{"id":"https://openalex.org/W2003567369","doi":"https://doi.org/10.1186/1752-0509-4-7","title":"In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene","display_name":"In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene","publication_year":2010,"publication_date":"2010-02-02","ids":{"openalex":"https://openalex.org/W2003567369","doi":"https://doi.org/10.1186/1752-0509-4-7","mag":"2003567369","pmid":"https://pubmed.ncbi.nlm.nih.gov/20122273"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-4-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-7","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-7","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067702764","display_name":"Stacey D. Finley","orcid":"https://orcid.org/0000-0001-6901-3692"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stacey D Finley","raw_affiliation_strings":["Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL 60208, USA","Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, IL 60208, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, USA","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054861635","display_name":"Linda J. Broadbelt","orcid":"https://orcid.org/0000-0003-4253-592X"},"institutions":[{"id":"https://openalex.org/I111979921","display_name":"Northwestern University","ror":"https://ror.org/000e0be47","country_code":"US","type":"education","lineage":["https://openalex.org/I111979921"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Linda J Broadbelt","raw_affiliation_strings":["Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA","Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA","institution_ids":["https://openalex.org/I111979921"]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Sciences, Northwestern University, Evanston, USA","institution_ids":["https://openalex.org/I111979921"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056011141","display_name":"Vassily Hatzimanikatis","orcid":"https://orcid.org/0000-0001-6432-4694"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Vassily Hatzimanikatis","raw_affiliation_strings":["Laboratory of Computational Systems Biotechnology, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), CH H4 625, Station 6, CH-1015, Lausanne, Switzerland","Laboratory of Computational Systems Biotechnology, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Systems Biotechnology, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), CH H4 625, Station 6, CH-1015, Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864","https://openalex.org/I12708293"]},{"raw_affiliation_string":"Laboratory of Computational Systems Biotechnology, Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.8593,"has_fulltext":true,"cited_by_count":104,"citation_normalized_percentile":{"value":0.90686814,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"4","issue":"1","first_page":"7","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.4693000018596649,"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":0.4693000018596649,"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/T10324","display_name":"Microbial bioremediation and biosurfactants","score":0.43050000071525574,"subfield":{"id":"https://openalex.org/subfields/2310","display_name":"Pollution"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12688","display_name":"Microbial metabolism and enzyme function","score":0.04490000009536743,"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/organism","display_name":"Organism","score":0.7199957966804504},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.6999785304069519},{"id":"https://openalex.org/keywords/bioremediation","display_name":"Bioremediation","score":0.6632688045501709},{"id":"https://openalex.org/keywords/biodegradation","display_name":"Biodegradation","score":0.6358932852745056},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.6158347129821777},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5588600635528564},{"id":"https://openalex.org/keywords/pseudomonas-putida","display_name":"Pseudomonas putida","score":0.5588576793670654},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5044511556625366},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.4831935465335846},{"id":"https://openalex.org/keywords/metabolic-engineering","display_name":"Metabolic engineering","score":0.46366244554519653},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4550110697746277},{"id":"https://openalex.org/keywords/metabolic-flux-analysis","display_name":"Metabolic flux analysis","score":0.4231511950492859},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4196015000343323},{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.41816315054893494},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37410447001457214},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.29539066553115845},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2119268774986267},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.16218256950378418},{"id":"https://openalex.org/keywords/metabolism","display_name":"Metabolism","score":0.1185966432094574},{"id":"https://openalex.org/keywords/contamination","display_name":"Contamination","score":0.08479002118110657},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08117818832397461},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07764589786529541}],"concepts":[{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.7199957966804504},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.6999785304069519},{"id":"https://openalex.org/C2124996","wikidata":"https://www.wikidata.org/wiki/Q816441","display_name":"Bioremediation","level":3,"score":0.6632688045501709},{"id":"https://openalex.org/C157021035","wikidata":"https://www.wikidata.org/wiki/Q696715","display_name":"Biodegradation","level":2,"score":0.6358932852745056},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.6158347129821777},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5588600635528564},{"id":"https://openalex.org/C2780543182","wikidata":"https://www.wikidata.org/wiki/Q2738168","display_name":"Pseudomonas