{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T07:38:23Z","timestamp":1762673903057},"reference-count":125,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9]]},"DOI":"10.1093\/bib\/bbt021","type":"journal-article","created":{"date-parts":[[2013,4,13]],"date-time":"2013-04-13T20:21:00Z","timestamp":1365884460000},"page":"771-782","source":"Crossref","is-referenced-by-count":32,"title":["Visualizing time-related data in biology, a review"],"prefix":"10.1093","volume":"15","author":[{"given":"Maria","family":"Secrier","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Reinhard","family":"Schneider","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,4,12]]},"reference":[{"issue":"4","key":"key\n\t\t\t\t20170523191953_bbt021-B1","doi-asserted-by":"crossref","first-page":"759","DOI":"10.4067\/S0716-97602004000500005","article-title":"Time in physics and biology","volume":"37","author":"Gunther","year":"2004","journal-title":"Biol Res"},{"issue":"1","key":"key\n\t\t\t\t20170523191953_bbt021-B2","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1093\/nar\/gkg113","article-title":"DSMM: a database of simulated molecular motions","volume":"31","author":"Finocchiaro","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B3","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/msb4100179","article-title":"Towards a theory of biological robustness","volume":"3","author":"Kitano","year":"2007","journal-title":"Mol Syst Biol"},{"issue":"4","key":"key\n\t\t\t\t20170523191953_bbt021-B4","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1007\/s001639870001","article-title":"Axiomatic design theory for systems","volume":"10","author":"Suh","year":"1998","journal-title":"Res Eng Des"},{"issue":"28","key":"key\n\t\t\t\t20170523191953_bbt021-B5","doi-asserted-by":"crossref","first-page":"12511","DOI":"10.1073\/pnas.1006283107","article-title":"Reverse engineering dynamic temporal models of biological processes and their relationships","volume":"107","author":"Ramakrishnan","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B6","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1126\/science.1199784","article-title":"Proteome half-life dynamics in living human cells","volume":"331","author":"Eden","year":"2011","journal-title":"Science"},{"issue":"6","key":"key\n\t\t\t\t20170523191953_bbt021-B7","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1038\/ng.821","article-title":"General properties of transcriptional time series in Escherichia coli","volume":"43","author":"So","year":"2011","journal-title":"Nat Genet"},{"issue":"1","key":"key\n\t\t\t\t20170523191953_bbt021-B8","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bib\/bbp057","article-title":"Toward the dynamic interactome: it's about time","volume":"11","author":"Przytycka","year":"2010","journal-title":"Brief Bioinform"},{"issue":"1","key":"key\n\t\t\t\t20170523191953_bbt021-B9","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.jmb.2010.02.020","article-title":"The subunit interfaces of weakly associated homodimeric proteins","volume":"398","author":"Dey","year":"2010","journal-title":"J Mol Biol"},{"issue":"10","key":"key\n\t\t\t\t20170523191953_bbt021-B10","doi-asserted-by":"crossref","first-page":"1233","DOI":"10.1016\/j.str.2010.08.007","article-title":"Transient protein-protein interactions: structural, functional, and network properties","volume":"18","author":"Perkins","year":"2010","journal-title":"Structure"},{"issue":"19","key":"key\n\t\t\t\t20170523191953_bbt021-B11","doi-asserted-by":"crossref","first-page":"5390","DOI":"10.1111\/j.1742-4658.2009.07251.x","article-title":"Dynamic interactions of proteins in complex networks: a more structured view","volume":"276","author":"Stein","year":"2009","journal-title":"FEBS J"},{"issue":"6","key":"key\n\t\t\t\t20170523191953_bbt021-B12","doi-asserted-by":"crossref","first-page":"1583","DOI":"10.1046\/j.1432-1327.2000.01197.x","article-title":"Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades","volume":"267","author":"Kholodenko","year":"2000","journal-title":"Eur J Biochem"},{"issue":"2","key":"key\n\t\t\t\t20170523191953_bbt021-B13","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1371\/journal.pcbi.0030015","article-title":"Robustness can evolve gradually in complex regulatory gene networks with varying topology","volume":"3","author":"Ciliberti","year":"2007","journal-title":"PLOS