavages during the apoptosis of multiple myeloma cells induced by kinase inhibition. Proteomics. PMID 26552366 DOI: 10.1002/Pmic.201500356  0.18
2022 Miao Y, Deng Y, Liu J, Wang J, Hu B, Hao S, Wang H, Zhang Z, Jin Z, Zhang Y, Li C, Zhang P, Wan H, Zhang S, Feng J, et al. Anti-cancer effect of targeting fibroblast activation protein alpha in glioblastoma through remodeling macrophage phenotype and suppressing tumor progression. Cns Neuroscience & Therapeutics. PMID 36382346 DOI: 10.1111/cns.14024  0.18
2011 Zhang Y, He X, Li X, Fu D, Chen J, Yu Z. The second bactericidal permeability increasing protein (BPI) and its revelation of the gene duplication in the Pacific oyster, Crassostrea gigas. Fish & Shellfish Immunology. 30: 954-63. PMID 21300156 DOI: 10.1016/j.fsi.2011.01.031  0.18
2018 Du J, Zhang Y, Zhao Q. New components of the Lignin Biosynthetic Metabolon. Trends in Plant Science. PMID 29843965 DOI: 10.1016/j.tplants.2018.05.007  0.18
2023 Li Y, Zhang C, Feng C, Pearce R, Lydia Freddolino P, Zhang Y. Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction. Nature Communications. 14: 5745. PMID 37717036 DOI: 10.1038/s41467-023-41303-9  0.179
2020 Zhang Y, Liu Y, Zeng XL, Wu J, Yu JL, Chen YH. Distinguishing the inverse spin Hall effect photocurrent of electrons and holes by comparing to the classical Hall effect. Optics Express. 28: 8331-8340. PMID 32225460 DOI: 10.1364/Oe.387692  0.178
2024 Zhang W, Zhang Y, Shi X, Wang S, Bao Y. Hemoglobin wonders: a fascinating gas transporter dive into molluscs. Critical Reviews in Biochemistry and Molecular Biology. 1-26. PMID 38189101 DOI: 10.1080/10409238.2023.2299381  0.177
2019 Xiao K, Liu C, Qin Q, Zhang Y, Wang X, Zhang J, Odle J, Lin X, Hu CA, Liu Y. EPA and DHA attenuate deoxynivalenol-induced intestinal porcine epithelial cell injury and protect barrier function integrity by inhibiting necroptosis signaling pathway. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. PMID 31909535 DOI: 10.1096/Fj.201902298R  0.177
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