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Volumn 2015-August, Issue , 2015, Pages 2019-2028

Predicting future scientific discoveries based on a networked analysis of the past literature

Author keywords

Hypothesis generation; Scientific discovery; Text mining

Indexed keywords

FACTORIZATION; FORECASTING; NATURAL LANGUAGE PROCESSING SYSTEMS; PROTEINS;

EID: 84954121316     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/2783258.2788609     Document Type: Conference Paper
Times cited : (33)

References (59)
  • 1
    • 77955287813 scopus 로고    scopus 로고
    • An overview of MetaMap: Historical perspective and recent advances
    • (May-Jun)
    • Aronson, A.R. and Lang, F.M., 2010. An overview of MetaMap: historical perspective and recent advances. J Am Med Inform Assoc 17, 3 (May-Jun), 229-236.
    • (2010) J Am Med Inform Assoc , vol.17 , Issue.3 , pp. 229-236
    • Aronson, A.R.1    Lang, F.M.2
  • 2
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • (May)
    • Ashburner, M., et al, 2000. Gene ontology: tool for the unification of biology. Nat Genet 25, 1 (May), 25-29.
    • (2000) Nat Genet , vol.25 , Issue.1 , pp. 25-29
    • Ashburner, M.1
  • 3
    • 34547198396 scopus 로고    scopus 로고
    • Algorithms and applications for approximate nonnegative matrix factorization
    • Berry, M.W., et al, 2007. Algorithms and applications for approximate nonnegative matrix factorization. Comp Statistics & Data Analysis 52, 1, 155-173.
    • (2007) Comp Statistics & Data Analysis , vol.52 , Issue.1 , pp. 155-173
    • Berry, M.W.1
  • 4
    • 33751255087 scopus 로고    scopus 로고
    • Evaluation of clustering algorithms for protein-protein interaction networks
    • Brohee, S. and Van Helden, J., 2006. Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7, 1, 488.
    • (2006) BMC Bioinformatics , vol.7 , Issue.1 , pp. 488
    • Brohee, S.1    Van Helden, J.2
  • 5
    • 84863922124 scopus 로고    scopus 로고
    • Comprehensive molecular characterization of human colon and rectal cancer
    • N. (Jul 19)
    • Cancer Genome Atlas, N., 2012. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 7407 (Jul 19), 330-337.
    • (2012) Nature , vol.487 , Issue.7407 , pp. 330-337
  • 6
    • 54549108740 scopus 로고    scopus 로고
    • Comprehensive genomic characterization defines human glioblastoma genes and core pathways
    • N. (Oct 23)
    • Cancer Genome Atlas Research, N., 2008. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 7216 (Oct 23), 1061-1068.
    • (2008) Nature , vol.455 , Issue.7216 , pp. 1061-1068
  • 7
    • 7444224120 scopus 로고    scopus 로고
    • On reduced rank nonnegative matrix factorization for symmetric nonnegative matrices
    • Catral, M., et al, 2004. On reduced rank nonnegative matrix factorization for symmetric nonnegative matrices. Linear Algebra and its Applications 393, 107-126.
    • (2004) Linear Algebra and its Applications , vol.393 , pp. 107-126
    • Catral, M.1
  • 8
    • 33746724092 scopus 로고    scopus 로고
    • Probabilistic prediction of protein-protein interactions from the protein sequences
    • (Oct)
    • Chinnasamy, A., et al, 2006. Probabilistic prediction of protein-protein interactions from the protein sequences. Comput Biol Med 36, 10 (Oct), 1143-1154.
    • (2006) Comput Biol Med , vol.36 , Issue.10 , pp. 1143-1154
    • Chinnasamy, A.1
  • 9
    • 17244380380 scopus 로고    scopus 로고
    • A survey of current work in biomedical text mining
    • (Mar)
    • Cohen, A.M. and Hersh, W.R., 2005. A survey of current work in biomedical text mining. Brief Bioinform 6, 1 (Mar), 57-71.
    • (2005) Brief Bioinform , vol.6 , Issue.1 , pp. 57-71
    • Cohen, A.M.1    Hersh, W.R.2
  • 10
    • 84894906101 scopus 로고    scopus 로고
    • Towards a protein-protein interaction information extraction system: Recognizing named entities
    • Danger, R., et al, 2014. Towards a Protein-Protein Interaction information extraction system: Recognizing named entities. Knowledge-Based Systems 57, 104-118.
