{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T10:10:53Z","timestamp":1781259053023,"version":"3.54.1"},"reference-count":54,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2006,5,19]],"date-time":"2006-05-19T00:00:00Z","timestamp":1147996800000},"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.0020051","type":"journal-article","created":{"date-parts":[[2006,5,16]],"date-time":"2006-05-16T18:24:29Z","timestamp":1147803869000},"page":"e51","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":157,"title":["Reverse Engineering the Gap Gene Network of Drosophila melanogaster"],"prefix":"10.1371","volume":"2","author":[{"given":"Theodore J","family":"Perkins","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johannes","family":"Jaeger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Reinitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leon","family":"Glass","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2006,5,19]]},"reference":[{"key":"pcbi-0020051-b001","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1242\/dev.101.1.1","article-title":"The molecular basis for metameric pattern in the Drosophila embryo.","volume":"101","year":"1987","journal-title":"Development"},{"key":"pcbi-0020051-b002","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/335025a0","article-title":"The molecular genetics of embryonic pattern formation in Drosophila.","volume":"335","year":"1988","journal-title":"Nature"},{"key":"pcbi-0020051-b003","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1016\/0168-9525(96)10044-5","article-title":"From gradients to stripes in Drosophila embryogenesis: Filling in the gaps.","volume":"12","year":"1996","journal-title":"Trends Genet"},{"key":"pcbi-0020051-b004","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1006\/jtbi.2001.2335","article-title":"A logical analysis of the gap gene system.","volume":"211","year":"2001","journal-title":"J Theor Biol"},{"key":"pcbi-0020051-b005","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/0925-4773(94)00310-J","article-title":"Mechanism of eve stripe formation.","volume":"49","year":"1995","journal-title":"Mechanisms of Development"},{"key":"pcbi-0020051-b006","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1038\/nature02678","article-title":"Dynamic control of positional information in the early Drosophila embryo.","volume":"430","year":"2004","journal-title":"Nature"},{"key":"pcbi-0020051-b007","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 Drosophila melanogaster.","volume":"167","year":"2004","journal-title":"Genetics"},{"key":"pcbi-0020051-b008","first-page":"41","article-title":"Linear modeling of mRNA expression levels during CNS development and injury.","volume":"3","year":"1999","journal-title":"Pac Symp Biocomput"},{"key":"pcbi-0020051-b009","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","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0020051-b010","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1006\/jcph.1998.6134","article-title":"Parallel simulated annealing by mixing of states.","volume":"148","year":"1999","journal-title":"J Comput Phys"},{"key":"pcbi-0020051-b011","unstructured":"ChuKW 2001 The existence and estimation of an optimal mixing regime [thesis] Stony Brook (New York) State University of New York at Stony Brook"},{"key":"pcbi-0020051-b012","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1016\/j.physd.2004.07.003","article-title":"Pattern formation and nuclear divisions are uncoupled in Drosophila segmentation: Comparison of spatially discrete and continuous models.","volume":"197","year":"2004","journal-title":"Physica D"},{"key":"pcbi-0020051-b013","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1006\/jtbi.1998.0701","article-title":"Dynamics of the genetic regulatory network for Arabidopsis thaliana flower morphogenesis.","volume":"193","year":"1998","journal-title":"J Theor Biol"},{"key":"pcbi-0020051-b014","first-page":"593","article-title":"Genetic control of flower morphogenesis in arabidopsis thaliana: A logical analysis.","volume":"14","year":"1999","journal-title":"Bioinformatics"},{"key":"pcbi-0020051-b015","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0022-5193(03)00035-3","article-title":"The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster.","volume":"223","year":"2003","journal-title":"J Theor Biol"},{"key":"pcbi-0020051-b016","doi-asserted-by":"crossref","first-page":"1896","DOI":"10.1126\/science.279.5358.1896","article-title":"Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene.","volume":"279","year":"1998","journal-title":"Science"},{"key":"pcbi-0020051-b017","doi-asserted-by":"crossref","first-page":"7702","DOI":"10.1073\/pnas.1230759100","article-title":"Detailed map of a cis-regulatory input function.","volume":"100","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0020051-b018","doi-asserted-by":"crossref","first-page":"2212","DOI":"10.1093\/bioinformatics\/bth222","article-title":"A database for management of gene expression data in