{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T11:50:06Z","timestamp":1775217006091,"version":"3.50.1"},"reference-count":66,"publisher":"Springer Science and Business Media LLC","issue":"S2","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,2]]},"DOI":"10.1186\/s12859-016-1443-5","type":"journal-article","created":{"date-parts":[[2017,2,15]],"date-time":"2017-02-15T10:35:57Z","timestamp":1487154957000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["A taxonomy of visualization tasks for the analysis of biological pathway data"],"prefix":"10.1186","volume":"18","author":[{"given":"Paul","family":"Murray","sequence":"first","affiliation":[]},{"given":"Fintan","family":"McGee","sequence":"additional","affiliation":[]},{"given":"Angus G.","family":"Forbes","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,2,15]]},"reference":[{"issue":"5","key":"1443_CR1","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","volume":"144","author":"D Hanahan","year":"2011","unstructured":"Hanahan D, Weinberg RA. Hallmarks of cancer: The next generation. Cell. 2011; 144(5):646\u201374.","journal-title":"Cell"},{"issue":"9","key":"1443_CR2","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1038\/nbt.1666","volume":"28","author":"E Demir","year":"2010","unstructured":"Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D\u2019Eustachio P, Schaefer C, Luciano J. The biopax community standard for pathway data sharing. Nat Biotechnol. 2010; 28(9):935\u201342.","journal-title":"Nat Biotechnol"},{"issue":"5560","key":"1443_CR3","doi-asserted-by":"crossref","first-page":"1662","DOI":"10.1126\/science.1069492","volume":"295","author":"H Kitano","year":"2002","unstructured":"Kitano H. Systems biology: A brief overview. Science. 2002; 295(5560):1662\u20134.","journal-title":"Science"},{"issue":"3","key":"1443_CR4","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1057\/palgrave.ivs.9500102","volume":"4","author":"P Saraiya","year":"2005","unstructured":"Saraiya P, North C, Duca K. Visualizing biological pathways: requirements analysis, systems evaluation and research agenda. Inf Vis. 2005; 4(3):191\u2013205.","journal-title":"Inf Vis"},{"issue":"2","key":"1443_CR5","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/nrc2981","volume":"11","author":"RA Cairns","year":"2011","unstructured":"Cairns RA, Harris IS, Mak TW. Regulation of cancer cell metabolism. Nat Rev Cancer. 2011; 11(2):85\u201395.","journal-title":"Nat Rev Cancer"},{"issue":"4","key":"1443_CR6","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/S1535-6108(03)00248-4","volume":"4","author":"J Luo","year":"2003","unstructured":"Luo J, Manning BD, Cantley LC. Targeting the PI3K-Akt pathway in human cancer: Rationale and promise. Cancer Cell. 2003; 4(4):257\u201362.","journal-title":"Cancer Cell"},{"issue":"6859","key":"1443_CR7","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/35102167","volume":"414","author":"T Reya","year":"2001","unstructured":"Reya T, Morrison SJ, Clarke MF, Weissman IL. Stem cells, cancer, and cancer stem cells. Nature. 2001; 414(6859):105\u201311.","journal-title":"Nature"},{"issue":"12","key":"1443_CR8","doi-asserted-by":"crossref","first-page":"2376","DOI":"10.1109\/TVCG.2013.124","volume":"19","author":"M Brehmer","year":"2013","unstructured":"Brehmer M, Munzner T. A multi-level typology of abstract visualization tasks. IEEE Trans Vis Comput Graph. 2013; 19(12):2376\u201385.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"20","key":"1443_CR9","doi-asserted-by":"crossref","first-page":"2651","DOI":"10.1093\/bioinformatics\/btm401","volume":"23","author":"M Suderman","year":"2007","unstructured":"Suderman M, Hallett M. Tools for visually exploring biological networks. Bioinformatics. 