putida","level":3,"score":0.5588576793670654},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5044511556625366},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.4831935465335846},{"id":"https://openalex.org/C6350086","wikidata":"https://www.wikidata.org/wiki/Q6822347","display_name":"Metabolic engineering","level":3,"score":0.46366244554519653},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4550110697746277},{"id":"https://openalex.org/C160941953","wikidata":"https://www.wikidata.org/wiki/Q6822342","display_name":"Metabolic flux analysis","level":3,"score":0.4231511950492859},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4196015000343323},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.41816315054893494},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37410447001457214},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.29539066553115845},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2119268774986267},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.16218256950378418},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.1185966432094574},{"id":"https://openalex.org/C112570922","wikidata":"https://www.wikidata.org/wiki/Q60528603","display_name":"Contamination","level":2,"score":0.08479002118110657},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08117818832397461},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07764589786529541},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001673","descriptor_name":"Biodegradation, Environmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001673","descriptor_name":"Biodegradation, Environmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001673","descriptor_name":"Biodegradation, Environmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002722","descriptor_name":"Chlorobenzenes","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D002722","descriptor_name":"Chlorobenzenes","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D002722","descriptor_name":"Chlorobenzenes","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D002722","descriptor_name":"Chlorobenzenes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002722","descriptor_name":"Chlorobenzenes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002722","descriptor_name":"Chlorobenzenes","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004785","descriptor_name":"Environmental Pollutants","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D004785","descriptor_name":"Environmental Pollutants","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D004785","descriptor_name":"Environmental Pollutants","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D004785","descriptor_name":"Environmental Pollutants","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004785","descriptor_name":"Environmental Pollutants","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004785","descriptor_name":"Environmental Pollutants","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005240","descriptor_name":"Feasibility Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005240","descriptor_name":"Feasibility Studies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005240","descriptor_name":"Feasibility Studies","qualifier_ui":null,"qualifier_name":null,"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":"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":"D016958","descriptor_name":"Pseudomonas putida","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016958","descriptor_name":"Pseudomonas putida","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016958","descriptor_name":"Pseudomonas putida","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1752-0509-4-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-7","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-7","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:20122273","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20122273","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:infoscience.epfl.ch:172808","is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/172808","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:infoscience.tind.io:172808","is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/75674","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"research article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2830930","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2830930","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-4-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-4-7","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-4-7","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320320915","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2003567369.pdf","grobid_xml":"https://content.openalex.org/works/W2003567369.