{"id":"https://openalex.org/W2527229771","doi":"https://doi.org/10.1093/bioinformatics/btw604","title":"DEF: an automated dead-end filling approach based on quasi-endosymbiosis","display_name":"DEF: an automated dead-end filling approach based on quasi-endosymbiosis","publication_year":2016,"publication_date":"2016-09-26","ids":{"openalex":"https://openalex.org/W2527229771","doi":"https://doi.org/10.1093/bioinformatics/btw604","mag":"2527229771","pmid":"https://pubmed.ncbi.nlm.nih.gov/28171511"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw604","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw604","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/3/405/25145886/btw604.pdf","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":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/3/405/25145886/btw604.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070464462","display_name":"Lili Liu","orcid":"https://orcid.org/0000-0001-9522-6229"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lili Liu","raw_affiliation_strings":["Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100764716","display_name":"Zijun Zhang","orcid":"https://orcid.org/0000-0003-2016-8014"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]},{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Zijun Zhang","raw_affiliation_strings":["Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China","Department of Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"Department of Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101070851","display_name":"Taotao Sheng","orcid":"https://orcid.org/0000-0003-3809-4885"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Taotao Sheng","raw_affiliation_strings":["Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100423292","display_name":"Ming Chen","orcid":"https://orcid.org/0000-0002-9677-1699"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ming Chen","raw_affiliation_strings":["Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I76130692"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5070464462"],"corresponding_institution_ids":["https://openalex.org/I76130692"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3335,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.68034804,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"33","issue":"3","first_page":"405","last_page":"413"},"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":0.9937000274658203,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9936000108718872,"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/endosymbiosis","display_name":"Endosymbiosis","score":0.8053499460220337},{"id":"https://openalex.org/keywords/dead-end","display_name":"Dead end","score":0.7850589752197266},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7083384990692139},{"id":"https://openalex.org/keywords/end-to-end-principle","display_name":"End-to-end principle","score":0.4168161153793335},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3265308141708374},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3169107735157013},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3085547685623169},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14338213205337524},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09087711572647095},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0754232108592987}],"concepts":[{"id":"https://openalex.org/C199733737","wikidata":"https://www.wikidata.org/wiki/Q4531856","display_name":"Endosymbiosis","level":5,"score":0.8053499460220337},{"id":"https://openalex.org/C2986709869","wikidata":"https://www.wikidata.org/wiki/Q398589","display_name":"Dead end","level":3,"score":0.7850589752197266},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7083384990692139},{"id":"https://openalex.org/C74296488","wikidata":"https://www.wikidata.org/wiki/Q2527392","display_name":"End-to-end principle","level":2,"score":0.4168161153793335},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3265308141708374},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3169107735157013},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3085547685623169},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14338213205337524},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09087711572647095},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0754232108592987},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C38349280","wikidata":"https://www.wikidata.org/wiki/Q1434290","display_name":"Flow (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C93829228","wikidata":"https://www.wikidata.org/wiki/Q165963","display_name":"Plastid","level":4,"score":0.0},{"id":"https://openalex.org/C69305403","wikidata":"https://www.wikidata.org/wiki/Q47263","display_name":"Chloroplast","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D013559","descriptor_name":"Symbiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013559","descriptor_name":"Symbiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013559","descriptor_name":"Symbiosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":2,"locations":[{"id":"doi:10.1093/bioinformatics/btw604","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw604","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/3/405/25145886/btw604.pdf","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:28171511","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28171511","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw604","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw604","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/3/405/25145886/btw604.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5892367096","display_name":null,"funder_award_id":"31371328","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8205675081","display_name":null,"funder_award_id":"31571366","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2527229771.pdf","grobid_xml":"https://content.openalex.org/works/W2527229771.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1537545744","https://openalex.org/W1976436531","https://openalex.org/W1986656046","https://openalex.org/W1997037290","https://openalex.org/W2005740697","https://openalex.org/W2009282793","https://openalex.org/W2041115195","https://openalex.org/W2057443273","https://openalex.org/W2073837631","https://openalex.org/W2075283200","https://openalex.org/W2091317547","https://openalex.org/W2096245011","https://openalex.org/W2104619491","https://openalex.org/W2105112252","https://openalex.org/W2107249189","https://openalex.org/W2107459209","https://openalex.org/W2132092950","https://openalex.org/W2141885858","https://openalex.org/W2142678478","https://openalex.org/W2147472054","https://openalex.org/W2154782854","https://openalex.org/W2159482845","https://openalex.org/W2161897808","https://openalex.org/W2170427655","https://openalex.org/W4242123597","https://openalex.org/W4285719527","https://openalex.org/W4294216483","https://openalex.org/W4320301318"],"related_works":["https://openalex.org/W3127005940","https://openalex.org/W3179968364","https://openalex.org/W3016188207","https://openalex.org/W4293268064","https://openalex.org/W2151749779","https://openalex.org/W4250565955","https://openalex.org/W2218833963","https://openalex.org/W2964709658","https://openalex.org/W2322650751","https://openalex.org/W2754236486"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}