2007; 23(20):2651\u20139.","journal-title":"Bioinformatics"},{"key":"1443_CR10","doi-asserted-by":"crossref","unstructured":"Pavlopoulos GA, Wegener AL, Schneider R. A survey of visualization tools for biological network analysis. BioData Min. 2008;1(12).","DOI":"10.1186\/1756-0381-1-12"},{"issue":"3","key":"1443_CR11","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nmeth.1436","volume":"7","author":"N Gehlenborg","year":"2010","unstructured":"Gehlenborg N, O\u2019Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC. Visualization of omics data for systems biology. Nat Methods. 2010; 7(3):56\u201368.","journal-title":"Nat Methods"},{"issue":"3","key":"1443_CR12","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1093\/bioinformatics\/btp665","volume":"26","author":"O Babur","year":"2010","unstructured":"Babur O, Dogrusoz U, Demir E, Sander C. ChiBE: Interactive visualization and manipulation of BioPAX pathway models. Bioinformatics. 2010; 26(3):429\u201331.","journal-title":"Bioinformatics"},{"issue":"12","key":"1443_CR13","doi-asserted-by":"crossref","first-page":"2536","DOI":"10.1109\/TVCG.2013.154","volume":"19","author":"A Lex","year":"2013","unstructured":"Lex A, Partl C, Kalkofen D, Streit M, Gratzl S, Wassermann AM, Schmalstieg D, Pfister H. Entourage: Visualizing relationships between biological pathways using contextual subsets. IEEE Trans Vis Comput Graph. 2013; 19(12):2536\u201345.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"D1","key":"1443_CR14","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1093\/nar\/gkt1102","volume":"42","author":"D Croft","year":"2014","unstructured":"Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, et al. The Reactome pathway knowledgebase. Nucleic Acids Res. 2014; 42(D1):472\u20137.","journal-title":"Nucleic Acids Res"},{"key":"1443_CR15","doi-asserted-by":"crossref","unstructured":"Hu Z, Mellor J, Wu J, DeLisi C. VisANT: An online visualization and analysis tool for biological interaction data. BMC Bioinforma. 2004; 5(17).","DOI":"10.1186\/1471-2105-5-17"},{"key":"1443_CR16","doi-asserted-by":"crossref","unstructured":"Bourqui R, Cottret L, Lacroix V, Auber D, Mary P, Sagot MF, Jourdan F. Metabolic network visualization eliminating node redundance and preserving metabolic pathways. BMC Syst Biol. 2007;1(29).","DOI":"10.1186\/1752-0509-1-29"},{"issue":"8","key":"1443_CR17","doi-asserted-by":"crossref","first-page":"1596","DOI":"10.1093\/bioinformatics\/bti153","volume":"21","author":"M Holford","year":"2005","unstructured":"Holford M, Li N, Nadkarni P, Zhao H. VitaPad: Visualization tools for the analysis of pathway data. Bioinformatics. 2005; 21(8):1596\u2013602.","journal-title":"Bioinformatics"},{"key":"1443_CR18","doi-asserted-by":"crossref","unstructured":"Longabaugh WJ. Combing the hairball with biofabric: a new approach for visualization of large networks. BMC Bioinforma. 2012;13(275).","DOI":"10.1186\/1471-2105-13-275"},{"issue":"11","key":"1443_CR19","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498\u2013504.","journal-title":"Genome Res"},{"issue":"6","key":"1443_CR20","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1109\/TVCG.2008.117","volume":"14","author":"A Barsky","year":"2008","unstructured":"Barsky A, Munzner T, Gardy J, Kincaid R. Cerebral: Visualizing multiple experimental conditions on a graph with biological context. IEEE Trans Vis Comput Graph. 2008; 14(6):1253\u201360.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"135","key":"1443_CR21","first-page":"1","volume":"16","author":"C Vehlow","year":"2015","unstructured":"Vehlow C, Kao DP, Bristow MR, Hunter LE, Weiskopf D, G\u00f6rg C. Visual analysis of biological data-knowledge networks. BMC Bioinforma. 2015; 16(135):1\u201315.","journal-title":"BMC Bioinforma"},{"issue":"6","key":"1443_CR22","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1753-6561-9-S6-S3","volume":"9","author":"TN Dang","year":"2015","unstructured":"Dang TN, Murray P, Forbes AG. PathwayMatrix: Visualizing binary relationships between proteins in biological pathways. BMC Proc. 2015; 9(6):3.","journal-title":"BMC Proc"},{"issue":"6","key":"1443_CR23","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1753-6561-9-S6-S6","volume":"9","author":"TN Dang","year":"2015","unstructured":"Dang TN, Murray P, Aurisano J, Forbes AG. ReactionFlow: An interactive visualization tool for causality analysis in biological pathways. BMC Proc. 2015; 9(6):6.","journal-title":"BMC Proc"},{"key":"1443_CR24","volume-title":"Proceedings of the IEEE Symposium on Information Visualization","author":"M Ghoniem","year":"2004","unstructured":"Ghoniem M, Fekete JD, Castagliola P. A comparison of the readability of graphs using node-link and matrix-based representations. In: Proceedings of the IEEE Symposium on Information Visualization. New York: IEEE: 2004. p. 17\u201324."