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W32351191","https://openalex.org/W226866151","https://openalex.org/W565006244","https://openalex.org/W1482758648","https://openalex.org/W1582368367","https://openalex.org/W1749993378","https://openalex.org/W1921101232","https://openalex.org/W1965399445","https://openalex.org/W1966855912","https://openalex.org/W1969253588","https://openalex.org/W1985687822","https://openalex.org/W1988896394","https://openalex.org/W1989981840","https://openalex.org/W1996529795","https://openalex.org/W1996912752","https://openalex.org/W1997598914","https://openalex.org/W2003489966","https://openalex.org/W2012860845","https://openalex.org/W2015751324","https://openalex.org/W2019631913","https://openalex.org/W2028492259","https://openalex.org/W2036099201","https://openalex.org/W2037512840","https://openalex.org/W2042067428","https://openalex.org/W2047228180","https://openalex.org/W2049929499","https://openalex.org/W2055521663","https://openalex.org/W2058141842","https://openalex.org/W2069139861","https://openalex.org/W2072280409","https://openalex.org/W2073150308","https://openalex.org/W2076262841","https://openalex.org/W2078627426","https://openalex.org/W2097248419","https://openalex.org/W2097553713","https://openalex.org/W2101155309","https://openalex.org/W2101536914","https://openalex.org/W2104619491","https://openalex.org/W2106246734","https://openalex.org/W2107409961","https://openalex.org/W2112840884","https://openalex.org/W2113860028","https://openalex.org/W2114205236","https://openalex.org/W2120612018","https://openalex.org/W2133657715","https://openalex.org/W2145996960","https://openalex.org/W2149948001","https://openalex.org/W2150575101","https://openalex.org/W2153344191","https://openalex.org/W2155286911","https://openalex.org/W2162082704","https://openalex.org/W2162237022","https://openalex.org/W2165674132","https://openalex.org/W2170427655","https://openalex.org/W2178117785","https://openalex.org/W2179170929","https://openalex.org/W2493129284","https://openalex.org/W2501240559","https://openalex.org/W2525293283","https://openalex.org/W2787847152","https://openalex.org/W3106353906","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W3012829536","https://openalex.org/W4249191815","https://openalex.org/W2027251495","https://openalex.org/W2171219265","https://openalex.org/W2613838074","https://openalex.org/W2133150343","https://openalex.org/W2081052511","https://openalex.org/W2991154838","https://openalex.org/W2148121172","https://openalex.org/W1989168955"],"abstract_inverted_index":{"BACKGROUND:":[0],"Bioremediation":[1],"offers":[2],"a":[3,73,91,186,208,222],"promising":[4,179],"pollution":[5],"treatment":[6],"method":[7],"in":[8,16,36,220,240],"the":[9,17,32,39,43,63,66,88,99,103,117,124,131,136,166,204,241],"reduction":[10],"and":[11,86,111,161,173,243],"elimination":[12],"of":[13,34,45,65,102,135,165,207,245],"man-made":[14],"compounds":[15],"environment.":[18,40,68],"Computational":[19],"tools":[20,234],"to":[21,30,56,78,126,154,189,237],"predict":[22],"novel":[23,46,80,118,200,246],"biodegradation":[24,81,201,248],"pathways":[25,47,89,104,119,180,202],"for":[26,83,94,216,228],"pollutants":[27],"allow":[28],"one":[29],"explore":[31],"capabilities":[33],"microorganisms":[35],"cleaning":[37],"up":[38],"However,":[41],"given":[42],"wealth":[44],"obtained":[48],"using":[49],"these":[50],"prediction":[51],"methods,":[52],"it":[53],"is":[54],"necessary":[55],"evaluate":[57],"their":[58],"relative":[59],"feasibility,":[60],"particularly":[61],"within":[62],"context":[64],"cellular":[67,100],"RESULTS:":[69],"We":[70,97,114,211],"have":[71,212],"utilized":[72],"computational":[74,233],"framework":[75],"called":[76],"BNICE":[77,122],"generate":[79,155],"routes":[82],"1,2,4-trichlorobenzene":[84],"(1,2,4-TCB)":[85],"incorporated":[87],"into":[90,185],"metabolic":[92,107,217],"model":[93],"Pseudomonas":[95],"putida.":[96],"studied":[98],"feasibility":[101],"by":[105,121],"applying":[106],"flux":[108,137],"analysis":[109],"(MFA)":[110],"thermodynamic":[112,163,174],"constraints.":[113],"found":[115],"that":[116,141,181,224],"generated":[120],"enabled":[123],"cell":[125],"produce":[127],"more":[128],"biomass":[129,145,156],"than":[130],"known":[132],"pathway.":[133,167],"Evaluation":[134],"distribution":[138],"profiles":[139],"revealed":[140],"several":[142,178],"properties":[143],"influenced":[144],"production:":[146],"1)":[147],"reducing":[148],"power":[149],"required,":[150],"2)":[151],"reactions":[152],"required":[153],"precursors,":[157],"3)":[158],"oxygen":[159],"utilization,":[160],"4)":[162],"topology":[164],"Based":[168],"on":[169],"pathway":[170],"analysis,":[171],"MFA,":[172],"properties,":[175],"we":[176],"identified":[177,213],"can":[182,225],"be":[183,226,238],"engineered":[184],"host":[187,209],"organism":[188],"accomplish":[190],"bioremediation.":[191,229],"CONCLUSIONS:":[192],"This":[193],"work":[194],"was":[195],"aimed":[196],"at":[197],"understanding":[198],"how":[199],"influence":[203],"existing":[205],"metabolism":[206],"organism.":[210],"attractive":[214],"targets":[215],"engineers":[218],"interested":[219],"constructing":[221],"microorganism":[223],"used":[227],"Through":[230],"this":[231],"work,":[232],"are":[235],"shown":[236],"useful":[239],"design":[242],"evaluation":[244],"xenobiotic":[247],"pathways,":[249],"identifying":[250],"cellularly":[251],"feasible":[252],"degradation":[253],"routes.":[254]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":8}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
