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Jianyang Zeng, Ph.D. - Publications

Affiliations: 
2011 Computer Science Duke University, Durham, NC 
Area:
Computer Science, General Biophysics
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35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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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