{"id":"https://openalex.org/W1738195056","doi":"https://doi.org/10.1186/1471-2105-14-s7-s7","title":"Quasi-cellular systems: stochastic simulation analysis at nanoscale range","display_name":"Quasi-cellular systems: stochastic simulation analysis at nanoscale range","publication_year":2013,"publication_date":"2013-04-01","ids":{"openalex":"https://openalex.org/W1738195056","doi":"https://doi.org/10.1186/1471-2105-14-s7-s7","mag":"1738195056","pmid":"https://pubmed.ncbi.nlm.nih.gov/23815522"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-s7-s7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s7-s7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S7-S7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S7-S7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062544718","display_name":"Lorenzo Calviello","orcid":"https://orcid.org/0000-0002-5600-0988"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Lorenzo Calviello","raw_affiliation_strings":["Dipartimento di Informatica, Universit\u00e0 di Pisa, L.go B. Pontecorvo 3, 56127 Pisa, Italy","Dipartimento di Informatica, Universit\u00e0 di Pisa, L.go B. Pontecorvo 3, 56127, Pisa, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica, Universit\u00e0 di Pisa, L.go B. Pontecorvo 3, 56127 Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]},{"raw_affiliation_string":"Dipartimento di Informatica, Universit\u00e0 di Pisa, L.go B. Pontecorvo 3, 56127, Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005149620","display_name":"Pasquale Stano","orcid":"https://orcid.org/0000-0002-2228-2825"},"institutions":[{"id":"https://openalex.org/I119003972","display_name":"Roma Tre University","ror":"https://ror.org/05vf0dg29","country_code":"IT","type":"education","lineage":["https://openalex.org/I119003972"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Pasquale Stano","raw_affiliation_strings":["Dipartimento di Biologia, Universit\u00e0 di Roma III, Via G. Marconi 446, 00146, Roma, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Biologia, Universit\u00e0 di Roma III, Via G. Marconi 446, 00146, Roma, Italy","institution_ids":["https://openalex.org/I119003972"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003346364","display_name":"Fabio Mavelli","orcid":null},"institutions":[{"id":"https://openalex.org/I5561750","display_name":"University of Bari Aldo Moro","ror":"https://ror.org/027ynra39","country_code":"IT","type":"education","lineage":["https://openalex.org/I5561750"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Fabio Mavelli","raw_affiliation_strings":["Dipartimento di Chimica, Universit\u00e0 di Bari, Via E. Orabona 4, 70121, Bari, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Chimica, Universit\u00e0 di Bari, Via E. Orabona 4, 70121, Bari, Italy","institution_ids":["https://openalex.org/I5561750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111955256","display_name":"Pier Luigi Luisi","orcid":null},"institutions":[{"id":"https://openalex.org/I119003972","display_name":"Roma Tre University","ror":"https://ror.org/05vf0dg29","country_code":"IT","type":"education","lineage":["https://openalex.org/I119003972"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Pier Luigi Luisi","raw_affiliation_strings":["Dipartimento di Biologia, Universit\u00e0 di Roma III, Via G. Marconi 446, 00146, Roma, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Biologia, Universit\u00e0 di Roma III, Via G. Marconi 446, 00146, Roma, Italy","institution_ids":["https://openalex.org/I119003972"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080527399","display_name":"Roberto Marangoni","orcid":"https://orcid.org/0000-0002-6603-6984"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]},{"id":"https://openalex.org/I4210143448","display_name":"Instituto di Biofisica","ror":"https://ror.org/041xzk838","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210143448","https://openalex.org/I4210155236"]}],"countries":["ES","IT"],"is_corresponding":true,"raw_author_name":"Roberto Marangoni","raw_affiliation_strings":["Dipartimento di Informatica, Universit\u00e0 di Pisa, L.go B. Pontecorvo 3, 56127, Pisa, Italy","Istituto di Biofisica del CNR, Via G. Moruzzi 1, 56124, Pisa, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica, Universit\u00e0 di Pisa, L.go B. Pontecorvo 3, 56127, Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]},{"raw_affiliation_string":"Istituto di Biofisica del CNR, Via G. Moruzzi 1, 56124, Pisa, Italy","institution_ids":["https://openalex.org/I4210143448"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5080527399"],"corresponding_institution_ids":["https://openalex.org/I108290504","https://openalex.org/I4210143448"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":2.0613,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.86360865,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"14","issue":"S7","first_page":"S7","last_page":"S7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.2287999987602234,"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/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.2287999987602234,"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/T10725","display_name":"RNA Interference and Gene Delivery","score":0.14300000667572021,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.09880000352859497,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.6331743597984314},{"id":"https://openalex.org/keywords/liposome","display_name":"Liposome","score":0.49948978424072266},{"id":"https://openalex.org/keywords/fluorescence","display_name":"Fluorescence","score":0.4786982834339142},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4714775085449219},{"id":"https://openalex.org/keywords/green-fluorescent-protein","display_name":"Green