situ.","volume":"20","year":"2004","journal-title":"Bioinformatics"},{"key":"pcbi-0020051-b019","first-page":"303","article-title":"Progression of the cell cycle through mitosis leads to abortion of nascent transcripts.","volume":"97","year":"1991","journal-title":"Cell"},{"key":"pcbi-0020051-b020","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1038\/337138a0","article-title":"The Bicoid protein is a positive regulator of hunchback transcription in the early Drosophila embryo.","volume":"337","year":"1989","journal-title":"Nature"},{"key":"pcbi-0020051-b021","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1038\/332281a0","article-title":"Regulation of the Drosophila segmentation gene hunchback by two maternal morphogenetic centres.","volume":"332","year":"1988","journal-title":"Nature"},{"key":"pcbi-0020051-b022","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1242\/dev.111.2.367","article-title":"Interactions of the Drosophila gap gene giant with maternal and zygotic pattern-forming genes.","volume":"111","year":"1991","journal-title":"Development"},{"key":"pcbi-0020051-b023","doi-asserted-by":"crossref","first-page":"2587","DOI":"10.1002\/j.1460-2075.1990.tb07440.x","article-title":"Cis-acting control elements for Kr\u00fcppel expression in the Drosophila embryo.","volume":"9","year":"1990","journal-title":"EMBO J"},{"key":"pcbi-0020051-b024","doi-asserted-by":"crossref","first-page":"2267","DOI":"10.1002\/j.1460-2075.1991.tb07763.x","article-title":"Gene expression mediated by cis-acting sequences of the Kr\u00fcppel gene in response to the Drosophila morphogens Bicoid and Hunchback.","volume":"10","year":"1991","journal-title":"EMBO J"},{"key":"pcbi-0020051-b025","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1038\/376253a0","article-title":"Activation of posterior gap gene expression in the Drosophila blastoderm.","volume":"376","year":"1995","journal-title":"Nature"},{"key":"pcbi-0020051-b026","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1242\/dev.110.2.621","article-title":"Pattern formation under the control of the terminal system in the Drosophila embryo.","volume":"110","year":"1990","journal-title":"Development"},{"key":"pcbi-0020051-b027","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/0012-1606(90)90053-L","article-title":"Control of the initiation of homeotic gene expression by the gap genes giant and tailless in Drosophila.","volume":"140","year":"1990","journal-title":"Dev Biol"},{"key":"pcbi-0020051-b028","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/0925-4773(91)90019-3","article-title":"Control and function of terminal gap gene activity in the posterior pole region of the Drosophila embryo.","volume":"35","year":"1991","journal-title":"Mech Dev"},{"key":"pcbi-0020051-b029","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1126\/science.1348871","article-title":"Competition for overlapping sites in the regulatory region of the Drosophila gene Kr\u00fcppel.","volume":"256","year":"1992","journal-title":"Science"},{"key":"pcbi-0020051-b030","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1126\/science.1546296","article-title":"Spatial control of the gap gene knirps in the Drosophila embryo by posterior morphogen system.","volume":"255","year":"1992","journal-title":"Science"},{"key":"pcbi-0020051-b031","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/341337a0","article-title":"Kr\u00fcppel requirement for knirps enhancement reflects overlapping gap gene activities in the Drosophila embryo.","volume":"341","year":"1989","journal-title":"Nature"},{"key":"pcbi-0020051-b032","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1242\/dev.111.2.601","article-title":"Spatial regulation of the gap gene giant during Drosophila development.","volume":"111","year":"1991","journal-title":"Development"},{"key":"pcbi-0020051-b033","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1242\/dev.111.2.611","article-title":"Mutually repressive interactions between the gap genes giant and Kr\u00fcppel define middle body regions of the Drosophila embryo.","volume":"111","year":"1991","journal-title":"Development"},{"key":"pcbi-0020051-b034","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1126\/science.1925599","article-title":"Dual role of the Drosophila pattern gene tailless in embryonic termini.","volume":"254","year":"1991","journal-title":"Science"},{"key":"pcbi-0020051-b035","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1242\/dev.114.1.99","article-title":"The giant gene of Drosophila encodes a b-ZIP DNA-binding protein that regulates the expression of other segmentation gap genes.","volume":"114","year":"1992","journal-title":"Development"},{"key":"pcbi-0020051-b036","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1038\/346577a0","article-title":"A morphogenetic gradient of Hunchback protein organizes the expression of the gap genes Kr\u00fcppel and knirps in the early Drosophila embryo.","volume":"346","year":"1990","journal-title":"Nature"},{"key":"pcbi-0020051-b037","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1016\/0925-4773(94)90069-8","article-title":"Identical