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Volumn 15, Issue 8, 2015, Pages 1356-1374

Open source libraries and frameworks for biological data visualisation: A guide for developers

Author keywords

Bioinformatics; Chart; Hierarchy; Network; Software library

Indexed keywords

ALGORITHM; BIOINFORMATICS; BIOMEDICINE; COMPUTER INTERFACE; COMPUTER LANGUAGE; COPY NUMBER VARIATION; DATA ANALYSIS; EXPERIMENTATION; GEL ELECTROPHORESIS; K NEAREST NEIGHBOR; MATHEMATICAL MODEL; MOLECULAR BIOLOGY; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; REVIEW; SCIENTIST; WORKFLOW; COMPUTER GRAPHICS; HUMAN; INFORMATION PROCESSING; LIBRARY; PHYSIOLOGY; PROCEDURES; PROTEIN PROTEIN INTERACTION; PROTEOMICS; SOFTWARE; STATISTICAL ANALYSIS;

EID: 84926513336     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400377     Document Type: Review
Times cited : (37)

References (122)
  • 8
    • 84875404794 scopus 로고    scopus 로고
    • The UCSC Genome Browser database: extensions and updates 2013
    • Meyer, L. R., Zweig, A. S., Hinrichs, A. S., Karolchik, D. et al., The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 2013, 41, D64-69.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D64-D69
    • Meyer, L.R.1    Zweig, A.S.2    Hinrichs, A.S.3    Karolchik, D.4
  • 9
    • 75949090753 scopus 로고    scopus 로고
    • The UCSC Genome Browser. Current protocols in bioinformatics
    • Unit 1.4.
    • Karolchik, D., Hinrichs, A. S., Kent, W. J., The UCSC Genome Browser. Current protocols in bioinformatics 2009, Chapter 1, Unit 1.4.
    • (2009) , Issue.1
    • Karolchik, D.1    Hinrichs, A.S.2    Kent, W.J.3
  • 10
    • 2442718832 scopus 로고    scopus 로고
    • The Ensembl Web site: mechanics of a genome browser
    • Stalker, J., Gibbins, B., Meidl, P., Smith, J. et al., The Ensembl Web site: mechanics of a genome browser. Genome Res. 2004, 14, 951-955.
    • (2004) Genome Res. , vol.14 , pp. 951-955
    • Stalker, J.1    Gibbins, B.2    Meidl, P.3    Smith, J.4
  • 12
    • 77951531009 scopus 로고    scopus 로고
    • GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs
    • Risueno, A., Fontanillo, C., Dinger, M. E., De Las Rivas, J., GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics 2010, 11, 221.
    • (2010) BMC Bioinformatics , vol.11 , pp. 221
    • Risueno, A.1    Fontanillo, C.2    Dinger, M.E.3    De Las Rivas, J.4
  • 13
    • 48449104742 scopus 로고    scopus 로고
    • Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments
    • Al-Shahrour, F., Carbonell, J., Minguez, P., Goetz, S. et al., Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. Nucleic Acids Res. 2008, 36, W341-346.
    • (2008) Nucleic Acids Res. , vol.36 , pp. W341-W346
    • Al-Shahrour, F.1    Carbonell, J.2    Minguez, P.3    Goetz, S.4
  • 14
    • 84863011685 scopus 로고    scopus 로고
    • PRIDE Inspector: a tool to visualize and validate MS proteomics data
    • Wang, R., Fabregat, A., Rios, D., Ovelleiro, D. et al., PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat. Biotechnol. 2012, 30, 135-137.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 135-137
    • Wang, R.1    Fabregat, A.2    Rios, D.3    Ovelleiro, D.4
  • 15
    • 77949695293 scopus 로고    scopus 로고
    • Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies
    • Searle, B. C., Scaffold: a bioinformatic tool for validating MS/MS-based proteomic studies. Proteomics 2010, 10, 1265-1269.
    • (2010) Proteomics , vol.10 , pp. 1265-1269
    • Searle, B.C.1
  • 16
    • 42249108173 scopus 로고    scopus 로고
    • OpenMS - an open-source software framework for mass spectrometry
    • Sturm, M., Bertsch, A., Gropl, C., Hildebrandt, A. et al., OpenMS - an open-source software framework for mass spectrometry. BMC Bioinformatics 2008, 9, 163.
    • (2008) BMC Bioinformatics , vol.9 , pp. 163
    • Sturm, M.1    Bertsch, A.2    Gropl, C.3    Hildebrandt, A.4
  • 18
    • 84876252208 scopus 로고    scopus 로고
    • BioJS: an open source javascript framework for biological data visualization
    • Gomez, J., Garcia, L. J., Salazar, G. A., Villaveces, J. et al., BioJS: an open source javascript framework for biological data visualization. Bioinformatics 2013, 29, 1103-1104.
