{"id":"https://openalex.org/W2142142506","doi":"https://doi.org/10.1093/bioinformatics/btq509","title":"The mRNA landscape at yeast translation initiation sites","display_name":"The mRNA landscape at yeast translation initiation sites","publication_year":2010,"publication_date":"2010-09-06","ids":{"openalex":"https://openalex.org/W2142142506","doi":"https://doi.org/10.1093/bioinformatics/btq509","mag":"2142142506","pmid":"https://pubmed.ncbi.nlm.nih.gov/20819958"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq509","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq509","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/21/2651/48851609/bioinformatics_26_21_2651.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/26/21/2651/48851609/bioinformatics_26_21_2651.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032960228","display_name":"Adam Robbins\u2010Pianka","orcid":null},"institutions":[{"id":"https://openalex.org/I100538780","display_name":"Wesleyan University","ror":"https://ror.org/05h7xva58","country_code":"US","type":"education","lineage":["https://openalex.org/I100538780"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"A. Robbins-Pianka","raw_affiliation_strings":["1 Department of Biology and 2Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biology and 2Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA","institution_ids":["https://openalex.org/I100538780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081498801","display_name":"Michael Rice","orcid":"https://orcid.org/0000-0001-5150-4792"},"institutions":[{"id":"https://openalex.org/I100538780","display_name":"Wesleyan University","ror":"https://ror.org/05h7xva58","country_code":"US","type":"education","lineage":["https://openalex.org/I100538780"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. D. Rice","raw_affiliation_strings":["1 Department of Biology and 2Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biology and 2Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA","institution_ids":["https://openalex.org/I100538780"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054954864","display_name":"Michael P. Weir","orcid":"https://orcid.org/0000-0002-5999-4199"},"institutions":[{"id":"https://openalex.org/I100538780","display_name":"Wesleyan University","ror":"https://ror.org/05h7xva58","country_code":"US","type":"education","lineage":["https://openalex.org/I100538780"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. P. Weir","raw_affiliation_strings":["1 Department of Biology and 2Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Biology and 2Department of Mathematics and Computer Science, Wesleyan University, Middletown, CT 06459, USA","institution_ids":["https://openalex.org/I100538780"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5032960228"],"corresponding_institution_ids":["https://openalex.org/I100538780"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.4539,"has_fulltext":false,"cited_by_count":41,"citation_normalized_percentile":{"value":0.81308957,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"26","issue":"21","first_page":"2651","last_page":"2655"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10604","display_name":"RNA Research and Splicing","score":0.9994000196456909,"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/T11482","display_name":"RNA modifications and cancer","score":0.9987999796867371,"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/translation","display_name":"Translation (biology)","score":0.6682950854301453},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6143826842308044},{"id":"https://openalex.org/keywords/ribosome","display_name":"Ribosome","score":0.5748947858810425},{"id":"https://openalex.org/keywords/eukaryotic-translation","display_name":"Eukaryotic translation","score":0.5432852506637573},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5083696246147156},{"id":"https://openalex.org/keywords/base-pair","display_name":"Base pair","score":0.48183098435401917},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.4675910174846649},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.45174241065979004},{"id":"https://openalex.org/keywords/protein-biosynthesis","display_name":"Protein biosynthesis","score":0.450038343667984},{"id":"https://openalex.org/keywords/downstream","display_name":"Downstream (manufacturing)","score":0.44771048426628113},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.447458416223526},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.44438204169273376},{"id":"https://openalex.org/keywords/nucleic-acid-secondary-structure","display_name":"Nucleic acid secondary structure","score":0.4432436227798462},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.4134438633918762},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.36303579807281494},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3256767988204956},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.29427796602249146},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13662117719650269},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08020138740539551}],"concepts":[{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.6682950854301453},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6143826842308044},{"id":"https://openalex.org/C88478588","wikidata":"https://www.wikidata.org/wiki/Q42244","display_name":"Ribosome","level":4,"score":0.5748947858810425},{"id":"https://openalex.org/C4718897","wikidata":"https://www.wikidata.org/wiki/Q5408698","display_name":"Eukaryotic translation","level":5,"score":0.5432852506637573},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5083696246147156},{"id":"https://openalex.org/C185581394","wikidata":"https://www.wikidata.org/wiki/Q145911","display_name":"Base pair","level":3,"score":0.48183098435401917},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.4675910174846649},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45174241065979004},{"id":"https://openalex.org/C3675279","wikidata":"https://www.wikidata.org/wiki/Q211935","display_name":"Protein