Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations

BMC Bioinformatics

Volumn 8, Issue SUPPL. 9, 2007, Pages

  Kim, Hyunsoo ^a   Park, Haesun ^a   Drake, Barry L ^a  

^a Georgia Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL HYPOTHESIS; BIOMEDICAL LITERATURE; GENE-GENE INTERACTION; LATENT SEMANTIC INDEXING; MATRIX FACTORIZATIONS; NONNEGATIVE MATRIX FACTORIZATION; NUMBER OF FACTORS; RETRIEVAL METHODS;

BIOINFORMATICS; DATA MINING; FACTORIZATION; TEXT PROCESSING;

GENES;

REELIN;

ALZHEIMER DISEASE; BIOINFORMATICS; BIOMEDICINE; CONFERENCE PAPER; DATA MINING; GENE INTERACTION; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; SEMANTICS; SIGNAL TRANSDUCTION; ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; CLUSTER ANALYSIS; COMPUTER INTERFACE; DATA BASE; MEDLINE; METHODOLOGY; NATURAL LANGUAGE PROCESSING; PROTEIN ANALYSIS; PUBLICATION;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CLUSTER ANALYSIS; DATABASE MANAGEMENT SYSTEMS; INFORMATION STORAGE AND RETRIEVAL; MEDLINE; NATURAL LANGUAGE PROCESSING; PATTERN RECOGNITION, AUTOMATED; PERIODICALS AS TOPIC; PROTEIN INTERACTION MAPPING; SEMANTICS; USER-COMPUTER INTERFACE;

EID: 38449084004     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-S9-S6     Document Type: Conference Paper

References (25)

1. Berry MW Dumais ST O'Brien GW Using linear algebra for intelligent information retrieval SIAM Review 1995 37 573-595 10.1137/1037127
2. Berry MW Drmac Z Jessup ER Matrices, vector spaces, and information retrieval SIAM Review 1999 41 335-362 10.1137/S0036144598347035
3. Homayouri R Heinrich K Wei L Berry MW Gene clustering by latent semantic indexing of MEDLINE abstracts Bioinformatics 2005 21 104-115 10.1093/ bioinformatics/bth464 15308538
4. Chu M Plemmons RJ Nonnegative matrix factorization and applications IMAGE 2005 34 1-5
5. Lee DD Seung HS Learning the parts of objects by non-negative matrix factorization Nature 1999 401 788-791 10.1038/44565 10548103
6. Pauca VP Shahnaz F Berry MW Plemmons RJ Text mining using non-negative matrix factorizations Proc SIAM Int'l Conf Data Mining (SDM'04) 2004
7. Kim PM Tidor B Subsystem identification through dimensionality reduction of large-scale gene expression data Genome Research 2003 13 1706-1718 403744 12840046 10.1101/gr.903503
8. Brunet JP Tamayo P Golub TR Mesirov JP Metagenes and molecular pattern discovery using matrix factorization Proc Natl Acad Sci USA 2004 101 12 4164-4169 384712 15016911 10.1073/pnas.0308531101
9. Lee DD Seung HS Algorithms for non-negative matrix factorization Proceedings of Neural Information Processing Systems 2000 556-562 http://citeseer.ist.psu.edu/lee01algorithms.html
10. Hoyer PO Non-negative matrix factorization with sparseness constraints Journal of Machine Learning Research 2004 5 1457-1469
11. Rice DS Curran T Role of the reelin signaling pathway in central nervous system development Annu Rev Neurosci 2001 24 1005-1039 10.1146/ annurev.neuro.24.1.1005 11520926
12. Tissir F Goffinet AM Reelin and brain development Nat Rev Neurosci 2003 4 496-505 10.1038/nrn1113 12778121
13. Keshvara L Magdaleno S Benhayon D Curran T Cyclin-dependent kinase 5 phosphorylates disabled 1 independently of Reelin signaling J Neurosci 2002 22 4869-4877 12077184
14. Arnaud L Ballif BA Forster E Cooper JA Fyn tyrosine kinase is a critical regulator of disabled-1 during brain development Curr Biol 2003 13 9-17 10.1016/S0960-9822(02)01397-0 12526739
15. Bock HH Herz J Reelin activates SRC family tyrosine kinases in neurons Curr Biol 2003 13 18-26 10.1016/S0960-9822(02)01403-3 12526740
16. Lee MS Tsai LH Cdk5: One of the links between senile plaques and neurofibrillary tangles J Alzheimers Dis 2003 5 127-137 12719630
17. Kanehisa M Goto S KEGG: Kyoto encyclopedia of genes and genomes Nucleic Acids Res 2000 28 27-30 102409 10592173 10.1093/nar/28.1.27
18. Neumann S Schobel S Jager S Trautwein A Haass C Pietrzik CU FLichtenthaler S Amyloid precursor-like protein 1 influences endocytosis and proteolytic processing of the amyloid precursor protein J Biol Chem 2006 281 11 7583-7594 10.1074/jbc.M508340200 16344553
19. Li Q Sudhof TC Cleavage of amyloid-beta precursor protein and amyloid-beta precursor-like protein by BACE 1 J Biol Chem 2004 279 11 10542-10550 10.1074/jbc.M310001200 14699153
20. Zeimpekis D Gallopoulos E Design of a MATLAB toolbox for term-document matrix generation Proc Workshop on Clustering High Dimensional Data and its Applications at the 5th SIAM Int'l Conf Data Mining (SDM'05), Newport Beach, CA Dhillon IS, Kogan J, Ghosh J 2005 38-48
21. Paatero P Tapper U Positive matrix factorization: A non-negative factor model with optimal utilization of error estimates of data values Environmetrics 1994 5 111-126 10.1002/env.3170050203
22. Lin CJ Projected gradient methods for non-negative matrix factorization Tech Rep Information and Support Service ISSTECH-95-013 Department of Computer Science, National Taiwan University 2005
23. van Benthem MH Keenan MR Fast algorithm for the solution of large-scale non-negativity-constrained least squares problems J Chemometrics 2004 18 441-450 10.1002/cem.889
24. Bro R de Jong S A fast non-negativity-constrained least squares algorithm J Chemometrics 1997 11 393-401 10.1002/(SICI)1099-128X(199709/ 10)11:5<393::AID-CEM483>3.0.CO;2-L
25. Lawson CL Hanson RJ Solving Least Squares Problems Englewood Cliffs, NJ: Prentice-Hall 1974