    • (2013) Bioinformatics , vol.29 , pp. 1103-1104
    • Gomez, J.1    Garcia, L.J.2    Salazar, G.A.3    Villaveces, J.4
  • 19
    • 79551587720 scopus 로고    scopus 로고
    • Cytoscape 2.8: new features for data integration and network visualization
    • Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P. L., Ideker, T., Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011, 27, 431-432.
    • (2011) Bioinformatics , vol.27 , pp. 431-432
    • Smoot, M.E.1    Ono, K.2    Ruscheinski, J.3    Wang, P.L.4    Ideker, T.5
  • 20
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks, J., Nekrutenko, A., Taylor, J., Galaxy, T., Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010, 11, R86.
    • (2010) Genome Biol. , vol.11 , pp. R86
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3    Galaxy, T.4
  • 21
    • 0034504973 scopus 로고    scopus 로고
    • A taxonomy of visualization techniques using the data state reference model
    • Chi, E. H., A taxonomy of visualization techniques using the data state reference model. IEEE Symp. Inf. Visual. 2000, 2000, 69-75.
    • (2000) IEEE Symp. Inf. Visual. , vol.2000 , pp. 69-75
    • Chi, E.H.1
  • 22
    • 80052450168 scopus 로고    scopus 로고
    • O'Reilly Media, Inc., Sebastopol, CA .
    • Pilgrim, M., HTML5: Up and Running, O'Reilly Media, Inc., Sebastopol, CA 2010.
    • (2010) HTML5: Up and Running
    • Pilgrim, M.1
  • 24
    • 84879501266 scopus 로고    scopus 로고
    • Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report
    • Perez-Riverol, Y., Hermjakob, H., Kohlbacher, O., Martens, L. et al., Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report. J. Proteomics 2013, 87, 134-138.
    • (2013) J. Proteomics , vol.87 , pp. 134-138
    • Perez-Riverol, Y.1    Hermjakob, H.2    Kohlbacher, O.3    Martens, L.4
  • 26
    • 84890425321 scopus 로고    scopus 로고
    • Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective
    • Perez-Riverol, Y., Wang, R., Hermjakob, H., Muller, M. et al., Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective. Biochimica et biophysica acta 2014, 1844, 63-76.
    • (2014) Biochimica et biophysica acta , vol.1844 , pp. 63-76
    • Perez-Riverol, Y.1    Wang, R.2    Hermjakob, H.3    Muller, M.4
  • 27
    • 0034315705 scopus 로고    scopus 로고
    • Evaluating visualizations: using a taxonomic guide
    • Morse, E., Lewis, M., Olsen, K. A., Evaluating visualizations: using a taxonomic guide. Int. J. Hum-Comput. St. 2000, 53, 637-662.
    • (2000) Int. J. Hum-Comput. St. , vol.53 , pp. 637-662
    • Morse, E.1    Lewis, M.2    Olsen, K.A.3
  • 29
    • 0029725135 scopus 로고    scopus 로고
    • The eyes have it: a task by data type taxonomy for information visualizations
    • Washington, DC -.
    • Shneiderman, B., The eyes have it: a task by data type taxonomy for information visualizations. Proceedings of the IEEE Symposium on Visual Languages, Washington, DC 1996, pp. 336-343.
    • (1996) Proceedings of the IEEE Symposium on Visual Languages , pp. 336-343
    • Shneiderman, B.1
  • 31
    • 77957835477 scopus 로고    scopus 로고
    • Protovis: a graphical toolkit for visualization
    • Bostock, M., Heer, J., Protovis: a graphical toolkit for visualization. IEEE Trans. Visual. Computer Graph. 2009, 15, 1121-1128.
    • (2009) IEEE Trans. Visual. Computer Graph. , vol.15 , pp. 1121-1128
    • Bostock, M.1    Heer, J.2
  • 32
    • 84904822242 scopus 로고    scopus 로고
    • PIQMIe: a web server for semi-quantitative proteomics data management and analysis
    • Kuzniar, A., Kanaar, R., PIQMIe: a web server for semi-quantitative proteomics data management and analysis. Nucleic Acids Res. 2014, 42, W100-106.
    • (2014) Nucleic Acids Res. , vol.42 , pp. W100-W106
    • Kuzniar, A.1    Kanaar, R.2
  • 33
    • 84876525081 scopus 로고    scopus 로고
    • Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
    • Lewis, T. E., Sillitoe, I., Andreeva, A., Blundell, T. L. et al., Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res. 2013, 41, D499-507.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D499-D507
    • Lewis, T.E.1    Sillitoe, I.2    Andreeva, A.3    Blundell, T.L.4
  • 34
    • 27644483321 scopus 로고    scopus 로고
    • JFreeChart, a free Java class library for generating charts
    • Publisher Full Text . Available at.
