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Expert Review of Proteomics Volume 8, 2011 - Issue 3
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Review

Recent progress in predicting protein sub-subcellular locations

Pufeng Du School of Computer Science and Technology, Tianjin University, Tianjin 300072, China; MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China;[email protected]
,
Tingting Li Department of Biomedical Informatics, Peking University Health Science Center, 38 Xueyuan Rd, Beijing 100191, China; Department of Biomedical Informatics, Peking University Health Science Center, 38 Xueyuan Rd, Beijing 100191, China
&
Xin Wang School of Computer Science and Technology, Tianjin University, Tianjin 300072, China; School of Computer Science and Technology, Tianjin University, Tianjin 300072, China
Pages 391-404 | Published online: 09 Jan 2014

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Pufeng Du & Chao Xu. (2013) Predicting multisite protein subcellular locations: progress and challenges. Expert Review of Proteomics 10:3, pages 227-237.
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Articles from other publishers (35)

Yajie Hu, Chen Liu, Jinghui Yang, Mingmei Zhong, Baojiang Qian, Juan Chen, Yunhui Zhang & Jie Song. (2023) HMGB1 is involved in viral replication and the inflammatory response in coxsackievirus A16-infected 16HBE cells via proteomic analysis and identification. Virology Journal 20:1.
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Jie Song, Guifang Zhao, Hui Li, Yan Yang, Yue Yu, Yunguang Hu, Yadong Li, Jiang Li & Yajie Hu. (2023) Tandem mass tag (TMT) labeling-based quantitative proteomic analysis reveals the cellular protein characteristics of 16HBE cells infected with coxsackievirus A10 and the potential effect of HMGB1 on viral replication. Archives of Virology 168:8.
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Ren-Hua Wang, Tao Luo, Han-Lin Zhang & Pu-Feng Du. (2023) PLA-GNN: Computational inference of protein subcellular location alterations under drug treatments with deep graph neural networks. Computers in Biology and Medicine 157, pages 106775.
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Minjie Mou, Ziqi Pan, Mingkun Lu, Huaicheng Sun, Yunxia Wang, Yongchao Luo & Feng Zhu. (2022) Application of Machine Learning in Spatial Proteomics. Journal of Chemical Information and Modeling 62:23, pages 5875-5895.
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Jian Sun & Pu-Feng Du. (2020) Predicting protein subchloroplast locations: the 10th anniversary. Frontiers of Computer Science 15:2.
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Guang-Ping Li, Pu-Feng Du, Zi-Ang Shen, Hang-Yu Liu & Tao Luo. (2020) DPPN-SVM: Computational Identification of Mis-Localized Proteins in Cancers by Integrating Differential Gene Expressions With Dynamic Protein-Protein Interaction Networks. Frontiers in Genetics 11.
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颜 王. (2020) Progress on Methods of Subcellular Localization of Chloroplast Protein in Plant Cells. Botanical Research 09:03, pages 268-273.
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Yang-Yang Miao, Wei Zhao, Guang-Ping Li, Yang Gao & Pu-Feng Du. (2019) Predicting Endoplasmic Reticulum Resident Proteins Using Auto-Cross Covariance Transformation With a U-Shaped Residue Weight-Transfer Function. Frontiers in Genetics 10.
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Shanping Qiao, Baoqiang Yan & Jing Li. (2017) Ensemble learning for protein multiplex subcellular localization prediction based on weighted KNN with different features. Applied Intelligence 48:7, pages 1813-1824.
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Ya-Sen Jiao & Pu-Feng Du. (2017) Predicting protein submitochondrial locations by incorporating the positional-specific physicochemical properties into Chou's general pseudo-amino acid compositions. Journal of Theoretical Biology 416, pages 81-87.
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Yasen Jiao & Pufeng Du. (2016) Performance measures in evaluating machine learning based bioinformatics predictors for classifications. Quantitative Biology 4:4, pages 320-330.
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Ya-Sen Jiao & Pu-Feng Du. (2016) Prediction of Golgi-resident protein types using general form of Chou's pseudo-amino acid compositions: Approaches with minimal redundancy maximal relevance feature selection. Journal of Theoretical Biology 402, pages 38-44.
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Lisa M. Breckels, Sean B. Holden, David Wojnar, Claire M. Mulvey, Andy Christoforou, Arnoud Groen, Matthew W. B. Trotter, Oliver Kohlbacher, Kathryn S. Lilley & Laurent Gatto. (2016) Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics. PLOS Computational Biology 12:5, pages e1004920.
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Ya-Sen Jiao & Pu-Feng Du. (2016) Predicting Golgi-resident protein types using pseudo amino acid compositions: Approaches with positional specific physicochemical properties. Journal of Theoretical Biology 391, pages 35-42.
