Predicting protein function via downward random walks on a gene ontology

[1]  Hailong Zhu,et al.  Predicting protein functions using incomplete hierarchical labels , 2015, BMC Bioinformatics.

[2]  Jun Wang,et al.  MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC) , 2014, BMC Bioinformatics.

[3]  Zhi-Hua Zhou,et al.  Genome-Wide Protein Function Prediction through Multi-Instance Multi-Label Learning , 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[4]  Predrag Radivojac,et al.  The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective , 2014, Bioinform..

[5]  Min-Ling Zhang,et al.  A Review on Multi-Label Learning Algorithms , 2014, IEEE Transactions on Knowledge and Data Engineering.

[6]  Michal Linial,et al.  The automated function prediction SIG looks back at 2013 and prepares for 2014 , 2014, Bioinform..

[7]  Giorgio Valentini,et al.  Hierarchical Ensemble Methods for Protein Function Prediction , 2014, ISRN bioinformatics.

[8]  Zhiwen Yu,et al.  Protein Function Prediction with Incomplete Annotations , 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[9]  Igor Jurisica,et al.  Knowledge Discovery and Data Mining in Biomedical Informatics: State-of-the-Art and Future Challenges , 2014 .

[10]  Karin M. Verspoor,et al.  Biomedical Text Mining: State-of-the-Art, Open Problems and Future Challenges , 2014, Interactive Knowledge Discovery and Data Mining in Biomedical Informatics.

[11]  Christophe Dessimoz,et al.  CAFA and the open world of protein function predictions. , 2013, Trends in genetics : TIG.

[12]  Janna Hastings,et al.  Exploiting disjointness axioms to improve semantic similarity measures , 2013, Bioinform..

[13]  Huzefa Rangwala,et al.  Protein Function Prediction Using Dependence Maximization , 2013, ECML/PKDD.

[14]  Zili Zhang,et al.  Protein Function Prediction by Integrating Multiple Kernels , 2013, IJCAI.

[15]  Predrag Radivojac,et al.  Information-theoretic evaluation of predicted ontological annotations , 2013, Bioinform..

[16]  Xiaoyan Liu,et al.  Measuring gene functional similarity based on group-wise comparison of GO terms , 2013, Bioinform..

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

[18]  Karin M. Verspoor,et al.  Combining heterogeneous data sources for accurate functional annotation of proteins , 2013, BMC Bioinformatics.

[19]  Daniel W. A. Buchan,et al.  A large-scale evaluation of computational protein function prediction , 2013, Nature Methods.

[20]  Patricia C. Babbitt,et al.  Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space , 2013, PLoS Comput. Biol..

[21]  Christophe Dessimoz,et al.  Quality of Computationally Inferred Gene Ontology Annotations , 2012, PLoS Comput. Biol..

[22]  Haixuan Yang,et al.  Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty , 2012, Bioinform..

[23]  Vipin Kumar,et al.  Computational Approaches to Protein Function Prediction , 2012 .

[24]  Noémie Elhadad,et al.  Redundancy in electronic health record corpora: analysis, impact on text mining performance and mitigation strategies , 2013, BMC Bioinformatics.

[25]  Nicolò Cesa-Bianchi,et al.  Synergy of multi-label hierarchical ensembles, data fusion, and cost-sensitive methods for gene functional inference , 2012, Machine Learning.

[26]  P. Radivojac,et al.  Analysis of protein function and its prediction from amino acid sequence , 2011, Proteins.

[27]  Giorgio Valentini,et al.  True Path Rule Hierarchical Ensembles for Genome-Wide Gene Function Prediction , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[28]  Cathy H. Wu,et al.  The Human Proteome Project: Current State and Future Direction , 2011, Molecular & Cellular Proteomics.

[29]  Carl Kingsford,et al.  Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction , 2011, RECOMB.

[30]  Zhi-Hua Zhou,et al.  Multi-Label Learning with Weak Label , 2010, AAAI.

[31]  Asa Ben-Hur,et al.  Hierarchical Classification of Gene Ontology Terms Using the Gostruct Method , 2010, J. Bioinform. Comput. Biol..

[32]  Purvesh Khatri,et al.  Predicting Novel Human Gene Ontology Annotations Using Semantic Analysis , 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[33]  Phillip W. Lord,et al.  Semantic Similarity in Biomedical Ontologies , 2009, PLoS Comput. Biol..

[34]  Vipin Kumar,et al.  Incorporating functional inter-relationships into protein function prediction algorithms , 2009, BMC Bioinformatics.

[35]  Knut Reinert,et al.  Robust consensus computation , 2008, BMC Bioinformatics.

[36]  Catia Pesquita,et al.  Metrics for GO based protein semantic similarity: a systematic evaluation , 2008, BMC Bioinformatics.

[37]  Christos Faloutsos,et al.  Random walk with restart: fast solutions and applications , 2008, Knowledge and Information Systems.

[38]  Carol Friedman,et al.  Information theory applied to the sparse gene ontology annotation network to predict novel gene function , 2007, ISMB/ECCB.

[39]  Zheng Guo,et al.  Globally predicting protein functions based on co-expressed protein-protein interaction networks and ontology taxonomy similarities. , 2007, Gene.

[40]  Philip S. Yu,et al.  A new method to measure the semantic similarity of GO terms , 2007, Bioinform..

[41]  R. Sharan,et al.  Network-based prediction of protein function , 2007, Molecular systems biology.

[42]  Rolf Apweiler,et al.  GOAnnotator: linking protein GO annotations to evidence text , 2006, Journal of biomedical discovery and collaboration.

[43]  Karin M. Verspoor,et al.  A categorization approach to automated ontological function annotation , 2006, Protein science : a publication of the Protein Society.

[44]  Neil R Smalheiser,et al.  Launching the "Journal of Biomedical Discovery and Collaboration" , 2006, Journal of Biomedical Discovery and Collaboration.

[45]  Zheng Guo,et al.  Broadly predicting specific gene functions with expression similarity and taxonomy similarity. , 2005, Gene.

[46]  S. Dwight,et al.  Predicting gene function from patterns of annotation. , 2003, Genome research.

[47]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

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