    • Gilbert, D., Morgner, T., JFreeChart, a free Java class library for generating charts. Publisher Full Text 2007. Available at http://www.jfree.org.
    • (2007)
    • Gilbert, D.1    Morgner, T.2
  • 35
    • 75249087912 scopus 로고    scopus 로고
    • SimBoolNet-a Cytoscape plugin for dynamic simulation of signaling networks
    • Zheng, J., Zhang, D., Przytycki, P. F., Zielinski, R. et al., SimBoolNet-a Cytoscape plugin for dynamic simulation of signaling networks. Bioinformatics 2010, 26, 141-142.
    • (2010) Bioinformatics , vol.26 , pp. 141-142
    • Zheng, J.1    Zhang, D.2    Przytycki, P.F.3    Zielinski, R.4
  • 36
    • 33747822950 scopus 로고    scopus 로고
    • JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information
    • Scheer, M., Klawonn, F., Munch, R., Grote, A. et al., JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information. Nucleic Acids Res. 2006, 34, W510-515.
    • (2006) Nucleic Acids Res. , vol.34 , pp. W510-W515
    • Scheer, M.1    Klawonn, F.2    Munch, R.3    Grote, A.4
  • 37
    • 77949681441 scopus 로고    scopus 로고
    • Rover: a tool to visualize and validate quantitative proteomics data from different sources
    • Colaert, N., Helsens, K., Impens, F., Vandekerckhove, J., Gevaert, K., Rover: a tool to visualize and validate quantitative proteomics data from different sources. Proteomics 2010, 10, 1226-1229.
    • (2010) Proteomics , vol.10 , pp. 1226-1229
    • Colaert, N.1    Helsens, K.2    Impens, F.3    Vandekerckhove, J.4    Gevaert, K.5
  • 38
    • 77649120044 scopus 로고    scopus 로고
    • FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data
    • Barsnes, H., Eidhammer, I., Martens, L., FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data. Proteomics 2010, 10, 1087-1090.
    • (2010) Proteomics , vol.10 , pp. 1087-1090
    • Barsnes, H.1    Eidhammer, I.2    Martens, L.3
  • 39
    • 79956021267 scopus 로고    scopus 로고
    • Peptide fractionation by acid pH SDS-free electrophoresis
    • Ramos, Y., Garcia, Y., Perez-Riverol, Y., Leyva, A. et al., Peptide fractionation by acid pH SDS-free electrophoresis. Electrophoresis 2011, 32, 1323-1326.
    • (2011) Electrophoresis , vol.32 , pp. 1323-1326
    • Ramos, Y.1    Garcia, Y.2    Perez-Riverol, Y.3    Leyva, A.4
  • 40
    • 84862798576 scopus 로고    scopus 로고
    • Isoelectric point optimization using peptide descriptors and support vector machines
    • Perez-Riverol, Y., Audain, E., Millan, A., Ramos, Y. et al., Isoelectric point optimization using peptide descriptors and support vector machines. J. Proteomics 2012, 75, 2269-2274.
    • (2012) J. Proteomics , vol.75 , pp. 2269-2274
    • Perez-Riverol, Y.1    Audain, E.2    Millan, A.3    Ramos, Y.4
  • 41
    • 84866849125 scopus 로고    scopus 로고
    • EpiExplorer: live exploration and global analysis of large epigenomic datasets
    • Halachev, K., Bast, H., Albrecht, F., Lengauer, T., Bock, C., EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biol. 2012, 13, R96.
    • (2012) Genome Biol. , vol.13 , pp. R96
    • Halachev, K.1    Bast, H.2    Albrecht, F.3    Lengauer, T.4    Bock, C.5
  • 42
    • 84891822499 scopus 로고    scopus 로고
    • EBI metagenomics-a new resource for the analysis and archiving of metagenomic data
    • Hunter, S., Corbett, M., Denise, H., Fraser, M. et al., EBI metagenomics-a new resource for the analysis and archiving of metagenomic data. Nucleic Acids Res. 2014, 42, D600-606.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D600-D606
    • Hunter, S.1    Corbett, M.2    Denise, H.3    Fraser, M.4
  • 43
    • 84883585774 scopus 로고    scopus 로고
    • SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments
    • Nim, T. H., White, J. K., Tucker-Kellogg, L., SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments. Nucleic Acids Res. 2013, 41, W187-191.