Comput Biol"},{"issue":"7065","key":"key\n\t\t\t\t20170523191953_bbt021-B14","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/nature04114","article-title":"A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression","volume":"438","author":"Rifkin","year":"2005","journal-title":"Nature"},{"issue":"4","key":"key\n\t\t\t\t20170523191953_bbt021-B15","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/S0169-5347(02)02497-7","article-title":"Gene flow and the limits to natural selection","volume":"17","author":"Lenormand","year":"2002","journal-title":"Trends Ecol Evol"},{"issue":"3\u20134","key":"key\n\t\t\t\t20170523191953_bbt021-B16","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1016\/j.physa.2004.07.011","article-title":"Robustness and network evolution - an entropic principle","volume":"346","author":"Demetrius","year":"2005","journal-title":"Physica A"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B17","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/1741-7007-5-29","article-title":"Evolution favors protein mutational robustness in sufficiently large populations","volume":"5","author":"Bloom","year":"2007","journal-title":"BMC Biol"},{"issue":"4","key":"key\n\t\t\t\t20170523191953_bbt021-B18","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/j.copbio.2008.06.008","article-title":"Sloppiness, robustness, and evolvability in systems biology","volume":"19","author":"Daniels","year":"2008","journal-title":"Curr Opin Biotech"},{"issue":"8","key":"key\n\t\t\t\t20170523191953_bbt021-B19","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1038\/nrm2446","article-title":"From the first protein structures to our current knowledge of protein folding: delights and scepticisms","volume":"9","author":"Fersht","year":"2008","journal-title":"Nat Rev Mol Cell Bio"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B20","author":"Strogatz"},{"issue":"3","key":"key\n\t\t\t\t20170523191953_bbt021-B21","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1038\/nmeth.1422","article-title":"Visualizing genomes: techniques and challenges","volume":"7","author":"Nielsen","year":"2010","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B22","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1007\/11784203_59","article-title":"Spatio-temporal visualization of battlefield entities and events","volume":"4035","author":"Fong","year":"2006","journal-title":"Lect Notes Comput Sci"},{"issue":"3","key":"key\n\t\t\t\t20170523191953_bbt021-B23","doi-asserted-by":"crossref","first-page":"627","DOI":"10.2307\/2409633","article-title":"Using phylogenetic trees to study speciation and extinction","volume":"46","author":"Hey","year":"1992","journal-title":"Evolution"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B24","author":"Alon"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B25","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1756-0381-1-12","article-title":"A survey of visualization tools for biological network analysis","volume":"1","author":"Pavlopoulos","year":"2008","journal-title":"BioData Min"},{"issue":"11","key":"key\n\t\t\t\t20170523191953_bbt021-B26","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1038\/nrm2787","article-title":"Evolution of biomolecular networks: lessons from metabolic and protein interactions","volume":"10","author":"Yamada","year":"2009","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"8","key":"key\n\t\t\t\t20170523191953_bbt021-B27","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nrg3244","article-title":"Study designs studying and modelling dynamic biological processes using time-series gene expression data","volume":"13","author":"Bar-Joseph","year":"2012","journal-title":"Nat Rev Genetics"},{"issue":"6","key":"key\n\t\t\t\t20170523191953_bbt021-B28","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1177\/074873099129000948","article-title":"Limit cycle models for circadian rhythms based on transcriptional regulation in Drosophila and Neurospora","volume":"14","author":"Leloup","year":"1999","journal-title":"J Biol Rhythms"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B29","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000422","article-title":"Predicting the distribution of spiral waves from cell properties in a developmental-path model of Dictyostelium pattern formation","volume":"5","author":"Geberth","year":"2009","journal-title":"PLOS Comput. Biol."