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Jian Peng - Publications

Affiliations: 
2007-2013 Computer Science Toyota Technological Institute 
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32 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
2019 Su Y, Luo Y, Zhao X, Liu Y, Peng J. Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction. Plos Computational Biology. 15: e1007283. PMID 31483777 DOI: 10.1371/Journal.Pcbi.1007283  0.348
2019 Cai Y, Guan K, Lobell D, Potgieter AB, Wang S, Peng J, Xu T, Asseng S, Zhang Y, You L, Peng B. Integrating satellite and climate data to predict wheat yield in Australia using machine learning approaches Agricultural and Forest Meteorology. 274: 144-159. DOI: 10.1016/J.Agrformet.2019.03.010  0.316
2018 Shang J, Jiang M, Tong W, Xiao J, Peng J, Han J. DPPred: An Effective Prediction Framework with Concise Discriminative Patterns. Ieee Transactions On Knowledge and Data Engineering. 30: 1226-1239. PMID 30745791 DOI: 10.1109/Tkde.2017.2757476  0.326
2018 Liu Y, Ye Q, Wang L, Peng J. Learning structural motif representations for efficient protein structure search. Bioinformatics (Oxford, England). 34: i773-i780. PMID 30423083 DOI: 10.1093/Bioinformatics/Bty585  0.446
2017 Liu Y, Palmedo P, Ye Q, Berger B, Peng J. Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks. Cell Systems. PMID 29275173 DOI: 10.1016/J.Cels.2017.11.014  0.44
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  0.308
2017 Ma X, Zhou G, Shang J, Wang J, Peng J, Han J. Detection of Complexes in Biological Networks Through Diversified Dense Subgraph Mining. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 28570104 DOI: 10.1089/Cmb.2017.0037  0.37
2017 Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, et al. Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways. Cell Systems. PMID 28131822 DOI: 10.1016/J.Cels.2016.12.011  0.3
2016 Cho H, Berger B, Peng J. Compact Integration of Multi-Network Topology for Functional Analysis of Genes. Cell Systems. PMID 27889536 DOI: 10.1016/J.Cels.2016.10.017  0.345
2016 Wang S, Peng J, Ma J, Xu J. Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields. Scientific Reports. 6: 18962. PMID 26752681 DOI: 10.1038/Srep18962  0.592
2015 Simmons S, Peng J, Bienkowska J, Berger B. Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 715-28. PMID 26098139 DOI: 10.1089/Cmb.2015.0085  0.31
2015 Wang S, Cho H, Zhai C, Berger B, Peng J. Exploiting ontology graph for predicting sparsely annotated gene function. Bioinformatics (Oxford, England). 31: i357-i364. PMID 26072504 DOI: 10.1093/Bioinformatics/Btv260  0.321
2015 Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, et al. Widespread macromolecular interaction perturbations in human genetic disorders. Cell. 161: 647-60. PMID 25910212 DOI: 10.1016/J.Cell.2015.04.013  0.312
2014 Taipale M, Tucker G, Peng J, Krykbaeva I, Lin ZY, Larsen B, Choi H, Berger B, Gingras AC, Lindquist S. A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways. Cell. 158: 434-48. PMID 25036637 DOI: 10.1016/J.Cell.2014.05.039  0.379
2013 Daniels NM, Gallant A, Peng J, Cowen LJ, Baym M, Berger B. Compressive genomics for protein databases. Bioinformatics (Oxford, England). 29: i283-90. PMID 23812995 DOI: 10.1093/Bioinformatics/Btt214  0.361
2013 Wang S, Ma J, Peng J, Xu J. Protein structure alignment beyond spatial proximity. Scientific Reports. 3: 1448. PMID 23486213 DOI: 10.7490/F1000Research.1093698.1  0.582
2012 Hosur R, Peng J, Vinayagam A, Stelzl U, Xu J, Perrimon N, Bienkowska J, Berger B. A computational framework for boosting confidence in high-throughput protein-protein interaction datasets. Genome Biology. 13: R76. PMID 22937800 DOI: 10.1186/Gb-2012-13-8-R76  0.582
2012 Källberg M, Wang H, Wang S, Peng J, Wang Z, Lu H, Xu J. Template-based protein structure modeling using the RaptorX web server. Nature Protocols. 7: 1511-22. PMID 22814390 DOI: 10.1038/Nprot.2012.085  0.601
2012 Ma J, Peng J, Wang S, Xu J. A conditional neural fields model for protein threading. Bioinformatics (Oxford, England). 28: i59-66. PMID 22689779 DOI: 10.7490/F1000Research.1093699.1  0.534
2012 Adhikari AN, Peng J, Wilde M, Xu J, Freed KF, Sosnick TR. Modeling large regions in proteins: applications to loops, termini, and folding. Protein Science : a Publication of the Protein Society. 21: 107-21. PMID 22095743 DOI: 10.1002/Pro.767  0.596
2011 Peng J, Xu J. RaptorX: exploiting structure information for protein alignment by statistical inference. Proteins. 79: 161-71. PMID 21987485 DOI: 10.1002/Prot.23175  0.593
2011 Wang Z, Zhao F, Peng J, Xu J. Protein 8-class secondary structure prediction using conditional neural fields Proteomics. 11: 3786-3792. PMID 21805636 DOI: 10.1002/Pmic.201100196  0.589
2011 Wang S, Peng J, Xu J. Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. Bioinformatics (Oxford, England). 27: 2537-45. PMID 21791532 DOI: 10.1093/Bioinformatics/Btr432  0.616
2011 Peng J, Xu J. A multiple-template approach to protein threading. Proteins. 79: 1930-9. PMID 21465564 DOI: 10.1002/Prot.23016  0.596
2011 Wang S, Peng J, Xu J. 3DCOMB: Alignment of distantly-related protein structures F1000research. 2. DOI: 10.7490/F1000Research.2059.1  0.574
2010 Zhao F, Peng J, Debartolo J, Freed KF, Sosnick TR, Xu J. A probabilistic and continuous model of protein conformational space for template-free modeling. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 783-98. PMID 20583926 DOI: 10.1089/Cmb.2009.0235  0.583
2010 Zhao F, Peng J, Xu J. Fragment-free approach to protein folding using conditional neural fields. Bioinformatics (Oxford, England). 26: i310-7. PMID 20529922 DOI: 10.1093/Bioinformatics/Btq193  0.596
2010 Peng J, Xu J. Low-homology protein threading. Bioinformatics (Oxford, England). 26: i294-300. PMID 20529920 DOI: 10.7490/F1000Research.320.1  0.558
2010 Zhao F, Peng J, Xu J. Efficient fragment-free approach to protein folding F1000research. 1. DOI: 10.7490/F1000Research.312.1  0.537
2009 Zhao F, Peng J, Debartolo J, Freed KF, Sosnick TR, Xu J. A Probabilistic Graphical Model for Ab Initio Folding. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 5541: 59-73. PMID 23459639 DOI: 10.1007/978-3-642-02008-7_5  0.561
2009 Peng J, Xu J. Boosting Protein Threading Accuracy. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 5541: 31-45. PMID 22506254 DOI: 10.1007/978-3-642-02008-7_3  0.519
2009 Xu J, Peng J, Zhao F. Template-based and free modeling by RAPTOR++ in CASP8. Proteins. 77: 133-7. PMID 19722267 DOI: 10.1002/Prot.22567  0.564
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