{"id":"https://openalex.org/W2134603954","doi":"https://doi.org/10.1093/bioinformatics/btl271","title":"Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in <i>Escherichia coli</i>","display_name":"Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in <i>Escherichia coli</i>","publication_year":2006,"publication_date":"2006-05-26","ids":{"openalex":"https://openalex.org/W2134603954","doi":"https://doi.org/10.1093/bioinformatics/btl271","mag":"2134603954","pmid":"https://pubmed.ncbi.nlm.nih.gov/16731694"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl271","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl271","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/15/1895/48839687/bioinformatics_22_15_1895.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/22/15/1895/48839687/bioinformatics_22_15_1895.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084996809","display_name":"Jordi Vidal Rodr\u00edguez","orcid":null},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"J. Vidal Rodr\u00edguez","raw_affiliation_strings":["Section Computational Science, Faculty of Science, University of Amsterdam 1 \u00a0 1 \u00a0 \u00a0 Kruislaan 403, 1098 SJ Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Section Computational Science, Faculty of Science, University of Amsterdam 1 \u00a0 1 \u00a0 \u00a0 Kruislaan 403, 1098 SJ Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091729787","display_name":"Jaap A. Kaandorp","orcid":"https://orcid.org/0000-0003-4558-7135"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jaap A. Kaandorp","raw_affiliation_strings":["Section Computational Science, Faculty of Science, University of Amsterdam 1 \u00a0 1 \u00a0 \u00a0 Kruislaan 403, 1098 SJ Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Section Computational Science, Faculty of Science, University of Amsterdam 1 \u00a0 1 \u00a0 \u00a0 Kruislaan 403, 1098 SJ Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088488937","display_name":"Maciej Dobrzy\u0144ski","orcid":"https://orcid.org/0000-0002-0208-7758"},"institutions":[{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Maciej Dobrzy\u0144ski","raw_affiliation_strings":["Center for Mathematics and Computer Science (CWI) 2 \u00a0 2 \u00a0 \u00a0 Kruislaan 413, 1098 SJ Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Center for Mathematics and Computer Science (CWI) 2 \u00a0 2 \u00a0 \u00a0 Kruislaan 413, 1098 SJ Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1341640284"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109878628","display_name":"Joke Blom","orcid":null},"institutions":[{"id":"https://openalex.org/I1341640284","display_name":"Centrum Wiskunde & Informatica","ror":"https://ror.org/00x7ekv49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1341640284","https://openalex.org/I2800991832"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Joke G. Blom","raw_affiliation_strings":["Center for Mathematics and Computer Science (CWI) 2 \u00a0 2 \u00a0 \u00a0 Kruislaan 413, 1098 SJ Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Center for Mathematics and Computer Science (CWI) 2 \u00a0 2 \u00a0 \u00a0 Kruislaan 413, 1098 SJ Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I1341640284"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5084996809"],"corresponding_institution_ids":["https://openalex.org/I887064364"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.1328,"has_fulltext":true,"cited_by_count":102,"citation_normalized_percentile":{"value":0.91713293,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"22","issue":"15","first_page":"1895","last_page":"1901"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9979000091552734,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9905999898910522,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phosphoenolpyruvate-carboxykinase","display_name":"Phosphoenolpyruvate carboxykinase","score":0.9617894887924194},{"id":"https://openalex.org/keywords/pep-group-translocation","display_name":"PEP group translocation","score":0.8395509719848633},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.7448604702949524},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.44558513164520264},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4428223967552185},{"id":"https://openalex.org/keywords/phosphotransferase","display_name":"Phosphotransferase","score":0.41814666986465454},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3483954668045044},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.2708362340927124},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14974603056907654}],"concepts":[{"id":"https://openalex.org/C143937172","wikidata":"https://www.wikidata.org/wiki/Q303568","display_name":"Phosphoenolpyruvate carboxykinase","level":3,"score":0.9617894887924194},{"id":"https://openalex.org/C45656491","wikidata":"https://www.wikidata.org/wiki/Q1538418","display_name":"PEP group