    • (2013) Nucleic Acids Res. , vol.41 , pp. W187-W191
    • Nim, T.H.1    White, J.K.2    Tucker-Kellogg, L.3
  • 44
    • 84875498250 scopus 로고    scopus 로고
    • CircaDB: a database of mammalian circadian gene expression profiles
    • Pizarro, A., Hayer, K., Lahens, N. F., Hogenesch, J. B., CircaDB: a database of mammalian circadian gene expression profiles. Nucleic Acids Res. 2013, 41, D1009-1013.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D1009-D1013
    • Pizarro, A.1    Hayer, K.2    Lahens, N.F.3    Hogenesch, J.B.4
  • 45
    • 34247493236 scopus 로고    scopus 로고
    • Matplotlib: a 2D graphics environment
    • Hunter, J. D., Matplotlib: a 2D graphics environment. Comput. Sci. Eng. 2007, 9, 90-95.
    • (2007) Comput. Sci. Eng. , vol.9 , pp. 90-95
    • Hunter, J.D.1
  • 47
    • 84908641515 scopus 로고    scopus 로고
    • ggplot2: elegant graphics for data analysis
    • Ginestet, C., ggplot2: elegant graphics for data analysis. J. R. Stat. Soc. Stat. 2011, 174, 245-245.
    • (2011) J. R. Stat. Soc. Stat. , vol.174 , pp. 245-245
    • Ginestet, C.1
  • 48
    • 65649092976 scopus 로고    scopus 로고
    • Biopython: freely available Python tools for computational molecular biology and bioinformatics
    • Cock, P. J., Antao, T., Chang, J. T., Chapman, B. A. et al., Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009, 25, 1422-1423.
    • (2009) Bioinformatics , vol.25 , pp. 1422-1423
    • Cock, P.J.1    Antao, T.2    Chang, J.T.3    Chapman, B.A.4
  • 50
    • 73449149044 scopus 로고    scopus 로고
    • Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data
    • Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., Bustamante, C. D., Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 2009, 5, e1000695.
    • (2009) PLoS Genet. , vol.5 , pp. e1000695
    • Gutenkunst, R.N.1    Hernandez, R.D.2    Williamson, S.H.3    Bustamante, C.D.4
  • 51
    • 84897411667 scopus 로고    scopus 로고
    • Generic software frameworks for GC-MS based metabolomics
    • IntechOpen, Viena .
    • Hoffmann, N., Stoye, J., Generic software frameworks for GC-MS based metabolomics. Metabolomics, IntechOpen, Viena 2012.
    • (2012) Metabolomics
    • Hoffmann, N.1    Stoye, J.2
  • 52
    • 84865321063 scopus 로고    scopus 로고
    • Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets
    • Hoffmann, N., Keck, M., Neuweger, H., Wilhelm, M. et al., Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinform. 2012, 13, 214.
    • (2012) BMC Bioinform. , vol.13 , pp. 214
    • Hoffmann, N.1    Keck, M.2    Neuweger, H.3    Wilhelm, M.4
  • 53
    • 84895511946 scopus 로고    scopus 로고
    • AHaH computing-from metastable switches to attractors to machine learning
    • Nugent, M. A., Molter, T. W., AHaH computing-from metastable switches to attractors to machine learning. PloS one 2014, 9, e85175.
    • (2014) PloS one , vol.9 , pp. e85175
    • Nugent, M.A.1    Molter, T.W.2
  • 54
    • 84882328986 scopus 로고    scopus 로고
    • WholeCellViz: data visualization for whole-cell models
    • Lee, R., Karr, J. R., Covert, M. W., WholeCellViz: data visualization for whole-cell models. BMC Bioinf. 2013, 14, 253.
    • (2013) BMC Bioinf. , vol.14 , pp. 253
    • Lee, R.1    Karr, J.R.2    Covert, M.W.3
  • 55
    • 84862753629 scopus 로고    scopus 로고
    • Relax with CouchDB-into the non-relational DBMS era of bioinformatics
    • Manyam, G., Payton, M. A., Roth, J. A., Abruzzo, L. V., Coombes, K. R., Relax with CouchDB-into the non-relational DBMS era of bioinformatics. Genomics 2012, 100, 1-7.
    • (2012) Genomics , vol.100 , pp. 1-7
    • Manyam, G.1    Payton, M.A.2    Roth, J.A.3    Abruzzo, L.V.4    Coombes, K.R.5
  • 56
    • 77953216762 scopus 로고    scopus 로고
    • A tour through the Visualization zoo
    • Heer, J., Bostock, M., Ogievetsky, V., A tour through the Visualization zoo. Commun. Acm. 2010, 53, 59-67.
    • (2010) Commun. Acm. , vol.53 , pp. 59-67
    • Heer, J.1    Bostock, M.2    Ogievetsky, V.3
  • 59
    • 54949155487 scopus 로고    scopus 로고
    • Rolling the dice: multidimensional visual exploration using scatterplot matrix navigation
    • Elmqvist, N., Dragicevic, P., Fekete, J. D., Rolling the dice: multidimensional visual exploration using scatterplot matrix navigation. IEEE Trans. Visual. Comp. Graph. 2008, 14, 1141-1148.