},{"key":"1443_CR25","volume-title":"Proceedings of the IFIP Conference on Human-Computer Interaction","author":"N Henry","year":"2007","unstructured":"Henry N, Fekete JD. MatLink: Enhanced matrix visualization for analyzing social networks. In: Proceedings of the IFIP Conference on Human-Computer Interaction. Berlin: Springer Berlin Heidelberg: 2007. p. 288\u2013302."},{"issue":"6","key":"1443_CR26","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1109\/TVCG.2007.70582","volume":"13","author":"N Henry","year":"2007","unstructured":"Henry N, Fekete JD, McGuffin MJ. NodeTrix: A hybrid visualization of social networks. IEEE Trans Vis Comput Graph. 2007; 13(6):1302\u20139.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"1","key":"1443_CR27","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000; 28(1):27\u201330.","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"1443_CR28","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","volume":"19","author":"M Hucka","year":"2003","unstructured":"Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H. The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics. 2003; 19(4):524\u201331.","journal-title":"Bioinformatics"},{"issue":"8","key":"1443_CR29","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/nbt.1558","volume":"27","author":"NL Novere","year":"2009","unstructured":"Novere NL, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villeger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. The Systems Biology Graphical Notation. Nat Biotechnol. 2009; 27(8):735\u201341.","journal-title":"Nat Biotechnol"},{"key":"1443_CR30","volume-title":"Proceedings of the First IEEE Conference on Visualization","author":"S Wehrend","year":"1990","unstructured":"Wehrend S, Lewis C. A problem-oriented classification of visualization techniques. In: Proceedings of the First IEEE Conference on Visualization. New York: IEEE: 1990. p. 139\u201343."},{"key":"1443_CR31","volume-title":"Proceedings of the IEEE Symposium on Visual Languages","author":"B Shneiderman","year":"1996","unstructured":"Shneiderman B. The eyes have it: A task by data type taxonomy for information visualizations. In: Proceedings of the IEEE Symposium on Visual Languages. New York: IEEE: 1996. p. 336\u201343."},{"key":"1443_CR32","volume-title":"Proceedings of the AVI Workshop on BEyond Time and Errors: Novel Evaluation Methods for Information Visualization. BELIV \u201906","author":"ERA Valiati","year":"2006","unstructured":"Valiati ERA, Pimenta MS, Freitas CMDS. A taxonomy of tasks for guiding the evaluation of multidimensional visualizations. In: Proceedings of the AVI Workshop on BEyond Time and Errors: Novel Evaluation Methods for Information Visualization. BELIV \u201906. New York: ACM: 2006."},{"key":"1443_CR33","volume-title":"Proceedings of the AVI Workshop on BEyond Time and Errors: Novel Evaluation Methods for Information Visualization. BELIV \u201906","author":"B Lee","year":"2006","unstructured":"Lee B, Plaisant C, Parr CS, Fekete JD, Henry N. Task taxonomy for graph visualization. In: Proceedings of the AVI Workshop on BEyond Time and Errors: Novel Evaluation Methods for Information Visualization. BELIV \u201906. New York: ACM: 2006."},{"key":"1443_CR34","volume-title":"Proceedings of the IEEE Symposium on Information Visualization","author":"R Amar","year":"2005","unstructured":"Amar R, Eagan J, Stasko J. Low-level components of analytic activity in information visualization. In: Proceedings of the IEEE Symposium on Information Visualization. New York: ACM: 2005. p. 111\u20137."