fluorescent protein","score":0.4662294387817383},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.4548620879650116},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4438480734825134},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4419354796409607},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.43199270963668823},{"id":"https://openalex.org/keywords/nanoscopic-scale","display_name":"Nanoscopic scale","score":0.4134064018726349},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.38179925084114075},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3718875050544739},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.2862222492694855},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2680506408214569},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23788994550704956},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1455632448196411},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11631852388381958},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1093912124633789}],"concepts":[{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.6331743597984314},{"id":"https://openalex.org/C185154212","wikidata":"https://www.wikidata.org/wiki/Q410454","display_name":"Liposome","level":2,"score":0.49948978424072266},{"id":"https://openalex.org/C91881484","wikidata":"https://www.wikidata.org/wiki/Q191807","display_name":"Fluorescence","level":2,"score":0.4786982834339142},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4714775085449219},{"id":"https://openalex.org/C142613039","wikidata":"https://www.wikidata.org/wiki/Q272983","display_name":"Green fluorescent protein","level":3,"score":0.4662294387817383},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.4548620879650116},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4438480734825134},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4419354796409607},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.43199270963668823},{"id":"https://openalex.org/C45206210","wikidata":"https://www.wikidata.org/wiki/Q2415817","display_name":"Nanoscopic scale","level":2,"score":0.4134064018726349},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.38179925084114075},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3718875050544739},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.2862222492694855},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2680506408214569},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23788994550704956},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1455632448196411},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11631852388381958},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1093912124633789},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002474","descriptor_name":"Cell-Free System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002474","descriptor_name":"Cell-Free System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002474","descriptor_name":"Cell-Free System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008081","descriptor_name":"Liposomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008081","descriptor_name":"Liposomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008081","descriptor_name":"Liposomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","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":"D049452","descriptor_name":"Green Fluorescent Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-14-s7-s7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s7-s7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S7-S7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23815522","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23815522","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 bioinformatics","raw_type":null},{"id":"pmh:oai:etd.adm.unipi.it:etd-06252012-133856","is_oa":true,"landing_page_url":"http://etd.adm.unipi.it/theses/available/etd-06252012-133856/","pdf_url":"https://etd.adm.unipi.it/theses/available/etd-06252012-133856/unrestricted/TesiMagistrale_Lorenzo_Calviello.pdf","source":{"id":"https://openalex.org/S4306401800","display_name":"Electronic Theses and Dissertations Repository (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://etd.adm.unipi.it/theses/available/etd-06252012-133856/","raw_type":"text"},{"id":"pmh:oai:europepmc.org:2631515","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3633058","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"},{"id":"pmh:oai:arpi.unipi.it:11568/853155","is_oa":true,"landing_page_url":"http://hdl.handle.net/11568/853155","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"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":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:ricerca.uniba.it:11586/33864","is_oa":false,"landing_page_url":"http://hdl.handle.net/11586/33864","pdf_url":null,"source":{"id":"https://openalex.org/S4377196296","display_name":"CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I5561750","host_organization_name":"University of Bari Aldo Moro","host_organization_lineage":["https://openalex.org/I5561750"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-14-s7-s7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s7-s7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S7-S7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1738195056.pdf","grobid_xml":"https://content.openalex.org/works/W1738195056.