Visualizing time-related data in biology, a review

Gunther, 2004, Time in physics and biology, Biol Res, 37, 759, 10.4067/S0716-97602004000500005

Finocchiaro, 2003, DSMM: a database of simulated molecular motions, Nucleic Acids Res, 31, 456, 10.1093/nar/gkg113

Kitano, 2007, Towards a theory of biological robustness, Mol Syst Biol, 3, 137, 10.1038/msb4100179

Suh, 1998, Axiomatic design theory for systems, Res Eng Des, 10, 189, 10.1007/s001639870001

Ramakrishnan, 2010, Reverse engineering dynamic temporal models of biological processes and their relationships, Proc Natl Acad Sci USA, 107, 12511, 10.1073/pnas.1006283107

Eden, 2011, Proteome half-life dynamics in living human cells, Science, 331, 764, 10.1126/science.1199784

So, 2011, General properties of transcriptional time series in Escherichia coli, Nat Genet, 43, 554, 10.1038/ng.821

Przytycka, 2010, Toward the dynamic interactome: it's about time, Brief Bioinform, 11, 15, 10.1093/bib/bbp057

Dey, 2010, The subunit interfaces of weakly associated homodimeric proteins, J Mol Biol, 398, 146, 10.1016/j.jmb.2010.02.020

Perkins, 2010, Transient protein-protein interactions: structural, functional, and network properties, Structure, 18, 1233, 10.1016/j.str.2010.08.007

Stein, 2009, Dynamic interactions of proteins in complex networks: a more structured view, FEBS J, 276, 5390, 10.1111/j.1742-4658.2009.07251.x

Kholodenko, 2000, Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades, Eur J Biochem, 267, 1583, 10.1046/j.1432-1327.2000.01197.x

Ciliberti, 2007, Robustness can evolve gradually in complex regulatory gene networks with varying topology, PLOS Comput Biol, 3, 164, 10.1371/journal.pcbi.0030015

Rifkin, 2005, A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression, Nature, 438, 220, 10.1038/nature04114

Lenormand, 2002, Gene flow and the limits to natural selection, Trends Ecol Evol, 17, 183, 10.1016/S0169-5347(02)02497-7

Demetrius, 2005, Robustness and network evolution - an entropic principle, Physica A, 346, 682, 10.1016/j.physa.2004.07.011

Bloom, 2007, Evolution favors protein mutational robustness in sufficiently large populations, BMC Biol, 5, 29, 10.1186/1741-7007-5-29

Daniels, 2008, Sloppiness, robustness, and evolvability in systems biology, Curr Opin Biotech, 19, 389, 10.1016/j.copbio.2008.06.008

Fersht, 2008, From the first protein structures to our current knowledge of protein folding: delights and scepticisms, Nat Rev Mol Cell Bio, 9, 650, 10.1038/nrm2446

Strogatz

Nielsen, 2010, Visualizing genomes: techniques and challenges, Nat Methods, 7, S5, 10.1038/nmeth.1422

Fong, 2006, Spatio-temporal visualization of battlefield entities and events, Lect Notes Comput Sci, 4035, 622, 10.1007/11784203_59

Hey, 1992, Using phylogenetic trees to study speciation and extinction, Evolution, 46, 627, 10.2307/2409633

Alon

Pavlopoulos, 2008, A survey of visualization tools for biological network analysis, BioData Min, 1, 12, 10.1186/1756-0381-1-12

Yamada, 2009, Evolution of biomolecular networks: lessons from metabolic and protein interactions, Nat Rev Mol Cell Biol, 10, 791, 10.1038/nrm2787

Bar-Joseph, 2012, Study designs studying and modelling dynamic biological processes using time-series gene expression data, Nat Rev Genetics, 13, 552, 10.1038/nrg3244

Leloup, 1999, Limit cycle models for circadian rhythms based on transcriptional regulation in Drosophila and Neurospora, J Biol Rhythms, 14, 433, 10.1177/074873099129000948

Geberth, 2009, Predicting the distribution of spiral waves from cell properties in a developmental-path model of Dictyostelium pattern formation, PLOS Comput. Biol., 5, 10.1371/journal.pcbi.1000422

Pavlopoulos, 2010, A reference guide for tree analysis and visualization, BioData Min, 3, 1, 10.1186/1756-0381-3-1

Barsky, 2007, Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation, Bioinformatics, 23, 1040, 10.1093/bioinformatics/btm057

