{"id":"https://openalex.org/W2106412306","doi":"https://doi.org/10.1145/2024724.2024892","title":"Design of robust metabolic pathways","display_name":"Design of robust metabolic pathways","publication_year":2011,"publication_date":"2011-06-05","ids":{"openalex":"https://openalex.org/W2106412306","doi":"https://doi.org/10.1145/2024724.2024892","mag":"2106412306"},"language":"en","primary_location":{"id":"doi:10.1145/2024724.2024892","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2024724.2024892","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 48th Design Automation Conference","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://dspace.mit.edu/bitstream/1721.1/101144/1/122-yp468-Nicosia.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091880579","display_name":"Renato Umeton","orcid":"https://orcid.org/0000-0002-5561-6932"},"institutions":[{"id":"https://openalex.org/I4210110987","display_name":"IIT@MIT","ror":"https://ror.org/01wp8zh54","country_code":"US","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210110987"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Renato Umeton","raw_affiliation_strings":["MIT Cambridge, MA","Department of Biological Engineering, MIT, Cambridge, MA 02139, USA"],"affiliations":[{"raw_affiliation_string":"MIT Cambridge, MA","institution_ids":["https://openalex.org/I4210110987"]},{"raw_affiliation_string":"Department of Biological Engineering, MIT, Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I4210110987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090224486","display_name":"Giovanni Stracquadanio","orcid":"https://orcid.org/0000-0001-9819-3645"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Giovanni Stracquadanio","raw_affiliation_strings":["Johns Hopkins University, Baltimore, MD","Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218 USA"],"affiliations":[{"raw_affiliation_string":"Johns Hopkins University, Baltimore, MD","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218 USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022075541","display_name":"Anilkumar Sorathiya","orcid":null},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Anilkumar Sorathiya","raw_affiliation_strings":["U. of Cambridge, Cambridge, UK","Computer Laboratory U. of Cambridge, UK CB3 0FD"],"affiliations":[{"raw_affiliation_string":"U. of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Computer Laboratory U. of Cambridge, UK CB3 0FD","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056748708","display_name":"P\u00edetro Li\u00f3","orcid":"https://orcid.org/0000-0002-0540-5053"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Pietro Li\u00f2","raw_affiliation_strings":["U. of Cambridge, Cambridge, UK","Computer Laboratory U. of Cambridge, UK CB3 0FD"],"affiliations":[{"raw_affiliation_string":"U. of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Computer Laboratory U. of Cambridge, UK CB3 0FD","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025685078","display_name":"Alessio Papini","orcid":"https://orcid.org/0000-0001-7904-0336"},"institutions":[{"id":"https://openalex.org/I45084792","display_name":"University of Florence","ror":"https://ror.org/04jr1s763","country_code":"IT","type":"education","lineage":["https://openalex.org/I45084792"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessio Papini","raw_affiliation_strings":["U. of Florence, Firenze, Italy","Dept. of Evolutionary Biology U. of Florence, Firenze, Italy I-50121"],"affiliations":[{"raw_affiliation_string":"U. of Florence, Firenze, Italy","institution_ids":["https://openalex.org/I45084792"]},{"raw_affiliation_string":"Dept. of Evolutionary Biology U. of Florence, Firenze, Italy I-50121","institution_ids":["https://openalex.org/I45084792"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026158192","display_name":"Giuseppe Nicosia","orcid":"https://orcid.org/0000-0002-0650-3157"},"institutions":[{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giuseppe Nicosia","raw_affiliation_strings":["U. of Catania, Catania, Italy","Dept. of Mathematics & Computer Science U. of Catania, Italy I-95125"],"affiliations":[{"raw_affiliation_string":"U. of Catania, Catania, Italy","institution_ids":["https://openalex.org/I39063666"]},{"raw_affiliation_string":"Dept. of Mathematics & Computer Science U. of Catania, Italy I-95125","institution_ids":["https://openalex.org/I39063666"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5091880579"],"corresponding_institution_ids":["https://openalex.org/I4210110987"],"apc_list":null,"apc_paid":null,"fwci":0.9338,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.74176905,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9997000098228455,"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":0.9997000098228455,"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10404","display_name":"Enzyme Catalysis and Immobilization","score":0.9944000244140625,"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/geobacter-sulfurreducens","display_name":"Geobacter sulfurreducens","score":0.9106822609901428},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.6358051896095276},{"id":"https://openalex.org/keywords/photosynthesis","display_name":"Photosynthesis","score":0.5906217098236084},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.529646635055542},{"id":"https://openalex.org/keywords/multi-objective-optimization","display_name":"Multi-objective optimization","score":0.5114961862564087},{"id":"https://openalex.org/keywords/estimator","display_name":"Estimator","score":0.46096986532211304},{"id":"https://openalex.org/keywords/yield","display_name":"Yield (engineering)","score":0.45564326643943787},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.4138319790363312},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4067001938819885},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.38749295473098755},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.32905372977256775},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20268458127975464},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17950230836868286},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15032446384429932},{"id":"https://openalex.org/keywords/metabolism","display_name":"Metabolism","score":0.1490761637687683},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1278754472732544},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.11759451031684875},{"id":"https://openalex.org/keywords/biofilm","display_name":"Biofilm","score":0.09992033243179321},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.09463238716125488},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.07745346426963806}],"concepts":[{"id":"https://openalex.org/C2779812452","wikidata":"https://www.wikidata.org/wiki/Q1502805","display_name":"Geobacter