translocation","level":4,"score":0.8395509719848633},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.7448604702949524},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.44558513164520264},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4428223967552185},{"id":"https://openalex.org/C2777504003","wikidata":"https://www.wikidata.org/wiki/Q3381520","display_name":"Phosphotransferase","level":3,"score":0.41814666986465454},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3483954668045044},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.2708362340927124},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14974603056907654}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D010728","descriptor_name":"Phosphoenolpyruvate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010728","descriptor_name":"Phosphoenolpyruvate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010728","descriptor_name":"Phosphoenolpyruvate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010770","descriptor_name":"Phosphotransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010770","descriptor_name":"Phosphotransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010770","descriptor_name":"Phosphotransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029968","descriptor_name":"Escherichia coli Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btl271","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl271","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/15/1895/48839687/bioinformatics_22_15_1895.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16731694","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16731694","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:dare.uva.nl:openaire_cris_publications/42c066da-14f9-411a-a106-ee6a5f1b905a","is_oa":false,"landing_page_url":"https://handle.uba.uva.nl/personal/pure/en/publications/spatial-stochastic-modelling-of-the-phosphoenolpyruvatedependent-phosphotransferase-pts-pathway-in-escherichia-coli(42c066da-14f9-411a-a106-ee6a5f1b905a).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400088","display_name":"UvA-DARE (University of Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887064364","host_organization_name":"University of Amsterdam","host_organization_lineage":["https://openalex.org/I887064364"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Vidal Rodr\u00edguez, J, Kaandorp, J A, Dobrzy\u0144ski, M & Blom, J G 2006, 'Spatial Stochastic Modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli', Bioinformatics, vol. 22, pp. 1895-1901. https://doi.org/10.1093/bioinformatics/btl271","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:dare.uva.nl:publications/42c066da-14f9-411a-a106-ee6a5f1b905a","is_oa":false,"landing_page_url":"http://dare.uva.nl/personal/pure/en/publications/spatial-stochastic-modelling-of-the-phosphoenolpyruvatedependent-phosphotransferase-pts-pathway-in-escherichia-coli(42c066da-14f9-411a-a106-ee6a5f1b905a).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400088","display_name":"UvA-DARE (University of Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887064364","host_organization_name":"University of Amsterdam","host_organization_lineage":["https://openalex.org/I887064364"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:uvapub:oai:dare.uva.nl:publications/42c066da-14f9-411a-a106-ee6a5f1b905a","is_oa":false,"landing_page_url":"https://dare.uva.nl/personal/pure/en/publications/spatial-stochastic-modelling-of-the-phosphoenolpyruvatedependent-phosphotransferase-pts-pathway-in-escherichia-coli(42c066da-14f9-411a-a106-ee6a5f1b905a).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 22, 1895 - 1901. Oxford University Press","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl271","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl271","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/15/1895/48839687/bioinformatics_22_15_1895.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2134603954.pdf","grobid_xml":"https://content.openalex.org/works/W2134603954.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W86248839","https://openalex.org/W1688739247","https://openalex.org/W1946177469","https://openalex.org/W1978408051","https://openalex.org/W1988498168","https://openalex.org/W2013194100","https://openalex.org/W2017260253","https://openalex.org/W2023688597","https://openalex.org/W2059053384","https://openalex.org/W2066100786","https://openalex.org/W2068359975","https://openalex.org/W2096015757","https://openalex.org/W2097242011","https://openalex.org/W2105627149","https://openalex.org/W2107342968","https://openalex.org/W2116620527","https://openalex.org/W2129502305","https://openalex.org/W2132898564","https://openalex.org/W2144258647","https://openalex.org/W2154892443","https://openalex.org/W2155418451","https://openalex.org/W2171539493","https://openalex.org/W6637006454"],"related_works":["https://openalex.org/W2033434138","https://openalex.org/W2913500940","https://openalex.org/W1974228300","https://openalex.org/W1682509349","https://openalex.org/W1984963993","https://openalex.org/W2468406986","https://openalex.org/W1518355276","https://openalex.org/W2076183099","https://openalex.org/W651806294","https://openalex.org/W1830877619"],"abstract_inverted_index":{"The":[0],"source":[1],"code":[2],"for":[3],"the":[4],"GMP":[5],"method":[6],"is":[7],"available":[8],"at":[9],"http://www.science.uva.nl/research/scs/CellMath/GMP.":[10]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":10}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2016-06-24T00:00:00"}