Zhan, 2011, Parameter estimation in systems biology models using spline approximation, BMC Syst Biol, 5, 14, 10.1186/1752-0509-5-14

Marwan, 2007, Recurrence plots for the analysis of complex systems, Phys Rep, 438, 237, 10.1016/j.physrep.2006.11.001

Müller, Visualization methods for time-dependent data - an overview, 10.1109/WSC.2003.1261490

Carvalho, 2008, A temporal focus plus context visualization model for handling valid-time spatial information, Inform Visual, 7, 265, 10.1057/PALGRAVE.IVS.9500188

Wall, 2003, Singular value decomposition and principal component analysis, In: A Practical Approach to Microarray Data Analysis, 91, 10.1007/0-306-47815-3_5

Yang, 2003, Mining biological data using self-organizing map, J Chem Inf Comput Sci, 43, 1748, 10.1021/ci034138n

Zbilut, 2002, Recurrence quantification analysis as a tool for nonlinear exploration of nonstationary cardiac signals, Med Eng Phys, 24, 53, 10.1016/S1350-4533(01)00112-6

Harris, 1998, The Fourier analysis of biological transients, J Neurosci Meth, 83, 15, 10.1016/S0165-0270(98)00080-6

Unser, 1996, A review of wavelets in biomedical applications, Proc IEEE, 84, 626, 10.1109/5.488704

Aach, 2001, Aligning gene expression time series with time warping algorithms, Bioinformatics, 17, 495, 10.1093/bioinformatics/17.6.495

Caporaso, 2011, Moving pictures of the human microbiome, Genome Biol, 12, R50, 10.1186/gb-2011-12-5-r50

Tsuchiya, 2007, Gene expression waves. Cell cycle independent collective dynamics in cultured cells, FEBS J, 274, 2878, 10.1111/j.1742-4658.2007.05822.x

Klevecz, 2008, Collective behavior in gene regulation: the cell is an oscillator, the cell cycle a developmental process, FEBS J, 275, 2372, 10.1111/j.1742-4658.2008.06399.x

Giuliani, 1998, A nonlinear explanation of aging-induced changes in heartbeat dynamics, Am J Physiol, 275, H1455

Yeung, 2002, Reverse engineering gene networks using singular value decomposition and robust regression, Proc Natl Acad Sci USA, 99, 6163, 10.1073/pnas.092576199

Alter, 2000, Singular value decomposition for genome-wide expression data processing and modeling, Proc Natl Acad Sci USA, 97, 10101, 10.1073/pnas.97.18.10101

Giuliani, 2002, Nonlinear signal analysis methods in the elucidation of protein sequence-structure relationships, Chem Rev, 102, 1471, 10.1021/cr0101499

Kitano, 2002, Systems biology: a brief overview, Science, 295, 1662, 10.1126/science.1069492

Meyer, 2010, MoDEL (molecular dynamics extended library): a database of atomistic molecular dynamics trajectories, Structure, 18, 1399, 10.1016/j.str.2010.07.013

Edgar, 2002, Gene Expression Omnibus: NCBI gene expression and hybridization array data repository, Nucleic Acids Res, 30, 207, 10.1093/nar/30.1.207

Kincaid, 2008, VistaClara: an expression browser plug-in for Cytoscape, Bioinformatics, 24, 2112, 10.1093/bioinformatics/btn368

Warsow, 2010, ExprEssence–revealing the essence of differential experimental data in the context of an interaction/regulation net-work, BMC Syst Biol, 4, 164, 10.1186/1752-0509-4-164

Westenberg, 2010, SpotXplore: a cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks, Bioinformatics, 26, 2922, 10.1093/bioinformatics/btq535

Gauthier, 2008, Cyclebase.org–a comprehensive multi-organism online database of cell-cycle experiments, Nucleic Acids Res, 36, D854

Case, 2005, The Amber biomolecular simulation programs, J Comput Chem, 26, 1668, 10.1002/jcc.20290

Van Der Spoel, 2005, Gromacs: fast, flexible, and free, J Comput Chem, 26, 1701, 10.1002/jcc.20291

Brooks, 2009, CHARMM: the biomolecular simulation program, J Comput Chem, 30, 1545, 10.1002/jcc.21287

Phillips, 2005, Scalable molecular dynamics with NAMD, J Comput Chem, 26, 1781, 10.1002/jcc.20289

Humphrey, 1996, VMD: visual molecular dynamics, J Mol Graph Model, 14, 33, 10.1016/0263-7855(96)00018-5

