{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,6]],"date-time":"2026-06-06T20:39:24Z","timestamp":1780778364050,"version":"3.54.1"},"reference-count":102,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2012,7,12]],"date-time":"2012-07-12T00:00:00Z","timestamp":1342051200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002589","type":"journal-article","created":{"date-parts":[[2012,7,13]],"date-time":"2012-07-13T16:22:31Z","timestamp":1342196551000},"page":"e1002589","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":85,"title":["Efficient Reverse-Engineering of a Developmental Gene Regulatory Network"],"prefix":"10.1371","volume":"8","author":[{"given":"Anton","family":"Crombach","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karl R.","family":"Wotton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Damjan","family":"Cicin-Sain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maksat","family":"Ashyraliyev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johannes","family":"Jaeger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2012,7,12]]},"reference":[{"key":"ref1","first-page":"253","article-title":"Gene circuits and their uses.","author":"J Reinitz","year":"1996"},{"key":"ref2","first-page":"18","article-title":"REVEAL, a general reverse engineering algorithm for inference of genetic network architectures.","volume":"1998","author":"S Liang","year":"1998","journal-title":"Pacific Symp Biocomput"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1093\/bioinformatics\/16.8.707","article-title":"Genetic network inference: from co-expression clustering to reverse engineering.","volume":"16","author":"P D'haeseleer","year":"2000","journal-title":"Bioinformatics"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.plrev.2005.01.001","article-title":"Reverse-engineering transcription control networks.","volume":"2","author":"TS Gardner","year":"2005","journal-title":"Phys Life Rev"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1038\/nature07633","article-title":"Reverse engineering the genotype-phenotype map with natural genetic variation.","volume":"456","author":"MV Rockman","year":"2008","journal-title":"Nature"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.jbiotec.2009.07.013","article-title":"Reverse engineering and verification of gene networks: Principles, assumptions, and limitations of present methods and future perspectives.","volume":"144","author":"F He","year":"2009","journal-title":"J Biotech"},{"key":"ref7","first-page":"9","article-title":"Reverse Engineering of Gene Regulatory Networks.","author":"J Jaeger","year":"2010"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"12182","DOI":"10.1073\/pnas.220392197","article-title":"Discovering functional relationships between RNA expression and chemotherapeutic susceptibility using relevance networks.","volume":"97","author":"AJ Butte","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"5944","DOI":"10.1073\/pnas.0933416100","article-title":"Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling.","volume":"100","author":"J Tegn\u00e9r","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1126\/science.1081900","article-title":"Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling.","volume":"301","author":"TS Gardner","year":"2003","journal-title":"Science"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1038\/ng1165","article-title":"Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data.","volume":"34","author":"E Segal","year":"2003","journal-title":"Nat Genet"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1038\/ng1532","article-title":"Reverse engineering of regulatory networks in human B cells.","volume":"37","author":"K Basso","year":"2005","journal-title":"Nat Genet"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1016\/j.cell.2007.10.053","article-title":"A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell.","volume":"131","author":"R Bonneau","year":"2007","journal-title":"Cell"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1016\/j.cell.2009.01.055","article-title":"A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches.","volume":"137","author":"I Cantone","year":"2009","journal-title":"Cell"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1817","DOI":"10.1039\/b908108a","article-title":"Transcription regulatory networks in <italic>Caeorhabditis elegans<\/italic> inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development.","volume":"5","author":"V Vermeirssen","year":"2009","journal-title":"Mol