{"id":"https://openalex.org/W2108443071","doi":"https://doi.org/10.1186/1752-0509-1-52","title":"Master equation simulation analysis of immunostained Bicoid morphogen gradient","display_name":"Master equation simulation analysis of immunostained Bicoid morphogen gradient","publication_year":2007,"publication_date":"2007-11-16","ids":{"openalex":"https://openalex.org/W2108443071","doi":"https://doi.org/10.1186/1752-0509-1-52","mag":"2108443071","pmid":"https://pubmed.ncbi.nlm.nih.gov/18021413"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-1-52","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-1-52","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-1-52","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-1-52","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111896288","display_name":"YuFeng Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"YuFeng Wu","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-3600, USA. yufeng1714@gmail.com","Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794-3600, USA. yufeng1714@gmail.com","institution_ids":["https://openalex.org/I59553526"]},{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048711176","display_name":"Ekaterina Myasnikova","orcid":"https://orcid.org/0000-0001-6301-1012"},"institutions":[{"id":"https://openalex.org/I212220629","display_name":"Peter the Great St. Petersburg Polytechnic University","ror":"https://ror.org/02x91aj62","country_code":"RU","type":"education","lineage":["https://openalex.org/I212220629"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ekaterina Myasnikova","raw_affiliation_strings":["Department of Computational Biology, Center of Advanced Studies, St.Petersburg State Polytechnic University, St.Petersburg, 195251, Russia","Department of Computational Biology, Center of Advanced Studies, St.Petersburg State Polytechnic University, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Biology, Center of Advanced Studies, St.Petersburg State Polytechnic University, St.Petersburg, 195251, Russia","institution_ids":["https://openalex.org/I212220629"]},{"raw_affiliation_string":"Department of Computational Biology, Center of Advanced Studies, St.Petersburg State Polytechnic University, Russia","institution_ids":["https://openalex.org/I212220629"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5041358651","display_name":"John Reinitz","orcid":"https://orcid.org/0000-0002-6314-9510"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Reinitz","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794-3600, USA","Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794-3600, USA","institution_ids":["https://openalex.org/I59553526"]},{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, USA","institution_ids":["https://openalex.org/I59553526"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5111896288"],"corresponding_institution_ids":["https://openalex.org/I59553526"],"apc_list":null,"apc_paid":null,"fwci":1.4798,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.81355359,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"1","issue":"1","first_page":"52","last_page":"52"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.47360000014305115,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.47360000014305115,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12417","display_name":"Morphological variations and asymmetry","score":0.1615000069141388,"subfield":{"id":"https://openalex.org/subfields/2608","display_name":"Geometry and Topology"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.07479999959468842,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/drosophila-embryogenesis","display_name":"Drosophila embryogenesis","score":0.9492483139038086},{"id":"https://openalex.org/keywords/morphogen","display_name":"Morphogen","score":0.8839855790138245},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.6245786547660828},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4430449903011322},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4133085608482361},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.36463040113449097},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.248254656791687},{"id":"https://openalex.org/keywords/embryo","display_name":"Embryo","score":0.22094973921775818},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18980970978736877},{"id":"https://openalex.org/keywords/embryogenesis","display_name":"Embryogenesis","score":0.11652383208274841},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09064063429832458}],"concepts":[{"id":"https://openalex.org/C167290458","wikidata":"https://www.wikidata.org/wiki/Q2035755","display_name":"Drosophila embryogenesis","level":4,"score":0.9492483139038086},{"id":"https://openalex.org/C2778386714","wikidata":"https://www.wikidata.org/wiki/Q417084","display_name":"Morphogen","level":3,"score":0.8839855790138245},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.6245786547660828},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4430449903011322},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4133085608482361},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.36463040113449097},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.248254656791687},{"id":"https://openalex.org/C196843134","wikidata":"https://www.wikidata.org/wiki/Q33196","display_name":"Embryo","level":2,"score":0.22094973921775818},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18980970978736877},{"id":"https://openalex.org/C87073359","wikidata":"https://www.wikidata.org/wiki/Q33196","display_name":"Embryogenesis","level":3,"score":0.11652383208274841},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09064063429832458},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D016012","descriptor_name":"Poisson Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016012","descriptor_name":"Poisson Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016012","descriptor_name":"Poisson Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/1752-0509-1-52","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-1-52","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-1-52","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:18021413","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18021413","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC systems biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2212647","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2212647","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-1-52","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-1-52","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-1-52","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8375956775","display_name":null,"funder_award_id":"RR07801","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2108443071.pdf","grobid_xml":"https://content.openalex.org/works/W2108443071.