Pettersen, 2004, UCSF Chimera–a visualization system for exploratory research and analysis, J Comput Chem, 25, 1605, 10.1002/jcc.20084

Moreland, 2005, The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications, BMC Bioinformatics, 6, 21, 10.1186/1471-2105-6-21

Schrödinger, 2012, Suite 2012: MacroModel [computer program]. Version 9.9

DeLano, 2005, PyMOL: a communications tool for computational models, Abstr Pap Am Chem Soc, 230, U1371

DeLano, 2009, PyMOL molecular viewer: updates and refinements, Abstr Pap Am Chem Soc, 238

Herraez, 2006, Biomolecules in the computer: Jmol to the rescue, Biochem Mol Biol Educ, 34, 255, 10.1002/bmb.2006.494034042644

O'Donoghue, 2010, Visualization of macromolecular structures, Nat Methods, 7, S42, 10.1038/nmeth.1427

Durrant, 2011, Molecular dynamics simulations and drug discovery, BMC Biol, 9, 71, 10.1186/1741-7007-9-71

Schena, 1995, Quantitative monitoring of gene-expression patterns with a complementary-DNA microarray, Science, 270, 467, 10.1126/science.270.5235.467

Lashkari, 1997, Yeast microarrays for genome wide parallel genetic and gene expression analysis, Proc Natl Acad Sci USA, 94, 13057, 10.1073/pnas.94.24.13057

Glas, 2006, Converting a breast cancer microarray signature into a high-throughput diagnostic test, BMC Genomics, 7, 278, 10.1186/1471-2164-7-278

Krupp, 2012, RNA-seq atlas–a reference database for gene expression profiling in normal tissue by next-generation sequencing, Bioinformatics, 28, 1184, 10.1093/bioinformatics/bts084

Ernst, 2006, STEM: a tool for the analysis of short time series gene expression data, BMC Bioinformatics, 7, 10.1186/1471-2105-7-191

MacArthur, 2010, GATE: software for the analysis and visualization of high-dimensional time series expression data, Bioinformatics, 26, 143, 10.1093/bioinformatics/btp628

Roy, 2010, Identification of functional elements and regulatory circuits by Drosophila modENCODE, Science, 330, 1787, 10.1126/science.1198374

Ernst, 2011, Mapping and analysis of chromatin state dynamics in nine human cell types, Nature, 473, 43, 10.1038/nature09906

Wu, 2006, Functional mapping - how to map and study the genetic architecture of dynamic complex traits, Nat Rev Genet, 7, 229, 10.1038/nrg1804

Das, 2011, A dynamic model for genome-wide association studies, Hum Genet, 129, 629, 10.1007/s00439-011-0960-6

Li, 2011, The Bayesian lasso for genome-wide association studies, Bioinformatics, 27, 516, 10.1093/bioinformatics/btq688

Funahashi, 2008, CellDesigner 3.5: a versatile modeling tool for biochemical networks, Proc IEEE, 96, 1254, 10.1109/JPROC.2008.925458

Hoops, 2006, Copasi–a complex pathway simulator, Bioinformatics, 22, 3067, 10.1093/bioinformatics/btl485

Mendes, 2009, Computational modeling of biochemical networks using Copasi, Methods Mol Biol, 500, 17, 10.1007/978-1-59745-525-1_2

Ramsey, 2005, Dizzy: stochastic simulation of large-scale genetic regulatory networks (supplementary material), J Bioinform Comput Biol, 3, 437, 10.1142/S0219720005001144

Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res, 13, 2498, 10.1101/gr.1239303

Junker, 2006, VANTED: a system for advanced data analysis and visualization in the context of biological networks, BMC Bioinformatics, 7, 109, 10.1186/1471-2105-7-109

Hu, 2008, VisANT: an integrative framework for networks in systems biology, Brief Bioinform, 9, 317, 10.1093/bib/bbn020

Hu, 2009, VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology, Nucleic Acids Res, 37, W115, 10.1093/nar/gkp406

Curtis, 2011, TVNviewer: an interactive visualization tool for exploring networks that change over time or space, Bioinformatics, 27, 1880, 10.1093/bioinformatics/btr273

Longabaugh, 2012, BioTapestry: a tool to visualize the dynamic properties of gene regulatory networks, Methods Mol Biol, 786, 359, 10.1007/978-1-61779-292-2_21

Enjalbert, 2011, Intuitive visualization and analysis of multi-omics data and application to Escherichia coli carbon metabolism, PLoS One, 6, e21318, 10.1371/journal.pone.0021318