    • (2008) IEEE Trans. Visual. Comp. Graph. , vol.14 , pp. 1141-1148
    • Elmqvist, N.1    Dragicevic, P.2    Fekete, J.D.3
  • 60
    • 78149255579 scopus 로고    scopus 로고
    • The flowvizmenu and parallel scatterplot matrix: hybrid multidimensional visualizations for network exploration
    • Viau, C., McGuffin, M. J., Chiricota, Y., Jurisica, I., The flowvizmenu and parallel scatterplot matrix: hybrid multidimensional visualizations for network exploration. IEEE Trans. Visualization Comp. Graph. 2010, 16, 1100-1108.
    • (2010) IEEE Trans. Visualization Comp. Graph. , vol.16 , pp. 1100-1108
    • Viau, C.1    McGuffin, M.J.2    Chiricota, Y.3    Jurisica, I.4
  • 61
    • 0034568109 scopus 로고    scopus 로고
    • 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns
    • RESEARCH0003
    • Hastie, T., Tibshirani, R., Eisen, M. B., Alizadeh, A. et al., 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome Biol. 2000, 1, RESEARCH0003.
    • (2000) Genome Biol. , vol.1
    • Hastie, T.1    Tibshirani, R.2    Eisen, M.B.3    Alizadeh, A.4
  • 62
    • 58149330446 scopus 로고    scopus 로고
    • Breast cancer diagnosis from proteomic mass spectrometry data: a comparative evaluation
    • Article 15.
    • Hand, D. J., Breast cancer diagnosis from proteomic mass spectrometry data: a comparative evaluation. Stat. Appl. Genet. Mol. 2008, 7, Article 15.
    • (2008) Stat. Appl. Genet. Mol. , vol.7
    • Hand, D.J.1
  • 63
    • 0038281453 scopus 로고    scopus 로고
    • Observing and interpreting correlations in metabolomic networks
    • Steuer, R., Kurths, J., Fiehn, O., Weckwerth, W., Observing and interpreting correlations in metabolomic networks. Bioinformatics 2003, 19, 1019-1026.
    • (2003) Bioinformatics , vol.19 , pp. 1019-1026
    • Steuer, R.1    Kurths, J.2    Fiehn, O.3    Weckwerth, W.4
  • 64
    • 84867625594 scopus 로고    scopus 로고
    • Volcano plots in analyzing differential expressions with mRNA microarrays
    • Li, W., Volcano plots in analyzing differential expressions with mRNA microarrays. J. Bioinf. Comput. Biol. 2012, 10, 1231003.
    • (2012) J. Bioinf. Comput. Biol. , vol.10 , pp. 1231003
    • Li, W.1
  • 65
    • 76949097340 scopus 로고    scopus 로고
    • Quantitative proteomics reveals subset-specific viral recognition in dendritic cells
    • Luber, C. A., Cox, J., Lauterbach, H., Fancke, B. et al., Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity 2010, 32, 279-289.
    • (2010) Immunity , vol.32 , pp. 279-289
    • Luber, C.A.1    Cox, J.2    Lauterbach, H.3    Fancke, B.4
  • 66
    • 77952344256 scopus 로고    scopus 로고
    • Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions
    • Hubner, N. C., Bird, A. W., Cox, J., Splettstoesser, B. et al., Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions. J. Cell Biol. 2010, 189, 739-754.
    • (2010) J. Cell Biol. , vol.189 , pp. 739-754
    • Hubner, N.C.1    Bird, A.W.2    Cox, J.3    Splettstoesser, B.4
  • 68
    • 3142769033 scopus 로고    scopus 로고
    • The murine testicular transcriptome: characterizing gene expression in the testis during the progression of spermatogenesis
    • Shima, J. E., McLean, D. J., McCarrey, J. R., Griswold, M. D., The murine testicular transcriptome: characterizing gene expression in the testis during the progression of spermatogenesis. Biol. Reprod. 2004, 71, 319-330.
    • (2004) Biol. Reprod. , vol.71 , pp. 319-330
    • Shima, J.E.1    McLean, D.J.2    McCarrey, J.R.3    Griswold, M.D.4
  • 69
    • 33744830828 scopus 로고    scopus 로고
    • Matrices or node-link diagrams: which visual representation is better for visualising connectivity models
    • Keller, R., Eckert, C. M., Clarkson, P. J., Matrices or node-link diagrams: which visual representation is better for visualising connectivity models? Inf. Visual. 2006, 5, 62-76.
    • (2006) Inf. Visual. , vol.5 , pp. 62-76
    • Keller, R.1    Eckert, C.M.2    Clarkson, P.J.3
  • 70
    • 16244398384 scopus 로고    scopus 로고
    • A comparison of the readability of graphs using node-link and matrix-based representations
    • IEEE Computer Society, Washington, DC -.