},{"issue":"1","key":"key\n\t\t\t\t20170523191953_bbt021-B30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1756-0381-3-1","article-title":"A reference guide for tree analysis and visualization","volume":"3","author":"Pavlopoulos","year":"2010","journal-title":"BioData Min"},{"issue":"8","key":"key\n\t\t\t\t20170523191953_bbt021-B31","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.1093\/bioinformatics\/btm057","article-title":"Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation","volume":"23","author":"Barsky","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B32","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1752-0509-5-14","article-title":"Parameter estimation in systems biology models using spline approximation","volume":"5","author":"Zhan","year":"2011","journal-title":"BMC Syst Biol"},{"issue":"5\u20136","key":"key\n\t\t\t\t20170523191953_bbt021-B33","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.physrep.2006.11.001","article-title":"Recurrence plots for the analysis of complex systems","volume":"438","author":"Marwan","year":"2007","journal-title":"Phys Rep"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B34","doi-asserted-by":"crossref","article-title":"Visualization methods for time-dependent data - an overview","author":"M\u00fcller","DOI":"10.1109\/WSC.2003.1261490"},{"issue":"3\u20134","key":"key\n\t\t\t\t20170523191953_bbt021-B35","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1057\/PALGRAVE.IVS.9500188","article-title":"A temporal focus plus context visualization model for handling valid-time spatial information","volume":"7","author":"Carvalho","year":"2008","journal-title":"Inform Visual"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B36","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/0-306-47815-3_5","article-title":"Singular value decomposition and principal component analysis","volume-title":"In: A Practical Approach to Microarray Data Analysis","author":"Wall","year":"2003"},{"issue":"6","key":"key\n\t\t\t\t20170523191953_bbt021-B37","doi-asserted-by":"crossref","first-page":"1748","DOI":"10.1021\/ci034138n","article-title":"Mining biological data using self-organizing map","volume":"43","author":"Yang","year":"2003","journal-title":"J Chem Inf Comput Sci"},{"issue":"1","key":"key\n\t\t\t\t20170523191953_bbt021-B38","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/S1350-4533(01)00112-6","article-title":"Recurrence quantification analysis as a tool for nonlinear exploration of nonstationary cardiac signals","volume":"24","author":"Zbilut","year":"2002","journal-title":"Med Eng Phys"},{"issue":"1","key":"key\n\t\t\t\t20170523191953_bbt021-B39","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/S0165-0270(98)00080-6","article-title":"The Fourier analysis of biological transients","volume":"83","author":"Harris","year":"1998","journal-title":"J Neurosci Meth"},{"issue":"4","key":"key\n\t\t\t\t20170523191953_bbt021-B40","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1109\/5.488704","article-title":"A review of wavelets in biomedical applications","volume":"84","author":"Unser","year":"1996","journal-title":"Proc IEEE"},{"issue":"6","key":"key\n\t\t\t\t20170523191953_bbt021-B41","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1093\/bioinformatics\/17.6.495","article-title":"Aligning gene expression time series with time warping algorithms","volume":"17","author":"Aach","year":"2001","journal-title":"Bioinformatics"},{"issue":"5","key":"key\n\t\t\t\t20170523191953_bbt021-B42","doi-asserted-by":"crossref","first-page":"R50","DOI":"10.1186\/gb-2011-12-5-r50","article-title":"Moving pictures of the human microbiome","volume":"12","author":"Caporaso","year":"2011","journal-title":"Genome Biol"},{"issue":"11","key":"key\n\t\t\t\t20170523191953_bbt021-B43","doi-asserted-by":"crossref","first-page":"2878","DOI":"10.1111\/j.1742-4658.2007.05822.x","article-title":"Gene expression waves. Cell cycle independent collective dynamics in cultured cells","volume":"274","author":"Tsuchiya","year":"2007","journal-title":"FEBS J"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B44","doi-asserted-by":"crossref","first-page":"2372","DOI":"10.1111\/j.1742-4658.2008.06399.x","article-title":"Collective behavior in gene regulation: the cell is an oscillator, the cell