BioSyst"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"13550","DOI":"10.1073\/pnas.1001107107","article-title":"Fourier analysis and systems identification of the p53 feedback loop.","volume":"107","author":"N Geva-Zatorsky","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.biosystems.2008.12.004","article-title":"Gene regulatory network inference: Data integration in dynamic models\u2014A review.","volume":"96","author":"M Hecker","year":"2009","journal-title":"BioSystems"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1126\/science.1094068","article-title":"Inferring Cellular Networks Using Probabilistic Graphical Models.","volume":"303","author":"N Friedman","year":"2004","journal-title":"Science"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/1471-2105-7-S1-S7","article-title":"ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context.","volume":"7","author":"AA Margolin","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"e8","DOI":"10.1371\/journal.pbio.0050008","article-title":"Large-Scale Mapping and Validation of <italic>Escherichia coli<\/italic> Transcriptional Regulation from a Compendium of Expression Profiles.","volume":"5","author":"JJ Faith","year":"2007","journal-title":"PLoS Biol"},{"key":"ref21","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":"MKS Yeung","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/nbt1075","article-title":"Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks.","volume":"23","author":"D di Bernardo","year":"2005","journal-title":"Nat Biotech"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1093\/bioinformatics\/btl003","article-title":"Inference of gene regulatory networks and compound node of action from time course gene expression profiles.","volume":"22","author":"M Bansal","year":"2006","journal-title":"Bioinformatics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1038\/msb4100120","article-title":"How to infer gene networks from expression profiles.","volume":"3","author":"M Bansal","year":"2007","journal-title":"Mol Syst Biol"},{"key":"ref25","article-title":"The inheritance of process: a dynamical systems approach.","author":"J Jaeger","year":"2012","journal-title":"J Exp Zool B (Mol Dev Evol)"},{"key":"ref26","article-title":"Life&apos;s Attractors: Understanding Developmental Systems Through Reverse Engineering and <italic>In Silico<\/italic> Evolution.","author":"J Jaeger","year":"2012"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1089\/10665270252833208","article-title":"Modeling and Simulation of Genetic Regulatory Systems: A Literature Review.","volume":"9","author":"H de Jong","year":"2002","journal-title":"J Comp Biol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.2174\/138161207780765945","article-title":"Computational and Experimental Approaches for Modeling Regulatory Networks.","volume":"13","author":"J Goutsias","year":"2007","journal-title":"Curr Pharm Design"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1038\/nrm2503","article-title":"Modelling and analysis of gene regulatory networks.","volume":"9","author":"G Karlebach","year":"2008","journal-title":"Nat Rev Genet"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/1752-0509-2-47","article-title":"Optimization in computational systems biology.","volume":"2","author":"JR Banga","year":"2008","journal-title":"BMC Syst Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1111\/j.1742-4658.2008.06844.x","article-title":"Systems biology: parameter estimation for biochemical models.","volume":"276","author":"M Ashyraliyev","year":"2009","journal-title":"FEBS J"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.devcel.2006.07.004","article-title":"Quantifying the Gurken Morphogen Gradient in <italic>Drosophila<\/italic> Oogenesis.","volume":"11","author":"LA Goentoro","year":"2006","journal-title":"Dev Cell"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"21707","DOI":"10.1073\/pnas.0912395106","article-title":"Dynamics of the Dorsal morphogen gradient.","volume":"106","author":"JS Kanodia","year":"2009","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/1752-0509-4-21","article-title":"Parameter estimation and inference for stochastic reaction-diffusion systems: application to morphogenesis in <italic>D. melanogaster<\/italic>.","volume":"4","author":"MA Dewar","year":"2010","journal-title":"BMC Syst Biol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1007\/s00018-010-0536-y","article-title":"The Gap Gene Network.","volume":"68","author":"J Jaeger","year":"2011","journal-title":"Cell Mol Life Sci"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1242\/dev.101.1.1","article-title":"The