{"id":"https://openalex.org/W1945070849","doi":"https://doi.org/10.1186/1471-2105-14-s9-s6","title":"MGC: a metagenomic gene caller","display_name":"MGC: a metagenomic gene caller","publication_year":2013,"publication_date":"2013-06-01","ids":{"openalex":"https://openalex.org/W1945070849","doi":"https://doi.org/10.1186/1471-2105-14-s9-s6","mag":"1945070849","pmid":"https://pubmed.ncbi.nlm.nih.gov/23901840"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-14-s9-s6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s9-s6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S9-S6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S9-S6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018240746","display_name":"Achraf El Allali","orcid":"https://orcid.org/0000-0002-4561-2161"},"institutions":[{"id":"https://openalex.org/I155781252","display_name":"University of South Carolina","ror":"https://ror.org/02b6qw903","country_code":"US","type":"education","lineage":["https://openalex.org/I155781252"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Achraf El Allali","raw_affiliation_strings":["Department of Computer Science and Engineering, University of South Carolina, 315 Main Street, Columbia, SC 29208, USA. eachraf@gmail.com","Department of Computer Science and Engineering, University of South Carolina, Columbia, (USA)"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of South Carolina, 315 Main Street, Columbia, SC 29208, USA. eachraf@gmail.com","institution_ids":["https://openalex.org/I155781252"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of South Carolina, Columbia, (USA)","institution_ids":["https://openalex.org/I155781252"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112054359","display_name":"John R. Rose","orcid":"https://orcid.org/0000-0001-7600-7215"},"institutions":[{"id":"https://openalex.org/I155781252","display_name":"University of South Carolina","ror":"https://ror.org/02b6qw903","country_code":"US","type":"education","lineage":["https://openalex.org/I155781252"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John R Rose","raw_affiliation_strings":["Department of Computer Science and Engineering, University of South Carolina, 315 Main Street., Columbia, SC, 29208, USA","Department of Computer Science and Engineering, University of South Carolina, Columbia, (USA)"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of South Carolina, 315 Main Street., Columbia, SC, 29208, USA","institution_ids":["https://openalex.org/I155781252"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of South Carolina, Columbia, (USA)","institution_ids":["https://openalex.org/I155781252"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5018240746"],"corresponding_institution_ids":["https://openalex.org/I155781252"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.7486,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.70501213,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"14","issue":"S9","first_page":"S6","last_page":"S6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.998199999332428,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9975000023841858,"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/orfs","display_name":"ORFS","score":0.9464209079742432},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.8113672137260437},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6528001427650452},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5725031495094299},{"id":"https://openalex.org/keywords/gc-content","display_name":"GC-content","score":0.5652202367782593},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.5073074698448181},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.504501461982727},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4742909073829651},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4520183205604553},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4404506981372833},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4379979372024536},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4332408905029297},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3955502510070801},{"id":"https://openalex.org/keywords/open-reading-frame","display_name":"Open reading frame","score":0.3731782138347626},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3503350019454956},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2627952992916107},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.13024002313613892}],"concepts":[{"id":"https://openalex.org/C2780530800","wikidata":"https://www.wikidata.org/wiki/Q7072921","display_name":"ORFS","level":5,"score":0.9464209079742432},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8113672137260437},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6528001427650452},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5725031495094299},{"id":"https://openalex.org/C42251679","wikidata":"https://www.wikidata.org/wiki/Q933491","display_name":"GC-content","level":4,"score":0.5652202367782593},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.5073074698448181},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.504501461982727},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4742909073829651},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4520183205604553},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4404506981372833},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4379979372024536},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4332408905029297},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3955502510070801},{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.3731782138347626},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3503350019454956},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2627952992916107},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.13024002313613892}],"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":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","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":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020745","descriptor_name":"Genome, Archaeal","qualifier_ui":null,"qualifier_name":null,"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":3,"locations":[{"id":"doi:10.1186/1471-2105-14-s9-s6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s9-s6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S9-S6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23901840","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23901840","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 bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2695786","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3698006","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-14-s9-s6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-14-s9-s6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-S9-S6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.8899999856948853}],"awards":[{"id":"https://openalex.org/G2216343635","display_name":null,"funder_award_id":"0959427","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1945070849.pdf","grobid_xml":"https://content.openalex.org/works/W1945070849.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W188371266","https://openalex.org/W1492088121","https://openalex.org/W1544324307","https://openalex.org/W1834463255","https://openalex.org/W2005122969","https://openalex.org/W2033705779","https://openalex.org/W2053697292","https://openalex.org/W2057021995","https://openalex.org/W2061246785","https://openalex.org/W2069689025","https://openalex.org/W2075970797","https://openalex.org/W2099006507","https://openalex.org/W2103210188","https://openalex.org/W2111051539","https://openalex.org/W2120267228","https://openalex.org/W2128617961","https://openalex.org/W2142749416","https://openalex.org/W2151017710","https://openalex.org/W2156701707","https://openalex.org/W2165999027","https://openalex.org/W2269046617","https://openalex.org/W2480943001","https://openalex.org/W4240982680","https://openalex.org/W4241391257","https://openalex.org/W4244288971"],"related_works":["https://openalex.org/W2017477982","https://openalex.org/W1978801575","https://openalex.org/W2029252138","https://openalex.org/W4306784270","https://openalex.org/W2101899141","https://openalex.org/W3031046715","https://openalex.org/W2017335389","https://openalex.org/W2358544099","https://openalex.org/W1976390578","https://openalex.org/W2072439611"],"abstract_inverted_index":{"Learning":[0],"separate":[1,61],"models":[2,65],"for":[3,52,63],"several":[4],"pre-defined":[5],"GC-content":[6,59],"regions":[7],"as":[8,22],"opposed":[9],"to":[10,60],"a":[11],"single":[12],"model":[13],"approach":[14],"improves":[15],"the":[16,19,25,41,50,56],"performance":[17],"of":[18,34,44,58],"neural":[20],"network":[21],"demonstrated":[23],"by":[24],"experimental":[26],"results":[27],"presented":[28],"in":[29,66],"this":[30],"paper.":[31],"The":[32],"inclusion":[33],"amino-acid":[35],"usage":[36],"features":[37],"also":[38],"helps":[39],"improve":[40],"overall":[42],"accuracy":[43],"our":[45],"algorithm.":[46],"MGC's":[47],"improvement":[48],"sets":[49],"ground":[51],"further":[53],"investigation":[54],"into":[55],"use":[57],"data":[62],"training":[64],"machine":[67],"learning":[68],"based":[69],"gene":[70],"finders.":[71]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}