    • (2014) Knowledge-Based Systems , vol.57 , pp. 104-118
    • Danger, R.1
  • 11
    • 78651317084 scopus 로고    scopus 로고
    • The comparative toxicogenomics database: Update 2011
    • Database issue (Jan)
    • Davis, A.P., et al, 2011. The Comparative Toxicogenomics Database: update 2011. Nucleic Acids Res 39, Database issue (Jan), D1067-1072.
    • (2011) Nucleic Acids Res , vol.39 , pp. D1067-D1072
    • Davis, A.P.1
  • 12
    • 0036805329 scopus 로고    scopus 로고
    • Bridging structural biology and genomics: Assessing protein interaction data with known complexes
    • (Oct)
    • Edwards, A.M., et al, 2002. Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet 18, 10 (Oct), 529-536.
    • (2002) Trends Genet , vol.18 , Issue.10 , pp. 529-536
    • Edwards, A.M.1
  • 13
    • 84876515907 scopus 로고    scopus 로고
    • STRING v9.1: Proteinprotein interaction networks, with increased coverage and integration
    • (Jan)
    • Franceschini, A., et al, 2013. STRING v9.1: proteinprotein interaction networks, with increased coverage and integration. Nucleic Acids Res 41, (Jan), D808-815.
    • (2013) Nucleic Acids Res , vol.41 , pp. D808-D815
    • Franceschini, A.1
  • 14
    • 33847294345 scopus 로고    scopus 로고
    • RelEx-relation extraction using dependency parse trees
    • Fundel, K., et al, 2007. RelEx-Relation extraction using dependency parse trees. Bioinformatics 23, 3, 365-371.
    • (2007) Bioinformatics , vol.23 , Issue.3 , pp. 365-371
    • Fundel, K.1
  • 15
    • 84984996500 scopus 로고    scopus 로고
    • The gene ontology project in 2008
    • Database issue (Jan)
    • Gene Ontology, C., 2008. The Gene Ontology project in 2008. Nucleic Acids Res 36, Database issue (Jan), D440-444.
    • (2008) Nucleic Acids Res , vol.36 , pp. D440-D444
    • Gene Ontology, C.1
  • 16
    • 75849158230 scopus 로고    scopus 로고
    • The gene ontology in 2010: Extensions and refinements
    • Database issue (Jan)
    • Gene Ontology, C., 2010. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 38, Database issue (Jan), D331-335.
    • (2010) Nucleic Acids Res , vol.38 , pp. D331-D335
    • Gene Ontology, C.1
  • 17
    • 84876569864 scopus 로고    scopus 로고
    • Genenames.org: The HGNC resources
    • (Jan)
    • Gray, K.A., et al, 2013. Genenames.org: the HGNC resources. Nucleic Acids Res 41, (Jan), D545-552.
    • (2013) Nucleic Acids Res , vol.41 , pp. D545-D552
    • Gray, K.A.1
  • 19
    • 33947112755 scopus 로고    scopus 로고
    • Reconstruction of reflectance spectra using robust nonnegative matrix factorization
    • Hamza, A.B. and Brady, D.J., 2006. Reconstruction of reflectance spectra using robust nonnegative matrix factorization. IEEE Transactions on Signal Processing 54, 9, 3637-3642.
    • (2006) IEEE Transactions on Signal Processing , vol.54 , Issue.9 , pp. 3637-3642
    • Hamza, A.B.1    Brady, D.J.2
  • 20
    • 0035224502 scopus 로고    scopus 로고
    • Disambiguating proteins, genes, and RNA in text: A machine learning approach
    • suppl 1
    • Hatzivassiloglou, V., et al, 2001. Disambiguating proteins, genes, and RNA in text: a machine learning approach. Bioinformatics 17 Suppl 1, suppl 1, S97-106.
    • (2001) Bioinformatics , vol.17 , pp. S97-S106
    • Hatzivassiloglou, V.1
  • 21
    • 67549137262 scopus 로고    scopus 로고
    • Multimodal networks: Structure and operations
    • (Apr-Jun)
    • Heath, L.S. and Sioson, A.A., 2009. Multimodal networks: structure and operations. IEEE/ACM Trans Comput Biol Bioinform 6, 2 (Apr-Jun), 321-332.
