Predicting Protein-Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization
暂无分享,去创建一个
Feiping Nie | Chris H. Q. Ding | Hua Wang | Heng Huang | C. Ding | Hua Wang | Heng Huang | F. Nie
[1] Fan Chung,et al. Spectral Graph Theory , 1996 .
[2] H. Sebastian Seung,et al. Learning the parts of objects by non-negative matrix factorization , 1999, Nature.
[3] Anton J. Enright,et al. Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.
[4] B. Schwikowski,et al. A network of protein–protein interactions in yeast , 2000, Nature Biotechnology.
[5] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[6] T. Ito,et al. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[7] F. Cohen,et al. Co-evolution of proteins with their interaction partners. , 2000, Journal of molecular biology.
[8] Jitendra Malik,et al. Normalized Cuts and Image Segmentation , 2000, IEEE Trans. Pattern Anal. Mach. Intell..
[9] S. Salzberg,et al. Prediction of operons in microbial genomes. , 2001, Nucleic acids research.
[10] C. DeLisi,et al. Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[11] J. Thornton,et al. Protein–protein interfaces: Analysis of amino acid conservation in homodimers , 2001, Proteins.
[12] Gary D Bader,et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.
[13] Jason Weston,et al. Mismatch String Kernels for SVM Protein Classification , 2002, NIPS.
[14] E. Marcotte,et al. Predicting functional linkages from gene fusions with confidence. , 2002, Applied bioinformatics.
[15] S. Teichmann. The constraints protein-protein interactions place on sequence divergence. , 2002, Journal of molecular biology.
[16] D. Eisenberg,et al. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach , 2003, Genome Biology.
[17] Frederick P. Roth,et al. Predicting co-complexed protein pairs using genomic and proteomic data integration , 2004, BMC Bioinformatics.
[18] R. Russell,et al. The relationship between sequence and interaction divergence in proteins. , 2003, Journal of molecular biology.
[19] Alessandro Vespignani,et al. Global protein function prediction from protein-protein interaction networks , 2003, Nature Biotechnology.
[20] J. Thornton,et al. Structural characterisation and functional significance of transient protein-protein interactions. , 2003, Journal of molecular biology.
[21] M. Gerstein,et al. A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data , 2003, Science.
[22] D. Frishman,et al. A domain interaction map based on phylogenetic profiling. , 2004, Journal of molecular biology.
[23] William Stafford Noble,et al. Kernel methods for predicting protein-protein interactions , 2005, ISMB.
[24] Yanjun Qi,et al. Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources , 2004, Pacific Symposium on Biocomputing.
[25] Chris H. Q. Ding,et al. On the Equivalence of Nonnegative Matrix Factorization and Spectral Clustering , 2005, SDM.
[26] Mei Liu,et al. Prediction of protein-protein interactions using random decision forest framework , 2005, Bioinform..
[27] Jean-Loup Faulon,et al. Predicting protein-protein interactions using signature products , 2005, Bioinform..
[28] Mona Singh,et al. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps , 2005, ISMB.
[29] E. Sprinzak,et al. Utilizing logical relationships in genomic data to decipher cellular processes , 2005, The FEBS journal.
[30] S. Hubbard,et al. Conservation of orientation and sequence in protein domain--domain interactions. , 2005, Journal of molecular biology.
[31] Chris H. Q. Ding,et al. Orthogonal nonnegative matrix t-factorizations for clustering , 2006, KDD '06.
[32] Mike Tyers,et al. BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..
[33] Juwen Shen,et al. Predicting protein–protein interactions based only on sequences information , 2007, Proceedings of the National Academy of Sciences.
[34] Benjamin A. Shoemaker,et al. Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases , 2007, PLoS Comput. Biol..
[35] Benjamin A. Shoemaker,et al. Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners , 2007, PLoS Comput. Biol..
[36] William Stafford Noble,et al. A structural alignment kernel for protein structures , 2007, Bioinform..
[37] Jiawei Han,et al. Non-negative Matrix Factorization on Manifold , 2008, 2008 Eighth IEEE International Conference on Data Mining.
[38] Chris H. Q. Ding,et al. Non-negative Laplacian Embedding , 2009, 2009 Ninth IEEE International Conference on Data Mining.
[39] Emmanuel J. Candès,et al. Exact Matrix Completion via Convex Optimization , 2009, Found. Comput. Math..
[40] Xue-wen Chen,et al. Sequence-based prediction of protein interaction sites with an integrative method , 2009, Bioinform..
[41] Quanquan Gu,et al. Co-clustering on manifolds , 2009, KDD.
[42] William Stafford Noble,et al. Large-scale prediction of protein-protein interactions from structures , 2010, BMC Bioinformatics.
[43] Olgica Milenkovic Wei Dai,et al. Low‐Rank Matrix Completion for Inference of Protein‐Protein Interaction Networks , 2010 .
[44] B. Frey,et al. Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis , 2010, The Journal of cell biology.
[45] Emmanuel J. Candès,et al. Matrix Completion With Noise , 2009, Proceedings of the IEEE.
[46] Fillia Makedon,et al. Fast Nonnegative Matrix Tri-Factorization for Large-Scale Data Co-Clustering , 2011, IJCAI.
[47] Chris H. Q. Ding,et al. Simultaneous clustering of multi-type relational data via symmetric nonnegative matrix tri-factorization , 2011, CIKM '11.
[48] Feiping Nie,et al. Cross-language web page classification via dual knowledge transfer using nonnegative matrix tri-factorization , 2011, SIGIR.
[49] Feiping Nie,et al. Nonnegative Matrix Tri-factorization Based High-Order Co-clustering and Its Fast Implementation , 2011, 2011 IEEE 11th International Conference on Data Mining.
[50] Feiping Nie,et al. Dyadic transfer learning for cross-domain image classification , 2011, 2011 International Conference on Computer Vision.