    • Ghoniem, M., Fekete, J. D., Castagliola, P., A comparison of the readability of graphs using node-link and matrix-based representations. Proceedings of the IEEE Symposium on Information Visualization, IEEE Computer Society, Washington, DC 2004, pp. 17-24.
    • (2004) Proceedings of the IEEE Symposium on Information Visualization , pp. 17-24
    • Ghoniem, M.1    Fekete, J.D.2    Castagliola, P.3
  • 71
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabasi, A. L., Oltvai, Z. N., Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 2004, 5, 101-U115.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 101-U115
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 72
    • 33747832812 scopus 로고    scopus 로고
    • BiologicalNetworks: visualization and analysis tool for systems biology
    • Baitaluk, M., Sedova, M., Ray, A., Gupta, A., BiologicalNetworks: visualization and analysis tool for systems biology. Nucleic Acids Res. 2006, 34, W466-W471.
    • (2006) Nucleic Acids Res. , vol.34 , pp. W466-W471
    • Baitaluk, M.1    Sedova, M.2    Ray, A.3    Gupta, A.4
  • 73
    • 65449162644 scopus 로고    scopus 로고
    • A survey of visualization tools for biological network analysis
    • Pavlopoulos, G. A., Wegener, A. L., Schneider, R., A survey of visualization tools for biological network analysis. BioData Mining 2008, 1, 12.
    • (2008) BioData Mining , vol.1 , pp. 12
    • Pavlopoulos, G.A.1    Wegener, A.L.2    Schneider, R.3
  • 75
    • 84920070787 scopus 로고    scopus 로고
    • Making proteomics data accessible and reusable: current state of proteomics databases and repositories
    • Perez-Riverol, Y., Alpi, E., Wang, R., Hermjakob, H., Vizcaino, J. A., Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics 2015, 15, 930-950.
    • (2015) Proteomics , vol.15 , pp. 930-950
    • Perez-Riverol, Y.1    Alpi, E.2    Wang, R.3    Hermjakob, H.4    Vizcaino, J.A.5
  • 76
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks
    • Maere, S., Heymans, K., Kuiper, M., BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21, 3448-3449.
    • (2005) Bioinformatics , vol.21 , pp. 3448-3449
    • Maere, S.1    Heymans, K.2    Kuiper, M.3
  • 77
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader, G. D., Hogue, C. W., An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinf. 2003, 4, 2.
    • (2003) BMC Bioinf. , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 78
    • 78149262301 scopus 로고    scopus 로고
    • GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop
    • Montojo, J., Zuberi, K., Rodriguez, H., Kazi, F. et al., GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics 2010, 26, 2927-2928.
    • (2010) Bioinformatics , vol.26 , pp. 2927-2928
    • Montojo, J.1    Zuberi, K.2    Rodriguez, H.3    Kazi, F.4
  • 79
    • 79952052352 scopus 로고    scopus 로고
    • iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence
    • baq023
    • Turner, B., Razick, S., Turinsky, A. L., Vlasblom, J. et al., iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database: J. Biol. Databases Curation 2010, 2010, baq023.
    • (2010) Database: J. Biol. Databases Curation , vol.2010
    • Turner, B.1    Razick, S.2    Turinsky, A.L.3    Vlasblom, J.4
  • 80
    • 84894356263 scopus 로고    scopus 로고
    • PathGuide - model-based generation of guideline-compliant pathways for the use in different hospital information systems
    • Bockmann, B., Heiden, K., PathGuide - model-based generation of guideline-compliant pathways for the use in different hospital information systems. Studies Health Technol. Inf. 2013, 192, 1089.
    • (2013) Studies Health Technol. Inf. , vol.192 , pp. 1089
    • Bockmann, B.1    Heiden, K.2
  • 82
    • 84891795660 scopus 로고    scopus 로고
    • Saccharomyces genome database provides new regulation data
    • Costanzo, M. C., Engel, S. R., Wong, E. D., Lloyd, P. et al., Saccharomyces genome database provides new regulation data. Nucleic Acids Res. 2014, 42, D717-725.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D717-D725
    • Costanzo, M.C.1    Engel, S.R.2    Wong, E.D.3    Lloyd, P.4
  • 83
    • 85166916238 scopus 로고    scopus 로고
    • Gephi: an open source software for exploring and manipulating networks
    • Bastian, M., Heymann, S., Jacomy, M., Gephi: an open source software for exploring and manipulating networks. ICWSM 2009, 8, 361-362.
    • (2009) ICWSM , vol.8 , pp. 361-362
    • Bastian, M.1    Heymann, S.2    Jacomy, M.3
  • 84
    • 84904402854 scopus 로고    scopus 로고
    • Dyconet: a gephi plugin for community detection in dynamic complex networks
    • Kauffman, J., Kittas, A., Bennett, L., Tsoka, S., Dyconet: a gephi plugin for community detection in dynamic complex networks. PloS one 2014, 9, e101357.