cycle a developmental process","volume":"275","author":"Klevecz","year":"2008","journal-title":"FEBS J"},{"issue":"4 Pt 2","key":"key\n\t\t\t\t20170523191953_bbt021-B45","first-page":"H1455","article-title":"A nonlinear explanation of aging-induced changes in heartbeat dynamics","volume":"275","author":"Giuliani","year":"1998","journal-title":"Am J Physiol"},{"issue":"9","key":"key\n\t\t\t\t20170523191953_bbt021-B46","doi-asserted-by":"crossref","first-page":"6163","DOI":"10.1073\/pnas.092576199","article-title":"Reverse engineering gene networks using singular value decomposition and robust regression","volume":"99","author":"Yeung","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B47","doi-asserted-by":"crossref","first-page":"10101","DOI":"10.1073\/pnas.97.18.10101","article-title":"Singular value decomposition for genome-wide expression data processing and modeling","volume":"97","author":"Alter","year":"2000","journal-title":"Proc Natl Acad Sci USA"},{"issue":"5","key":"key\n\t\t\t\t20170523191953_bbt021-B48","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1021\/cr0101499","article-title":"Nonlinear signal analysis methods in the elucidation of protein sequence-structure relationships","volume":"102","author":"Giuliani","year":"2002","journal-title":"Chem Rev"},{"issue":"5560","key":"key\n\t\t\t\t20170523191953_bbt021-B49","doi-asserted-by":"crossref","first-page":"1662","DOI":"10.1126\/science.1069492","article-title":"Systems biology: a brief overview","volume":"295","author":"Kitano","year":"2002","journal-title":"Science"},{"issue":"11","key":"key\n\t\t\t\t20170523191953_bbt021-B50","doi-asserted-by":"crossref","first-page":"1399","DOI":"10.1016\/j.str.2010.07.013","article-title":"MoDEL (molecular dynamics extended library): a database of atomistic molecular dynamics trajectories","volume":"18","author":"Meyer","year":"2010","journal-title":"Structure"},{"issue":"1","key":"key\n\t\t\t\t20170523191953_bbt021-B51","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res"},{"issue":"18","key":"key\n\t\t\t\t20170523191953_bbt021-B52","doi-asserted-by":"crossref","first-page":"2112","DOI":"10.1093\/bioinformatics\/btn368","article-title":"VistaClara: an expression browser plug-in for Cytoscape","volume":"24","author":"Kincaid","year":"2008","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B53","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1186\/1752-0509-4-164","article-title":"ExprEssence\u2013revealing the essence of differential experimental data in the context of an interaction\/regulation net-work","volume":"4","author":"Warsow","year":"2010","journal-title":"BMC Syst Biol"},{"issue":"22","key":"key\n\t\t\t\t20170523191953_bbt021-B54","doi-asserted-by":"crossref","first-page":"2922","DOI":"10.1093\/bioinformatics\/btq535","article-title":"SpotXplore: a cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks","volume":"26","author":"Westenberg","year":"2010","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"key\n\t\t\t\t20170523191953_bbt021-B55","first-page":"D854","article-title":"Cyclebase.org\u2013a comprehensive multi-organism online database of cell-cycle experiments","volume":"36","author":"Gauthier","year":"2008","journal-title":"Nucleic Acids Res"},{"issue":"16","key":"key\n\t\t\t\t20170523191953_bbt021-B56","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1002\/jcc.20290","article-title":"The Amber biomolecular simulation programs","volume":"26","author":"Case","year":"2005","journal-title":"J Comput Chem"},{"issue":"16","key":"key\n\t\t\t\t20170523191953_bbt021-B57","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1002\/jcc.20291","article-title":"Gromacs: fast, flexible, and free","volume":"26","author":"Van Der Spoel","year":"2005","journal-title":"J Comput Chem"},{"issue":"10","key":"key\n\t\t\t\t20170523191953_bbt021-B58","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1002\/jcc.21287","article-title":"CHARMM: the biomolecular simulation program","volume":"30","author":"Brooks","year":"2009","journal-title":"J Comput Chem"},{"issue":"16","key":"key\n\t\t\t\t20170523191953_bbt021-B59","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1002\/jcc.20289","article-title":"Scalable molecular dynamics with NAMD","volume":"26","author":"Phillips","year":"2005","journal-title":"J Comput