{"id":"https://openalex.org/W2098984028","doi":"https://doi.org/10.1093/bioinformatics/bth075","title":"Poorly conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins","display_name":"Poorly conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins","publication_year":2004,"publication_date":"2004-02-10","ids":{"openalex":"https://openalex.org/W2098984028","doi":"https://doi.org/10.1093/bioinformatics/bth075","mag":"2098984028","pmid":"https://pubmed.ncbi.nlm.nih.gov/14871864"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bth075","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth075","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/8/1248/48905453/bioinformatics_20_8_1248.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/20/8/1248/48905453/bioinformatics_20_8_1248.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009948326","display_name":"Hagay Shmuely","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"H. Shmuely","raw_affiliation_strings":["Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel","Department of Life Sciences#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel","institution_ids":["https://openalex.org/I124227911"]},{"raw_affiliation_string":"Department of Life Sciences#TAB#","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108222071","display_name":"E. Dinitz","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"E. Dinitz","raw_affiliation_strings":["Department of Life Sciences#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Life Sciences#TAB#","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036277729","display_name":"Idit Dahan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"I. Dahan","raw_affiliation_strings":["Department of Life Sciences#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Life Sciences#TAB#","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023221161","display_name":"Jerry Eichler","orcid":"https://orcid.org/0000-0001-9409-8026"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. Eichler","raw_affiliation_strings":["Department of Life Sciences#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Life Sciences#TAB#","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048857636","display_name":"Daniel Fischer","orcid":"https://orcid.org/0000-0002-7513-683X"},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"D. Fischer","raw_affiliation_strings":["Department of Bioinformatics and Computer Science, Ben Gurion University of the Negev, PO Box 653, Beersheva 84015, Israel#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Computer Science, Ben Gurion University of the Negev, PO Box 653, Beersheva 84015, Israel#TAB#","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002696188","display_name":"Boaz Shaanan","orcid":"https://orcid.org/0000-0001-8925-4362"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"B. Shaanan","raw_affiliation_strings":["Department of Life Sciences#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Life Sciences#TAB#","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5009948326"],"corresponding_institution_ids":["https://openalex.org/I124227911"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1975,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.76880867,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"20","issue":"8","first_page":"1248","last_page":"1253"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3084999918937683,"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":0.3084999918937683,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.20340000092983246,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.14959999918937683,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/orfs","display_name":"ORFS","score":0.9921040534973145},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7952016592025757},{"id":"https://openalex.org/keywords/archaea","display_name":"Archaea","score":0.7696505188941956},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6916647553443909},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6347458362579346},{"id":"https://openalex.org/keywords/open-reading-frame","display_name":"Open reading frame","score":0.5539735555648804},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4682264029979706},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.4601131081581116},{"id":"https://openalex.org/keywords/halobacterium","display_name":"Halobacterium","score":0.45310115814208984},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39925453066825867},{"id":"https://openalex.org/keywords/halophile","display_name":"Halophile","score":0.3003684878349304},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.2325960099697113},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.17181098461151123}],"concepts":[{"id":"https://openalex.org/C2780530800","wikidata":"https://www.wikidata.org/wiki/Q7072921","display_name":"ORFS","level":5,"score":0.9921040534973145},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7952016592025757},{"id":"https://openalex.org/C550995028","wikidata":"https://www.wikidata.org/wiki/Q10872","display_name":"Archaea","level":3,"score":0.7696505188941956},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6916647553443909},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6347458362579346},{"id":"https://openalex.org/C47289529","wikidata":"https://www.wikidata.org/wiki/Q908550","display_name":"Open reading