{"id":"https://openalex.org/W2159046100","doi":"https://doi.org/10.1186/s12918-014-0131-1","title":"Spatial localization of the first and last enzymes effectively connects active metabolic pathways in bacteria","display_name":"Spatial localization of the first and last enzymes effectively connects active metabolic pathways in bacteria","publication_year":2014,"publication_date":"2014-12-01","ids":{"openalex":"https://openalex.org/W2159046100","doi":"https://doi.org/10.1186/s12918-014-0131-1","mag":"2159046100","pmid":"https://pubmed.ncbi.nlm.nih.gov/25495800"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-014-0131-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-014-0131-1","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-014-0131-1","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/s12918-014-0131-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046474433","display_name":"Pablo Meyer","orcid":"https://orcid.org/0000-0001-5281-4661"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pablo Meyer","raw_affiliation_strings":["IBM Computational Biology Center, Yorktown Heights, NY, USA. pmeyerr@us.ibm.com","IBM Computational Biology Center, Yorktown Heights, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Computational Biology Center, Yorktown Heights, NY, USA. pmeyerr@us.ibm.com","institution_ids":[]},{"raw_affiliation_string":"IBM Computational Biology Center, Yorktown Heights, NY, USA","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065396462","display_name":"Guillermo Cecchi","orcid":"https://orcid.org/0000-0003-1013-8348"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guillermo Cecchi","raw_affiliation_strings":["IBM Computational Biology Center, Yorktown Heights, NY, USA. gcecchi@us.ibm.com","IBM Computational Biology Center, Yorktown Heights, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Computational Biology Center, Yorktown Heights, NY, USA. gcecchi@us.ibm.com","institution_ids":[]},{"raw_affiliation_string":"IBM Computational Biology Center, Yorktown Heights, NY, USA","institution_ids":["https://openalex.org/I1341412227"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000065699","display_name":"Gustavo Stolovitzky","orcid":"https://orcid.org/0000-0002-9618-2819"},"institutions":[{"id":"https://openalex.org/I1341412227","display_name":"IBM (United States)","ror":"https://ror.org/05hh8d621","country_code":"US","type":"company","lineage":["https://openalex.org/I1341412227"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gustavo Stolovitzky","raw_affiliation_strings":["IBM Computational Biology Center, Yorktown Heights, NY, USA. gustavo@us.ibm.com","IBM Computational Biology Center, Yorktown Heights, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Computational Biology Center, Yorktown Heights, NY, USA. gustavo@us.ibm.com","institution_ids":[]},{"raw_affiliation_string":"IBM Computational Biology Center, Yorktown Heights, NY, USA","institution_ids":["https://openalex.org/I1341412227"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5046474433"],"corresponding_institution_ids":["https://openalex.org/I1341412227"],"apc_list":null,"apc_paid":null,"fwci":0.5691,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.68151973,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"8","issue":"1","first_page":"131","last_page":"131"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.4490000009536743,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.4490000009536743,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.1695999950170517,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.05429999902844429,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.7540633678436279},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6751240491867065},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.6413282155990601},{"id":"https://openalex.org/keywords/cytoplasm","display_name":"Cytoplasm","score":0.6058684587478638},{"id":"https://openalex.org/keywords/exponential-growth","display_name":"Exponential growth","score":0.5154586434364319},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.4979720115661621},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.45607832074165344},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.45290714502334595},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.4483081102371216},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.44773828983306885},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39570552110671997}],"concepts":[{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.7540633678436279},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6751240491867065},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.6413282155990601},{"id":"https://openalex.org/C190062978","wikidata":"https://www.wikidata.org/wiki/Q79899","display_name":"Cytoplasm","level":2,"score":0.6058684587478638},{"id":"https://openalex.org/C75235859","wikidata":"https://www.wikidata.org/wiki/Q582659","display_name":"Exponential