Year |
Citation |
Score |
2023 |
Li S, Tian T, Zhang Z, Zou Z, Zhao D, Zeng J. PocketAnchor: Learning structure-based pocket representations for protein-ligand interaction prediction. Cell Systems. PMID 37516103 DOI: 10.1016/j.cels.2023.05.005 |
0.335 |
|
2021 |
He X, Zhang S, Zhang Y, Lei Z, Jiang T, Zeng J. Characterizing RNA Pseudouridylation by Convolutional Neural Networks. Genomics, Proteomics & Bioinformatics. PMID 33631424 DOI: 10.1016/j.gpb.2019.11.015 |
0.446 |
|
2020 |
Wan F, Zhu Y, Hu H, Dai A, Cai X, Chen L, Gong H, Xia T, Yang D, Wang M, Zeng J. DeepCPI: A Deep Learning-based Framework for Large-scale in silico Drug Screening. Genomics, Proteomics & Bioinformatics. PMID 32035227 DOI: 10.1016/J.Gpb.2019.04.003 |
0.357 |
|
2020 |
Li S, Wan F, Shu H, Jiang T, Zhao D, Zeng J. MONN: A Multi-objective Neural Network for Predicting Compound-Protein Interactions and Affinities Cell Systems. 10. DOI: 10.1016/J.Cels.2020.03.002 |
0.351 |
|
2019 |
Hu Y, Wang Z, Hu H, Wan F, Chen L, Yuanpeng X, Wang X, Zhao D, Huang W, Zeng J. ACME: Pan-specific peptide-MHC class I binding prediction through attention-based deep neural networks. Bioinformatics (Oxford, England). PMID 31120490 DOI: 10.1093/Bioinformatics/Btz427 |
0.304 |
|
2019 |
Abbas A, He X, Niu J, Zhou B, Zhu G, Ma T, Song J, Gao J, Zhang MQ, Zeng J. Integrating Hi-C and FISH data for modeling of the 3D organization of chromosomes. Nature Communications. 10: 2049. PMID 31053705 DOI: 10.1038/S41467-019-10005-6 |
0.321 |
|
2018 |
Hu H, Xiao A, Zhang S, Li Y, Shi X, Jiang T, Zhang L, Zhang L, Zeng J. DeepHINT: Understanding HIV-1 integration via deep learning with attention. Bioinformatics (Oxford, England). PMID 30295703 DOI: 10.1093/Bioinformatics/Bty842 |
0.442 |
|
2018 |
Zhu G, Deng W, Hu H, Ma R, Zhang S, Yang J, Peng J, Kaplan T, Zeng J. Reconstructing spatial organizations of chromosomes through manifold learning. Nucleic Acids Research. PMID 29408992 DOI: 10.1093/Nar/Gky065 |
0.503 |
|
2017 |
Zhou J, Ma S, Wang D, Zeng J, Jiang T. FreePSI: an alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome. Nucleic Acids Research. PMID 29136203 DOI: 10.1093/Nar/Gkx1059 |
0.36 |
|
2017 |
Zhang S, Hu H, Zhou J, He X, Jiang T, Zeng J. Analysis of Ribosome Stalling and Translation Elongation Dynamics by Deep Learning. Cell Systems. 5: 212-220.e6. PMID 28957655 DOI: 10.1016/J.Cels.2017.08.004 |
0.568 |
|
2017 |
Luo Y, Zhao X, Zhou J, Yang J, Zhang Y, Kuang W, Peng J, Chen L, Zeng J. A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information. Nature Communications. 8: 573. PMID 28924171 DOI: 10.1038/S41467-017-00680-8 |
0.318 |
|
2017 |
Zhang S, Hu H, Jiang T, Zhang L, Zeng J. TITER: predicting translation initiation sites by deep learning. Bioinformatics (Oxford, England). 33: i234-i242. PMID 28881981 DOI: 10.1093/Bioinformatics/Btx247 |
0.513 |
|
2017 |
Li S, Dong F, Wu Y, Zhang S, Zhang C, Liu X, Jiang T, Zeng J. A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data. Nucleic Acids Research. PMID 28575488 DOI: 10.1093/Nar/Gkx492 |
0.531 |
|
2017 |
Xiong D, Zeng J, Gong H. A deep learning framework for improving long-range residue-residue contact prediction using a hierarchical strategy. Bioinformatics (Oxford, England). PMID 28472263 DOI: 10.1093/Bioinformatics/Btx296 |
0.454 |
|
2017 |
Zhou Y, Donald BR, Zeng J. Parallel Computational Protein Design. Methods in Molecular Biology (Clifton, N.J.). 1529: 265-277. PMID 27914056 DOI: 10.1007/978-1-4939-6637-0_13 |
0.68 |
|
2016 |
Zhou Y, Wu Y, Zeng J. Computational Protein Design Using AND/OR Branch-and-Bound Search. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 27167301 DOI: 10.1089/Cmb.2015.0212 |
0.535 |
|
2016 |
Gong H, Zhang S, Wang J, Gong H, Zeng J. Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 23: 300-10. PMID 27159632 DOI: 10.1089/Cmb.2015.0184 |