Chem"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B60"},{"issue":"1","key":"key\n\t\t\t\t20170523191953_bbt021-B61","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J Mol Graph Model"},{"issue":"13","key":"key\n\t\t\t\t20170523191953_bbt021-B62","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2013a visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J Comput Chem"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B63"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B64","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/1471-2105-6-21","article-title":"The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications","volume":"6","author":"Moreland","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B65","volume-title":"Suite 2012: MacroModel [computer program]. Version 9.9","author":"Schr\u00f6dinger","year":"2012"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B66"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B67","first-page":"U1371","article-title":"PyMOL: a communications tool for computational models","volume":"230","author":"DeLano","year":"2005","journal-title":"Abstr Pap Am Chem Soc"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B68","article-title":"PyMOL molecular viewer: updates and refinements","volume":"238","author":"DeLano","year":"2009","journal-title":"Abstr Pap Am Chem Soc"},{"issue":"4","key":"key\n\t\t\t\t20170523191953_bbt021-B69","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1002\/bmb.2006.494034042644","article-title":"Biomolecules in the computer: Jmol to the rescue","volume":"34","author":"Herraez","year":"2006","journal-title":"Biochem Mol Biol Educ"},{"issue":"3","key":"key\n\t\t\t\t20170523191953_bbt021-B70","doi-asserted-by":"crossref","first-page":"S42","DOI":"10.1038\/nmeth.1427","article-title":"Visualization of macromolecular structures","volume":"7","author":"O'Donoghue","year":"2010","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B71","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/1741-7007-9-71","article-title":"Molecular dynamics simulations and drug discovery","volume":"9","author":"Durrant","year":"2011","journal-title":"BMC Biol"},{"issue":"5235","key":"key\n\t\t\t\t20170523191953_bbt021-B72","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1126\/science.270.5235.467","article-title":"Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray","volume":"270","author":"Schena","year":"1995","journal-title":"Science"},{"issue":"24","key":"key\n\t\t\t\t20170523191953_bbt021-B73","doi-asserted-by":"crossref","first-page":"13057","DOI":"10.1073\/pnas.94.24.13057","article-title":"Yeast microarrays for genome wide parallel genetic and gene expression analysis","volume":"94","author":"Lashkari","year":"1997","journal-title":"Proc Natl Acad Sci USA"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B74","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1186\/1471-2164-7-278","article-title":"Converting a breast cancer microarray signature into a high-throughput diagnostic test","volume":"7","author":"Glas","year":"2006","journal-title":"BMC Genomics"},{"issue":"8","key":"key\n\t\t\t\t20170523191953_bbt021-B75","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1093\/bioinformatics\/bts084","article-title":"RNA-seq atlas\u2013a reference database for gene expression profiling in normal tissue by next-generation sequencing","volume":"28","author":"Krupp","year":"2012","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B76","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-7-191","article-title":"STEM: a tool for the analysis of short time series gene expression data","volume":"7","author":"Ernst","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B77"},{"issue":"1","key":"key\n\t\t\t\t20170523191953_bbt021-B78","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1093\/bioinformatics\/btp628","article-title":"GATE: software for the analysis and visualization of high-dimensional time series expression data","volume":"26","author":"MacArthur","year":"2010","journal-title":"Bioinformatics"},{"issue":"6012","key":"key\n\t\t\t\t20170523191953_bbt021-B79","doi-asserted-by":"crossref","first-page":"1787","DOI":"10.1126\/science.1198374","article-title":"Identification of functional elements and regulatory circuits by Drosophila modENCODE","volume":"330","author":"Roy","year":"2010","journal-title":"Science"},{"issue":"7345","key":"key\n\t\t\t\t20170523191953_bbt021-B80","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nature09906","article-title":"Mapping