molecular basis for metameric pattern in the <italic>Drosophila<\/italic> embryo.","volume":"101","author":"M Akam","year":"1987","journal-title":"Development"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/335025a0","article-title":"The molecular genetics of embryonic pattern formation in <italic>Drosophila<\/italic>.","volume":"335","author":"PW Ingham","year":"1988","journal-title":"Nature"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1016\/S0022-5193(05)80391-1","article-title":"A connectionist model of development.","volume":"152","author":"E Mjolsness","year":"1991","journal-title":"J Theor Biol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/0925-4773(94)00310-J","article-title":"Mechanism of <italic>eve<\/italic> stripe formation.","volume":"49","author":"J Reinitz","year":"1995","journal-title":"Mech Dev"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.mod.2006.11.001","article-title":"Known maternal gradients are not sufficient for the establishment of gap domains in <italic>Drosophila melanogaster<\/italic>.","volume":"124","author":"J Jaeger","year":"2007","journal-title":"Mech Dev"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1007\/s004270050184","article-title":"Rapid preparation of a panel of polyclonal antibodies to <italic>Drosophila<\/italic> segmentation proteins.","volume":"208","author":"D Kosman","year":"1998","journal-title":"Dev Genes Evol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1093\/bioinformatics\/17.1.3","article-title":"Registration of the expression patterns of <italic>Drosophila<\/italic> segmentation genes by two independent methods.","volume":"17","author":"E Myasnikova","year":"2001","journal-title":"Bioinformatics"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1016\/j.ydbio.2007.10.037","article-title":"Characterization of the <italic>Drosophila<\/italic> segment determination morphome.","volume":"313","author":"S Surkova","year":"2008","journal-title":"Dev Biol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1","DOI":"10.4161\/fly.6060","article-title":"Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images.","volume":"2","author":"S Surkova","year":"2008","journal-title":"Fly"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1002\/jez.1402710106","article-title":"Cooperative control of positional information in <italic>Drosophila<\/italic> by <italic>bicoid<\/italic> and maternal <italic>hunchback<\/italic>.","volume":"271","author":"J Reinitz","year":"1995","journal-title":"J Exp Zool B (Mol Dev Evol)"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/nature02678","article-title":"Dynamic control of positional information in the early <italic>Drosophila<\/italic> embryo.","volume":"430","author":"J Jaeger","year":"2004","journal-title":"Nature"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"e1000303","DOI":"10.1371\/journal.pcbi.1000303","article-title":"Canalization of Gene Expression and Domain Shifts in the <italic>Drosophila<\/italic> Blastoderm by Dynamical Attractors.","volume":"5","author":"SurkovaS Manu","year":"2009","journal-title":"PLoS Comp Biol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1534\/genetics.104.027334","article-title":"Dynamical analysis of regulatory interactions in the gap gene system of <italic>Drosophila melanogaster<\/italic>.","volume":"167","author":"J Jaeger","year":"2004","journal-title":"Genetics"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"e1000548","DOI":"10.1371\/journal.pcbi.1000548","article-title":"Gene Circuit Analysis of the Terminal Gap Gene <italic>huckebein<\/italic>.","volume":"5","author":"M Ashyraliyev","year":"2009","journal-title":"PLoS Comp Biol"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"e51","DOI":"10.1371\/journal.pcbi.0020051","article-title":"Reverse Engineering the Gap Gene Network.","volume":"2","author":"TJ Perkins","year":"2006","journal-title":"PLoS Comp Biol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"e1000049","DOI":"10.1371\/journal.pbio.1000049","article-title":"Canalization of Gene Expression in the <italic>Drosophila<\/italic> Blastoderm by Gap Gene Cross Regulation.","volume":"7","author":"SurkovaS Manu","year":"2009","journal-title":"PLoS Biol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1007\/BF00291041","article-title":"A non-radioactive in situ hybridization method for the localization of specific RNAs in <italic>Drosophila<\/italic> embryos reveals translational control of the segmentation gene <italic>hunchback<\/italic>.","volume":"98","author":"D