{"id":"https://openalex.org/W2126416152","doi":"https://doi.org/10.1093/bioinformatics/btl139","title":"GRAST: a new way of genome reduction analysis using comparative genomics","display_name":"GRAST: a new way of genome reduction analysis using comparative genomics","publication_year":2006,"publication_date":"2006-04-06","ids":{"openalex":"https://openalex.org/W2126416152","doi":"https://doi.org/10.1093/bioinformatics/btl139","mag":"2126416152","pmid":"https://pubmed.ncbi.nlm.nih.gov/16601001"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl139","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl139","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/13/1551/48839248/bioinformatics_22_13_1551.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/22/13/1551/48839248/bioinformatics_22_13_1551.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011612471","display_name":"Christina Toft","orcid":"https://orcid.org/0000-0003-1714-6703"},"institutions":[{"id":"https://openalex.org/I157286207","display_name":"National University of Ireland, Maynooth","ror":"https://ror.org/048nfjm95","country_code":"IE","type":"education","lineage":["https://openalex.org/I157286207"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Christina Toft","raw_affiliation_strings":["Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland \u00a0 Maynooth","Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland Maynooth#TAB#"],"affiliations":[{"raw_affiliation_string":"Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland \u00a0 Maynooth","institution_ids":["https://openalex.org/I157286207"]},{"raw_affiliation_string":"Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland Maynooth#TAB#","institution_ids":["https://openalex.org/I157286207"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026642450","display_name":"Mario A. Fares","orcid":"https://orcid.org/0000-0002-4345-3013"},"institutions":[{"id":"https://openalex.org/I157286207","display_name":"National University of Ireland, Maynooth","ror":"https://ror.org/048nfjm95","country_code":"IE","type":"education","lineage":["https://openalex.org/I157286207"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Mario A. Fares","raw_affiliation_strings":["Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland \u00a0 Maynooth","Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland Maynooth#TAB#"],"affiliations":[{"raw_affiliation_string":"Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland \u00a0 Maynooth","institution_ids":["https://openalex.org/I157286207"]},{"raw_affiliation_string":"Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland Maynooth#TAB#","institution_ids":["https://openalex.org/I157286207"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5011612471"],"corresponding_institution_ids":["https://openalex.org/I157286207"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2649,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.57499291,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"22","issue":"13","first_page":"1551","last_page":"1561"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9994999766349792,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9994999766349792,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9966999888420105,"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/reduction","display_name":"Reduction (mathematics)","score":0.5995758175849915},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5694502592086792},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.5345040559768677},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5306991934776306},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.520438015460968},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.49837160110473633},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3353508710861206},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3272906541824341},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.144383043050766},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12041082978248596}],"concepts":[{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.5995758175849915},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5694502592086792},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.5345040559768677},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5306991934776306},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.520438015460968},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49837160110473633},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3353508710861206},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3272906541824341},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.144383043050766},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12041082978248596},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001042","descriptor_name":"Aphids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001042","descriptor_name":"Aphids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001042","descriptor_name":"Aphids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btl139","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl139","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/13/1551/48839248/bioinformatics_22_13_1551.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:16601001","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16601001","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/btl139","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl139","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/13/1551/48839248/bioinformatics_22_13_1551.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":[],"funders":[{"id":"https://openalex.org/F4320320847","display_name":"Science Foundation Ireland","ror":"https://ror.org/0271asj38"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2126416152.pdf","grobid_xml":"https://content.openalex.org/works/W2126416152.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1520910643","https://openalex.org/W1807210160","https://openalex.org/W1951480739","https://openalex.org/W1952540142","https://openalex.org/W1968179480","https://openalex.org/W1976339007","https://openalex.org/W1990403227","https://openalex.org/W1990453950","https://openalex.org/W1999536502","https://openalex.org/W2012886161","https://openalex.org/W2015213608","https://openalex.org/W2015225927","https://openalex.org/W2016588572","https://openalex.org/W2022518804","https://openalex.org/W2034229618","https://openalex.org/W2049119361","https://openalex.org/W2057804750","https://openalex.org/W2068787541","https://openalex.org/W2087784763","https://openalex.org/W2087880457","https://openalex.org/W2097646748","https://openalex.org/W2102131597","https://openalex.org/W2105507932","https://openalex.org/W2106726141","https://openalex.org/W2108621157","https://openalex.org/W2115539957","https://openalex.org/W2123500593","https://openalex.org/W2124681451","https://openalex.org/W2150227488","https://openalex.org/W2155606054","https://openalex.org/W2156273926","https://openalex.org/W2156524568","https://openalex.org/W2157748357","https://openalex.org/W2158714788","https://openalex.org/W2160244495","https://openalex.org/W2161996227","https://openalex.org/W2163481135","https://openalex.org/W2167895990","https://openalex.org/W6638336419"],"related_works":["https://openalex.org/W2414506155","https://openalex.org/W1565527690","https://openalex.org/W2752117239","https://openalex.org/W1493660383","https://openalex.org/W2759519215","https://openalex.org/W2170130581","https://openalex.org/W4318240630","https://openalex.org/W2353729507","https://openalex.org/W2560359598","https://openalex.org/W3023271652"],"abstract_inverted_index":{"Investigation":[0],"of":[1,16,23,59],"genome":[2,39],"reduction":[3],"and":[4,32,44],"rearrangements":[5],"in":[6],"endosymbionts":[7],"using":[8],"a":[9],"novel":[10],"computational":[11],"tool":[12],"(GRAST)":[13],"identified":[14,37],"gathering":[15],"genes":[17,26],"with":[18],"similar":[19],"functions.":[20],"Conserved":[21],"clusters":[22],"functionally":[24],"related":[25],"(CGSCs)":[27],"were":[28],"detected.":[29],"Heterogeneous":[30],"gene":[31,33,42,50],"cluster":[34],"non-functionalization/loss":[35],"are":[36],"between":[38],"regions,":[40],"functional":[41],"categories":[43],"during":[45,54],"evolution.":[46],"Results":[47],"show":[48],"that":[49],"non-functionalisation":[51],"has":[52],"accelerated":[53],"the":[55],"last":[56],"50":[57],"MY":[58],"Buchnera's":[60],"evolution":[61],"while":[62],"CGSCs":[63],"have":[64],"been":[65],"static.":[66]},"counts_by_year":[{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}