},{"issue":"3","key":"1443_CR35","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1109\/TVCG.2013.238","volume":"20","author":"J-w Ahn","year":"2014","unstructured":"Ahn J-w, Plaisant C, Shneiderman B. A task taxonomy for network evolution analysis. IEEE Trans Vis Comput Graph. 2014; 20(3):365\u201376.","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"1443_CR36","volume-title":"Multivariate Network Visualization","author":"AJ Pretorius","year":"2014","unstructured":"Pretorius AJ, Purchase HC, Stasko JT. Tasks for multivariate network analysis. In: Multivariate Network Visualization. Heidelberg, Germany: Springer: 2014. p. 77\u201395."},{"issue":"19","key":"1443_CR37","first-page":"1","volume":"14","author":"C Partl","year":"2013","unstructured":"Partl C, Lex A, Streit M, Kalkofen D, Kashofer K, Schmalstieg D. enroute: Dynamic path extraction from biological pathway maps for exploring heterogeneous experimental datasets. BMC Bioinforma. 2013; 14(19):1\u201316.","journal-title":"BMC Bioinforma"},{"key":"1443_CR38","unstructured":"Hadlak S, Schumann H, Schulz HJ. A survey of multi-faceted graph visualization. In: Eurographics Conference on Visualization (EuroVis). The Eurographics Association: 2015. p. 1\u201320."},{"key":"1443_CR39","unstructured":"Vehlow C, Beck F, Weiskopf D. The state of the art in visualizing group structures in graphs. In: Eurographics Conference on Visualization (EuroVis) - STARs. The Eurographics Association: 2015. p. 21\u201340."},{"issue":"4","key":"1443_CR40","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1109\/TVCG.2005.53","volume":"11","author":"P Saraiya","year":"2005","unstructured":"Saraiya P, North C, Duca K. An insight-based methodology for evaluating bioinformatics visualizations. IEEE Trans Vis Comput Graph. 2005; 11(4):443\u201356.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"6","key":"1443_CR41","doi-asserted-by":"crossref","first-page":"2070","DOI":"10.1371\/journal.pone.0128985","volume":"10","author":"M Sari","year":"2015","unstructured":"Sari M, Bahceci I, Dogrusoz U, Sumer SO, Aksoy BA, Babur \u00d6, Demir E. SBGNViz: A tool for visualization and complexity management of SBGN process description maps. PloS one. 2015; 10(6):2070\u20139.","journal-title":"PloS one"},{"issue":"12","key":"1443_CR42","doi-asserted-by":"crossref","first-page":"2070","DOI":"10.1109\/TVCG.2013.220","volume":"19","author":"R Shadoan","year":"2013","unstructured":"Shadoan R, Weaver C. Visual analysis of higher-order conjunctive relationships in multidimensional data using a hypergraph query system. IEEE Trans Vis Comput Graph. 2013; 19(12):2070\u20139.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"12","key":"1443_CR43","doi-asserted-by":"crossref","first-page":"2310","DOI":"10.1109\/TVCG.2014.2346441","volume":"20","author":"S Van Den Elzen","year":"2014","unstructured":"Van Den Elzen S, Van Wijk JJ. Multivariate network exploration and presentation: From detail to overview via selections and aggregations. IEEE Trans Vis Comput Graph. 2014; 20(12):2310\u20139.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"6","key":"1443_CR44","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1109\/TVCG.2007.70589","volume":"13","author":"W Willett","year":"2007","unstructured":"Willett W, Heer J, Agrawala M. Scented widgets: Improving navigation cues with embedded visualizations. IEEE Trans Vis Comput Graph. 2007; 13(6):1129\u201336.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"4","key":"1443_CR45","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1177\/1473871611416549","volume":"10","author":"M Gleicher","year":"2011","unstructured":"Gleicher M, Albers D, Walker R, Jusufi I, Hansen CD, Roberts JC. Visual comparison for information visualization. Inf Vis. 2011; 10(4):289\u2013309.","journal-title":"Inf Vis"},{"issue":"12","key":"1443_CR46","doi-asserted-by":"crossref","first-page":"2556","DOI":"10.1109\/TVCG.2013.149","volume":"19","author":"S Rufiange","year":"2013","unstructured":"Rufiange S, McGuffin MJ. Diffani: Visualizing dynamic graphs with a hybrid of difference maps and animation. IEEE Trans Vis Comput Graph. 