Jinbo Xu

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Sheng WangZelixir BiotechVerified email at zelixir.com
Jian PengHelixonVerified email at helixon.com
Jianzhu MaTsinghua UniversityVerified email at tsinghua.edu.cn
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 SinghDuke UniversityVerified email at duke.edu
Dongbo BuBioinformatics lab, Institute 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
Morten KallbergIllumina incVerified email at illumina.com
Xin GaoProfessor, Computer Sciences; Director, Computational Bioscience Research CenterVerified email at kaust.edu.sa
Ying XuProfessor, Southern University of Science and Technology (2023/01/15 - )Verified email at uga.edu
Boqiao LaiToyota Technological Institute at ChicagoVerified email at ttic.edu
Serafim BatzoglouSeerVerified email at seer.bio
Laksshman SundaramGraduate Student in Computer Science, Stanford UniversityVerified email at stanford.edu
Kyle Kai-How FarhPrincipal Investigator, Illumina AI LabVerified email at illumina.com
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
Xiaoyang JingVerified email at ttic.edu

Jinbo Xu

Professor, Toyota Technological Institute at Chicago

Verified email at ttic.edu - Homepage

Machine Learning Algorithm and Optimization Computational Biology


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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	2330	2018
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	1958	2012
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	1057	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	1057	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	841	2008
Protein secondary structure prediction using deep convolutional neural fields S Wang, J Peng, J Ma, J Xu Scientific reports 6, 2016	713	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	610	2016
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	458	2018
RaptorX: exploiting structure information for protein alignment by statistical inference J Peng, J Xu Proteins: Structure, Function, and Bioinformatics 79 (S10), 161-171, 2011	458	2011
Distance-based protein folding powered by deep learning J Xu Proceedings of the National Academy of Sciences 116 (34), 16856-16865, 2019	429	2019
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	405	2007
Predicting protein–protein interactions through sequence-based deep learning S Hashemifar, B Neyshabur, AA Khan, J Xu Bioinformatics 34 (17), i802-i810, 2018	375	2018
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	358	2003
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	318	2014
Identification of let-7–regulated oncofetal genes B Boyerinas, SM Park, N Shomron, MM Hedegaard, J Vinther, ... Cancer research 68 (8), 2587, 2008	290	2008
Critical assessment of protein intrinsic disorder prediction M Necci, D Piovesan, CPJ Xu), DP Curators, SCE Tosatto Nature Methods, 2021	279	2021
Improved protein structure prediction by deep learning irrespective of co-evolution information J Xu, M Mcpartlon, J Li Nature Machine Intelligence, 2021	241	2021
Conditional neural fields J Peng, L Bo, J Xu Advances in neural information processing systems 22, 1419-1427, 2009	229	2009
Protein structure alignment beyond spatial proximity S Wang, J Ma, J Peng, J Xu Scientific reports 3, 1448, 2013	223	2013
Protein threading using context-specific alignment potential J Ma, S Wang, F Zhao, J Xu Bioinformatics 29 (13), i257-i265, 2013	181	2013

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