    • (2014) PloS one , vol.9 , pp. e101357
    • Kauffman, J.1    Kittas, A.2    Bennett, L.3    Tsoka, S.4
  • 85
    • 84902603261 scopus 로고    scopus 로고
    • ForceAtlas2, a continuous graph layout algorithm for handy network visualization designed for the gephi software
    • Jacomy, M., Venturini, T., Heymann, S., Bastian, M., ForceAtlas2, a continuous graph layout algorithm for handy network visualization designed for the gephi software. PloS one 2014, 9, e98679.
    • (2014) PloS one , vol.9 , pp. e98679
    • Jacomy, M.1    Venturini, T.2    Heymann, S.3    Bastian, M.4
  • 87
    • 77956267975 scopus 로고    scopus 로고
    • A model-driven traceability framework for software product lines
    • Anquetil, N., Kulesza, U., Mitschke, R., Moreira, A. et al., A model-driven traceability framework for software product lines. Softw. Syst. Model 2010, 9, 427-451.
    • (2010) Softw. Syst. Model , vol.9 , pp. 427-451
    • Anquetil, N.1    Kulesza, U.2    Mitschke, R.3    Moreira, A.4
  • 90
    • 35448966196 scopus 로고    scopus 로고
    • Protege: a tool for managing and using terminology in radiology applications
    • Rubin, D. L., Noy, N. F., Musen, M. A., Protege: a tool for managing and using terminology in radiology applications. J. Digit. Imaging 2007, 20, 34-46.
    • (2007) J. Digit. Imaging , vol.20 , pp. 34-46
    • Rubin, D.L.1    Noy, N.F.2    Musen, M.A.3
  • 93
    • 0035042776 scopus 로고    scopus 로고
    • A literature network of human genes for high-throughput analysis of gene expression
    • Jenssen, T. K., Laegreid, A., Komorowski, J., Hovig, E., A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet. 2001, 28, 21-28.
    • (2001) Nat. Genet. , vol.28 , pp. 21-28
    • Jenssen, T.K.1    Laegreid, A.2    Komorowski, J.3    Hovig, E.4
  • 94
    • 0035228039 scopus 로고    scopus 로고
    • PIES, a protein interaction extraction system
    • Hawaii
    • Wong, L., PIES, a protein interaction extraction system. Pacific Symposium on Biocomputing, Hawaii 2001, 520-531.
    • (2001) Pacific Symposium on Biocomputing , pp. 520-531
    • Wong, L.1
  • 96
    • 84904801714 scopus 로고    scopus 로고
    • NetworkAnalyst - integrative approaches for protein-protein interaction network analysis and visual exploration
    • Xia, J., Benner, M. J., Hancock, R. E., NetworkAnalyst - integrative approaches for protein-protein interaction network analysis and visual exploration. Nucleic Acids Res. 2014, 42, W167-174.
    • (2014) Nucleic Acids Res. , vol.42 , pp. W167-W174
    • Xia, J.1    Benner, M.J.2    Hancock, R.E.3
  • 97
    • 84891817932 scopus 로고    scopus 로고
    • NeXO Web: the NeXO ontology database and visualization platform
    • Dutkowski, J., Ono, K., Kramer, M., Yu, M. et al., NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Res. 2014, 42, D1269-1274.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D1269-D1274
    • Dutkowski, J.1    Ono, K.2    Kramer, M.3    Yu, M.4
  • 98
    • 84872417708 scopus 로고    scopus 로고
    • A knowledge-based decision support system in bioinformatics: an application to protein complex extraction
    • Fiannaca, A., La Rosa, M., Urso, A., Rizzo, R., Gaglio, S., A knowledge-based decision support system in bioinformatics: an application to protein complex extraction. BMC Bioinf. 2013, 14(Suppl 1), S5.
    • (2013) BMC Bioinf. , vol.14 , pp. S5
    • Fiannaca, A.1    La Rosa, M.2    Urso, A.3    Rizzo, R.4    Gaglio, S.5
  • 100
    • 79954524892 scopus 로고    scopus 로고
    • GBOOST: a GPU-based tool for detecting gene-gene interactions in genome-wide case control studies
    • Yung, L. S., Yang, C., Wan, X., Yu, W., GBOOST: a GPU-based tool for detecting gene-gene interactions in genome-wide case control studies. Bioinformatics 2011, 27, 1309-1310.
    • (2011) Bioinformatics , vol.27 , pp. 1309-1310
    • Yung, L.S.1    Yang, C.2    Wan, X.3    Yu, W.4
  • 101
    • 74549204784 scopus 로고    scopus 로고
    • Graphstream: a tool for bridging the gap between complex systems and dynamic graphs
    • Preprint . arXiv:0803.2093.
