{"id":"https://openalex.org/W2165932090","doi":"https://doi.org/10.1093/bioinformatics/btp557","title":"In response to \u2018Can sugars be produced from fatty acids? A test case for pathway analysis tools\u2019","display_name":"In response to \u2018Can sugars be produced from fatty acids? A test case for pathway analysis tools\u2019","publication_year":2009,"publication_date":"2009-09-23","ids":{"openalex":"https://openalex.org/W2165932090","doi":"https://doi.org/10.1093/bioinformatics/btp557","mag":"2165932090","pmid":"https://pubmed.ncbi.nlm.nih.gov/19776213"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp557","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp557","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"letter","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042337539","display_name":"Karoline Faust","orcid":"https://orcid.org/0000-0001-7129-2803"},"institutions":[{"id":"https://openalex.org/I132053463","display_name":"Universit\u00e9 Libre de Bruxelles","ror":"https://ror.org/01r9htc13","country_code":"BE","type":"education","lineage":["https://openalex.org/I132053463"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Karoline Faust","raw_affiliation_strings":["Laboratoire de Bioinformatique des G\u00e9nomes et des R\u00e9seaux (BiGRe), Universit\u00e9 Libre de Bruxelles, Campus Plaine,CP 263, Bld du Triomphe, B-1050 Bruxelles, Belgium"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Bioinformatique des G\u00e9nomes et des R\u00e9seaux (BiGRe), Universit\u00e9 Libre de Bruxelles, Campus Plaine,CP 263, Bld du Triomphe, B-1050 Bruxelles, Belgium","institution_ids":["https://openalex.org/I132053463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034771876","display_name":"Didier Croes","orcid":null},"institutions":[{"id":"https://openalex.org/I132053463","display_name":"Universit\u00e9 Libre de Bruxelles","ror":"https://ror.org/01r9htc13","country_code":"BE","type":"education","lineage":["https://openalex.org/I132053463"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Didier Croes","raw_affiliation_strings":["Laboratoire de Bioinformatique des G\u00e9nomes et des R\u00e9seaux (BiGRe), Universit\u00e9 Libre de Bruxelles, Campus Plaine,CP 263, Bld du Triomphe, B-1050 Bruxelles, Belgium"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Bioinformatique des G\u00e9nomes et des R\u00e9seaux (BiGRe), Universit\u00e9 Libre de Bruxelles, Campus Plaine,CP 263, Bld du Triomphe, B-1050 Bruxelles, Belgium","institution_ids":["https://openalex.org/I132053463"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056821549","display_name":"Jacques van Helden","orcid":"https://orcid.org/0000-0002-8799-8584"},"institutions":[{"id":"https://openalex.org/I132053463","display_name":"Universit\u00e9 Libre de Bruxelles","ror":"https://ror.org/01r9htc13","country_code":"BE","type":"education","lineage":["https://openalex.org/I132053463"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Jacques van Helden","raw_affiliation_strings":["Laboratoire de Bioinformatique des G\u00e9nomes et des R\u00e9seaux (BiGRe), Universit\u00e9 Libre de Bruxelles, Campus Plaine,CP 263, Bld du Triomphe, B-1050 Bruxelles, Belgium"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Bioinformatique des G\u00e9nomes et des R\u00e9seaux (BiGRe), Universit\u00e9 Libre de Bruxelles, Campus Plaine,CP 263, Bld du Triomphe, B-1050 Bruxelles, Belgium","institution_ids":["https://openalex.org/I132053463"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5042337539"],"corresponding_institution_ids":["https://openalex.org/I132053463"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.71595094,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.696386,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"25","issue":"23","first_page":"3202","last_page":"3205"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9970999956130981,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.6012033224105835},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5988495349884033},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.5751940011978149},{"id":"https://openalex.org/keywords/test","display_name":"Test (biology)","score":0.5340114235877991},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.504799485206604},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42082759737968445},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.338228702545166},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.33444106578826904},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32441073656082153},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2562969923019409},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.134872168302536},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1071624755859375},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.09076985716819763}],"concepts":[{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.6012033224105835},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5988495349884033},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.5751940011978149},{"id":"https://openalex.org/C2777267654","wikidata":"https://www.wikidata.org/wiki/Q3519023","display_name":"Test (biology)","level":2,"score":0.5340114235877991},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.504799485206604},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42082759737968445},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.338228702545166},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.33444106578826904},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32441073656082153},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2562969923019409},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.134872168302536},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1071624755859375},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.09076985716819763}],"mesh":[{"descriptor_ui":"D000105","descriptor_name":"Acetyl Coenzyme A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000105","descriptor_name":"Acetyl Coenzyme