and analysis of chromatin state dynamics in nine human cell types","volume":"473","author":"Ernst","year":"2011","journal-title":"Nature"},{"issue":"3","key":"key\n\t\t\t\t20170523191953_bbt021-B81","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1038\/nrg1804","article-title":"Functional mapping - how to map and study the genetic architecture of dynamic complex traits","volume":"7","author":"Wu","year":"2006","journal-title":"Nat Rev Genet"},{"issue":"6","key":"key\n\t\t\t\t20170523191953_bbt021-B82","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1007\/s00439-011-0960-6","article-title":"A dynamic model for genome-wide association studies","volume":"129","author":"Das","year":"2011","journal-title":"Hum Genet"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B83","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1093\/bioinformatics\/btq688","article-title":"The Bayesian lasso for genome-wide association studies","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"issue":"8","key":"key\n\t\t\t\t20170523191953_bbt021-B84","doi-asserted-by":"crossref","first-page":"1254","DOI":"10.1109\/JPROC.2008.925458","article-title":"CellDesigner 3.5: a versatile modeling tool for biochemical networks","volume":"96","author":"Funahashi","year":"2008","journal-title":"Proc IEEE"},{"issue":"24","key":"key\n\t\t\t\t20170523191953_bbt021-B85","doi-asserted-by":"crossref","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","article-title":"Copasi\u2013a complex pathway simulator","volume":"22","author":"Hoops","year":"2006","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B86","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1007\/978-1-59745-525-1_2","article-title":"Computational modeling of biochemical networks using Copasi","volume":"500","author":"Mendes","year":"2009","journal-title":"Methods Mol Biol"},{"issue":"2","key":"key\n\t\t\t\t20170523191953_bbt021-B87","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1142\/S0219720005001144","article-title":"Dizzy: stochastic simulation of large-scale genetic regulatory networks (supplementary material)","volume":"3","author":"Ramsey","year":"2005","journal-title":"J Bioinform Comput Biol"},{"issue":"11","key":"key\n\t\t\t\t20170523191953_bbt021-B88","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B89","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1186\/1471-2105-7-109","article-title":"VANTED: a system for advanced data analysis and visualization in the context of biological networks","volume":"7","author":"Junker","year":"2006","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"key\n\t\t\t\t20170523191953_bbt021-B90","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1093\/bib\/bbn020","article-title":"VisANT: an integrative framework for networks in systems biology","volume":"9","author":"Hu","year":"2008","journal-title":"Brief Bioinform"},{"issue":"Web Server issue","key":"key\n\t\t\t\t20170523191953_bbt021-B91","doi-asserted-by":"crossref","first-page":"W115","DOI":"10.1093\/nar\/gkp406","article-title":"VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology","volume":"37","author":"Hu","year":"2009","journal-title":"Nucleic Acids Res"},{"issue":"13","key":"key\n\t\t\t\t20170523191953_bbt021-B92","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1093\/bioinformatics\/btr273","article-title":"TVNviewer: an interactive visualization tool for exploring networks that change over time or space","volume":"27","author":"Curtis","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B93","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/978-1-61779-292-2_21","article-title":"BioTapestry: a tool to visualize the dynamic properties of gene regulatory networks","volume":"786","author":"Longabaugh","year":"2012","journal-title":"Methods Mol Biol"},{"issue":"6","key":"key\n\t\t\t\t20170523191953_bbt021-B94","doi-asserted-by":"crossref","first-page":"e21318","DOI":"10.1371\/journal.pone.0021318","article-title":"Intuitive visualization and analysis of multi-omics data and application to Escherichia coli carbon metabolism","volume":"6","author":"Enjalbert","year":"2011","journal-title":"PLoS One"},{"issue":"10","key":"key\n\t\t\t\t20170523191953_bbt021-B95","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1038\/nprot.2009.177","article-title":"Network