Recent Advances on Prediction of Protein Subcellular Localization

[1]  Philip Resnik,et al.  Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language , 1999, J. Artif. Intell. Res..

[2]  Pufeng Du,et al.  PseAAC-General: Fast Building Various Modes of General Form of Chou’s Pseudo-Amino Acid Composition for Large-Scale Protein Datasets , 2014, International journal of molecular sciences.

[3]  K. Chou,et al.  iLoc-Virus: a multi-label learning classifier for identifying the subcellular localization of virus proteins with both single and multiple sites. , 2011, Journal of theoretical biology.

[4]  M. K. Sekhwal,et al.  Identification of MFS proteins in sorghum using semantic similarity , 2013, Theory in Biosciences.

[5]  Sun-Yuan Kung,et al.  HybridGO-Loc: Mining Hybrid Features on Gene Ontology for Predicting Subcellular Localization of Multi-Location Proteins , 2014, PloS one.

[6]  E. Mumcuoglu,et al.  Subcellular Localization Prediction with New Protein Encoding Schemes , 2007, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[7]  K. Chou,et al.  Recent progress in protein subcellular location prediction. , 2007, Analytical biochemistry.

[8]  Chunyu Wang,et al.  A novel insight into Gene Ontology semantic similarity. , 2013, Genomics.

[9]  K. Chou,et al.  Hum-PLoc: a novel ensemble classifier for predicting human protein subcellular localization. , 2006, Biochemical and biophysical research communications.

[10]  Guo-Zheng Li,et al.  Multilabel Learning via Random Label Selection for Protein Subcellular Multilocations Prediction , 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[11]  K. Chou,et al.  PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition. , 2008, Analytical biochemistry.

[12]  Doheon Lee,et al.  A method to improve protein subcellular localization prediction by integrating various biological data sources , 2009, BMC Bioinformatics.

[13]  Kuo-Chen Chou,et al.  Using optimized evidence-theoretic K-nearest neighbor classifier and pseudo-amino acid composition to predict membrane protein types. , 2005, Biochemical and biophysical research communications.

[14]  Carole A. Goble,et al.  Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation , 2003, Bioinform..

[15]  K. Chou,et al.  Virus-mPLoc: A Fusion Classifier for Viral Protein Subcellular Location Prediction by Incorporating Multiple Sites , 2010, Journal of biomolecular structure & dynamics.

[16]  K. Chou,et al.  iLoc-Euk: A Multi-Label Classifier for Predicting the Subcellular Localization of Singleplex and Multiplex Eukaryotic Proteins , 2011, PloS one.

[17]  Xin Wang,et al.  PseAAC-Builder: a cross-platform stand-alone program for generating various special Chou's pseudo-amino acid compositions. , 2012, Analytical biochemistry.

[18]  K. Chou,et al.  REVIEW : Recent advances in developing web-servers for predicting protein attributes , 2009 .

[19]  K. Chou,et al.  Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. , 2007, Journal of proteome research.

[20]  Dong-Sheng Cao,et al.  propy: a tool to generate various modes of Chou's PseAAC , 2013, Bioinform..

[21]  K. Chou,et al.  Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms , 2008, Nature Protocols.

[22]  Xiaoqi Zheng,et al.  Prediction of bacterial protein subcellular localization by incorporating various features into Chou's PseAAC and a backward feature selection approach. , 2014, Biochimie.

[23]  K. Chou.  Prediction of protein cellular attributes using pseudo‐amino acid composition , 2001, Proteins.

[24]  Kuo-Chen Chou,et al.  Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes , 2005, Bioinform..

[25]  Kuo-Chen Chou,et al.  Large‐scale plant protein subcellular location prediction , 2007, Journal of cellular biochemistry.

[26]  Yuan Zhang,et al.  Prediction of protein subcellular multi-localization based on the general form of Chou's pseudo amino acid composition. , 2012, Protein and peptide letters.

[27]  Sun-Yuan Kung,et al.  mGOASVM: Multi-label protein subcellular localization based on gene ontology and support vector machines , 2012, BMC Bioinformatics.

[28]  Guo-Zheng Li,et al.  A Multi-Label Predictor for Identifying the Subcellular Locations of Singleplex and Multiplex Eukaryotic Proteins , 2012, PloS one.

[29]  Zhirong Sun,et al.  Support vector machine approach for protein subcellular localization prediction , 2001, Bioinform..

[30]  K. Chou,et al.  Hum-mPLoc: an ensemble classifier for large-scale human protein subcellular location prediction by incorporating samples with multiple sites. , 2007, Biochemical and biophysical research communications.

[31]  Liang Kong,et al.  Predict protein structural class for low-similarity sequences by evolutionary difference information into the general form of Chou's pseudo amino acid composition. , 2014, Journal of theoretical biology.