    • (2009) IEEE/ACM Trans Comput Biol Bioinform , vol.6 , Issue.2 , pp. 321-332
    • Heath, L.S.1    Sioson, A.A.2
  • 22
    • 3042786293 scopus 로고    scopus 로고
    • A gene network for navigating the literature
    • (Jul)
    • Hoffmann, R. and Valencia, A., 2004. A gene network for navigating the literature. Nat Genet 36, 7 (Jul), 664.
    • (2004) Nat Genet , vol.36 , Issue.7 , pp. 664
    • Hoffmann, R.1    Valencia, A.2
  • 23
    • 84941120469 scopus 로고    scopus 로고
    • PhosphoSitePlus, 2014: Mutations, PTMs and recalibrations
    • Database issue (Jan)
    • Hornbeck, P.V., et al, 2015. PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res 43, Database issue (Jan), D512-520.
    • (2015) Nucleic Acids Res , vol.43 , pp. D512-D520
    • Hornbeck, P.V.1
  • 24
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • C. (Oct 21)
    • International Human Genome Sequencing, C., 2004. Finishing the euchromatic sequence of the human genome. Nature 431, 7011 (Oct 21), 931-945.
    • (2004) Nature , vol.431 , Issue.7011 , pp. 931-945
  • 25
    • 0035042776 scopus 로고    scopus 로고
    • A literature network of human genes for high-throughput analysis of gene expression
    • (May)
    • Jenssen, T.K., et al, 2001. A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 28, 1 (May), 21-28.
    • (2001) Nat Genet , vol.28 , Issue.1 , pp. 21-28
    • Jenssen, T.K.1
  • 26
    • 11144327494 scopus 로고    scopus 로고
    • Fisher nonnegative matrix factorization for learning local features
    • Jia, Y.W.Y. and Turk, C.H.M., 2004 Fisher nonnegative matrix factorization for learning local features. In Proc. Asian Conf. on Comp. Vision, 27-30.
    • (2004) Proc. Asian Conf. on Comp. Vision , pp. 27-30
    • Jia, Y.W.Y.1    Turk, C.H.M.2
  • 27
    • 84868088476 scopus 로고    scopus 로고
    • Reactome - A curated knowledgebase of biological pathways: Megakaryocytes and platelets
    • Jupe, S., et al, 2012. Reactome - a curated knowledgebase of biological pathways: megakaryocytes and platelets. Journal of Thrombosis and Haemostasis: JTH, 10(11), 2399-2402.
    • (2012) Journal of Thrombosis and Haemostasis: JTH , vol.10 , Issue.11 , pp. 2399-2402
    • Jupe, S.1
  • 29
    • 70049106408 scopus 로고    scopus 로고
    • Geometric de-noising of protein-protein interaction networks
    • (Aug)
    • Kuchaiev, O., et al, 2009. Geometric de-noising of protein-protein interaction networks. PLoS Comput Biol 5, 8 (Aug), e1000454.
    • (2009) PLoS Comput Biol , vol.5 , Issue.8
    • Kuchaiev, O.1
  • 31
    • 0033592606 scopus 로고    scopus 로고
    • Learning the parts of objects by non-negative matrix factorization
    • (Oct 21)
    • Lee, D.D. and Seung, H.S., 1999. Learning the parts of objects by non-negative matrix factorization. Nature 401, 6755 (Oct 21), 788-791.
    • (1999) Nature , vol.401 , Issue.6755 , pp. 788-791
    • Lee, D.D.1    Seung, H.S.2
  • 32
    • 0001093042 scopus 로고    scopus 로고
    • Algorithms for nonnegative matrix factorization
    • Lee, D.D. and Seung, H.S., 2000. Algorithms for Nonnegative Matrix Factorization. In NIPS, 556-562.
    • (2000) NIPS , pp. 556-562
    • Lee, D.D.1    Seung, H.S.2
  • 33
    • 77953130163 scopus 로고    scopus 로고
    • Untangling complex networks: Risk minimization in financial markets through accessible spin glass ground states
    • (Aug 15)
    • Lisewski, A.M. and Lichtarge, O., 2010. Untangling complex networks: risk minimization in financial markets through accessible spin glass ground states. Physica A 389, 16 (Aug 15), 3250-3253.