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Yong H Woo, Hifzur Ansari, Thomas D Otto, Christen M Klinger, Martin Kolisko, Jan Michálek, Alka Saxena, Dhanasekaran Shanmugam, Annageldi Tayyrov, Alaguraj Veluchamy, Shahjahan Ali, Axel Bernal, Javier del Campo, Jaromír Cihlář, Pavel Flegontov, Sebastian G Gornik, Eva Hajdušková, Aleš Horák, Jan Janouškovec, Nicholas J Katris, Fred D Mast, Diego Miranda-Saavedra, Tobias Mourier, Raeece Naeem, Mridul Nair, Aswini K Panigrahi, Neil D Rawlings, Eriko Padron-Regalado, Abhinay Ramaprasad, Nadira Samad, Aleš Tomčala, Jon Wilkes, Daniel E Neafsey, Christian Doerig, Chris Bowler, Patrick J Keeling, David S Roos, Joel B Dacks, Thomas J Templeton, Ross F Waller, Julius Lukeš, Miroslav Oborník & Arnab Pain. (2015) Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. eLife 4.
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Guohua Huang, Yin Lu, Changhong Lu, Mingyue Zheng & Yu-Dong Cai. (2015) Prediction of Drug Indications Based on Chemical Interactions and Chemical Similarities. BioMed Research International 2015, pages 1-14.
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Zhanpeng Jiang, Rui Xu & Changchun Dong. (2015) Identification of Chemical Toxicity Using Ontology Information of Chemicals. Computational and Mathematical Methods in Medicine 2015, pages 1-5.
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Shao-Ping Shi, Hao-Dong Xu, Ping-Ping Wen & Jian-Ding Qiu. (2015) Progress and challenges in predicting protein methylation sites. Molecular BioSystems 11:10, pages 2610-2619.
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Xiaomei Li, Xindong Wu & Gongqing Wu. (2014) Robust feature generation for protein subchloroplast location prediction with a weighted GO transfer model. Journal of Theoretical Biology 347, pages 84-94.
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Andy Christoforou, Claire Mulvey, Lisa M. Breckels, Laurent Gatto & Kathryn S. Lilley. 2014. Quantitative Proteomics. Quantitative Proteomics 185 210 .
Jing Lu, Guohua Huang, Hai-Peng Li, Kai-Yan Feng, Lei Chen, Ming-Yue Zheng & Yu-Dong Cai. (2014) Prediction of Cancer Drugs by Chemical-Chemical Interactions. PLoS ONE 9:2, pages e87791.
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Pufeng Du & Lusheng Wang. (2014) Predicting Human Protein Subcellular Locations by the Ensemble of Multiple Predictors via Protein-Protein Interaction Network with Edge Clustering Coefficients. PLoS ONE 9:1, pages e86879.
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Shan Ping Qiao. (2014) Bioinformatics Study with an Implementation of Two Feature Extraction Algorithms for Protein Sequences. Advanced Materials Research 886, pages 576-579.
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Lei Chen, Jing Lu, Ning Zhang, Tao Huang & Yu-Dong Cai. (2014) A hybrid method for prediction and repositioning of drug Anatomical Therapeutic Chemical classes. Molecular BioSystems 10:4, pages 868.
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Lianping Yang, Xiangde Zhang & Hegui Zhu. (2013) Alignment free comparison: k word voting model and its applications. Journal of Theoretical Biology 335, pages 276-282.
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L.M. Breckels, L. Gatto, A. Christoforou, A.J. Groen, K.S. Lilley & M.W.B. Trotter. (2013) The effect of organelle discovery upon sub-cellular protein localisation. Journal of Proteomics 88, pages 129-140.
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Hao Lin, Wei Chen, Lu-Feng Yuan, Zi-Qiang Li & Hui Ding. (2013) Using Over-Represented Tetrapeptides to Predict Protein Submitochondria Locations. Acta Biotheoretica 61:2, pages 259-268.
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Chad P. Satori, Michelle M. Henderson, Elyse A. Krautkramer, Vratislav Kostal, Mark M. Distefano & Edgar A. Arriaga. (2013) Bioanalysis of Eukaryotic Organelles. Chemical Reviews 113:4, pages 2733-2811.
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Lei Chen, Jing Lu, Jian Zhang, Kai-Rui Feng, Ming-Yue Zheng & Yu-Dong Cai. (2013) Predicting Chemical Toxicity Effects Based on Chemical-Chemical Interactions. PLoS ONE 8:2, pages e56517.
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Tao Zhang, Min Jiang, Lei Chen, Bing Niu & Yudong Cai. (2013) Prediction of Gene Phenotypes Based on GO and KEGG Pathway Enrichment Scores. BioMed Research International 2013, pages 1-7.
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Lei Chen, Tao Huang, Jian Zhang, Ming-Yue Zheng, Kai-Yan Feng, Yu-Dong Cai & Kuo-Chen Chou. (2013) Predicting Drugs Side Effects Based on Chemical-Chemical Interactions and Protein-Chemical Interactions. BioMed Research International 2013, pages 1-8.
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Pufeng Du & Yuan Yu. (2013) SubMito-PSPCP: Predicting Protein Submitochondrial Locations by Hybridizing Positional Specific Physicochemical Properties with Pseudoamino Acid Compositions. BioMed Research International 2013, pages 1-7.
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Samuel T. Mindaye, Moonjin Ra, Jessica Lo Surdo, Steven R. Bauer & Michail A. Alterman. (2013) Improved proteomic profiling of the cell surface of culture-expanded human bone marrow multipotent stromal cells. Journal of Proteomics 78, pages 1-14.
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Pufeng Du, Yang Tian & Yan Yan. (2012) Subcellular localization prediction for human internal and organelle membrane proteins with projected gene ontology scores. Journal of Theoretical Biology 313, pages 61-67.
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Lianping Yang, Xiangde Zhang & Hegui Zhu. (2012) Alignment free comparison: Similarity distribution between the DNA primary sequences based on the shortest absent word. Journal of Theoretical Biology 295, pages 125-131.
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