{"id":"https://openalex.org/W2594731494","doi":"https://doi.org/10.2390/biecoll-jib-2016-285","title":"Estimation of biomass composition from genomic and transcriptomic information","display_name":"Estimation of biomass composition from genomic and transcriptomic information","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2594731494","doi":"https://doi.org/10.2390/biecoll-jib-2016-285","mag":"2594731494","pmid":"https://pubmed.ncbi.nlm.nih.gov/28187415"},"language":"en","primary_location":{"id":"pmid:28187415","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28187415","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":"Journal of integrative bioinformatics","raw_type":null},"type":"article","indexed_in":["datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/1822/44986","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067144800","display_name":"Sophia Santos","orcid":"https://orcid.org/0000-0003-4700-6066"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Santos, Sophia","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5079343705","display_name":"Isabel Rocha","orcid":"https://orcid.org/0000-0001-9494-3410"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rocha, Isabel","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5067144800"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.8705,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.77579729,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"13","issue":"2","first_page":"285","last_page":"285"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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":1.0,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9958999752998352,"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":0.9939000010490417,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6232183575630188},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5781269669532776},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.47343993186950684},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45568349957466125},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43751439452171326},{"id":"https://openalex.org/keywords/biomass","display_name":"Biomass (ecology)","score":0.4362291693687439},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.419489324092865},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2968302071094513},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16722732782363892},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16086655855178833},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.13061752915382385}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6232183575630188},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5781269669532776},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.47343993186950684},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45568349957466125},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43751439452171326},{"id":"https://openalex.org/C115540264","wikidata":"https://www.wikidata.org/wiki/Q2945560","display_name":"Biomass (ecology)","level":2,"score":0.4362291693687439},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.419489324092865},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2968302071094513},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16722732782363892},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16086655855178833},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.13061752915382385}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018533","descriptor_name":"Biomass","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018533","descriptor_name":"Biomass","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018533","descriptor_name":"Biomass","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"pmid:28187415","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28187415","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:biecoll.ub.uni-bielefeld.de:5440","is_oa":false,"landing_page_url":"http://biecoll.ub.uni-bielefeld.de/volltexte/2017/5440/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/article.php?aid=285","raw_type":"Journal Article"},{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/44986","is_oa":true,"landing_page_url":"http://hdl.handle.net/1822/44986","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"","raw_type":"journal article"},{"id":"pmh:oai:repositorium.uminho.pt:1822/44986","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/44986","pdf_url":null,"source":{"id":"https://openalex.org/S4306400624","display_name":"Reposit\u00f3riUM (Universidade do Minho)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99682543","host_organization_name":"University of Minho","host_organization_lineage":["https://openalex.org/I99682543"],"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":null,"raw_type":"journal article"},{"id":"doi:10.2390/biecoll-jib-2016-285","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2016-285","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/44986","is_oa":true,"landing_page_url":"http://hdl.handle.net/1822/44986","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"","raw_type":"journal article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1167214205","display_name":null,"funder_award_id":"COMPETE","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1516346500","display_name":null,"funder_award_id":"01-0145","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G1578237752","display_name":null,"funder_award_id":"COMPETE","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G1763632427","display_name":null,"funder_award_id":"POCI-01-0145","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G2534777963","display_name":null,"funder_award_id":"POCI-01-0145-FEDER-006684","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G274581676","display_name":null,"funder_award_id":"POCI-01","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G2905247347","display_name":null,"funder_award_id":"UID/BIO/04469","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G3114003372","display_name":null,"funder_award_id":"NORTE-01-0145-FEDER-000004","funder_id":"https://openalex.org/F4320323642","funder_display_name":"Minist\u00e9rio