2013; 19(12):2556\u201365.","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"1443_CR47","volume-title":"Multivariate Network Visualization","author":"O Kohlbacher","year":"2014","unstructured":"Kohlbacher O, Schreiber F, Ward MO. Multivariate networks in the life sciences. In: Multivariate Network Visualization. Heidelberg, Germany: Springer: 2014. p. 61\u201373."},{"issue":"suppl 1","key":"1443_CR48","first-page":"433","volume":"33","author":"C Von Mering","year":"2005","unstructured":"Von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P. STRING: Known and predicted protein\u2013protein associations, integrated and transferred across organisms. Nucleic Acids Res. 2005; 33(suppl 1):433\u20137.","journal-title":"Nucleic Acids Res"},{"key":"1443_CR49","volume-title":"Proceedings of the 9th International Symposium on Visual Information Communication and Interaction (VINCI)","author":"F Paduano","year":"2016","unstructured":"Paduano F, Etemadpour R, Forbes AG. BranchingSets: Interactively visualizing categories on node-link diagrams. In: Proceedings of the 9th International Symposium on Visual Information Communication and Interaction (VINCI). Dallas: ACM: 2016. p. 9\u201316."},{"issue":"3","key":"1443_CR50","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1111\/cgf.12882","volume":"35","author":"T Dang","year":"2016","unstructured":"Dang T, Pendar N, Forbes AG. TimeArcs: Visualizing fluctuations in dynamic networks. Comput Graph Forum. 2016; 35(3):61\u20139.","journal-title":"Comput Graph Forum"},{"issue":"1","key":"1443_CR51","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1057\/ivs.2009.1","volume":"9","author":"M Skeels","year":"2010","unstructured":"Skeels M, Lee B, Smith G, Robertson GG. Revealing uncertainty for information visualization. Inf Vis. 2010; 9(1):70\u201381.","journal-title":"Inf Vis"},{"issue":"12","key":"1443_CR52","doi-asserted-by":"crossref","first-page":"2526","DOI":"10.1109\/TVCG.2012.285","volume":"18","author":"Y Wu","year":"2012","unstructured":"Wu Y, Yuan GX, Ma KL. Visualizing flow of uncertainty through analytical processes. IEEE Trans Vis Comput Graph. 2012; 18(12):2526\u201335.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"1","key":"1443_CR53","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1109\/TVCG.2015.2467691","volume":"22","author":"Y Wang","year":"2016","unstructured":"Wang Y, Shen Q, Archambault D, Zhou Z, Zhu M, Yang S, Qu H. AmbiguityVis: Visualization of ambiguity in graph layouts. IEEE Trans Vis Comput Graph. 2016; 22(1):359\u201368.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"3","key":"1443_CR54","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1111\/j.1467-8659.2008.01231.x","volume":"27","author":"AJ Pretorius","year":"2008","unstructured":"Pretorius AJ, van Wijk JJ. Visual inspection of multivariate graphs. Comput Graph Forum. 2008; 27(3):967\u201374.","journal-title":"Comput Graph Forum"},{"issue":"12","key":"1443_CR55","doi-asserted-by":"crossref","first-page":"2032","DOI":"10.1109\/TVCG.2013.223","volume":"19","author":"S Ghani","year":"2013","unstructured":"Ghani S, Kwon BC, Lee S, Yi JS, Elmqvist N. Visual analytics for multimodal social network analysis: A design study with social scientists. IEEE Trans Vis Comput Graph. 2013; 19(12):2032\u201341.","journal-title":"IEEE Trans Vis Comput Graph"},{"key":"1443_CR56","volume-title":"Proceedings of the ACM SIGCHI Conference on Human Factors in Computing Systems","author":"D Holten","year":"2009","unstructured":"Holten D, van Wijk JJ. A user study on visualizing directed edges in graphs. In: Proceedings of the ACM SIGCHI Conference on Human Factors in Computing Systems. New York: ACM: 2009. p. 2299\u2013308."},{"issue":"6","key":"1443_CR57","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1109\/TVCG.2009.122","volume":"15","author":"C Collins","year":"2009","unstructured":"Collins C, Penn G, Carpendale S. Bubble sets: Revealing set relations with isocontours over existing visualizations. IEEE Trans Vis Comput Graph. 