Background

Xiaoyong Pan worked till December 201i8 as postdoc in the Department of Medical informatics at Erasmus MC, Rotterdam, The Netherlands. He obtained a Ph.D. from University of Copenhagen in 2017, and a M.E. from Shanghai Jiaotong University in 2011. From 2011 to 2013, he worked as a software engineer in IBM Corporation for two and half years before starting his Ph.D in University of Copenhagen. He was supported by a Ph.D. fellowship from Copenhagen University from 2013 to 2016 and his Thesis title is "computational analysis of long non-coding RNAs and their functions". In 2013, he received outstanding master thesis award from Shanghai Education Commission. he have published over 20 papers at prominent journals, and serve as a leading Guest Editor for IEEE Access. 

Publications

• Xiaoyong Pan, Anne Wenzel, Lars Juhl Jensen, Jan Gorodkin. Genome-Wide Identification of Clusters of Predicted MicroRNA Binding Sites as MicroRNA Sponge Candidates. Plos One. In press. [Webserver]

• Xiaoyong Pan, Hong-Bin Shen. Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks. Bioinformatics. In press. [Code]

• Xiaoyong Pan, Peter Rijnbeek, Junchi Yan, Hong-Bin Shen. Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks. BMC Genomics, 2018. In press.[Code]

• Zhen Cao*, Xiaoyong Pan*, Yang Yang*, Yan Huang, Hong-Bin Shen^. The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier. Bioinformatics, in press (shared first author). [Webserver]

   

• Xiaoyong Pan, Hong-Bin Shen. Learning distributed representations of RNA sequences and its application for predicting RNA-protein binding sites with a convolutional neural network. Neurocomputing. 305: 51-58. [Code]

• Lei Chen*, Xiaoyong Pan*, XiaoHua Hu*, Yu-Hang Zhang, ShaoPeng Wang, Tao Huang, Yu-Dong Cai. Gene expression differences among different MSI statuses in colorectal cancer. International Journal of Cancer. In press (shared first author).

• Yong-Xian Fan, Xiaoyong Pan, Yang Zhang^ and Hong-Bin Shen^. LabCaS for ranking potential calpain substrate cleavage sites from amino acid sequence. Methods in Molecular Biology, In press [Webserver]

• Xiaoyong Pan, Junchi Yan. Attention based convolutional neural network for predicting RNA-protein binding sites. NIPS Workshop on Machine Learning in Computational Biology, 2017. [Code]

• Lei Chen, Yu-Hang Zhang, Guohua Huang, Xiaoyong Pan, ShaoPeng Wang, Tao Huang, Yu-Dong Cai. Discriminating circRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm with feature selection. Molecular Genetics and Genomics. 2017 Sep 14. doi: 10.1007/s00438-017-1372-7.

• Xiaoyong Pan, Hong-Bin Shen. RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach . BMC bioinformatics, 2017, 18(1):136. [Code]

• Alexander Junge, Jan C. Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos, Ferhat Alkan, Christian Anthon, Christian von Mering, Christopher T. Workman, Lars Juhl Jensen, and Jan Gorodkin. RAIN: RNA-protein Association and Interaction Networks. Database (Oxford), 2017, baw167.

• Xiaoyong Pan, Yong-Xian Fan, Junchi Yan, Hong-Bin Shen. IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction. BMC genomics, 2016, 17(1): 582.

• Xiaoyong Pan, Hong-Bin Shen. OUGENE: a disease associated over-expressed and under-expressed gene database. Science Bulletin, 2016, 61(10):752-754.

• Xiaoyong Pan, Kai Xiong. PredcircRNA: computational classification of circular RNA from other long non-coding RNA using hybrid features. Molecular BioSystems, 2015, 11(8): 2219-2226.

• Aashiq H Mirza, Claus HB Berthelsen, Stefan E Seemann, Xiaoyong Pan, Klaus S Frederiksen, Mogens Vilien, Jan Gorodkin, Flemming Pociot. Transcriptomic landscape of lncRNAs in inflammatory bowel disease. Genome medicine, 2015, 7(1):39.

• Xiaoyong Pan, Lin Zhu, Yong-Xian Fan, Junchi Yan. Predicting protein–RNA interaction amino acids using random forest based on submodularity subset selection. Computational biology and chemistry, 2014, 53,:324-330.

• Xiao-Yong Pan, Ye Tian, Yan Huang, Hong-Bin Shen. Towards better accuracy for missing value estimation of epistatic miniarray profiling data by a novel ensemble approach. Genomics, 2011, 97(5): 257-264.

• Ya-Nan Zhang, Xiao-Yong Pan, Yan Huang, Hong-Bin Shen. Adaptive compressive learning for prediction of protein–protein interactions from primary sequence. Journal of theoretical biology, 2011, 283(1): 44-52.

• Xiao-Yong Pan, Ya-Nan Zhang, Hong-Bin Shen. Large-Scale prediction of human protein− protein interactions from amino acid sequence based on latent topic features. Journal of Proteome Research, 2010, 9(10): 4992-5001.

• Xue-Mei Ding, Xiao-Yong Pan, Chen Xu, Hong-Bin Shen. Computational prediction of DNA-protein interactions: a review. Current computer-aided drug design, 2010, 6(3): 197-206.

• Xiao-Yong Pan, Hong-Bin Shen. Robust prediction of B-factor profile from sequence using two-stage SVR based on random forest feature selection. Protein and peptide letters, 2009, 16 (12), 1447-1454.