| Year |
Citation |
Score |
| 2024 |
Jing X, Wu F, Luo X, Xu J. Single-sequence protein structure prediction by integrating protein language models. Proceedings of the National Academy of Sciences of the United States of America. 121: e2308788121. PMID 38507445 DOI: 10.1073/pnas.2308788121 |
0.477 |
|
| 2023 |
Wu F, Wu L, Radev D, Xu J, Li SZ. Integration of pre-trained protein language models into geometric deep learning networks. Communications Biology. 6: 876. PMID 37626165 DOI: 10.1038/s42003-023-05133-1 |
0.363 |
|
| 2023 |
Chen B, Xie Z, Qiu J, Ye Z, Xu J, Tang J. Improved the heterodimer protein complex prediction with protein language models. Briefings in Bioinformatics. PMID 37328552 DOI: 10.1093/bib/bbad221 |
0.363 |
|
| 2023 |
McPartlon M, Xu J. An end-to-end deep learning method for protein side-chain packing and inverse folding. Proceedings of the National Academy of Sciences of the United States of America. 120: e2216438120. PMID 37253017 DOI: 10.1073/pnas.2216438120 |
0.357 |
|
| 2022 |
Wu F, Jing X, Luo X, Xu J. Improving protein structure prediction using templates and sequence embedding. Bioinformatics (Oxford, England). PMID 36355462 DOI: 10.1093/bioinformatics/btac723 |
0.446 |
|
| 2022 |
Kong L, Ju F, Zheng WM, Zhu J, Sun S, Xu J, Bu D. ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 35073170 DOI: 10.1089/cmb.2021.0430 |
0.495 |
|
| 2022 |
Lai B, Xu J. Accurate protein function prediction via graph attention networks with predicted structure information. Briefings in Bioinformatics. 23. PMID 34882195 DOI: 10.1093/bib/bbab502 |
0.475 |
|
| 2021 |
Jing X, Xu J. Fast and effective protein model refinement using deep graph neural networks. Nature Computational Science. 1: 462-469. PMID 35321360 DOI: 10.1038/s43588-021-00098-9 |
0.396 |
|
| 2021 |
Tran NH, Xu J, Li M. A tale of solving two computational challenges in protein science: neoantigen prediction and protein structure prediction. Briefings in Bioinformatics. PMID 34891158 DOI: 10.1093/bib/bbab493 |
0.384 |
|
| 2021 |
Xie Z, Xu J. Deep graph learning of inter-protein contacts. Bioinformatics (Oxford, England). PMID 34755837 DOI: 10.1093/bioinformatics/btab761 |
0.407 |
|
| 2021 |
Xu J, Mcpartlon M, Li J. Improved protein structure prediction by deep learning irrespective of co-evolution information. Nature Machine Intelligence. 3: 601-609. PMID 34368623 DOI: 10.1038/s42256-021-00348-5 |
0.452 |
|
| 2021 |
Li J, Xu J. Study of Real-Valued Distance Prediction for Protein Structure Prediction with Deep Learning. Bioinformatics (Oxford, England). PMID 33961022 DOI: 10.1093/bioinformatics/btab333 |
0.363 |
|
| 2021 |
Wu F, Xu J. Deep template-based protein structure prediction. Plos Computational Biology. 17: e1008954. PMID 33939695 DOI: 10.1371/journal.pcbi.1008954 |
0.44 |
|
| 2020 |
Jing X, Xu J. Improved Protein Model Quality Assessment By Integrating Sequential And Pairwise Features Using Deep Learning. Bioinformatics (Oxford, England). PMID 33325480 DOI: 10.1093/bioinformatics/btaa1037 |
0.34 |
|
| 2020 |
Jing X, Zeng H, Wang S, Xu J. A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning. Methods in Molecular Biology (Clifton, N.J.). 2074: 67-80. PMID 31583631 DOI: 10.1007/978-1-4939-9873-9_6 |
0.528 |
|
| 2019 |
Xu J, Wang S. Analysis of distance-based protein structure prediction by deep learning in CASP13. Proteins. PMID 31471916 DOI: 10.1002/Prot.25810 |
0.424 |
|
| 2019 |
Xu J. Distance-based protein folding powered by deep learning. Proceedings of the National Academy of Sciences of the United States of America. PMID 31399549 DOI: 10.1073/Pnas.1821309116 |
0.53 |
|
| 2018 |
Hashemifar S, Neyshabur B, Khan AA, Xu J. Predicting protein-protein interactions through sequence-based deep learning. Bioinformatics (Oxford, England). 34: i802-i810. PMID 30423091 DOI: 10.1093/Bioinformatics/Bty573 |
0.486 |
|
| 2018 |
