Jinbo Xu

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Sheng WangZelixir BiotechVerified email at zelixir.com
Jian PengUniversity of Illinois at Urbana-ChampaignVerified email at illinois.edu
Jianzhu MaPeking UniversityVerified email at pku.edu.cn
Ming LiUniversity Professor, University of WaterlooVerified email at uwaterloo.ca
Bonnie BergerMITVerified email at mit.edu
Zhiyong WangToyota Technological Institute at ChicagoVerified email at ttic.edu
Siqi SunAssociate Professor; Fudan University, Shanghai AI LabVerified email at fudan.edu.cn
Rohit SinghMITVerified email at mit.edu
Dongbo BuInstitute of Computing Technology, Chinese Academy of SciencesVerified email at ict.ac.cn
Shuai Cheng LiDepartment of Computer Science, City University of Hong KongVerified email at cityu.edu.hk
Somaye HashemifarColumbia UniversityVerified email at cumc.columbia.edu
Morten KallbergIllumina incVerified email at illumina.com
Xin GaoProfessor, Computer Sciences; Associate Director, Computational Bioscience Research CenterVerified email at kaust.edu.sa
Zhen LiAssistant Professor, the Chinese University of Hong Kong, Shenzhen (CUHKSZ)Verified email at cuhk.edu.cn
Ying XuProfessor of Biochemistry and Molecular Biology, University of GeorgiaVerified email at uga.edu
Tobin SosnickProfessor of Biochemistry and Molecular Biology, University of ChicagoVerified email at uchicago.edu
Karl F. FreedProfessor of Chemistry, Emeritis, U of ChicagoVerified email at uchicago.edu
Natalia MaltsevResearch Professor, Department of Human Genetics, The University of ChicagoVerified email at uchicago.edu
Serafim BatzoglouSeerVerified email at seer.bio
Laksshman SundaramGraduate Student in Computer Science, Stanford UniversityVerified email at stanford.edu

Jinbo Xu

Professor, Toyota Technological Institute at Chicago

Verified email at ttic.edu - Homepage

Machine Learning Algorithm and Optimization Computational Biology


Title Sort by citations Sort by year Sort by title	Cited by Cited by	Year
Template-based protein structure modeling using the RaptorX web server M Källberg, H Wang, S Wang, J Peng, Z Wang, H Lu, J Xu Nature protocols 7 (8), 1511-1522, 2012	1591	2012
Opportunities And Obstacles For Deep Learning In Biology And Medicine T Ching, DS Himmelstein, BK Beaulieu-Jones, AA Kalinin, BT Do, ... J R Soc Interface 15 (141), 2018	1291	2018
Accurate de novo prediction of protein contact map by ultra-deep learning model S Wang, S Sun, Z Li, R Zhang, J Xu PLoS computational biology 13 (1), e1005324, 2017	726	2017
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model S Wang, S Sun, Z Li, R Zhang, J Xu PLOS Computational Biology 13 (1), e1005324, 2017	726	2017
Global alignment of multiple protein interaction networks with application to functional orthology detection R Singh, J Xu, B Berger Proceedings of the National Academy of Sciences 105 (35), 12763-12768, 2008	680	2008
Protein secondary structure prediction using deep convolutional neural fields S Wang, J Peng, J Ma, J Xu Scientific reports 6, 2016	508	2016
RaptorX-Property: a web server for protein structure property prediction S Wang, W Li, S Liu, J Xu Nucleic acids research 44 (W1), W430-W435, 2016	393	2016
Pairwise global alignment of protein interaction networks by matching neighborhood topology R Singh, J Xu, B Berger Annual International Conference on Research in Computational Molecular …, 2007	377	2007
RaptorX: exploiting structure information for protein alignment by statistical inference J Peng, J Xu Proteins: Structure, Function, and Bioinformatics 79 (S10), 161-171, 2011	376	2011
RAPTOR: optimal protein threading by linear programming J Xu, M Li, D Kim, Y Xu Journal of Bioinformatics and Computational Biology 1 (01), 95-117, 2003	337	2003
Distance-based protein folding powered by deep learning J Xu Proceedings of the National Academy of Sciences 116 (34), 16856-16865, 2019	283	2019
Identification of let-7–regulated oncofetal genes B Boyerinas, SM Park, N Shomron, MM Hedegaard, J Vinther, ... Cancer research 68 (8), 2587, 2008	270	2008
RaptorX server: a resource for template-based protein structure modeling M Källberg, G Margaryan, S Wang, J Ma, J Xu Protein Structure Prediction, 17-27, 2014	242	2014
Predicting the clinical impact of human mutation with deep neural networks L Sundaram, H Gao, SR Padigepati, JF McRae, Y Li, JA Kosmicki, ... Nature genetics 50 (8), 1161-1170, 2018	224	2018
Conditional neural fields J Peng, L Bo, J Xu Advances in neural information processing systems 22, 1419-1427, 2009	222	2009
Predicting protein–protein interactions through sequence-based deep learning S Hashemifar, B Neyshabur, AA Khan, J Xu Bioinformatics 34 (17), i802-i810, 2018	189	2018
Protein structure alignment beyond spatial proximity S Wang, J Ma, J Peng, J Xu Scientific reports 3, 1448, 2013	168	2013
Protein threading using context-specific alignment potential J Ma, S Wang, F Zhao, J Xu Bioinformatics 29 (13), i257-i265, 2013	156	2013
Protein 8‐class secondary structure prediction using conditional neural fields Z Wang, F Zhao, J Peng, J Xu Proteomics 11 (19), 3786-3792, 2011	153	2011
Predicting protein contact map using evolutionary and physical constraints by integer programming Z Wang, J Xu Bioinformatics 29 (13), i266-i273, 2013	144	2013

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