[32]  K. Chou,et al.  iLoc-Plant: a multi-label classifier for predicting the subcellular localization of plant proteins with both single and multiple sites. , 2011, Molecular bioSystems.

[33]  Dekang Lin,et al.  An Information-Theoretic Definition of Similarity , 1998, ICML.

[34]  Zhen-Hui Zhang,et al.  A novel method for apoptosis protein subcellular localization prediction combining encoding based on grouped weight and support vector machine , 2006, FEBS letters.

[35]  Deendayal Dinakarpandian,et al.  Finding disease similarity based on implicit semantic similarity , 2012, J. Biomed. Informatics.

[36]  Nicola J. Mulder,et al.  The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines , 2014, Front. Genet..

[37]  Evaluating long-term relationship of protein sequence by use of D-interval conditional probability and its impact on protein structural class prediction. , 2009, Protein and peptide letters.

[38]  K. Chou,et al.  Support vector machines for predicting membrane protein types by using functional domain composition. , 2003, Biophysical journal.

[39]  Guo-Ping Zhou,et al.  Subcellular location prediction of apoptosis proteins , 2002, Proteins.

[40]  Kuo-Chen Chou,et al.  Predicting protein localization in budding Yeast , 2005, Bioinform..

[41]  Kuo-Chen Chou,et al.  A top-down approach to enhance the power of predicting human protein subcellular localization: Hum-mPLoc 2.0. , 2009, Analytical biochemistry.

[42]  Zheng Yuan.  Prediction of protein subcellular locations using Markov chain models , 1999, FEBS letters.

[43]  Yan Li,et al.  A protein structural classes prediction method based on PSI-BLAST profile. , 2014, Journal of theoretical biology.

[44]  Changqing Li,et al.  An Ensemble Classifier for Eukaryotic Protein Subcellular Location Prediction Using Gene Ontology Categories and Amino Acid Hydrophobicity , 2012, PloS one.

[45]  David W. Conrath,et al.  Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy , 1997, ROCLING/IJCLCLP.

[46]  S. Kung,et al.  GOASVM: a subcellular location predictor by incorporating term-frequency gene ontology into the general form of Chou's pseudo-amino acid composition. , 2013, Journal of theoretical biology.

[47]  K. Chou.  Some remarks on protein attribute prediction and pseudo amino acid composition , 2010, Journal of Theoretical Biology.

[48]  Shiow-Fen Hwang,et al.  ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization , 2008, BMC Bioinformatics.

[49]  Liaofu Luo,et al.  Use of  tetrapeptide signals for protein secondary-structure prediction , 2008, Amino Acids.

[50]  K. Chou,et al.  Virus-PLoc: a fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells. , 2007, Biopolymers.

[51]  G. Pollastri,et al.  SCLpredT: Ab initio and homology-based prediction of subcellular localization by N-to-1 neural networks , 2013, SpringerPlus.

[52]  Q Gu,et al.  Prediction of G-protein-coupled receptor classes in low homology using Chou's pseudo amino acid composition with approximate entropy and hydrophobicity patterns. , 2010, Protein and peptide letters.

[53]  Xiaoqi Zheng,et al.  Accurate prediction of protein structural class using auto covariance transformation of PSI-BLAST profiles , 2011, Amino Acids.

[54]  K. Chou,et al.  Using Functional Domain Composition and Support Vector Machines for Prediction of Protein Subcellular Location* , 2002, The Journal of Biological Chemistry.

[55]  Kuo-Chen Chou,et al.  A New Method for Predicting the Subcellular Localization of Eukaryotic Proteins with Both Single and Multiple Sites: Euk-mPLoc 2.0 , 2010, PloS one.

[56]  Yu-Yen Ou,et al.  Protein disorder prediction by condensed PSSM considering propensity for order or disorder , 2006, BMC Bioinformatics.

[57]  K. Chou,et al.  Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins. , 2007, Protein engineering, design & selection : PEDS.

[58]  K. Chou,et al.  Protein subcellular location prediction. , 1999, Protein engineering.

[59]  K Nishikawa,et al.  Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies. , 1994, Journal of molecular biology.

[60]  K. Chou,et al.  Plant-mPLoc: A Top-Down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization , 2010, PloS one.

[61]  K. Chou,et al.  Prediction of protein structural classes. , 1995, Critical reviews in biochemistry and molecular biology.

[62]  Thomas Lengauer,et al.  A new measure for functional similarity of gene products based on Gene Ontology , 2006, BMC Bioinformatics.

[63]  Paul Pavlidis,et al.  Gene Ontology term overlap as a measure of gene functional similarity , 2008, BMC Bioinformatics.

[64]  Thomas L. Madden,et al.  Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. , 2001, Nucleic acids research.

[65]  Kuo-Chen Chou,et al.  Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-Nearest Neighbor classifiers. , 2006, Journal of proteome research.