da Ci\u00eancia, Tecnologia e Ensino Superior"},{"id":"https://openalex.org/G344822066","display_name":null,"funder_award_id":"NORTE-01-0145-FEDER-000004","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G3491971210","display_name":null,"funder_award_id":"COMPETE 2020","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G4176497637","display_name":null,"funder_award_id":"COMPETE 2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G4455079242","display_name":null,"funder_award_id":"POCI-01-","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G5224927334","display_name":null,"funder_award_id":"POCI-01-","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G5256422550","display_name":null,"funder_award_id":"UID/BIO/04469/2013","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G6193589897","display_name":null,"funder_award_id":"POCI-01-0145","funder_id":"https://openalex.org/F4320323642","funder_display_name":"Minist\u00e9rio da Ci\u00eancia, Tecnologia e Ensino Superior"},{"id":"https://openalex.org/G6469001316","display_name":null,"funder_award_id":"UID/BIO/04469","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6623037509","display_name":null,"funder_award_id":"POCI-01-0145-FEDER-006684","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G7142320195","display_name":null,"funder_award_id":"UID/BIO/04469/2013 unit","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G7584003722","display_name":null,"funder_award_id":"NORTE-01-0145","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G836519787","display_name":null,"funder_award_id":"UID/BIO/04469/2013","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G8862270368","display_name":null,"funder_award_id":"POCI-01-0145-FEDER","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G8884816653","display_name":null,"funder_award_id":"POCI-01-0145-FEDER","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G8928600714","display_name":null,"funder_award_id":"NORTE-01-0145-FEDER-000004","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320323642","display_name":"Minist\u00e9rio da Ci\u00eancia, Tecnologia e Ensino Superior","ror":"https://ror.org/045b9pr88"},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W102715436","https://openalex.org/W1512810258","https://openalex.org/W1597762351","https://openalex.org/W1925984292","https://openalex.org/W1982309495","https://openalex.org/W1990025317","https://openalex.org/W1992844569","https://openalex.org/W2029403511","https://openalex.org/W2046527060","https://openalex.org/W2046914949","https://openalex.org/W2049883153","https://openalex.org/W2077460182","https://openalex.org/W2078775934","https://openalex.org/W2097588479","https://openalex.org/W2115575148","https://openalex.org/W2123698848","https://openalex.org/W2123966372","https://openalex.org/W2127336775","https://openalex.org/W2135557896","https://openalex.org/W2143273383","https://openalex.org/W2150908245","https://openalex.org/W2152280797","https://openalex.org/W2156409537","https://openalex.org/W2162373261","https://openalex.org/W2163240970","https://openalex.org/W2165762336","https://openalex.org/W2170427655","https://openalex.org/W2739999456"],"related_works":["https://openalex.org/W3133318625","https://openalex.org/W2189228649","https://openalex.org/W2567468476","https://openalex.org/W2128744222","https://openalex.org/W3123532558","https://openalex.org/W2900780313","https://openalex.org/W2064745061","https://openalex.org/W2263557753","https://openalex.org/W3017400003","https://openalex.org/W2062714820"],"abstract_inverted_index":{"Given":[0],"the":[1,6,25,49,80,123,131,164],"great":[2],"potential":[3],"impact":[4],"of":[5,9,15,27,35,48,62,82,166],"growing":[7],"number":[8],"complete":[10],"genome-scale":[11,37],"metabolic":[12,38],"network":[13],"reconstructions":[14],"microorganisms,":[16],"bioinformatics":[17],"tools":[18],"are":[19,156],"needed":[20],"to":[21,129,159],"simplify":[22],"and":[23,68,102,106,117,134,169,175],"accelerate":[24],"course":[26],"knowledge":[28],"in":[29,55,99,114,122,147],"this":[30,87,154],"field.":[31],"One":[32],"essential":[33],"component":[34],"a":[36,89,137,180],"model":[39],"is":[40,46,92,135,179,187],"its":[41],"biomass":[42,97],"equation,":[43],"whose":[44],"maximization":[45],"one":[47],"most":[50],"common":[51],"objective":[52],"functions":[53],"used":[54],"Flux":[56],"Balance":[57],"Analysis":[58],"formulations.":[59],"Some":[60],"components":[61],"biomass,":[63],"such":[64],"as":[65,110],"amino":[66,100,167],"acids":[67,101],"nucleotides,":[69,103],"can":[70],"be":[71],"estimated":[72],"from":[73,104,172,176],"genome":[74,105,173],"information,":[75,108],"providing":[76],"reliable":[77],"data":[78,121,178,186],"without":[79],"need":[81],"performing":[83],"lab":[84],"experiments.":[85],"In":[86],"work":[88],"java":[90],"tool":[91,139,155],"proposed":[93],"that":[94,163],"estimates":[95],"microbial":[96],"composition":[98],"transcriptomic":[107,120,177],"using":[109,153],"input":[111],"files":[112,118],"sequences":[113],"FASTA":[115],"format":[116],"with":[119,142],"csv":[124],"format.":[125],"This":[126],"application":[127],"allows":[128],"obtain":[130],"results":[132,151],"rapidly":[133],"also":[136],"user-friendly":[138],"for":[140],"users":[141],"any":[143],"or":[144],"little":[145],"background":[146],"informatics":[148],"(http://darwin.di.uminho.pt/biomass/).":[149],"The":[150],"obtained":[152],"fairly":[157],"close":[158],"experimental":[160,185],"data,":[161],"showing":[162],"estimation":[165],"acid":[168],"nucleotide":[170],"compositions":[171],"information":[174],"good":[181],"alternative":[182],"when":[183],"no":[184],"available.":[188]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-07T08:38:57.713557","created_date":"2025-10-10T00:00:00"}