Wang S, Fei S, Wang Z, Li Y, Xu J, Zhao F, Gao X. PredMP: a web server for de novo prediction and visualization of membrane proteins. Bioinformatics (Oxford, England). PMID 30084960 DOI: 10.1093/Bioinformatics/Bty684 |
0.446 |
|
| 2018 |
Zhu J, Wang S, Bu D, Xu J. Protein threading using residue co-variation and deep learning. Bioinformatics (Oxford, England). 34: i263-i273. PMID 29949980 DOI: 10.1093/bioinformatics/bty278 |
0.479 |
|
| 2018 |
Zeng H, Wang S, Zhou T, Zhao F, Li X, Wu Q, Xu J. ComplexContact: a web server for inter-protein contact prediction using deep learning. Nucleic Acids Research. PMID 29790960 DOI: 10.1093/Nar/Gky420 |
0.512 |
|
| 2018 |
Gao Y, Wang S, Deng M, Xu J. RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning. Bmc Bioinformatics. 19: 100. PMID 29745828 DOI: 10.1186/S12859-018-2065-X |
0.491 |
|
| 2018 |
Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, ... ... Xu J, et al. Opportunities and obstacles for deep learning in biology and medicine. Journal of the Royal Society, Interface. 15. PMID 29618526 DOI: 10.1098/Rsif.2017.0387 |
0.302 |
|
| 2017 |
Wozniak PP, Konopka BM, Xu J, Vriend G, Kotulska M. Forecasting residue-residue contact prediction accuracy. Bioinformatics (Oxford, England). PMID 29036497 DOI: 10.1093/Bioinformatics/Btx416 |
0.477 |
|
| 2017 |
Wang S, Li Z, Yu Y, Xu J. Folding Membrane Proteins by Deep Transfer Learning. Cell Systems. 5: 202-211.e3. PMID 28957654 DOI: 10.1016/J.Cels.2017.09.001 |
0.472 |
|
| 2017 |
Wang S, Sun S, Xu J. Analysis of deep learning methods for blind protein contact prediction in CASP12. Proteins. PMID 28845538 DOI: 10.1002/Prot.25377 |
0.477 |
|
| 2017 |
Wang S, Sun S, Li Z, Zhang R, Xu J. Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. Plos Computational Biology. 13: e1005324. PMID 28056090 DOI: 10.1371/Journal.Pcbi.1005324 |
0.533 |
|
| 2017 |
Wang S, Xu J. De Novo Protein Structure Prediction by Big Data and Deep Learning Biophysical Journal. 112: 55a. DOI: 10.1016/J.Bpj.2016.11.334 |
0.496 |
|
| 2016 |
Wang S, Ma J, Xu J. AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields. Bioinformatics (Oxford, England). 32: i672-i679. PMID 27587688 DOI: 10.1093/Bioinformatics/Btw446 |
0.446 |
|
| 2016 |
Hashemifar S, Ma J, Naveed H, Canzar S, Xu J. ModuleAlign: module-based global alignment of protein-protein interaction networks. Bioinformatics (Oxford, England). 32: i658-i664. PMID 27587686 DOI: 10.1093/Bioinformatics/Btw447 |
0.447 |
|
| 2016 |
Hashemifar S, Huang Q, Xu J. Joint Alignment of Multiple Protein-Protein Interaction Networks via Convex Optimization. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 27428933 DOI: 10.1089/Cmb.2016.0025 |
0.428 |
|
| 2016 |
Wang S, Li W, Liu S, Xu J. RaptorX-Property: a web server for protein structure property prediction. Nucleic Acids Research. PMID 27112573 DOI: 10.1093/Nar/Gkw306 |
0.479 |
|
| 2016 |
Wang S, Li W, Zhang R, Liu S, Xu J. CoinFold: a web server for protein contact prediction and contact-assisted protein folding. Nucleic Acids Research. PMID 27112569 DOI: 10.1093/Nar/Gkw307 |
0.488 |
|
| 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 |
0.615 |
|
| 2015 |
Ma J, Wang S, Wang Z, Xu J. Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning. Bioinformatics (Oxford, England). PMID 26275894 DOI: 10.1093/Bioinformatics/Btv472 |
0.506 |
|
| 2015 |
Xie B, Agam G, Balasubramanian S, Xu J, Gilliam TC, Maltsev N, Börnigen D. Disease gene prioritization using network and feature. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 313-23. PMID 25844670 DOI: 10.1089/Cmb.2015.0001 |
0.313 |
|
| 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 |
0.325 |
|
| 2014 |
Dubchak I, Balasubramanian S, Wang S, Meyden C, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski AR, Mirzaa GM, Dave P, Agam G, Xu J, et al. An integrative computational approach for prioritization of genomic variants. Plos One. 9: e114903. PMID 25506935 DOI: 10.1371/Journal.Pone.0114903 |