frame","level":4,"score":0.5539735555648804},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4682264029979706},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.4601131081581116},{"id":"https://openalex.org/C2776733701","wikidata":"https://www.wikidata.org/wiki/Q139014","display_name":"Halobacterium","level":4,"score":0.45310115814208984},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39925453066825867},{"id":"https://openalex.org/C80642116","wikidata":"https://www.wikidata.org/wiki/Q946633","display_name":"Halophile","level":3,"score":0.3003684878349304},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2325960099697113},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.17181098461151123}],"mesh":[{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D006217","descriptor_name":"Halobacterium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006217","descriptor_name":"Halobacterium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006217","descriptor_name":"Halobacterium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bth075","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth075","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/8/1248/48905453/bioinformatics_20_8_1248.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:14871864","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14871864","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:CiteSeerX.psu:10.1.1.515.4600","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.515.4600","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/20/8/1248.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bth075","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bth075","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/20/8/1248/48905453/bioinformatics_20_8_1248.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":[{"score":0.6499999761581421,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320323051","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2098984028.pdf"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1487061466","https://openalex.org/W1497175644","https://openalex.org/W1568167276","https://openalex.org/W1582255757","https://openalex.org/W1668462635","https://openalex.org/W1882986874","https://openalex.org/W1966306076","https://openalex.org/W1971596502","https://openalex.org/W1974383394","https://openalex.org/W1987934913","https://openalex.org/W2001660787","https://openalex.org/W2003690139","https://openalex.org/W2019377841","https://openalex.org/W2019591778","https://openalex.org/W2019750654","https://openalex.org/W2022589976","https://openalex.org/W2024194735","https://openalex.org/W2024228623","https://openalex.org/W2024751051","https://openalex.org/W2026582002","https://openalex.org/W2028762212","https://openalex.org/W2036848170","https://openalex.org/W2081219382","https://openalex.org/W2090424274","https://openalex.org/W2090438401","https://openalex.org/W2109628984","https://openalex.org/W2115843776","https://openalex.org/W2124037112","https://openalex.org/W2143199763","https://openalex.org/W2150044006","https://openalex.org/W2154478075","https://openalex.org/W2160582562","https://openalex.org/W2165979915","https://openalex.org/W2166865790","https://openalex.org/W2169382386","https://openalex.org/W2169748335"],"related_works":["https://openalex.org/W2142984901","https://openalex.org/W1964697181","https://openalex.org/W4242567973","https://openalex.org/W2149155835","https://openalex.org/W4206448586","https://openalex.org/W2338753080","https://openalex.org/W2007710100","https://openalex.org/W2165255936","https://openalex.org/W4240421871","https://openalex.org/W2601041732"],"abstract_inverted_index":{"MOTIVATION:":[0],"A":[1,82],"large":[2],"fraction":[3],"of":[4,24,51,86,129],"open":[5],"reading":[6],"frames":[7],"(ORFs)":[8],"identified":[9],"as":[10],"'hypothetical'":[11],"proteins":[12,33],"correspond":[13,152],"to":[14,22,31,39,153,186],"either":[15],"'conserved":[16],"hypothetical'":[17],"proteins,":[18,142],"representing":[19],"sequences":[20],"homologous":[21],"ORFs":[23,41,60,101],"unknown":[25],"function":[26],"from":[27],"other":[28,40,117,170],"organisms,":[29],"or":[30,57],"hypothetical":[32],"lacking":[34],"any":[35],"significant":[36],"sequence":[37],"similarity":[38],"in":[42,89,107,116,167,192],"the":[43,46,90,108,130,188,193],"databases.":[44],"Elucidating":[45],"functions":[47,181],"and":[48,160,169,182],"three-dimensional":[49],"structures":[50],"such":[52],"orphan":[53],"ORFs,":[54],"termed":[55],"ORFans":[56,74],"poorly":[58],"conserved":[59],"(PCOs),":[61],"is":[62,124],"essential":[63],"for":[64,78,126],"understanding":[65],"biodiversity.":[66],"However,":[67],"it":[68],"has":[69],"been":[70],"claimed":[71],"that":[72,122,145],"many":[73],"may":[75],"not":[76],"encode":[77],"expressed":[79,155],"proteins.":[80,156],"RESULTS:":[81],"genome-wide":[83],"experimental":[84,161],"study":[85],"'paralogous":[87],"PCOs'":[88,180],"halophilic":[91],"archaea":[92],"Halobacterium":[93,131,147],"sp.":[94,132,148],"NRC-1":[95,133,149],"was":[96],"conducted.":[97],"Paralogous":[98],"PCOs":[99,151,166],"are":[100,172],"with":[102,112],"at":[103,164],"least":[104],"one":[105],"homolog":[106],"same":[109],"organism,":[110],"but":[111],"no":[113],"clear":[114],"homologs":[115],"organisms.":[118],"The":[119],"results":[120],"reveal":[121],"mRNA":[123],"synthesized":[125],"a":[127],"majority":[128],"paralogous":[134,150],"PCO":[135],"families,":[136],"including":[137],"those":[138],"comprising":[139],"relatively":[140],"short":[141],"strongly":[143],"suggesting":[144],"these":[146],"true,":[154],"Hence,":[157],"further":[158],"computational":[159],"studies":[162],"aimed":[163],"characterizing":[165],"this":[168],"organisms":[171],"merited.":[173],"Such":[174],"efforts":[175],"could":[176],"shed":[177],"light":[178],"on":[179],"origins,":[183],"thereby":[184],"serving":[185],"elucidate":[187],"vast":[189],"diversity":[190],"observed":[191],"genetic":[194],"material.":[195]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