sulfurreducens","level":4,"score":0.9106822609901428},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.6358051896095276},{"id":"https://openalex.org/C183688256","wikidata":"https://www.wikidata.org/wiki/Q11982","display_name":"Photosynthesis","level":2,"score":0.5906217098236084},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.529646635055542},{"id":"https://openalex.org/C68781425","wikidata":"https://www.wikidata.org/wiki/Q2052203","display_name":"Multi-objective optimization","level":2,"score":0.5114961862564087},{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.46096986532211304},{"id":"https://openalex.org/C134121241","wikidata":"https://www.wikidata.org/wiki/Q899301","display_name":"Yield (engineering)","level":2,"score":0.45564326643943787},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.4138319790363312},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4067001938819885},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.38749295473098755},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.32905372977256775},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20268458127975464},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17950230836868286},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15032446384429932},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.1490761637687683},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1278754472732544},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.11759451031684875},{"id":"https://openalex.org/C58123911","wikidata":"https://www.wikidata.org/wiki/Q467410","display_name":"Biofilm","level":3,"score":0.09992033243179321},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.09463238716125488},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.07745346426963806},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C191897082","wikidata":"https://www.wikidata.org/wiki/Q11467","display_name":"Metallurgy","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1145/2024724.2024892","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2024724.2024892","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 48th Design Automation Conference","raw_type":"proceedings-article"},{"id":"pmh:oai:dspace.mit.edu:1721.1/101144","is_oa":true,"landing_page_url":"http://hdl.handle.net/1721.1/101144","pdf_url":"https://dspace.mit.edu/bitstream/1721.1/101144/1/122-yp468-Nicosia.pdf","source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Umeton","raw_type":"http://purl.org/eprint/type/ConferencePaper"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.299.2594","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.299.2594","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.dmi.unict.it/~nicosia/papers/conferences/Nicosia-DAC-2011.pdf","raw_type":"text"},{"id":"pmh:oai:flore.unifi.it:2158/592786","is_oa":false,"landing_page_url":"http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5981995","pdf_url":null,"source":{"id":"https://openalex.org/S4306402033","display_name":"Florence Research (University of Florence)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45084792","host_organization_name":"University of Florence","host_organization_lineage":["https://openalex.org/I45084792"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"},{"id":"pmh:oai:repository.essex.ac.uk:18707","is_oa":false,"landing_page_url":"http://repository.essex.ac.uk/18707/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401236","display_name":"Open Access at Essex (University of Essex)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I110002522","host_organization_name":"University of Essex","host_organization_lineage":["https://openalex.org/I110002522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference or Workshop Item"}],"best_oa_location":{"id":"pmh:oai:dspace.mit.edu:1721.1/101144","is_oa":true,"landing_page_url":"http://hdl.handle.net/1721.1/101144","pdf_url":"https://dspace.mit.edu/bitstream/1721.1/101144/1/122-yp468-Nicosia.pdf","source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Umeton","raw_type":"http://purl.org/eprint/type/ConferencePaper"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2106412306.pdf","grobid_xml":"https://content.openalex.org/works/W2106412306.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1556517310","https://openalex.org/W1564638059","https://openalex.org/W2003010595","https://openalex.org/W2031808864","https://openalex.org/W2091507629","https://openalex.org/W2114185778","https://openalex.org/W2122266551","https://openalex.org/W2126105956","https://openalex.org/W2126392233","https://openalex.org/W2126729622","https://openalex.org/W2130364940","https://openalex.org/W2133034074","https://openalex.org/W2133769848","https://openalex.org/W2143381319","https://openalex.org/W2147120117","https://openalex.org/W2147472054","https://openalex.org/W2150689124","https://openalex.org/W2154174174","https://openalex.org/W2166152646","https://openalex.org/W2171092495","https://openalex.org/W2178309719","https://openalex.org/W4238101851"],"related_works":["https://openalex.org/W2501695202","https://openalex.org/W2801931653","https://openalex.org/W4252209016","https://openalex.org/W2531264461","https://openalex.org/W4224069007","https://openalex.org/W2123437519","https://openalex.org/W4252071083","https://openalex.org/W3131618642","https://openalex.org/W2227096786","https://openalex.org/W2143043177"],"abstract_inverted_index":{"In":[0],"this":[1],"paper":[2],"we":[3,16,29,39,50],"investigate":[4],"plant":[5],"photosynthesis":[6,28],"and":[7,18],"microbial":[8],"fuel":[9],"cells.":[10],"We":[11],"report":[12],"the":[13,31,41],"following:":[14],"1)":[15],"introduce":[17],"validate":[19],"a":[20],"novel":[21],"multi-objective":[22],"optimization":[23],"algorithm,":[24],"PMO2;":[25],"2)":[26],"in":[27,36],"increase":[30],"yield":[32],"of":[33,56],"135%,":[34],"while":[35],"Geobacter":[37],"sulfurreducens":[38],"determine":[40],"tradeoff":[42],"for":[43],"growth":[44],"versus":[45],"redox":[46],"properties;":[47],"3)":[48],"finally,":[49],"discuss":[51],"Pareto-Front":[52],"as":[53],"an":[54],"estimator":[55],"robust":[57],"metabolic":[58],"pathways.":[59]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}