Tautz","year":"1989","journal-title":"Chromosoma"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"846","DOI":"10.1126\/science.1099247","article-title":"Multiplex Detection of RNA Expression in <italic>Drosophila<\/italic> Embryos.","volume":"305","author":"D Kosman","year":"2004","journal-title":"Science"},{"key":"ref54","article-title":"Digital Image Processing","author":"RC Gonzalez","year":"2002"},{"key":"ref55","article-title":"Morphological Image Analysis: Principles and Applications","author":"P Soille","year":"2003"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1007\/s00427-005-0484-y","article-title":"A high-throughput method for quantifying gene expression data from early <italic>Drosophila<\/italic> embryos.","volume":"215","author":"H Janssens","year":"2005","journal-title":"Dev Genes Evol"},{"key":"ref57","article-title":"Computer Graphics: Principles and Practice","author":"JD Foley","year":"1995"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/0925-4773(90)90135-9","article-title":"Regulation of <italic>Kr\u00fcppel<\/italic> expression in the anlage of the Malpighian tubules in the <italic>Drosophila<\/italic> embryo.","volume":"33","author":"U Gaul","year":"1990","journal-title":"Mech Dev"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1109\/34.24792","article-title":"Principal Warps: Thin Plate Splines and the Decomposition of Deformations.","volume":"11","author":"FL Bookstein","year":"1989","journal-title":"IEEE Trans Patt Analysis Machine Intel"},{"key":"ref60","article-title":"An efficient simulated annealing schedule: derivation. New Haven, CT: Yale Electrical Engineering Department.","volume":"8816","author":"J Lam","year":"1988","journal-title":"Technical Report"},{"key":"ref61","article-title":"An efficient simulated annealing schedule: implementation and evaluation. New Haven, CT: Yale Electrical Engineering Department.","volume":"8817","author":"J Lam","year":"1988","journal-title":"Technical Report"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1006\/jcph.1998.6134","article-title":"Parallel simulated annealing by mixing of states.","volume":"148","author":"KW Chu","year":"1999","journal-title":"J Comp Phys"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"3356","DOI":"10.1093\/bioinformatics\/btm433","article-title":"Efficient parameter estimation for spatio-temporal models of pattern formation: case study of <italic>Drosophila melanogaster<\/italic>.","volume":"23","author":"Y Fomekong-Nanfack","year":"2007","journal-title":"Bioinformatics"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1186\/1752-0509-2-83","article-title":"Parameter estimation and determinability analysis applied to <italic>Drosophila<\/italic> gap gene circuits.","volume":"2","author":"M Ashyraliyev","year":"2008","journal-title":"BMC Syst Biol"},{"key":"ref65","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4612-1768-8_11","article-title":"System Identification: Theory for the User","author":"L Ljung","year":"1998"},{"key":"ref66","article-title":"Parameter Estimation and Inverse Problems","author":"RC Aster","year":"2005"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1038\/nrm2030","article-title":"Linking data to models: data regression.","volume":"7","author":"K Jaqaman","year":"2006","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1145\/1089014.1089020","article-title":"SUNDIALS: Suite of nonlinear and differential\/algebraic equation solvers.","volume":"31","author":"AC Hindmarsh","year":"2005","journal-title":"ACM Trans Math Software"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"2212","DOI":"10.1093\/bioinformatics\/bth222","article-title":"A database for management of gene expression data <italic>in situ<\/italic>.","volume":"20","author":"E Poustelnikova","year":"2004","journal-title":"Bioinformatics"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"D560","DOI":"10.1093\/nar\/gkn717","article-title":"FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution.","volume":"37","author":"A Pisarev","year":"2009","journal-title":"Nuc Acids Res"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1038\/327383a0","article-title":"Finger protein of novel structure encoded by <italic>hunchback<\/italic>, a second member of the gap class of <italic>Drosophila<\/italic> segmentation genes.","volume":"327","author":"D Tautz","year":"1987","journal-title":"Nature"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"2881","DOI":"10.1002\/j.1460-2075.1988.tb03145.x","article-title":"Differential regulation of the two transcripts from the <italic>Drosophila<\/italic> gap segmentation gene <italic>hunchback<\/italic>.","volume":"7","author":"C Schr\u00f6der","year":"1988","journal-title":"EMBO J"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"3067","DOI":"10.1242\/dev.121.9.3067","article-title":"Posterior stripe expression of <italic>hunchback<\/italic> is driven from two promoters by a common enhancer element.","volume":"121","author":"JS Margolis","year":"1995","journal-title":"Development"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"2795","DOI":"10.1242\/dev.051300","article-title":"The time to measure positional information: maternal Hunchback is required for the synchrony of the Bicoid transcriptional response at teh onset of zygotic transcription.","volume":"137","author":"A Porcher","year":"2010","journal-title":"Development"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"3446","DOI":"10.1128\/MCB.26.9.3446-3454.2006","article-title":"The Tailless Nuclear Receptor Acts as a Dedicated Repressor in the Early <italic>Drosophila<\/italic> Embryo.","volume":"26","author":"E Mor\u00e1n","year":"2006","journal-title":"Mol Cell Biol"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1242\/dev.110.3.759","article-title":"Dose-dependent regulation of pair-rule stripes by gap proteins and the initiation of segment polarity.","volume":"110","author":"R Warrior","year":"1990","journal-title":"Development"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1038\/nature02189","article-title":"A self-organizing system of repressor gradients establishes segmental complexity in <italic>Drosophila<\/italic>.","volume":"426","author":"DE Clyde","year":"2003","journal-title":"Nature"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1038\/415798a","article-title":"Establishment of developmental precision and proportions in the early <italic>Drosophila<\/italic> embryo.","volume":"415","author":"B Houchmandzadeh","year":"2002","journal-title":"Nature"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1111\/j.1742-4658.2008.06843.x","article-title":"Systems biology: experimental design.","volume":"276","author":"C Kreutz","year":"2009","journal-title":"FEBS J"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1042\/bse0450195","article-title":"Parameter estimation and optimal experimental design.","volume":"45","author":"JR Banga","year":"2008","journal-title":"Essays Biochem"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1049\/iet-syb:20070069","article-title":"Computational procedures for optimal experimental design in biological systems.","volume":"2","author":"E Balsa-Canto","year":"2008","journal-title":"IET Syst Biol"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"e1000558","DOI":"10.1371\/journal.pcbi.1000558","article-title":"Optimal experimental design for parameter estimation of a cell signaling model.","volume":"5","author":"S Bandara","year":"2008","journal-title":"PLoS Comp Biol"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"0088","DOI":"10.1186\/gb-2002-3-12-research0088","article-title":"Systematic determination of patterns of gene expression during <italic>Drosophila<\/italic> embryogenesis.","volume":"3","author":"P Tomancak","year":"2002","journal-title":"Genome Biol"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"R145","DOI":"10.1186\/gb-2007-8-7-r145","article-title":"Global analysis of patterns of gene expression during <italic>Drosophila<\/italic> embryogenesis.","volume":"8","author":"P Tomancak","year":"2007","journal-title":"Genome Biol"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1006\/dbio.2002.0652","article-title":"Dorsal gradient networks in the <italic>Drosophila<\/italic> embryo.","volume":"246","author":"A Stathopoulos","year":"2002","journal-title":"Dev Biol"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"R887","DOI":"10.1016\/j.cub.2005.10.026","article-title":"Dorsoventral Axis Formation in the <italic>Drosophila<\/italic> Embryo\u2014Shaping and Transducing a Morphogen Gradient.","volume":"15","author":"B Moussian","year":"2005","journal-title":"Curr Biol"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1242\/dev.02214","article-title":"Shaping BMP morphogen gradients in the <italic>Drosophila<\/italic> embryo and pupal wing.","volume":"133","author":"MB O'Connor","year":"2006","journal-title":"Development"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.semcdb.2006.12.001","article-title":"Heart development in <italic>Drosophila<\/italic>.","volume":"18","author":"Y Tao","year":"2007","journal-title":"Semin Cell Dev Biol"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1016\/j.bbagrm.2008.09.002","article-title":"Cardiac