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GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins.
Durand P, Labarre L, Meil A, Divo JL, Vandenbrouck Y, Viari A, Wojcik J.
BMC Bioinformatics. 2006 Jan 17;7:21.
PMID: 16417636 [PubMed - indexed for MEDLINE]
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ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.
Huan T, Sivachenko AY, Harrison SH, Chen JY.
BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S5.
PMID: 18793469 [PubMed - indexed for MEDLINE]
SAGA: a subgraph matching tool for biological graphs.
Tian Y, McEachin RC, Santos C, States DJ, Patel JM.
Bioinformatics. 2007 Jan 15;23(2):232-9. Epub 2006 Nov 16.
PMID: 17110368 [PubMed - indexed for MEDLINE]
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PathSys: integrating molecular interaction graphs for systems biology.
Baitaluk M, Qian X, Godbole S, Raval A, Ray A, Gupta A.
BMC Bioinformatics. 2006 Feb 7;7:55.
PMID: 16464251 [PubMed - indexed for MEDLINE]
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool.
Sealfon RS, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG.
BMC Bioinformatics. 2006 Oct 10;7:443.
PMID: 17032457 [PubMed - indexed for MEDLINE]
A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila.
Pacifico S, Liu G, Guest S, Parrish JR, Fotouhi F, Finley RL Jr.
BMC Bioinformatics. 2006 Apr 7;7:195.
PMID: 16603075 [PubMed - indexed for MEDLINE]
Dynamic visualization of coexpression in systems genetics data.
New J, Kendall W, Huang J, Chesler E.
IEEE Trans Vis Comput Graph. 2008 Sep-Oct;14(5):1081-94.
PMID: 18599919 [PubMed - indexed for MEDLINE]
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EnsMart: a generic system for fast and flexible access to biological data.
Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, Hammond M, Rocca-Serra P, Cox T, Birney E.
Genome Res. 2004 Jan;14(1):160-9.
PMID: 14707178 [PubMed - indexed for MEDLINE]
Cerebral: visualizing multiple experimental conditions on a graph with biological context.
Barsky A, Munzner T, Gardy J, Kincaid R.
IEEE Trans Vis Comput Graph. 2008 Nov-Dec;14(6):1253-60.
PMID: 18988971 [PubMed - indexed for MEDLINE]
The Graphical Query Language: a tool for analysis of gene expression time-courses.
Costa IG, Schönhuth A, Schliep A.
Bioinformatics. 2005 May 15;21(10):2544-5. Epub 2005 Feb 8.
PMID: 15701683 [PubMed - indexed for MEDLINE]
Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures.
Koehler J, Rawlings C, Verrier P, Mitchell R, Skusa A, Ruegg A, Philippi S.
In Silico Biol. 2005;5(1):33-44.
PMID: 15972003 [PubMed - indexed for MEDLINE]
GrouseFlocks: steerable exploration of graph hierarchy space.
Archambault D, Munzner T, Auber D.
IEEE Trans Vis Comput Graph. 2008 Jul-Aug;14(4):900-13.
PMID: 18467763 [PubMed - indexed for MEDLINE]
BioMart--biological queries made easy.
Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A.
BMC Genomics. 2009 Jan 14;10:22.
PMID: 19144180 [PubMed - indexed for MEDLINE]
A model diagram layout extension for SBML.
Gauges R, Rost U, Sahle S, Wegner K.
Bioinformatics. 2006 Aug 1;22(15):1879-85. Epub 2006 May 18.
PMID: 16709586 [PubMed - indexed for MEDLINE]
WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data.
Yi M, Horton JD, Cohen JC, Hobbs HH, Stephens RM.
BMC Bioinformatics. 2006 Jan 19;7:30.
PMID: 16423281 [PubMed - indexed for MEDLINE]
jSquid: a Java applet for graphical on-line network exploration.
Klammer M, Roopra S, Sonnhammer EL.
Bioinformatics. 2008 Jun 15;24(12):1467-8. Epub 2008 Apr 29.
PMID: 18445606 [PubMed - indexed for MEDLINE]
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration.
Teber ET, Crawford E, Bolton KB, Van Dyk D, Schofield PR, Kapoor V, Church WB.
BMC Bioinformatics. 2006 Jan 23;7:33.
PMID: 16426464 [PubMed - indexed for MEDLINE]
Advanced query mechanisms for biological databases.
Chen IM, Kosky AS, Markowitz VM, Szeto E, Topaloglou T.
Proc Int Conf Intell Syst Mol Biol. 1998;6:43-51.
PMID: 9783208 [PubMed - indexed for MEDLINE]
Modeling biochemical transformation processes and information processing with Narrator.
Mandel JJ, Fuss H, Palfreyman NM, Dubitzky W.
BMC Bioinformatics. 2007 Mar 27;8:103.
PMID: 17389034 [PubMed - indexed for MEDLINE]
The mouse genome database (MGD): new features facilitating a model system.
Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE; Mouse Genome Database Group.
Nucleic Acids Res. 2007 Jan;35(Database issue):D630-7. Epub 2006 Nov 29.
PMID: 17135206 [PubMed - indexed for MEDLINE]