biosynthesis","level":2,"score":0.450038343667984},{"id":"https://openalex.org/C2776207758","wikidata":"https://www.wikidata.org/wiki/Q5303302","display_name":"Downstream (manufacturing)","level":2,"score":0.44771048426628113},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.447458416223526},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.44438204169273376},{"id":"https://openalex.org/C85468374","wikidata":"https://www.wikidata.org/wiki/Q6589957","display_name":"Nucleic acid secondary structure","level":4,"score":0.4432436227798462},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.4134438633918762},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36303579807281494},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3256767988204956},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29427796602249146},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13662117719650269},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08020138740539551},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014176","descriptor_name":"Protein Biosynthesis","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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btq509","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq509","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/21/2651/48851609/bioinformatics_26_21_2651.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:20819958","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20819958","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/btq509","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq509","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/21/2651/48851609/bioinformatics_26_21_2651.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/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2142142506.pdf","grobid_xml":"https://content.openalex.org/works/W2142142506.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W144075901","https://openalex.org/W1518926766","https://openalex.org/W1543796220","https://openalex.org/W1982980697","https://openalex.org/W1984675364","https://openalex.org/W1984708728","https://openalex.org/W1994244877","https://openalex.org/W2003796236","https://openalex.org/W2005000247","https://openalex.org/W2013947447","https://openalex.org/W2025569664","https://openalex.org/W2025763720","https://openalex.org/W2026487666","https://openalex.org/W2027055740","https://openalex.org/W2045348184","https://openalex.org/W2063779182","https://openalex.org/W2072971665","https://openalex.org/W2077546945","https://openalex.org/W2079517684","https://openalex.org/W2080099684","https://openalex.org/W2083070222","https://openalex.org/W2091607609","https://openalex.org/W2146335626","https://openalex.org/W2148627082","https://openalex.org/W2153521373","https://openalex.org/W2154128645","https://openalex.org/W2160689765","https://openalex.org/W2168847939"],"related_works":["https://openalex.org/W2558432341","https://openalex.org/W1975806245","https://openalex.org/W3047450301","https://openalex.org/W2345156963","https://openalex.org/W1971402940","https://openalex.org/W2919479895","https://openalex.org/W2131054067","https://openalex.org/W3196523453","https://openalex.org/W2021868453","https://openalex.org/W1978187259"],"abstract_inverted_index":{"Although":[0],"translation":[1,24,179,214],"initiation":[2,25,180],"has":[3,54],"been":[4,56],"well":[5],"studied,":[6],"many":[7],"questions":[8],"remain":[9],"in":[10,63,116,166,170],"elucidating":[11],"its":[12],"mechanisms.":[13],"An":[14],"ongoing":[15],"challenge":[16],"is":[17,74,201],"to":[18,58,107,144,159],"understand":[19],"how":[20],"ribosomes":[21],"choose":[22],"a":[23,68,78,97,104,117,126,137],"site":[26],"(TIS).":[27],"To":[28],"gain":[29],"new":[30],"insights,":[31],"we":[32,82,124],"analyzed":[33],"large":[34],"sets":[35,205],"of":[36,41,48,67,91,112,120,129,135,139,163,194,206,224],"TISs":[37,162,207],"with":[38,208,217],"the":[39,64,88,92,109,130,140,151,161,195,198,225],"aim":[40],"identifying":[42],"common":[43],"characteristics":[44],"that":[45,132,177,220],"are":[46,185],"potentially":[47],"functional":[49],"importance.":[50],"Nucleotide":[51],"sequence":[52,210],"context":[53],"previously":[55],"demonstrated":[57],"play":[59],"an":[60],"important":[61],"role":[62],"ribosome's":[65],"selection":[66],"TIS,":[69],"and":[70,173,181,192],"mRNA":[71,84],"secondary":[72,85,114,189,221],"structure":[73,86,115,190,222],"also":[75],"emerging":[76],"as":[77],"contributing":[79],"factor.":[80],"Here,":[81],"analyze":[83],"using":[87,103],"folding":[89],"predictions":[90],"RNAfold":[93],"algorithm.":[94],"We":[95],"present":[96],"method":[98],"for":[99,204,213],"analyzing":[100],"these":[101],"results":[102],"rank-ordering":[105],"approach":[106],"assess":[108],"overall":[110],"degree":[111],"predicted":[113],"given":[118],"region":[119],"mRNA.":[121],"In":[122],"addition,":[123],"used":[125],"modified":[127],"version":[128],"algorithm":[131],"makes":[133],"use":[134],"only":[136],"subset":[138],"standard":[141],"version's":[142],"output":[143],"incorporate":[145],"base-pairing":[146,174],"polarity":[147],"constraints":[148],"suggested":[149],"by":[150,187],"ribosome":[152,226],"scanning":[153],"process.":[154],"These":[155],"methods":[156],"were":[157],"employed":[158],"study":[160],"1735":[164],"genes":[165],"Saccharomyces":[167],"cerevisiae.":[168],"Trends":[169],"base":[171],"composition":[172],"probabilities":[175],"suggest":[176],"efficient":[178],"high":[182],"protein":[183],"expression":[184],"aided":[186],"reduced":[188],"upstream":[191],"downstream":[193,199,223],"TIS.":[196],"However,":[197],"reduction":[200],"not":[202],"observed":[203],"nucleotide":[209],"contexts":[211],"unfavorable":[212],"initiation,":[215],"consistent":[216],"previous":[218],"suggestions":[219],"can":[227],"facilitate":[228],"TIS":[229],"recognition.":[230]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