0.303 |
|
| 2014 |
Hashemifar S, Xu J. HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks. Bioinformatics (Oxford, England). 30: i438-44. PMID 25161231 DOI: 10.1093/Bioinformatics/Btu450 |
0.416 |
|
| 2014 |
Ma J, Wang S, Wang Z, Xu J. MRFalign: protein homology detection through alignment of Markov random fields. Plos Computational Biology. 10: e1003500. PMID 24675572 DOI: 10.1371/Journal.Pcbi.1003500 |
0.502 |
|
| 2014 |
Källberg M, Margaryan G, Wang S, Ma J, Xu J. RaptorX server: a resource for template-based protein structure modeling. Methods in Molecular Biology (Clifton, N.J.). 1137: 17-27. PMID 24573471 DOI: 10.1007/978-1-4939-0366-5_2 |
0.541 |
|
| 2013 |
Wang Z, Xu J. Predicting protein contact map using evolutionary and physical constraints by integer programming. Bioinformatics (Oxford, England). 29: i266-73. PMID 23812992 DOI: 10.1093/Bioinformatics/Btt211 |
0.431 |
|
| 2013 |
Ma J, Wang S, Zhao F, Xu J. Protein threading using context-specific alignment potential. Bioinformatics (Oxford, England). 29: i257-65. PMID 23812991 DOI: 10.7490/F1000Research.1094039.1 |
0.451 |
|
| 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 |
0.599 |
|
| 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 |
0.596 |
|
| 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 |
0.621 |
|
| 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 |
0.51 |
|
| 2012 |
Zhao F, Xu J. A position-specific distance-dependent statistical potential for protein structure and functional study. Structure (London, England : 1993). 20: 1118-26. PMID 22608968 DOI: 10.1016/J.Str.2012.04.003 |
0.353 |
|
| 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 |
0.619 |
|
| 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 |
0.604 |
|
| 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 |
0.615 |
|
| 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 |
0.635 |
|
| 2011 |
Li SC, Bu D, Xu J, Li M. Finding nearly optimal GDT scores. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 693-704. PMID 21554017 DOI: 10.1089/Cmb.2010.0123 |
0.366 |
|
| 2011 |
Peng J, Xu J. A multiple-template approach to protein threading. Proteins. 79: 1930-9. PMID 21465564 DOI: 10.1002/Prot.23016 |
0.615 |
|
| 2011 |
Hosur R, Xu J, Bienkowska J, Berger B. iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. Journal of Molecular Biology. 405: 1295-310. PMID 21130772 DOI: 10.1016/J.Jmb.2010.11.025 |
0.466 |
|
| 2011 |
Wang S, Peng J, Xu J. 3DCOMB: Alignment of distantly-related protein structures F1000research. 2. DOI: 10.7490/F1000Research.2059.1 |
0.584 |
|
| 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 |
0.588 |
|
| 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 |
0.609 |
|
| 2010 |
Peng J, Xu J. Low-homology protein threading. Bioinformatics (Oxford, England). 26: i294-300. PMID 20529920 DOI: 10.7490/F1000Research.320.1 |
0.56 |
|
| 2010 |
Singh R, Park D, Xu J, Hosur R, Berger B. Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. Nucleic Acids Research. 38: W508-15. PMID 20513650 DOI: 10.1093/Nar/Gkq481 |
0.499 |
|
| 2010 |
DeBartolo J, Hocky G, Wilde M, Xu J, Freed KF, Sosnick TR. Protein structure prediction enhanced with evolutionary diversity: SPEED. Protein Science : a Publication of the Protein Society. 19: 520-34. PMID 20066664 DOI: 10.1002/Pro.330 |
0.551 |
|
| 2010 |
Zhao F, Peng J, Xu J. Efficient fragment-free approach to protein folding F1000research. 1. DOI: 10.7490/F1000Research.312.1 |
0.522 |
|
| 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 |
0.569 |
|
| 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 |
0.525 |
|
| 2009 |
Gao X, Xu J, Li SC, Li M. Predicting local quality of a sequence-structure alignment. Journal of Bioinformatics and Computational Biology. 7: 789-810. PMID 19785046 DOI: 10.1142/S0219720009004345 |