A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000105","descriptor_name":"Acetyl Coenzyme A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002241","descriptor_name":"Carbohydrates","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D002241","descriptor_name":"Carbohydrates","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D002241","descriptor_name":"Carbohydrates","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D005227","descriptor_name":"Fatty Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005227","descriptor_name":"Fatty Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005227","descriptor_name":"Fatty Acids","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019298","descriptor_name":"Glucose-6-Phosphate","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D019298","descriptor_name":"Glucose-6-Phosphate","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D019298","descriptor_name":"Glucose-6-Phosphate","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050260","descriptor_name":"Carbohydrate Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp557","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp557","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19776213","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19776213","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:dipot.ulb.ac.be:2013/59624","is_oa":false,"landing_page_url":"https://dipot.ulb.ac.be/dspace/bitstream/2013/59624/3/doi_35894.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306401063","display_name":"D\u00e9p\u00f4t institutionnel de l'Universit\u00e9 libre de Bruxelles (Universit\u00e9 Libre de Bruxelles)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I132053463","host_organization_name":"Universit\u00e9 Libre de Bruxelles","host_organization_lineage":["https://openalex.org/I132053463"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 25 (23","raw_type":"info:ulb-repo/semantics/openurl/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1489268516","https://openalex.org/W1598572316","https://openalex.org/W1684307508","https://openalex.org/W1814099126","https://openalex.org/W1873506857","https://openalex.org/W1964491374","https://openalex.org/W1967638237","https://openalex.org/W1977353955","https://openalex.org/W1983710275","https://openalex.org/W1993464554","https://openalex.org/W1998505309","https://openalex.org/W2008818443","https://openalex.org/W2025060809","https://openalex.org/W2028681077","https://openalex.org/W2070745137","https://openalex.org/W2071902637","https://openalex.org/W2073612090","https://openalex.org/W2088226054","https://openalex.org/W2089035513","https://openalex.org/W2091317547","https://openalex.org/W2092899907","https://openalex.org/W2093241068","https://openalex.org/W2103708054","https://openalex.org/W2111031006","https://openalex.org/W2111086098","https://openalex.org/W2114205236","https://openalex.org/W2119913016","https://openalex.org/W2123060905","https://openalex.org/W2133298156","https://openalex.org/W2133319394","https://openalex.org/W2133579817","https://openalex.org/W2135206190","https://openalex.org/W2135460645","https://openalex.org/W2152776677","https://openalex.org/W2153344191","https://openalex.org/W2154066017","https://openalex.org/W2158069895","https://openalex.org/W2169517653","https://openalex.org/W2170326567","https://openalex.org/W2292783450","https://openalex.org/W4298203020","https://openalex.org/W4298226842"],"related_works":["https://openalex.org/W2063475537","https://openalex.org/W2341681417","https://openalex.org/W1961707331","https://openalex.org/W2012938657","https://openalex.org/W1578136679","https://openalex.org/W2096004952","https://openalex.org/W2087715585","https://openalex.org/W2147962989","https://openalex.org/W4309835295","https://openalex.org/W4223538309"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"In":[2,149],"their":[3,95,121],"article":[4,56],"entitled":[5],"\u2018Can":[6],"sugars":[7],"be":[8,166],"produced":[9],"from":[10,44],"fatty":[11],"acids?":[12],"A":[13],"test":[14,50],"case":[15],"for":[16,59,69],"pathway":[17,29],"analysis":[18,158],"tools\u2019":[19],"de":[20,110],"Figueiredo":[21,111],"and":[22,34,112,155,164],"co-authors":[23],"assess":[24],"the":[25,39,63,70,79,106,116,128,141],"performance":[26,119],"of":[27,41,74,120,143],"three":[28,60],"prediction":[30],"tools":[31,72,97,144],"(METATOOL,":[32],"PathFinding":[33],"Pathway":[35],"Hunter":[36],"Tool)":[37],"using":[38],"synthesis":[40],"glucose-6-phosphate":[42],"(G6P)":[43],"acetyl-CoA":[45],"in":[46,130,140],"humans":[47],"as":[48,67,168],"a":[49,137],"case.":[51],"We":[52,104,134],"think":[53],"that":[54,115,145],"this":[55],"is":[57,81,124],"biased":[58],"reasons:":[61],"(i)":[62],"metabolic":[64,152],"networks":[65],"used":[66],"input":[68,131],"respective":[71],"were":[73],"very":[75],"different":[76,147,161],"sizes;":[77],"(ii)":[78],"\u2018assessment\u2019":[80],"restricted":[82],"to":[83,93,127],"two":[84],"study":[85],"cases;":[86],"(iii)":[87],"developers":[88],"are":[89,159,180],"inherently":[90],"more":[91],"skilled":[92],"use":[94],"own":[96],"than":[98,171],"those":[99],"developed":[100],"by":[101,109],"other":[102],"people.":[103],"extended":[105],"analyses":[107],"led":[108],"clearly":[113],"show":[114],"apparent":[117],"superior":[118],"tool":[122],"(METATOOL)":[123],"partly":[125],"due":[126],"differences":[129],"network":[132],"sizes.":[133],"also":[135],"see":[136],"conceptual":[138],"problem":[139],"comparison":[142],"serve":[146],"purposes.":[148],"our":[150],"opinion,":[151],"path":[153],"finding":[154],"elementary":[156],"mode":[157],"answering":[160],"biological":[162],"questions,":[163],"should":[165],"considered":[167],"complementary":[169],"rather":[170],"competitive":[172],"approaches.":[173],"Contact:":[174],"kfaust@ulb.ac.be":[175],"Supplementary":[176,178],"information:":[177],"data":[179],"available":[181],"at":[182],"Bioinformatics":[183],"online.":[184]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2025-10-10T00:00:00"}