    • (2010) Physica A , vol.389 , Issue.16 , pp. 3250-3253
    • Lisewski, A.M.1    Lichtarge, O.2
  • 36
    • 84859837637 scopus 로고    scopus 로고
    • Using slot grammar
    • Center, Yorktown Heights, NY, IBM Res. Rep. RC23978
    • Mccord, M.C. and Bernth, A., 2010. Using slot grammar. IBM TJ Watson Res. Center, Yorktown Heights, NY, IBM Res. Rep. RC23978.
    • (2010) IBM TJ Watson Res.
    • Mccord, M.C.1    Bernth, A.2
  • 37
    • 59549091756 scopus 로고    scopus 로고
    • Evaluating contributions of natural language parsers to protein-protein interaction extraction
    • (Feb 1)
    • Miyao, Y., et al, 2009. Evaluating contributions of natural language parsers to protein-protein interaction extraction. Bioinformatics 25, 3 (Feb 1), 394-400.
    • (2009) Bioinformatics , vol.25 , Issue.3 , pp. 394-400
    • Miyao, Y.1
  • 39
    • 0028561099 scopus 로고
    • Positive matrix factorization: A non-negative factor model with optimal utilization of error estimates of data values
    • Paatero, P. and Tapper, U., 1994. Positive matrix factorization: A non-negative factor model with optimal utilization of error estimates of data values. Environmetrics 5, 2, 111-126.
    • (1994) Environmetrics , vol.5 , Issue.2 , pp. 111-126
    • Paatero, P.1    Tapper, U.2
  • 40
    • 84911386442 scopus 로고    scopus 로고
    • Literome: PubMed-scale genomic knowledge base in the cloud
    • (Oct)
    • Poon, H., et al, 2014. Literome: PubMed-scale genomic knowledge base in the cloud. Bioinformatics 30, 19 (Oct), 2840-2842.
    • (2014) Bioinformatics , vol.30 , Issue.19 , pp. 2840-2842
    • Poon, H.1
  • 41
    • 33847608309 scopus 로고    scopus 로고
    • BioInfer: A corpus for information extraction in the biomedical domain
    • Pyysalo, S., et al, 2007. BioInfer: a corpus for information extraction in the biomedical domain. BMC Bioinformatics 8, 50.
    • (2007) BMC Bioinformatics , vol.8 , pp. 50
    • Pyysalo, S.1
  • 42
    • 84904470880 scopus 로고    scopus 로고
    • An unsupervised text mining method for relation extraction from biomedical literature
    • Quan, C., et al, 2014. An unsupervised text mining method for relation extraction from biomedical literature. PLoS One 9, 7, e102039.
    • (2014) PLoS One , vol.9 , Issue.7
    • Quan, C.1
  • 43
    • 12144290446 scopus 로고    scopus 로고
    • GeneWays: A system for extracting, analyzing, visualizing, and integrating molecular pathway data
    • (Feb)
    • Rzhetsky, A., et al, 2004. GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J Biomed Inform 37, 1 (Feb), 43-53.
    • (2004) J Biomed Inform , vol.37 , Issue.1 , pp. 43-53
    • Rzhetsky, A.1
  • 45
    • 84907033471 scopus 로고    scopus 로고
    • Automated hypothesis generation based on mining scientific literature
    • New York, New York, USA
    • Scott, S., et al, 2014. Automated hypothesis generation based on mining scientific literature. In Proceedings of the 20th ACM SIGKDD, New York, New York, USA, 1877-1886.
    • (2014) Proceedings of the 20th ACM SIGKDD , pp. 1877-1886
    • Scott, S.1
  • 46
    • 84907033471 scopus 로고    scopus 로고
    • Automated hypothesis generation based on mining scientific literature
    • New York, USA
    • Scott, S., et al, 2014. Automated hypothesis generation based on mining scientific literature. In Proceedings of the 20th ACM SIGKDD, New York, USA, 1877-1886.
    • (2014) Proceedings of the 20th ACM SIGKDD , pp. 1877-1886
    • Scott, S.1
  • 47
    • 44349113144 scopus 로고    scopus 로고
    • Estimating the size of the human interactome
    • (May 13)
    • Stumpf, M.P., et al, 2008. Estimating the size of the human interactome. Proc Natl Acad Sci U S A 105, 19 (May 13), 6959-6964.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.19 , pp. 6959-6964
    • Stumpf, M.P.1
  • 48
    • 0036678776 scopus 로고    scopus 로고
    • Tagging gene and protein names in biomedical text
    • (Aug)
    • Tanabe, L. and Wilbur, W.J., 2002. Tagging gene and protein names in biomedical text. Bioinformatics 18, 8 (Aug), 1124-1132.