0.484 |
|
| 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 |
0.562 |
|
| 2009 |
Gao X, Bu D, Xu J, Li M. Improving consensus contact prediction via server correlation reduction. Bmc Structural Biology. 9: 28. PMID 19419562 DOI: 10.1186/1472-6807-9-28 |
0.49 |
|
| 2009 |
Bu D, Li M, Li SC, Qian J, Xu J. Finding compact structural motifs Theoretical Computer Science. 410: 2834-2839. DOI: 10.1016/J.Tcs.2009.03.023 |
0.423 |
|
| 2008 |
Singh R, Xu J, Berger B. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proceedings of the National Academy of Sciences of the United States of America. 105: 12763-8. PMID 18725631 DOI: 10.1073/Pnas.0806627105 |
0.387 |
|
| 2008 |
Li SC, Bu D, Xu J, Li M. Fragment-HMM: a new approach to protein structure prediction. Protein Science : a Publication of the Protein Society. 17: 1925-34. PMID 18723665 DOI: 10.1110/Ps.036442.108 |
0.481 |
|
| 2008 |
Li SC, Bu D, Gao X, Xu J, Li M. Designing succinct structural alphabets. Bioinformatics (Oxford, England). 24: i182-9. PMID 18586712 DOI: 10.1093/bioinformatics/btn165 |
0.312 |
|
| 2008 |
Zhao F, Li S, Sterner BW, Xu J. Discriminative learning for protein conformation sampling. Proteins. 73: 228-40. PMID 18412258 DOI: 10.1002/Prot.22057 |
0.511 |
|
| 2008 |
Singh R, Xu J, Berger B. Global alignment of multiple protein interaction networks. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 303-14. PMID 18229695 |
0.309 |
|
| 2008 |
Xu J, Jiao F, Yu L. Protein structure prediction using threading. Methods in Molecular Biology (Clifton, N.J.). 413: 91-121. PMID 18075163 DOI: 10.1007/978-1-59745-574-9_4 |
0.524 |
|
| 2007 |
Gao X, Bu D, Li SC, Xu J, Li M. FragQA: predicting local fragment quality of a sequence-structure alignment. Genome Informatics. International Conference On Genome Informatics. 19: 27-39. PMID 18546502 DOI: 10.11234/Gi1990.19.27 |
0.486 |
|
| 2007 |
Gao X, Bu D, Li SC, Li M, Xu J. Consensus contact prediction by linear programming. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 6: 323-34. PMID 17951835 |
0.349 |
|
| 2007 |
Xu J, Jiao F, Berger B. A parameterized algorithm for protein structure alignment. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 564-77. PMID 17683261 DOI: 10.1089/Cmb.2007.R003 |
0.456 |
|
| 2006 |
Jiao F, Xu J, Yu L, Schuurmans D. Protein fold recognition using the gradient boost algorithm. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 43-53. PMID 17369624 |
0.374 |
|
| 2006 |
Singh R, Xu J, Berger B. Struct2net: integrating structure into protein-protein interaction prediction. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 403-14. PMID 17094256 |
0.448 |
|
| 2006 |
Xu J, Berger B. Fast and accurate algorithms for protein side-chain packing Journal of the Acm (Jacm). 53: 533-557. DOI: 10.1145/1162349.1162350 |
0.446 |
|
| 2005 |
Xu J. Fold recognition by predicted alignment accuracy. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 2: 157-65. PMID 17044180 DOI: 10.1109/Tcbb.2005.24 |
0.441 |
|
| 2005 |
Tang T, Xu J, Li M. Discovering sequence-structure motifs from protein segments and two applications. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 370-81. PMID 15759642 |
0.35 |
|
| 2004 |
Xu J, Li M, Xu Y. Protein Threading by Linear Programming: Theoretical Analysis and Computational Results Journal of Combinatorial Optimization. 8: 403-418. DOI: 10.1007/S10878-004-4834-X |
0.385 |
|
| 2003 |
Xu J, Li M, Kim D, Xu Y. RAPTOR: optimal protein threading by linear programming. Journal of Bioinformatics and Computational Biology. 1: 95-117. PMID 15290783 DOI: 10.1142/S0219720003000186 |
0.402 |
|
| 2003 |
Xu J, Li M. Assessment of RAPTOR's linear programming approach in CAFASP3. Proteins. 53: 579-84. PMID 14579349 DOI: 10.1002/Prot.10531 |
0.35 |
|
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