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] Jason Weston,et al. Mismatch String Kernels for SVM Protein Classification , 2002, NIPS.
[2] Emmanuel J. Candès,et al. Matrix Completion With Noise , 2009, Proceedings of the IEEE.
[3] J. Thornton,et al. Protein–protein interfaces: Analysis of amino acid conservation in homodimers , 2001, Proteins.
[4] D. Frishman,et al. A domain interaction map based on phylogenetic profiling. , 2004, Journal of molecular biology.
[5] Benjamin A. Shoemaker,et al. Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners , 2007, PLoS Comput. Biol..
[6] Feiping Nie,et al. Dyadic transfer learning for cross-domain image classification , 2011, 2011 International Conference on Computer Vision.
[7] Benjamin A. Shoemaker,et al. Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases , 2007, PLoS Comput. Biol..
[8] 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.
[9] Yanjun Qi,et al. Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources , 2004, Pacific Symposium on Biocomputing.
[10] Mei Liu,et al. Prediction of protein-protein interactions using random decision forest framework , 2005, Bioinform..
[11] Alessandro Vespignani,et al. Global protein function prediction from protein-protein interaction networks , 2003, Nature Biotechnology.
[12] Raja Jothi,et al. Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. , 2006, Journal of molecular biology.
[13] E. Marcotte,et al. Predicting functional linkages from gene fusions with confidence. , 2002, Applied bioinformatics.
[14] B. Schwikowski,et al. A network of protein–protein interactions in yeast , 2000, Nature Biotechnology.
[15] Chris H. Q. Ding,et al. Convex and Semi-Nonnegative Matrix Factorizations , 2010, IEEE Transactions on Pattern Analysis and Machine Intelligence.
[16] Feiping Nie,et al. Cross-language web page classification via dual knowledge transfer using nonnegative matrix tri-factorization , 2011, SIGIR.
[17] Julio Collado-Vides,et al. A powerful non-homology method for the prediction of operons in prokaryotes , 2002, ISMB.
[18] Mark Pagel,et al. Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes , 2005, 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05).
[19] H. Sebastian Seung,et al. Learning the parts of objects by non-negative matrix factorization , 1999, Nature.
[20] Matteo Pellegrini,et al. Prolinks: a database of protein functional linkages derived from coevolution , 2004, Genome Biology.
[21] J. Thornton,et al. Structural characterisation and functional significance of transient protein-protein interactions. , 2003, Journal of molecular biology.
[22] Jiawei Han,et al. Non-negative Matrix Factorization on Manifold , 2008, 2008 Eighth IEEE International Conference on Data Mining.
[23] Temple F. Smith,et al. Operons in Escherichia coli: genomic analyses and predictions. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[24] S. Salzberg,et al. Prediction of operons in microbial genomes. , 2001, Nucleic acids research.
[25] Jean-Loup Faulon,et al. Predicting protein-protein interactions using signature products , 2005, Bioinform..
[26] E. Sprinzak,et al. Utilizing logical relationships in genomic data to decipher cellular processes , 2005, The FEBS journal.
[27] 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.
[28] Mike Tyers,et al. BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..
[29] 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.
[30] Fillia Makedon,et al. Fast Nonnegative Matrix Tri-Factorization for Large-Scale Data Co-Clustering , 2011, IJCAI.
[31] Chris H. Q. Ding,et al. Simultaneous clustering of multi-type relational data via symmetric nonnegative matrix tri-factorization , 2011, CIKM '11.
[32] Chris H. Q. Ding,et al. Non-negative Laplacian Embedding , 2009, 2009 Ninth IEEE International Conference on Data Mining.
[33] Gary D Bader,et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.
[34] C. Ding,et al. On the Equivalence of Nonnegative Matrix Factorization and K-means - Spectral Clustering , 2005 .
[35] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[36] Chris H. Q. Ding,et al. Orthogonal nonnegative matrix t-factorizations for clustering , 2006, KDD '06.
[37] Philip Resnik,et al. Using Information Content to Evaluate Semantic Similarity in a Taxonomy , 1995, IJCAI.
[38] U. Feige,et al. Spectral Graph Theory , 2015 .
[39] William Stafford Noble,et al. A structural alignment kernel for protein structures , 2007, Bioinform..
[40] Quanquan Gu,et al. Co-clustering on manifolds , 2009, KDD.
[41] David L. Wheeler,et al. GenBank , 2015, Nucleic Acids Res..
[42] Frederick P. Roth,et al. Predicting co-complexed protein pairs using genomic and proteomic data integration , 2004, BMC Bioinformatics.
[43] Jitendra Malik,et al. Normalized cuts and image segmentation , 1997, Proceedings of IEEE Computer Society Conference on Computer Vision and Pattern Recognition.
[44] D. Eisenberg,et al. Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.
[45] 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.
[46] F. Cohen,et al. Co-evolution of proteins with their interaction partners. , 2000, Journal of molecular biology.
[47] Emmanuel J. Candès,et al. Exact Matrix Completion via Convex Optimization , 2008, Found. Comput. Math..
[48] R. Russell,et al. The relationship between sequence and interaction divergence in proteins. , 2003, Journal of molecular biology.
[49] M. Gerstein,et al. A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data , 2003, Science.
[50] Anton J. Enright,et al. Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.
[51] Emmanuel J. Candès,et al. Exact Matrix Completion via Convex Optimization , 2009, Found. Comput. Math..
[52] Thomas Madej,et al. Evolutionary plasticity of protein families: Coupling between sequence and structure variation , 2005, Proteins.
[53] S. Hubbard,et al. Conservation of orientation and sequence in protein domain--domain interactions. , 2005, Journal of molecular biology.
[54] William Stafford Noble,et al. Large-scale prediction of protein-protein interactions from structures , 2010, BMC Bioinformatics.
[55] Juwen Shen,et al. Predicting protein–protein interactions based only on sequences information , 2007, Proceedings of the National Academy of Sciences.
[56] D. Eisenberg,et al. Use of Logic Relationships to Decipher Protein Network Organization , 2004, Science.
[57] William Stafford Noble,et al. Kernel methods for predicting protein-protein interactions , 2005, ISMB.
[58] 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.
[59] Olgica Milenkovic Wei Dai,et al. Low‐Rank Matrix Completion for Inference of Protein‐Protein Interaction Networks , 2010 .
[60] Mona Singh,et al. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps , 2005, ISMB.
[61] Xue-wen Chen,et al. Sequence-based prediction of protein interaction sites with an integrative method , 2009, Bioinform..
[62] S. Teichmann. The constraints protein-protein interactions place on sequence divergence. , 2002, Journal of molecular biology.
[63] Arun K. Ramani,et al. Exploiting the co-evolution of interacting proteins to discover interaction specificity. , 2003, Journal of molecular biology.