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1781095925","https://openalex.org/W1982903250","https://openalex.org/W1991927908","https://openalex.org/W1992487208","https://openalex.org/W1993009001","https://openalex.org/W1999556680","https://openalex.org/W1999777663","https://openalex.org/W2019562739","https://openalex.org/W2037768790","https://openalex.org/W2038701440","https://openalex.org/W2042321087","https://openalex.org/W2057230078","https://openalex.org/W2059053384","https://openalex.org/W2073881036","https://openalex.org/W2077046573","https://openalex.org/W2097242011","https://openalex.org/W2103957060","https://openalex.org/W2105057212","https://openalex.org/W2105293708","https://openalex.org/W2107342968","https://openalex.org/W2115260641","https://openalex.org/W2122121413","https://openalex.org/W2132898564","https://openalex.org/W2141688036","https://openalex.org/W2143368326","https://openalex.org/W2147745135","https://openalex.org/W2149994559","https://openalex.org/W2155418451","https://openalex.org/W2156375169","https://openalex.org/W2165526493","https://openalex.org/W2171005709","https://openalex.org/W2171280873","https://openalex.org/W2171327609","https://openalex.org/W2177489649","https://openalex.org/W2326628181","https://openalex.org/W4244164795"],"related_works":["https://openalex.org/W2021185324","https://openalex.org/W2950545321","https://openalex.org/W2043525390","https://openalex.org/W2117465991","https://openalex.org/W2601406067","https://openalex.org/W2067927099","https://openalex.org/W1990631690","https://openalex.org/W2138260287","https://openalex.org/W2610251648","https://openalex.org/W2112636327"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"concentration":[2],"gradient":[3,21,55,76,134,258,280],"of":[4,36,45,52,70,73,87,103,130,165,182,232,252,265,291,300],"Bicoid":[5,54,74,96,104,218,238],"protein":[6],"which":[7,117,317],"determines":[8],"the":[9,17,23,43,53,68,71,79,85,88,95,127,147,161,187,196,210,217,236,250,253,257,262,266,269,276,333],"developmental":[10,28],"pathways":[11],"in":[12,94,106,146,160,200,241,249,339],"early":[13],"Drosophila":[14,108],"embryo":[15,152],"is":[16,39,135,327],"best":[18],"characterized":[19],"morphogen":[20,75],"at":[22,78],"molecular":[24,59,80,219,239,278],"level.":[25],"Because":[26],"different":[27,34],"fates":[29],"can":[30,63,143,185,202,321],"be":[31,64,144,245,322],"elicited":[32],"by":[33,48],"concentrations":[35],"Bicoid,":[37],"it":[38],"important":[40],"to":[41,66,261,309],"probe":[42],"limits":[44,338],"this":[46,319],"specification":[47],"analyzing":[49],"intrinsic":[50,128,158],"fluctuations":[51],"arising":[56],"from":[57,150,157],"small":[58,180],"number.":[60],"Stochastic":[61],"simulations":[62,303],"applied":[65],"further":[67],"understanding":[69],"dynamics":[72],"formation":[77],"number":[81,220,240,279],"level,":[82],"and":[83,121,154,178,214,221,255,285,293],"determine":[84,310],"source":[86],"nucleus-to-nucleus":[89],"expression":[90],"variation":[91,222],"(noise)":[92],"observed":[93],"gradient.":[97],"RESULTS:":[98],"We":[99,124,138,170,193,274],"compared":[100],"quantitative":[101],"observations":[102],"levels":[105],"immunostained":[107,305],"embryos":[109,233],"with":[110,282,304],"a":[111,205,228,242,287],"spatially":[112],"extended":[113],"Master":[114,301],"Equation":[115,302],"model":[116],"represents":[118],"diffusion,":[119],"decay,":[120],"anterior":[122],"synthesis.":[123],"show":[125,171],"that":[126,195,235],"noise":[129,142,159,184,188,198,326],"an":[131,166],"autonomous":[132],"reaction-diffusion":[133],"Poisson":[136],"distributed.":[137],"demonstrate":[139,194],"how":[140,172,179],"experimental":[141],"identified":[145],"logarithm":[148],"domain":[149,164],"single":[151],"analysis,":[153],"then":[155],"separated":[156],"normalized":[162],"variance":[163,230,295],"ensemble":[167,231],"statistical":[168],"analysis.":[169],"measurement":[173,283],"sensitivity":[174],"affects":[175],"our":[176],"observations,":[177],"amounts":[181],"rescaling":[183],"perturb":[186],"strength":[189],"(Fano":[190],"factor)":[191],"observed.":[192],"biological":[197],"level":[199],"data":[201,306],"serve":[203],"as":[204,330],"physical":[206],"constraint":[207],"for":[208,215,313,318],"restricting":[209],"model's":[211],"parameter":[212],"space,":[213],"predicting":[216],"range.":[223],"An":[224],"estimate":[225],"based":[226],"on":[227],"low":[229],"suggests":[234],"steady-state":[237],"nucleus":[243],"should":[244,259],"larger":[246],"than":[247],"300":[248],"middle":[251],"embryo,":[254,267],"hence":[256],"extend":[260],"posterior":[263],"end":[264],"beyond":[268],"previously":[270],"assumed":[271],"background":[272],"limit.":[273],"exhibit":[275],"predicted":[277],"together":[281],"effects,":[284],"make":[286],"comparison":[288,299],"between":[289],"conditions":[290],"higher":[292],"lower":[294],"respectively.":[296],"CONCLUSION:":[297],"Quantitative":[298],"enabled":[307],"us":[308],"narrow":[311],"ranges":[312],"key":[314],"biophysical":[315],"parameters,":[316],"system":[320],"independently":[323],"validated.":[324],"Intrinsic":[325],"clearly":[328],"detectable":[329],"well,":[331],"although":[332],"staining":[334],"process":[335],"introduces":[336],"certain":[337],"resolution.":[340]},"counts_by_year":[{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":5}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