0.632 |
|
2016 |
Pan Y, Dong Y, Zhou J, Hallen M, Donald BR, Zeng J, Xu W. cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 27154509 DOI: 10.1089/Cmb.2015.0234 |
0.638 |
|
2015 |
Zhang S, Zhou J, Hu H, Gong H, Chen L, Cheng C, Zeng J. A deep learning framework for modeling structural features of RNA-binding protein targets. Nucleic Acids Research. PMID 26467480 DOI: 10.1093/Nar/Gkv1025 |
0.571 |
|
2015 |
Liang M, Li Z, Chen T, Zeng J. Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 12: 928-37. PMID 26357333 DOI: 10.1109/Tcbb.2014.2377729 |
0.313 |
|
2015 |
Xiong D, Zeng J, Gong H. RBRIdent: An algorithm for improved identification of RNA-binding residues in proteins from primary sequences. Proteins. 83: 1068-77. PMID 25846271 DOI: 10.1002/Prot.24806 |
0.427 |
|
2015 |
Wang S, Xu J, Zeng J. Inferential modeling of 3D chromatin structure. Nucleic Acids Research. 43: e54. PMID 25690896 DOI: 10.1093/Nar/Gkv100 |
0.417 |
|
2014 |
Zhou Y, Xu W, Donald BR, Zeng J. An efficient parallel algorithm for accelerating computational protein design. Bioinformatics (Oxford, England). 30: i255-i263. PMID 24931991 DOI: 10.1093/Bioinformatics/Btu264 |
0.71 |
|
2014 |
Liu Y, Zeng J, Gong H. Improving the orientation-dependent statistical potential using a reference state. Proteins. 82: 2383-93. PMID 24810843 DOI: 10.1002/Prot.24600 |
0.372 |
|
2013 |
Zeng J, Zhou P, Donald BR. HASH: a program to accurately predict protein Hα shifts from neighboring backbone shifts. Journal of Biomolecular Nmr. 55: 105-18. PMID 23242797 DOI: 10.1007/S10858-012-9693-7 |
0.672 |
|
2012 |
Tripathy C, Zeng J, Zhou P, Donald BR. Protein loop closure using orientational restraints from NMR data. Proteins. 80: 433-53. PMID 22161780 DOI: 10.1002/Prot.23207 |
0.8 |
|
2011 |
Zeng J, Roberts KE, Zhou P, Donald BR. A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1661-79. PMID 21970619 DOI: 10.1089/Cmb.2011.0172 |
0.754 |
|
2011 |
Zeng J, Zhou P, Donald BR. Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data. Journal of Biomolecular Nmr. 50: 371-95. PMID 21706248 DOI: 10.1007/S10858-011-9522-4 |
0.722 |
|
2011 |
Tripathy C, Zeng J, Zhou P, Donald BR. Protein loop closure using orientational restraints from NMR data Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6577: 483-498. DOI: 10.1007/978-3-642-20036-6_43 |
0.807 |
|
2010 |
Zeng J, Zhou P, Donald BR. A Markov random field framework for protein side-chain resonance assignment Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6044: 550-570. DOI: 10.1007/978-3-642-12683-3_36 |
0.728 |
|
2009 |
Zeng J, Boyles J, Tripathy C, Wang L, Yan A, Zhou P, Donald BR. High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations. Journal of Biomolecular Nmr. 45: 265-81. PMID 19711185 DOI: 10.1007/S10858-009-9366-3 |
0.73 |
|
2008 |
Zeng J, Tripathy C, Zhou P, Donald BR. A Hausdorff-based NOE assignment algorithm using protein backbone determined from residual dipolar couplings and rotamer patterns. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 7: 169-81. PMID 19642278 |
0.807 |
|
2008 |
Zeng JM, Tripathy C, Zhou P, Donald BR. A HAUSDORFF-BASED NOE ASSIGNMENT ALGORITHM USING PROTEIN BACKBONE DETERMINED FROM RESIDUAL DIPOLAR COUPLINGS AND ROTAMER PATTERNS. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 2008: 169-181. PMID 19122773 |
0.807 |
|
2008 |
Zeng J, Hsu W. Conflict-free container routing in mesh yard layouts Robotics and Autonomous Systems. 56: 451-460. DOI: 10.1016/J.Robot.2007.09.007 |
0.37 |
|
2006 |
Zeng J, Hsu W. Optimal Routing in a Small-World Network Journal of Computer Science and Technology. 21: 476-481. DOI: 10.1007/S11390-006-0476-Z |
0.317 |
|
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