visualization and analysis of gene expression data using BioLayout Express(3D)","volume":"4","author":"Theocharidis","year":"2009","journal-title":"Nat Protoc"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B96","doi-asserted-by":"crossref","first-page":"S26","DOI":"10.1038\/nmeth.1431","article-title":"Visualization of image data from cells to organisms","volume":"7","author":"Walter","year":"2010","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B97","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1186\/1471-2105-12-126","article-title":"STSE: spatio-temporal simulation environment dedicated to biology","volume":"12","author":"Stoma","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B98"},{"issue":"2","key":"key\n\t\t\t\t20170523191953_bbt021-B99","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1187\/cbe.04-07-0047","article-title":"Molecular and cellular biology animations: development and impact on student learning","volume":"4","author":"McClean","year":"2005","journal-title":"Cell Biol Educ"},{"issue":"2","key":"key\n\t\t\t\t20170523191953_bbt021-B100","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1016\/j.cell.2012.05.044","article-title":"A whole-cell computational model predicts phenotype from genotype","volume":"150","author":"Karr","year":"2012","journal-title":"Cell"},{"issue":"1","key":"key\n\t\t\t\t20170523191953_bbt021-B101","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1093\/bioinformatics\/15.1.72","article-title":"E-Cell: Software environment for whole-cell simulation","volume":"15","author":"Tomita","year":"1999","journal-title":"Bioinformatics"},{"issue":"10","key":"key\n\t\t\t\t20170523191953_bbt021-B102","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/S0167-7799(01)01740-1","article-title":"The Virtual Cell: a software environment for computational cell biology","volume":"19","author":"Loew","year":"2001","journal-title":"Trends Biotechnol"},{"issue":"9","key":"key\n\t\t\t\t20170523191953_bbt021-B103","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1093\/bioinformatics\/btp125","article-title":"Illoura: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data","volume":"25","author":"McComb","year":"2009","journal-title":"Bioinformatics"},{"issue":"51","key":"key\n\t\t\t\t20170523191953_bbt021-B104","doi-asserted-by":"crossref","first-page":"20374","DOI":"10.1073\/pnas.0808725105","article-title":"Four-dimensional realistic modeling of pancreatic organogenesis","volume":"105","author":"Setty","year":"2008","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2\u20133","key":"key\n\t\t\t\t20170523191953_bbt021-B105","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1016\/j.pbiomolbio.2004.02.004","article-title":"Towards whole-organ modelling of tumour growth","volume":"85","author":"Alarcon","year":"2004","journal-title":"Prog Biophys Mol Biol"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B106","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1186\/1752-0509-2-104","article-title":"Arena3D: visualization of biological networks in 3D","volume":"2","author":"Pavlopoulos","year":"2008","journal-title":"BMC Syst Biol"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B107","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/1471-2105-13-45","article-title":"Arena3D: visualizing time-driven phenotypic differences in biological systems","volume":"13","author":"Secrier","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B108","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-3516-1","volume-title":"Mathematical Models in Population Biology and Epidemiology","author":"Brauer","year":"2001","edition":"1st edn"},{"issue":"20","key":"key\n\t\t\t\t20170523191953_bbt021-B109","doi-asserted-by":"crossref","first-page":"2910","DOI":"10.1093\/bioinformatics\/btr481","article-title":"SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics","volume":"27","author":"Bielejec","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B110","first-page":"Unit 2.3","article-title":"Multiple sequence alignment using ClustalW and ClustalX","volume":"Chapter 2","author":"Thompson","year":"2002","journal-title":"Curr Protoc Bioinformatics"},{"issue":"3","key":"key\n\t\t\t\t20170523191953_bbt021-B111","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1093\/bioinformatics\/btg430","article-title":"The