    • Pigné, Y., Dutot, A., Guinand, F., Olivier, D., Graphstream: a tool for bridging the gap between complex systems and dynamic graphs. Preprint 2008. arXiv:0803.2093.
    • (2008)
    • Pigné, Y.1    Dutot, A.2    Guinand, F.3    Olivier, D.4
  • 103
    • 84858999278 scopus 로고    scopus 로고
    • Nodetrix: Hybrid representation for analyzing social networks
    • Preprint arXiv:0705.0599.
    • Henry, N., Fekete, J.-D., Mcguffin, M., Nodetrix: Hybrid representation for analyzing social networks. Preprint 2007 arXiv:0705.0599.
    • (2007)
    • Henry, N.1    Fekete, J.-D.2    Mcguffin, M.3
  • 104
    • 84860916660 scopus 로고    scopus 로고
    • Hive plots-rational approach to visualizing networks
    • Krzywinski, M., Birol, I., Jones, S. J., Marra, M. A., Hive plots-rational approach to visualizing networks. Brief. Bioinf. 2012, 13, 627-644.
    • (2012) Brief. Bioinf. , vol.13 , pp. 627-644
    • Krzywinski, M.1    Birol, I.2    Jones, S.J.3    Marra, M.A.4
  • 107
    • 35948936372 scopus 로고    scopus 로고
    • Visualizing changes of hierarchical data using treemaps
    • Tu, Y., Shen, H. W., Visualizing changes of hierarchical data using treemaps. IEEE Trans. Visual. Comput. Graph. 2007, 13, 1286-1293.
    • (2007) IEEE Trans. Visual. Comput. Graph. , vol.13 , pp. 1286-1293
    • Tu, Y.1    Shen, H.W.2
  • 108
    • 84865083935 scopus 로고    scopus 로고
    • Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython
    • Talevich, E., Invergo, B. M., Cock, P. J., Chapman, B. A., Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics 2012, 13, 209.
    • (2012) BMC Bioinformatics , vol.13 , pp. 209
    • Talevich, E.1    Invergo, B.M.2    Cock, P.J.3    Chapman, B.A.4
  • 113
    • 70349198953 scopus 로고    scopus 로고
    • Trelgol Publishing, Spanish Fork, UT .
    • Oliphant, T. E., A Guide to NumPy, Trelgol Publishing, Spanish Fork, UT 2006.
    • (2006) A Guide to NumPy
    • Oliphant, T.E.1
  • 114
    • 23744500479 scopus 로고    scopus 로고
    • SciPy: open source scientific tools for Python
    • Jones, E., Oliphant, T., Peterson, P., SciPy: open source scientific tools for Python. http://www.scipy.org/ 2001.
    • (2001)
    • Jones, E.1    Oliphant, T.2    Peterson, P.3
  • 117
    • 84903742389 scopus 로고    scopus 로고
    • OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals
    • Douzery, E. J., Scornavacca, C., Romiguier, J., Belkhir, K. et al., OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals. Mol. Biol. Evol. 2014, 31, 1923-1928.
    • (2014) Mol. Biol. Evol. , vol.31 , pp. 1923-1928
    • Douzery, E.J.1    Scornavacca, C.2    Romiguier, J.3    Belkhir, K.4
  • 119
    • 0029178750 scopus 로고
    • A focus+ context technique based on hyperbolic geometry for visualizing large hierarchies
    • ACM Press/Addison-Wesley Publishing Co., New York, NY -.
    • Lamping, J., Rao, R., Pirolli, P., A focus+ context technique based on hyperbolic geometry for visualizing large hierarchies. Proceedings of the SIGCHI conference on Human factors in computing systems, ACM Press/Addison-Wesley Publishing Co., New York, NY 1995, pp. 401-408.
    • (1995) Proceedings of the SIGCHI conference on Human factors in computing systems , pp. 401-408
    • Lamping, J.1    Rao, R.2    Pirolli, P.3
  • 121
    • 84885034028 scopus 로고    scopus 로고
    • Data visualization in environmental proteomics
    • Mehlan, H., Schmidt, F., Weiss, S., Schuler, J. et al., Data visualization in environmental proteomics. Proteomics 2013, 13, 2805-2821.
    • (2013) Proteomics , vol.13 , pp. 2805-2821
    • Mehlan, H.1    Schmidt, F.2    Weiss, S.3    Schuler, J.4
  • 122
    • 84866983714 scopus 로고    scopus 로고
    • More than meets the eye
    • Rinaldi, A., More than meets the eye. EMBO Rep. 2012, 13, 895-899.
    • (2012) EMBO Rep. , vol.13 , pp. 895-899
    • Rinaldi, A.1


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