{"id":"https://openalex.org/W2246614158","doi":"https://doi.org/10.1093/bib/bbv111","title":"A study of bias and increasing organismal complexity from their post-translational modifications and reaction site interplays","display_name":"A study of bias and increasing organismal complexity from their post-translational modifications and reaction site interplays","publication_year":2016,"publication_date":"2016-01-13","ids":{"openalex":"https://openalex.org/W2246614158","doi":"https://doi.org/10.1093/bib/bbv111","mag":"2246614158","pmid":"https://pubmed.ncbi.nlm.nih.gov/26764274"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv111","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv111","pdf_url":"https://academic.oup.com/bib/article-pdf/18/1/69/25408504/bbv111.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/18/1/69/25408504/bbv111.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028954340","display_name":"Oliver Bonham-Carter","orcid":"https://orcid.org/0000-0001-9032-0398"},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Oliver Bonham-Carter","raw_affiliation_strings":["School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, USA","[School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, USA","institution_ids":["https://openalex.org/I122266389"]},{"raw_affiliation_string":"[School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, USA]","institution_ids":["https://openalex.org/I122266389"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008692578","display_name":"Ishwor Thapa","orcid":"https://orcid.org/0000-0002-3594-1631"},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ishwor Thapa","raw_affiliation_strings":["School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, USA","School of Interdisciplinary Informatics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, USA","institution_ids":["https://openalex.org/I122266389"]},{"raw_affiliation_string":"School of Interdisciplinary Informatics","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111565634","display_name":"Steven G. From","orcid":null},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven From","raw_affiliation_strings":["Department of Mathematics, University of Nebraska at Omaha, Omaha, NE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Nebraska at Omaha, Omaha, NE, USA","institution_ids":["https://openalex.org/I122266389"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036016911","display_name":"Dhundy Bastola","orcid":"https://orcid.org/0000-0003-1128-4451"},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dhundy Bastola","raw_affiliation_strings":["School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, USA","School of Interdisciplinary Informatics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, USA","institution_ids":["https://openalex.org/I122266389"]},{"raw_affiliation_string":"School of Interdisciplinary Informatics","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I122266389"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.1709,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.62266465,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"18","issue":"1","first_page":"69","last_page":"84"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9987000226974487,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9987000226974487,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.7267597913742065},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.6091790795326233},{"id":"https://openalex.org/keywords/posttranslational-modification","display_name":"Posttranslational modification","score":0.5949507355690002},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5345456004142761},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4786756634712219},{"id":"https://openalex.org/keywords/rss","display_name":"RSS","score":0.43431463837623596},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.31757837533950806},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2811073660850525},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.27879226207733154},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22717419266700745},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.08352792263031006},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.07473939657211304}],"concepts":[{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.7267597913742065},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.6091790795326233},{"id":"https://openalex.org/C100631289","wikidata":"https://www.wikidata.org/wiki/Q898362","display_name":"Posttranslational modification","level":3,"score":0.5949507355690002},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5345456004142761},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4786756634712219},{"id":"https://openalex.org/C2385561","wikidata":"https://www.wikidata.org/wiki/Q45432","display_name":"RSS","level":2,"score":0.43431463837623596},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.31757837533950806},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2811073660850525},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.27879226207733154},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22717419266700745},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.08352792263031006},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.07473939657211304}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbv111","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv111","pdf_url":"https://academic.oup.com/bib/article-pdf/18/1/69/25408504/bbv111.