Jalview java alignment editor","volume":"20","author":"Clamp","year":"2004","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B112","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi0602s01","article-title":"Visualizing phylogenetic trees using TreeView","author":"Page","year":"2002","journal-title":"Curr Protoc Bioinformatics"},{"issue":"10","key":"key\n\t\t\t\t20170523191953_bbt021-B113","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods","volume":"28","author":"Tamura","year":"2011","journal-title":"Mol Biol Evol"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B114","doi-asserted-by":"crossref","first-page":"S16","DOI":"10.1038\/nmeth.1434","article-title":"Visualization of multiple alignments, phylogenies and gene family evolution","volume":"7","author":"Procter","year":"2010","journal-title":"Nat Methods"},{"issue":"9","key":"key\n\t\t\t\t20170523191953_bbt021-B115","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res"},{"issue":"Web Server issue","key":"key\n\t\t\t\t20170523191953_bbt021-B116","doi-asserted-by":"crossref","first-page":"W273","DOI":"10.1093\/nar\/gkh458","article-title":"Vista: computational tools for comparative genomics","volume":"32","author":"Frazer","year":"2004","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"key\n\t\t\t\t20170523191953_bbt021-B117","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1109\/TVCG.2009.167","article-title":"MizBee: a multiscale synteny browser","volume":"15","author":"Meyer","year":"2009","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"1","key":"key\n\t\t\t\t20170523191953_bbt021-B118","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/bioinformatics\/btl529","article-title":"Interactive Tree of Life (iTOL): an online tool for phylogenetic tree display and annotation","volume":"23","author":"Letunic","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B119","doi-asserted-by":"crossref","first-page":"61","DOI":"10.4137\/EBO.S8814","article-title":"EvoluCode: evolutionary barcodes as a unifying framework for multilevel evolutionary data","volume":"8","author":"Linard","year":"2012","journal-title":"Evol Bioinform Online"},{"issue":"1512","key":"key\n\t\t\t\t20170523191953_bbt021-B120","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1098\/rspb.2002.2218","article-title":"Biological identifications through DNA barcodes","volume":"270","author":"Hebert","year":"2003","journal-title":"Proc Biol Sci"},{"issue":"7","key":"key\n\t\t\t\t20170523191953_bbt021-B121","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0040425","article-title":"The cervical microbiome over 7 years and a comparison of methodologies for its characterization","volume":"7","author":"Smith","year":"2012","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B122","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1111\/j.1467-985X.2006.00414_11.x","article-title":"Statistical methods in molecular evolution","volume":"169","author":"Cannings","year":"2006","journal-title":"J R Stat Soc Ser A"},{"key":"key\n\t\t\t\t20170523191953_bbt021-B123"},{"issue":"9","key":"key\n\t\t\t\t20170523191953_bbt021-B124","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1038\/nrg2857","article-title":"Computational solutions to large-scale data management and analysis","volume":"11","author":"Schadt","year":"2010","journal-title":"Nat Rev Genet"},{"issue":"7209","key":"key\n\t\t\t\t20170523191953_bbt021-B125","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/455047a","article-title":"Big data: the future of biocuration","volume":"455","author":"Howe","year":"2008","journal-title":"Nature"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/15\/5\/771\/17488522\/bbt021.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,7,12]],"date-time":"2019-07-12T09:53:25Z","timestamp":1562925205000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article-lookup\/doi\/10.1093\/bib\/bbt021"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,4,12]]},"references-count":125,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2013,4,12]]},"published-print":{"date-parts":[[2014,9]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbt021","relation":{},"ISSN":["1477-4054","1467-5463"],"issn-type":[{"value":"1477-4054","type":"electronic"},{"value":"1467-5463","type":"print"}],"subject":[],"published":{"date-parts":[[2013,4,12]]}}}