    • (2002) Bioinformatics , vol.18 , Issue.8 , pp. 1124-1132
    • Tanabe, L.1    Wilbur, W.J.2
  • 49
    • 78049245506 scopus 로고    scopus 로고
    • A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature
    • Tikk, D., et al, 2010. A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature. PLoS Comput Biol 6, 7, e1000837.
    • (2010) PLoS Comput Biol , vol.6 , Issue.7
    • Tikk, D.1
  • 50
    • 80052411919 scopus 로고    scopus 로고
    • Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM
    • (Sep)
    • Tuncbag, N., et al, 2011. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc 6, 9 (Sep), 1341-1354.
    • (2011) Nat Protoc , vol.6 , Issue.9 , pp. 1341-1354
    • Tuncbag, N.1
  • 51
    • 84874724662 scopus 로고    scopus 로고
    • Update on activities at the universal protein resource (UniProt) in 2013
    • Database issue (Jan)
    • Uniprot, C., 2013. Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res 41, Database issue (Jan), D43-47.
    • (2013) Nucleic Acids Res , vol.41 , pp. D43-D47
    • Uniprot, C.1
  • 52
    • 84876273527 scopus 로고    scopus 로고
    • Large-scale event extraction from literature with multi-level gene normalization
    • Van Landeghem, S., et al, 2013. Large-scale event extraction from literature with multi-level gene normalization. PLoS One 8, 4, e55814.
    • (2013) PLoS One , vol.8 , Issue.4
    • Van Landeghem, S.1
  • 53
    • 84876235880 scopus 로고    scopus 로고
    • Predicting protein-protein interactions from multimodal biological data sources via nonnegative matrix tri-factorization
    • (Apr)
    • Wang, H., et al, 2013. Predicting protein-protein interactions from multimodal biological data sources via nonnegative matrix tri-factorization. J Comput Biol 20, 4 (Apr), 344-358.
    • (2013) J Comput Biol , vol.20 , Issue.4 , pp. 344-358
    • Wang, H.1
  • 54
    • 0037252705 scopus 로고    scopus 로고
    • Database resources of the national center for biotechnology
    • (Jan 1)
    • Wheeler, D.L., et al, 2003. Database resources of the National Center for Biotechnology. Nucleic Acids Res 31, 1 (Jan 1), 28-33.
    • (2003) Nucleic Acids Res , vol.31 , Issue.1 , pp. 28-33
    • Wheeler, D.L.1
  • 55
    • 58149202163 scopus 로고    scopus 로고
    • HMDB: A knowledgebase for the human metabolome
    • Database issue (Jan)
    • Wishart, D.S., et al, 2009. HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res 37, Database issue (Jan), D603-610.
    • (2009) Nucleic Acids Res , vol.37 , pp. D603-D610
    • Wishart, D.S.1
  • 56
    • 77950472891 scopus 로고    scopus 로고
    • HPDI: A database of experimental human protein-DNA interactions
    • (Jan 15)
    • Xie, Z., et al, 2010. hPDI: a database of experimental human protein-DNA interactions. Bioinformatics 26, 2 (Jan 15), 287-289.
    • (2010) Bioinformatics , vol.26 , Issue.2 , pp. 287-289
    • Xie, Z.1
  • 57
    • 84883162967 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis
    • You, Z.H., et al, 2013. Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis. BMC bioinformatics 14 Suppl 8, S10.
    • (2013) BMC Bioinformatics , vol.14 , pp. S10
    • You, Z.H.1
  • 58
    • 84867881743 scopus 로고    scopus 로고
    • Structure-based prediction of protein-protein interactions on a genome-wide scale
    • (Oct 25)
    • Zhang, Q.C., et al, 2012. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490, 7421 (Oct 25), 556-560.
    • (2012) Nature , vol.490 , Issue.7421 , pp. 556-560
    • Zhang, Q.C.1
  • 59
    • 84889679014 scopus 로고    scopus 로고
    • Discovering disease-disease associations by fusing systems-level molecular data
    • Zitnik, M., et al, 2013. Discovering disease-disease associations by fusing systems-level molecular data. Sci Rep 3, 3202.
    • (2013) Sci Rep , vol.3 , pp. 3202
    • Zitnik, M.1


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