growth","level":2,"score":0.5154586434364319},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.4979720115661621},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.45607832074165344},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.45290714502334595},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.4483081102371216},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.44773828983306885},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39570552110671997},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003593","descriptor_name":"Cytoplasm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003593","descriptor_name":"Cytoplasm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003593","descriptor_name":"Cytoplasm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D053898","descriptor_name":"Biosynthetic Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D053898","descriptor_name":"Biosynthetic Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D053898","descriptor_name":"Biosynthetic Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D062206","descriptor_name":"Spatial Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062206","descriptor_name":"Spatial Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062206","descriptor_name":"Spatial Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/s12918-014-0131-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-014-0131-1","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-014-0131-1","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:25495800","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25495800","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:europepmc.org:3269317","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4279816","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-014-0131-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-014-0131-1","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-014-0131-1","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":[{"display_name":"Life in Land","score":0.44999998807907104,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320308318","display_name":"Helen Hay Whitney Foundation","ror":"https://ror.org/037ebw447"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2159046100.pdf","grobid_xml":"https://content.openalex.org/works/W2159046100.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1568106481","https://openalex.org/W1642162696","https://openalex.org/W1843350440","https://openalex.org/W1968913339","https://openalex.org/W1970556744","https://openalex.org/W1979242519","https://openalex.org/W1979682650","https://openalex.org/W1988027333","https://openalex.org/W2007325299","https://openalex.org/W2009994916","https://openalex.org/W2011803261","https://openalex.org/W2024184910","https://openalex.org/W2037663758","https://openalex.org/W2042638652","https://openalex.org/W2043450929","https://openalex.org/W2050846271","https://openalex.org/W2070695257","https://openalex.org/W2072796170","https://openalex.org/W2079905392","https://openalex.org/W2081320341","https://openalex.org/W2082658471","https://openalex.org/W2105627149","https://openalex.org/W2110585845","https://openalex.org/W2112795872","https://openalex.org/W2114085934","https://openalex.org/W2124254997","https://openalex.org/W2132105526","https://openalex.org/W2132490111","https://openalex.org/W2135386829","https://openalex.org/W2147189708","https://openalex.org/W2156737316","https://openalex.org/W2159131031","https://openalex.org/W2170427655","https://openalex.org/W2308740962","https://openalex.org/W4250838544"],"related_works":["https://openalex.org/W2063475537","https://openalex.org/W2341681417","https://openalex.org/W1961707331","https://openalex.org/W2012938657","https://openalex.org/W2133150343","https://openalex.org/W1578136679","https://openalex.org/W2072067873","https://openalex.org/W2096004952","https://openalex.org/W2087715585","https://openalex.org/W2147962989"],"abstract_inverted_index":{"BACKGROUND:":[0],"Although":[1],"much":[2],"is":[3,15],"understood":[4],"about":[5,17],"the":[6,18,31,59,63,66,149,155,184,203,211,215],"enzymatic":[7],"cascades":[8],"that":[9,20,44,82,137,165,179],"underlie":[10],"cellular":[11,23,152],"biosynthesis,":[12],"comparatively":[13],"little":[14],"known":[16],"rules":[19],"determine":[21],"their":[22,113,193,196],"organization.":[24],"We":[25,42,177],"performed":[26],"a":[27,54,91,96,104,141,190],"detailed":[28],"analysis":[29,76,119],"of":[30,33,46,71,77,107,120,126,151,154,214],"localization":[32,57,153],"E.coli":[34],"GFP-tagged":[35],"enzymes":[36,122,159,166,198],"for":[37,145],"cells":[38],"growing":[39,134],"exponentially.":[40],"RESULTS:":[41],"found":[43,164],"out":[45],"857":[47],"globular":[48],"enzymes,":[49,84],"at":[50],"least":[51],"219":[52],"have":[53,95],"discrete":[55],"punctuate":[56],"in":[58,69,85,133,160],"cytoplasm":[60,185],"and":[61,100,109,163,207],"catalyze":[62],"first":[64,194],"or":[65,195],"last":[67,197],"reaction":[68],"60%":[70],"biosynthetic":[72],"pathways.":[73],"A":[74,116],"graph-theoretic":[75],"E.coli's":[78],"metabolic":[79,131,143,217],"network":[80],"shows":[81],"localized":[83],"contrast":[86],"to":[87,129,200],"non-localized":[88,114],"ones,":[89],"form":[90],"tree-like":[92],"hierarchical":[93],"structure,":[94],"higher":[97,105],"within-group":[98],"connectivity,":[99],"are":[101,186],"traversed":[102],"by":[103],"number":[106],"feed-forward":[108],"feedback":[110],"loops":[111],"than":[112],"counterparts.":[115],"Gene":[117],"Ontology":[118],"these":[121,138],"reveals":[123],"an":[124],"enrichment":[125],"terms":[127],"related":[128],"essential":[130],"functions":[132],"cells.":[135],"Given":[136],"findings":[139],"suggest":[140],"distinct":[142],"role":[144],"localization,":[146],"we":[147],"studied":[148],"dynamics":[150],"cell":[156],"wall":[157],"synthesizing":[158],"B.":[161],"subtilis":[162],"localize":[167,199],"during":[168,173],"exponential":[169],"growth":[170],"but":[171],"not":[172],"stationary":[174],"growth.":[175],"CONCLUSIONS:":[176],"conclude":[178],"active":[180,205],"biochemical":[181],"pathways":[182,206],"inside":[183],"organized":[187],"spatially":[188],"following":[189],"rule":[191],"where":[192],"effectively":[201],"connect":[202],"different":[204],"thus":[208],"could":[209],"reflect":[210],"activity":[212],"state":[213],"cell's":[216],"network.":[218]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":3}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}