transacting factor requirement for knirps and knirps-related gene expression in the anterior but not in the posterior region of the Drosophila embryo.","volume":"46","year":"1994","journal-title":"Mech Dev"},{"key":"pcbi-0020051-b038","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1038\/nature02189","article-title":"A self-organizing system of repressor gradients establishes segmental complexity in Drosophila.","volume":"426","year":"2003","journal-title":"Nature"},{"key":"pcbi-0020051-b039","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1038\/324668a0","article-title":"Cross-regulatory interactions among the gap genes of Drosophila.","volume":"324","year":"1986","journal-title":"Nature"},{"key":"pcbi-0020051-b040","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1016\/0092-8674(87)90124-3","article-title":"Pole region-dependent repression of the Drosophila gap gene Kr\u00fcppel by maternal gene products.","volume":"51","year":"1987","journal-title":"Cell"},{"key":"pcbi-0020051-b041","first-page":"3155","article-title":"Analysis of maternal effect mutant combinations elucidates regulation and function of the overlap of hunchback and Kr\u00fcppel gene expression in the Drosophila blastoderm embryo.","volume":"120","year":"1989","journal-title":"Development"},{"key":"pcbi-0020051-b042","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1016\/S0092-8674(94)90622-X","article-title":"Synergy between the Hunchback and Bicoid morphogens is required for anterior patterning in Drosophila.","volume":"78","year":"1994","journal-title":"Cell"},{"key":"pcbi-0020051-b043","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","year":"1990","journal-title":"Development"},{"key":"pcbi-0020051-b044","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/0092-8674(92)90405-2","article-title":"Control of Drosophila body pattern by the hunchback morphogen gradient.","volume":"69","year":"1992","journal-title":"Cell"},{"key":"pcbi-0020051-b045","doi-asserted-by":"crossref","first-page":"3043","DOI":"10.1242\/dev.120.10.3043","article-title":"Autonomous concentration-dependent activation and repression of Kr\u00fcppel by hunchback in the Drosophila embryo.","volume":"120","year":"1994","journal-title":"Development"},{"key":"pcbi-0020051-b046","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, giant, of Drosophila.","volume":"8","year":"1989","journal-title":"EMBO J"},{"key":"pcbi-0020051-b047","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1038\/327383a0","article-title":"Finger protein of novel structure encoded by hunchback, a second member of the gap class of Drosophila segmentation genes.","volume":"327","year":"1987","journal-title":"Nature"},{"key":"pcbi-0020051-b048","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/S0303-2647(98)00014-8","article-title":"Prediction of mutant expression patterns using gene circuits.","volume":"47","year":"1998","journal-title":"Biosystems"},{"key":"pcbi-0020051-b049","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1007\/s004270050184","article-title":"Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins.","volume":"208","year":"1998","journal-title":"Dev Genes Evol"},{"key":"pcbi-0020051-b050","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1093\/bioinformatics\/17.1.3","article-title":"Registration of the expression patterns of Drosophila segmentation genes by two independent methods.","volume":"17","year":"2001","journal-title":"Bioinformatics"},{"key":"pcbi-0020051-b051","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 Drosophila embryos.","volume":"215","year":"2005","journal-title":"Dev Genes Evol"},{"key":"pcbi-0020051-b052","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1007\/s00427-005-0472-2","article-title":"Removal of background signal from in situ data on the expression of segmentation gene in Drosophila.","volume":"215","year":"2005","journal-title":"Dev Genes Evol"},{"key":"pcbi-0020051-b053","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1242\/jcs.61.1.31","article-title":"Studies of nuclear and cytoplasmic behaviour during the five mitotic cycles that precede gastrulation in Drosophila embryogenesis.","volume":"61","year":"1983","journal-title":"J Cell Sci"},{"key":"pcbi-0020051-b054","doi-asserted-by":"crossref","unstructured":"Campos-OrtegaJAHartensteinV 1985 The Embryonic Development of Drosophila melanogaster Heidelberg (Germany) Springer 227 p.","DOI":"10.1007\/978-3-662-02454-6"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0020051","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,27]],"date-time":"2021-07-27T08:54:34Z","timestamp":1627376074000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0020051"}},"subtitle":[],"editor":[{"given":"Barbara","family":"Bryant","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2006,5,19]]},"references-count":54,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2006,5,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0020051","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006,5,19]]}}}