1 |
Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, et al. Using graph theory to analyze biological networks. BioData Min 2011;4:10.
DOI
|
2 |
Sharan R, Ideker T. Modeling cellular machinery through biological network comparison. Nat Biotechnol 2006;24:427-433.
DOI
|
3 |
Lysenko A, Roznovat IA, Saqi M, Mazein A, Rawlings CJ, Auffray C. Representing and querying disease networks using graph databases. BioData Min 2016;9:23.
DOI
|
4 |
Angles R, Gutierrez C. Survey of graph database models. ACM Comput Surv 2008;40:1.
|
5 |
Henkel R, Wolkenhauer O, Waltemath D. Combining computational models, semantic annotations and simulation experiments in a graph database. Database (Oxford) 2015;2015:bau130.
DOI
|
6 |
Mullen J, Cockell SJ, Woollard P, Wipat A. An integrated data driven approach to drug repositioning using gene-disease associations. PLoS One 2016;11:e0155811.
DOI
|
7 |
Balaur I, Saqi M, Barat A, Lysenko A, Mazein A, Rawlings CJ, et al. EpiGeNet: a graph database of interdependencies between genetic and epigenetic events in colorectal cancer. J Comput Biol 2016 Sep 14 [Epub]. https://doi.org/10.1089/cmb.2016.0095.
|
8 |
Robinson I, Webber J, Eifrem E. Graph Databases: New Opportunities for Connected Data. 2nd ed. Sebastopol: O'Reilly Media, Inc., 2015.
|
9 |
Neo Technology Inc. The Neo4j Operations Manual v3.0, Performance [Internet]. Baltimore: Neo Technology, Inc., 2016 [cited 2016 Jan 10]. Available from: https://neo4j.com/docs/operations-manual/current.
|
10 |
Van Bruggen R. Learning Neo4j. Birmingham: Packt Publishing Ltd., 2014.
|
11 |
Bravo A, Cases M, Queralt-Rosinach N, Sanz F, Furlong LI. A knowledge-driven approach to extract disease-related biomarkers from the literature. Biomed Res Int 2014;2014:253128.
|
12 |
Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006;34:D535-D539.
DOI
|
13 |
Solomon BD, Nguyen AD, Bear KA, Wolfsberg TG. Clinical genomic database. Proc Natl Acad Sci U S A 2013;110:9851-9855.
DOI
|
14 |
Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, et al. ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 2012;40:D1100-D1107.
DOI
|
15 |
Mattingly CJ, Colby GT, Forrest JN, Boyer JL. The Comparative Toxicogenomics Database (CTD). Environ Health Perspect 2003;111:793-795.
DOI
|
16 |
Liu CC, Tseng YT, Li W, Wu CY, Mayzus I, Rzhetsky A, et al. DiseaseConnect: a comprehensive web server for mechanismbased disease-disease connections. Nucleic Acids Res 2014;42:W137-W146.
DOI
|
17 |
Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 2006;34:D668-D672.
DOI
|
18 |
Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res 2014;42:D1001-D1006.
DOI
|
19 |
Lipscomb CE. Medical Subject Headings (MeSH). Bull Med Libr Assoc 2000;88:265-266.
|
20 |
Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA; Mouse Genome Database Group. The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res 2008;36:D724-D728.
|
21 |
Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, et al. MINT: the Molecular INTeraction database. Nucleic Acids Res 2007;35:D572-D574.
DOI
|
22 |
Peters LB, Bahr N, Bodenreider O. Evaluating drug-drug interaction information in NDF-RT and DrugBank. J Biomed Semantics 2015;6:19.
DOI
|
23 |
Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005;33:D514-D517.
|
24 |
Schriml LM, Arze C, Nadendla S, Chang YW, Mazaitis M, Felix V, et al. Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res 2012;40:D940-D946.
DOI
|
25 |
Rohde DD. The Orphan Drug Act: an engine of innovation? At what cost? Food Drug Law J 2000;55:125-143.
|
26 |
Twigger SN, Shimoyama M, Bromberg S, Kwitek AE, Jacob HJ; RGD Team. The Rat Genome Database, update 2007: easing the path from disease to data and back again. Nucleic Acids Res 2007;35:D658-D662.
DOI
|
27 |
Krallinger M, Valencia A, Hirschman L. Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biol 2008;9 Suppl 2:S8.
|
28 |
Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P. A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol 2010;6:343.
|
29 |
Chen X, Ji ZL, Chen YZ. TTD: Therapeutic Target Database. Nucleic Acids Res 2002;30:412-415.
DOI
|
30 |
UniProt Consortium. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 2014;42:D191-D198.
DOI
|
31 |
Gottlieb A, Stein GY, Ruppin E, Sharan R. PREDICT: a method for inferring novel drug indications with application to personalized medicine. Mol Syst Biol 2011;7:496.
|
32 |
Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature 1999;402(6761 Suppl):C47-C52.
DOI
|
33 |
Kitano H. Computational systems biology. Nature 2002;420:206-210.
DOI
|
34 |
Koonin EV, Wolf YI, Karev GP. The structure of the protein universe and genome evolution. Nature 2002;420:218-223.
DOI
|
35 |
Alon U. Biological networks: the tinkerer as an engineer. Science 2003;301:1866-1867.
DOI
|
36 |
Bray D. Molecular networks: the top-down view. Science 2003;301:1864-1865.
DOI
|
37 |
Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004;5:101-113.
DOI
|
38 |
Li J, Zhao PX. Mining functional modules in heterogeneous biological networks using multiplex PageRank approach. Front Plant Sci 2016;7:903.
|