gene regulatory networks in <italic>Drosophila<\/italic>.","volume":"1789","author":"AL Bryantsev","year":"2009","journal-title":"Biochim Biophys Acta"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"3715","DOI":"10.1242\/dev.031534","article-title":"The extracellular regulation of bone morphogenetic protein signaling.","volume":"136","author":"D Umulis","year":"2009","journal-title":"Development"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1242\/dev.126.7.1349","article-title":"The development and evolution of bristle patterns in Diptera.","volume":"126","author":"P Simpson","year":"1999","journal-title":"Development"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1016\/j.tig.2007.04.006","article-title":"The stars and stripes of animal bodies: evolution of regulatory elements mediating pigment and bristle patterns in <italic>Drosophila<\/italic>.","volume":"23","author":"P Simpson","year":"2007","journal-title":"Trends Genet"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/j.cub.2011.02.040","article-title":"Quantitative Variation in Autocrine Signaling and Pathway Crosstalk in the <italic>Caenorhabditis<\/italic> Vulval Network.","volume":"21","author":"E Hoyos","year":"2011","journal-title":"Curr Biol"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"2489","DOI":"10.1242\/dev.009324","article-title":"Pattern formation in the vertebrate neural tube: a sonic hedgehog morphogen-regulated transcriptional network.","volume":"135","author":"E Dessaud","year":"2008","journal-title":"Development"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1038\/324668a0","article-title":"Cross-regulatory interactions among the gap genes of <italic>Drosophila<\/italic>.","volume":"324","author":"H J\u00e4ckle","year":"1986","journal-title":"Nature"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1093\/genetics\/138.1.125","article-title":"Differential regulation of target genes by different alleles of the segmentation gene <italic>hunchback<\/italic> in <italic>Drosophila<\/italic>.","volume":"138","author":"M H\u00fclskamp","year":"1994","journal-title":"Genetics"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"3765","DOI":"10.1242\/dev.125.19.3765","article-title":"Two distinct mechanisms for differential positioning of gene expression borders involving the <italic>Drosophila<\/italic> gap protein <italic>giant<\/italic>.","volume":"125","author":"X Wu","year":"1998","journal-title":"Development"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"1539","DOI":"10.1002\/j.1460-2075.1989.tb03538.x","article-title":"A novel spatial transcription pattern associated with the segmentation gene, <italic>giant<\/italic>, of <italic>Drosophila<\/italic>.","volume":"8","author":"J Mohler","year":"1989","journal-title":"EMBO J"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1242\/dev.111.2.367","article-title":"Interactions of the <italic>Drosophila<\/italic> gap gene <italic>giant<\/italic> with maternal and zygotic pattern-forming genes.","volume":"111","author":"ED Eldon","year":"1991","journal-title":"Development"},{"key":"ref100","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1242\/dev.111.2.601","article-title":"Spatial regulation of the gap gene <italic>giant<\/italic> during <italic>Drosophila<\/italic> development.","volume":"111","author":"R Kraut","year":"1991","journal-title":"Development"},{"key":"ref101","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1242\/dev.114.1.99","article-title":"The <italic>giant<\/italic> gene of <italic>Drosophila<\/italic> encodes a b-ZIP DNA-binding protein that regulates the expression of other segmentation gap genes.","volume":"114","author":"M Capovilla","year":"1992","journal-title":"Development"},{"key":"ref102","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1006\/dbio.2001.0454","article-title":"Role of CtBP in transcriptional repression by the <italic>Drosophila giant<\/italic> protein.","volume":"239","author":"B Strunk","year":"2001","journal-title":"Dev Biol"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002589","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,21]],"date-time":"2022-01-21T02:01:39Z","timestamp":1642730499000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002589"}},"subtitle":[],"editor":[{"given":"Satoru","family":"Miyano","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2012,7,12]]},"references-count":102,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2012,7,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002589","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,7,12]]}}}