Theocharidis, 2009, Network visualization and analysis of gene expression data using BioLayout Express(3D), Nat Protoc, 4, 1535, 10.1038/nprot.2009.177

Walter, 2010, Visualization of image data from cells to organisms, Nat Methods, 7, S26, 10.1038/nmeth.1431

Stoma, 2011, STSE: spatio-temporal simulation environment dedicated to biology, BMC Bioinformatics, 12, 126, 10.1186/1471-2105-12-126

McClean, 2005, Molecular and cellular biology animations: development and impact on student learning, Cell Biol Educ, 4, 169, 10.1187/cbe.04-07-0047

Karr, 2012, A whole-cell computational model predicts phenotype from genotype, Cell, 150, 389, 10.1016/j.cell.2012.05.044

Tomita, 1999, E-Cell: Software environment for whole-cell simulation, Bioinformatics, 15, 72, 10.1093/bioinformatics/15.1.72

Loew, 2001, The Virtual Cell: a software environment for computational cell biology, Trends Biotechnol, 19, 401, 10.1016/S0167-7799(01)01740-1

McComb, 2009, Illoura: a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data, Bioinformatics, 25, 1208, 10.1093/bioinformatics/btp125

Setty, 2008, Four-dimensional realistic modeling of pancreatic organogenesis, Proc Natl Acad Sci USA, 105, 20374, 10.1073/pnas.0808725105

Alarcon, 2004, Towards whole-organ modelling of tumour growth, Prog Biophys Mol Biol, 85, 451, 10.1016/j.pbiomolbio.2004.02.004

Pavlopoulos, 2008, Arena3D: visualization of biological networks in 3D, BMC Syst Biol, 2, 104, 10.1186/1752-0509-2-104

Secrier, 2012, Arena3D: visualizing time-driven phenotypic differences in biological systems, BMC Bioinformatics, 13, 45, 10.1186/1471-2105-13-45

Brauer, 2001, Mathematical Models in Population Biology and Epidemiology, 1st edn, 10.1007/978-1-4757-3516-1

Bielejec, 2011, SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics, Bioinformatics, 27, 2910, 10.1093/bioinformatics/btr481

Thompson, 2002, Multiple sequence alignment using ClustalW and ClustalX, Curr Protoc Bioinformatics, Chapter 2, Unit 2.3

Clamp, 2004, The Jalview java alignment editor, Bioinformatics, 20, 426, 10.1093/bioinformatics/btg430

Page, 2002, Visualizing phylogenetic trees using TreeView, Curr Protoc Bioinformatics, 10.1002/0471250953.bi0602s01

Tamura, 2011, MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol Biol Evol, 28, 2731, 10.1093/molbev/msr121

Procter, 2010, Visualization of multiple alignments, phylogenies and gene family evolution, Nat Methods, 7, S16, 10.1038/nmeth.1434

Krzywinski, 2009, Circos: an information aesthetic for comparative genomics, Genome Res, 19, 1639, 10.1101/gr.092759.109

Frazer, 2004, Vista: computational tools for comparative genomics, Nucleic Acids Res, 32, W273, 10.1093/nar/gkh458

Meyer, 2009, MizBee: a multiscale synteny browser, IEEE Trans Vis Comput Graph, 15, 897, 10.1109/TVCG.2009.167

Letunic, 2007, Interactive Tree of Life (iTOL): an online tool for phylogenetic tree display and annotation, Bioinformatics, 23, 127, 10.1093/bioinformatics/btl529

Linard, 2012, EvoluCode: evolutionary barcodes as a unifying framework for multilevel evolutionary data, Evol Bioinform Online, 8, 61, 10.4137/EBO.S8814

Hebert, 2003, Biological identifications through DNA barcodes, Proc Biol Sci, 270, 313, 10.1098/rspb.2002.2218

Smith, 2012, The cervical microbiome over 7 years and a comparison of methodologies for its characterization, PLoS One, 7, 10.1371/journal.pone.0040425

Cannings, 2006, Statistical methods in molecular evolution, J R Stat Soc Ser A, 169, 391, 10.1111/j.1467-985X.2006.00414_11.x

Schadt, 2010, Computational solutions to large-scale data management and analysis, Nat Rev Genet, 11, 647, 10.1038/nrg2857

Howe, 2008, Big data: the future of biocuration, Nature, 455, 47, 10.1038/455047a