2009; 15(6):1009\u201316.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"11","key":"1443_CR58","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1109\/TVCG.2014.2315995","volume":"20","author":"R Jianu","year":"2014","unstructured":"Jianu R, Rusu A, Hu Y, Taggart D. How to display group information on node-link diagrams: An evaluation. IEEE Trans Vis Comput Graph. 2014; 20(11):1530\u201341.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"6","key":"1443_CR59","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/1753-6561-9-S6-S4","volume":"9","author":"F Paduano","year":"2015","unstructured":"Paduano F, Forbes AG. Extended LineSets: A visualization technique for the interactive inspection of biological pathways. BMC Proc. 2015; 9(6):4.","journal-title":"BMC Proc"},{"key":"1443_CR60","doi-asserted-by":"crossref","unstructured":"Felciano RM, Bavari S, Richards DR, Billaud J-n, Warren T, Panchal R, Kr\u00e4mer A. Predictive systems biology approach to broad-spectrum, host-directed drug target discovery in infectious diseases. In: Proceedings of the Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing: 2013. p. 17\u201328.","DOI":"10.1142\/9789814447973_0003"},{"issue":"4","key":"1443_CR61","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1093\/bioinformatics\/btt703","volume":"30","author":"A Kr\u00e4mer","year":"2014","unstructured":"Kr\u00e4mer A, Green J, Pollard J, Tugendreich S. Causal analysis approaches in ingenuity pathway analysis. Bioinformatics. 2014; 30(4):523\u201330.","journal-title":"Bioinformatics"},{"key":"1443_CR62","volume-title":"Multivariate Network Visualization","author":"D Archambault","year":"2014","unstructured":"Archambault D, Abello J, Kennedy J, Kobourov S, Ma KL, Miksch S, Muelder C, Telea AC. Temporal multivariate networks. In: Multivariate Network Visualization. Heidelberg, Germany: Springer: 2014. p. 151\u201374."},{"issue":"1","key":"1443_CR63","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1177\/1473871615576758","volume":"15","author":"D Archambault","year":"2016","unstructured":"Archambault D, Purchase HC. On the effective visualisation of dynamic attribute cascades. Inf Vis. 2016; 15(1):51\u201363.","journal-title":"Inf Vis"},{"issue":"8","key":"1443_CR64","doi-asserted-by":"crossref","first-page":"1254","DOI":"10.1109\/JPROC.2008.925458","volume":"96","author":"A Funahashi","year":"2008","unstructured":"Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H. Celldesigner 3.5: a versatile modeling tool for biochemical networks. Proc IEEE. 2008; 96(8):1254\u201365.","journal-title":"Proc IEEE"},{"key":"1443_CR65","volume-title":"Proceedings of the Ninth ACM International Conference on Interactive Tabletops and Surfaces. ITS \u201914","author":"SK Badam","year":"2014","unstructured":"Badam SK, Elmqvist N. Polychrome: A cross-device framework for collaborative web visualization. In: Proceedings of the Ninth ACM International Conference on Interactive Tabletops and Surfaces. ITS \u201914. New York: ACM: 2014. p. 109\u201318."},{"issue":"4","key":"1443_CR66","doi-asserted-by":"crossref","first-page":"1206","DOI":"10.1086\/421509","volume":"110","author":"J Moody","year":"2005","unstructured":"Moody J, McFarland D, Bender-deMoll S. Dynamic network visualization. Am J Sociol. 2005; 110(4):1206\u201341.","journal-title":"Am J Sociol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-1443-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,15]],"date-time":"2025-06-15T11:15:50Z","timestamp":1749986150000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-1443-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,2]]},"references-count":66,"journal-issue":{"issue":"S2","published-print":{"date-parts":[[2017,2]]}},"alternative-id":["1443"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-1443-5","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,2]]},"article-number":"21"}}