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26764274","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26764274","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bib:18/1/69","is_oa":false,"landing_page_url":"http://bib.oxfordjournals.org/cgi/content/short/18/1/69","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:5221421","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5221421","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbv111","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv111","pdf_url":"https://academic.oup.com/bib/article-pdf/18/1/69/25408504/bbv111.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6800000071525574,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G4029151897","display_name":null,"funder_award_id":"P20 GM103427","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7652910328","display_name":null,"funder_award_id":"P20 RR016469","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2246614158.pdf"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1516721652","https://openalex.org/W1558717344","https://openalex.org/W1569287373","https://openalex.org/W1576058481","https://openalex.org/W1626483287","https://openalex.org/W1963911852","https://openalex.org/W1965687515","https://openalex.org/W1967567143","https://openalex.org/W1967843471","https://openalex.org/W1970081438","https://openalex.org/W1970161309","https://openalex.org/W1971423919","https://openalex.org/W1971705061","https://openalex.org/W1973312670","https://openalex.org/W1974116969","https://openalex.org/W1983411526","https://openalex.org/W1993825796","https://openalex.org/W1995286508","https://openalex.org/W1998674552","https://openalex.org/W2004805642","https://openalex.org/W2005678965","https://openalex.org/W2005893121","https://openalex.org/W2009826707","https://openalex.org/W2013340095","https://openalex.org/W2015115860","https://openalex.org/W2026197201","https://openalex.org/W2036733318","https://openalex.org/W2045381070","https://openalex.org/W2046099871","https://openalex.org/W2055529686","https://openalex.org/W2059225545","https://openalex.org/W2062041233","https://openalex.org/W2075319133","https://openalex.org/W2075730510","https://openalex.org/W2075797628","https://openalex.org/W2096525273","https://openalex.org/W2098550162","https://openalex.org/W2104694670","https://openalex.org/W2105947350","https://openalex.org/W2114972602","https://openalex.org/W2125729063","https://openalex.org/W2132022337","https://openalex.org/W2136920174","https://openalex.org/W2136951727","https://openalex.org/W2148013311","https://openalex.org/W2154139219","https://openalex.org/W2162434225","https://openalex.org/W2165812499","https://openalex.org/W2171963266","https://openalex.org/W2198387358","https://openalex.org/W2214508850","https://openalex.org/W2786774014","https://openalex.org/W4245543257"],"related_works":["https://openalex.org/W2316833920","https://openalex.org/W4377098514","https://openalex.org/W2970701885","https://openalex.org/W2290118617","https://openalex.org/W1975345997","https://openalex.org/W4387564043","https://openalex.org/W2019197244","https://openalex.org/W2054792938","https://openalex.org/W2967223254","https://openalex.org/W4234452205"],"abstract_inverted_index":{"Post-translational":[0],"modifications":[1],"(PTMs)":[2],"are":[3,42,88,102],"important":[4],"steps":[5],"in":[6,45,240],"the":[7,27,36,93,114,118,158,182,188,210,217],"biosynthesis":[8],"of":[9,24,30,33,38,66,68,73,124,139,146,161,185,194,212,219],"proteins.":[10],"Aside":[11],"from":[12,52],"their":[13],"integral":[14],"contributions":[15],"to":[16,48,82,128,134,175,203,208,224],"protein":[17,83,173],"development,":[18],"i.e.":[19],"perform":[20],"specialized":[21],"proteolytic":[22],"cleavage":[23],"regulatory":[25],"subunits,":[26],"covalent":[28],"addition":[29],"functional":[31],"groups":[32],"proteins":[34,47],"or":[35],"degradation":[37],"entire":[39],"proteins,":[40],"PTMs":[41,101,153,220],"also":[43],"involved":[44],"enabling":[46],"withstand":[49],"and":[50,59,121,141,171,190,196,206,221],"recover":[51],"temporary":[53],"environmental":[54,234],"stresses":[55],"(heat":[56],"shock,":[57],"microgravity":[58],"many":[60,72,89],"others).":[61],"The":[62],"literature":[63],"supports":[64],"evidence":[65,211],"thousands":[67],"recently":[69],"discovered":[70],"PTMs,":[71,140,187],"which":[74,230],"may":[75,231],"likely":[76],"contribute":[77],"similarly":[78],"(perhaps,":[79],"even,":[80],"interchangeably)":[81],"stress":[84,235],"response.":[85],"Although":[86],"there":[87],"PTM":[90,115,163],"actors":[91],"on":[92],"biological":[94],"stage,":[95],"our":[96],"study":[97,113],"determines":[98],"that":[99,130,216,233],"these":[100,201],"generally":[103],"cast":[104],"into":[105],"organism-specific,":[106],"preferential":[107],"roles.":[108],"In":[109],"this":[110,241],"work,":[111],"we":[112,168],"compositions":[116,193],"across":[117,165],"mitochondrial":[119],"(Mt)":[120],"non-Mt":[122,197],"proteomes":[123],"11":[125],"diverse":[126],"organisms":[127],"illustrate":[129,176,209],"each":[131],"organism":[132],"appears":[133,223],"have":[135],"a":[136,238],"unique":[137,144],"list":[138,145],"an":[142],"equally":[143],"PTM-associated":[147],"residue":[148],"reaction":[149],"sites":[150],"(RSs),":[151],"where":[152],"interact":[154],"with":[155,227],"protein.":[156],"Despite":[157],"present":[159],"limitation":[160],"available":[162],"data":[164,174,202],"different":[166],"species,":[167],"apply":[169,200],"existing":[170],"current":[172],"particular":[177],"organismal":[178,228],"biases.":[179],"We":[180,199,214],"explore":[181],"relative":[183],"frequencies":[184],"observed":[186],"RSs":[189,222],"general":[191],"amino-acid":[192],"Mt":[195],"proteomes.":[198],"create":[204],"networks":[205],"heatmaps":[207],"bias.":[213,242],"show":[215],"number":[218],"grow":[225],"along":[226],"complexity,":[229],"imply":[232],"could":[236],"play":[237],"role":[239]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