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1587481053","https://openalex.org/W1974156076","https://openalex.org/W1975115468","https://openalex.org/W1984121585","https://openalex.org/W1984704432","https://openalex.org/W1984983643","https://openalex.org/W1987445483","https://openalex.org/W2000840693","https://openalex.org/W2004628972","https://openalex.org/W2011598430","https://openalex.org/W2014625274","https://openalex.org/W2025235840","https://openalex.org/W2026612033","https://openalex.org/W2029132648","https://openalex.org/W2031867321","https://openalex.org/W2033473419","https://openalex.org/W2036684586","https://openalex.org/W2042321087","https://openalex.org/W2047202960","https://openalex.org/W2049004176","https://openalex.org/W2049492969","https://openalex.org/W2058652191","https://openalex.org/W2081250164","https://openalex.org/W2087044877","https://openalex.org/W2092205415","https://openalex.org/W2097002638","https://openalex.org/W2113895609","https://openalex.org/W2117147910","https://openalex.org/W2128651447","https://openalex.org/W2139161084","https://openalex.org/W2140937954","https://openalex.org/W2167154952","https://openalex.org/W2169381840","https://openalex.org/W4235033012","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2057769265","https://openalex.org/W2338895903","https://openalex.org/W2024161258","https://openalex.org/W1911418903","https://openalex.org/W3044523069","https://openalex.org/W2126646394","https://openalex.org/W2211443823","https://openalex.org/W3144585500","https://openalex.org/W4211049090","https://openalex.org/W2136248167"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,62,214,284],"wet-lab":[2],"synthesis":[3],"of":[4,8,64,83,141,166,177,190,195,212,217,247,298],"the":[5,34,46,57,81,99,111,129,146,150,158,163,180,187,191,199,210,218,233,256,261,288,293,295,299,314,329,335,343,348],"simplest":[6],"forms":[7],"life":[9],"(minimal":[10],"cells)":[11],"is":[12,42,69,76,251,287,308],"a":[13,70,77,93,332],"challenging":[14],"aspect":[15],"in":[16,39,66,80,127,157,198,292,318],"modern":[17],"synthetic":[18],"biology.":[19],"Quasi-cellular":[20],"systems":[21],"able":[22,206],"to":[23,44,117,125,137,182,207,223,254,260,275,278,302],"produce":[24],"proteins":[25],"directly":[26],"from":[27,119],"DNA":[28,51],"can":[29],"be":[30],"obtained":[31],"by":[32,327],"encapsulating":[33],"cell-free":[35],"transcription/translation":[36],"system":[37],"PURESYSTEM(PS)":[38],"liposomes.":[40],"It":[41],"possible":[43],"detect":[45],"intra-vesicle":[47,257],"protein":[48],"production":[49,316],"using":[50,328],"encoding":[52],"for":[53,173,242],"GFP":[54,315],"and":[55,152,325,339],"monitoring":[56],"fluorescence":[58,131],"emission":[59],"over":[60],"time.":[61],"entrapment":[63,264,349],"solutes":[65,337],"small-volume":[67,243],"liposomes":[68,175,244],"fundamental":[71],"open":[72],"problem.":[73],"Stochastic":[74],"simulation":[75,95,330],"valuable":[78],"tool":[79],"study":[82,241],"biochemical":[84],"reaction":[85],"at":[86,312],"nanoscale":[87],"range.":[88],"QDC":[89],"(Quick":[90],"Direct-Method":[91],"Controlled),":[92],"stochastic":[94,296],"software":[96],"based":[97],"on":[98,232,342],"well-known":[100],"Gillespie's":[101,167],"SSA":[102],"algorithm,":[103],"was":[104,115],"used.":[105],"A":[106],"suitable":[107,138],"model":[108],"formally":[109],"describing":[110,291],"PS":[112,181,200],"reactions":[113],"network":[114],"developed,":[116],"predict,":[118],"inner":[120],"species":[121],"concentrations":[122,189],"(very":[123],"difficult":[124],"measure":[126],"small-volumes),":[128],"resulting":[130],"signal":[132],"(experimentally":[133],"observable).":[134],"RESULTS:":[135],"Thanks":[136,301],"features":[139],"specific":[140],"QDC,":[142],"we":[143,204,238],"successfully":[144],"formalized":[145],"dynamical":[147],"coupling":[148],"between":[149],"transcription":[151],"translation":[153],"processes":[154],"that":[155,272],"occurs":[156],"real":[159],"PS,":[160],"thus":[161],"bypassing":[162],"concurrent-only":[164],"environment":[165],"algorithm.":[168],"Simulations":[169],"were":[170,205],"firstly":[171],"performed":[172],"large":[174],"(2.67\u00b5m":[176],"diameter)":[178],"entrapping":[179],"synthetize":[183],"GFP.":[184],"By":[185],"varying":[186],"initial":[188,235],"three":[192,225],"main":[193],"classes":[194],"molecules":[196],"involved":[197],"(DNA,":[201],"enzymes,":[202],"consumables),":[203],"stochastically":[208],"simulate":[209],"time-course":[211],"GFP-production.":[213],"sigmoid":[215],"fit":[216],"GFP-production":[219],"curves":[220],"allowed":[221],"us":[222],"extract":[224],"quantitative":[226],"parameters":[227],"which":[228],"are":[229,273],"significantly":[230,279],"dependent":[231],"various":[234],"states.":[236],"Then":[237],"extended":[239],"this":[240],"(575":[245],"nm":[246],"diameter),":[248],"where":[249],"it":[250],"more":[252],"complex":[253],"infer":[255],"composition,":[258],"due":[259],"expected":[262],"anomalous":[263],"phenomena.":[265],"We":[266],"identified":[267],"almost":[268],"two":[269],"extreme":[270],"states":[271],"forecasted":[274],"give":[276],"rise":[277],"different":[280],"experimental":[281,306],"observables.":[282],"CONCLUSIONS:":[283],"present":[285],"work":[286],"first":[289],"one":[290],"detail":[294],"behavior":[297],"PS.":[300],"our":[303],"results,":[304],"an":[305],"approach":[307],"now":[309],"possible,":[310],"aimed":[311],"recording":[313],"kinetics":[317],"very":[319],"small":[320],"micro-emulsion":[321],"droplets":[322],"or":[323],"liposomes,":[324],"inferring,":[326],"as":[331],"reverse-engineering":[333],"procedure,":[334],"internal":[336],"distribution,":[338],"shed":[340],"light":[341],"still":[344],"unknown":[345],"forces":[346],"driving":[347],"phenomenon.":[350]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-12T21:12:35.861297","created_date":"2025-10-10T00:00:00"}
