{"id":"https://openalex.org/W2104504949","doi":"https://doi.org/10.1093/bioinformatics/bti812","title":"In silico sequence evolution with site-specific interactions along phylogenetic trees","display_name":"In silico sequence evolution with site-specific interactions along phylogenetic trees","publication_year":2005,"publication_date":"2005-12-06","ids":{"openalex":"https://openalex.org/W2104504949","doi":"https://doi.org/10.1093/bioinformatics/bti812","mag":"2104504949","pmid":"https://pubmed.ncbi.nlm.nih.gov/16332711"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti812","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/6/716/48839868/bioinformatics_22_6_716.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4811","1367-4803"],"is_oa":true,"is_in_doaj":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":null,"version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/22/6/716/48839868/bioinformatics_22_6_716.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049682751","display_name":"Tanja Gesell","orcid":"https://orcid.org/0000-0002-0733-7605"},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tanja Gesell","raw_affiliation_string":"Heinrich-Heine University Duesseldorf, Universitaetsstrasse 1 1 \u00a0 1 \u00a0 \u00a0 40225 Duesseldorf, Germany","raw_affiliation_strings":["Heinrich-Heine University Duesseldorf, Universitaetsstrasse 1 1 \u00a0 1 \u00a0 \u00a0 40225 Duesseldorf, Germany"]},{"author_position":"last","author":{"id":"https://openalex.org/A5085983122","display_name":"Arndt von Haeseler","orcid":"https://orcid.org/0000-0002-3366-4458"},"institutions":[{"id":"https://openalex.org/I2802916955","display_name":"Max Perutz Labs","ror":"https://ror.org/05cz70a34","country_code":"AT","type":"facility","lineage":["https://openalex.org/I2802916955"]},{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]},{"id":"https://openalex.org/I76134821","display_name":"Medical University of Vienna","ror":"https://ror.org/05n3x4p02","country_code":"AT","type":"education","lineage":["https://openalex.org/I76134821"]},{"id":"https://openalex.org/I150540706","display_name":"University of Veterinary Medicine Vienna","ror":"https://ror.org/01w6qp003","country_code":"AT","type":"education","lineage":["https://openalex.org/I150540706"]}],"countries":["AT"],"is_corresponding":true,"raw_author_name":"Arndt Von Haeseler","raw_affiliation_string":"Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories 2 \u00a0 2 \u00a0 \u00a0 Dr. Bohr-Gasse 9, A-1030 Vienna, Austria; Medical University of Vienna 4 \u00a0 4 \u00a0 \u00a0 Austria; University of Veterinary Medicine Vienna 5 \u00a0 5 \u00a0 \u00a0 Austria; University of Vienna 3 \u00a0 3 \u00a0 \u00a0 Austria","raw_affiliation_strings":["Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories 2 \u00a0 2 \u00a0 \u00a0 Dr. Bohr-Gasse 9, A-1030 Vienna, Austria","Medical University of Vienna 4 \u00a0 4 \u00a0 \u00a0 Austria","University of Veterinary Medicine Vienna 5 \u00a0 5 \u00a0 \u00a0 Austria","University of Vienna 3 \u00a0 3 \u00a0 \u00a0 Austria"]}],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5085983122"],"corresponding_institution_ids":["https://openalex.org/I2802916955","https://openalex.org/I129774422","https://openalex.org/I76134821","https://openalex.org/I150540706"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618,"provenance":"doaj"},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618,"provenance":"doaj"},"has_fulltext":true,"fulltext_origin":"ngrams","cited_by_count":31,"cited_by_percentile_year":{"min":91,"max":92},"biblio":{"volume":"22","issue":"6","first_page":"716","last_page":"722"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"RNA Sequencing Data Analysis","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/T10015","display_name":"RNA Sequencing Data Analysis","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/T10521","display_name":"Ribosome Structure and Translation Mechanisms","score":0.9995,"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":"Prediction of Protein Subcellular Localization","score":0.9919,"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":[{"keyword":"sequence evolution","score":0.5237},{"keyword":"trees","score":0.3585},{"keyword":"site-specific","score":0.25}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.7255003},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.59175664},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.58237344},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5651237},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.55432814},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.49796176},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39975742},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31647262},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1695714},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16648528},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16114959},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.16080457},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.12451029},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.09487888},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D020137","descriptor_name":"Base Pair Mismatch","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020137","descriptor_name":"Base Pair Mismatch","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti812","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/6/716/48839868/bioinformatics_22_6_716.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4811","1367-4803"],"is_oa":true,"is_in_doaj":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16332711","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":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":["National Institutes of Health"],"type":"repository"},"license":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti812","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/6/716/48839868/bioinformatics_22_6_716.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4811","1367-4803"],"is_oa":true,"is_in_doaj":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":null,"version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[{"score":0.5,"display_name":"Sustainable cities and communities","id":"https://metadata.un.org/sdg/11"}],"grants":[],"referenced_works_count":44,"referenced_works":["https://openalex.org/W1525734744","https://openalex.org/W1543796220","https://openalex.org/W1914379396","https://openalex.org/W1941675760","https://openalex.org/W1970074020","https://openalex.org/W1976361312","https://openalex.org/W1993968482","https://openalex.org/W1994388332","https://openalex.org/W1995470277","https://openalex.org/W2009596137","https://openalex.org/W2009736453","https://openalex.org/W2031206741","https://openalex.org/W2044247083","https://openalex.org/W2047354232","https://openalex.org/W2052576140","https://openalex.org/W2053929098","https://openalex.org/W2065461553","https://openalex.org/W2066331031","https://openalex.org/W2076634000","https://openalex.org/W2081443406","https://openalex.org/W2091851394","https://openalex.org/W2094548241","https://openalex.org/W2096619551","https://openalex.org/W2097386339","https://openalex.org/W2101546326","https://openalex.org/W2102424972","https://openalex.org/W2107010419","https://openalex.org/W2107721261","https://openalex.org/W2116503869","https://openalex.org/W2118676074","https://openalex.org/W2123758939","https://openalex.org/W2135753651","https://openalex.org/W2137188869","https://openalex.org/W2137640371","https://openalex.org/W2138178197","https://openalex.org/W2147307434","https://openalex.org/W2149608597","https://openalex.org/W2151538750","https://openalex.org/W2152303410","https://openalex.org/W2153505916","https://openalex.org/W2160659074","https://openalex.org/W2169239541","https://openalex.org/W4247016878","https://openalex.org/W4251866352"],"related_works":["https://openalex.org/W1503050251","https://openalex.org/W4299941255","https://openalex.org/W2383147678","https://openalex.org/W1983230203","https://openalex.org/W1993951481","https://openalex.org/W2949462032","https://openalex.org/W2952753948","https://openalex.org/W2165098423","https://openalex.org/W2950764994","https://openalex.org/W1588193375"],"ngrams_url":"https://api.openalex.org/works/W2104504949/ngrams","abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"A":[2],"biological":[3],"sequence":[4,29,39,100,151],"usually":[5],"has":[6],"many":[7],"sites":[8],"whose":[9],"evolution":[10,40,101,116,147],"depends":[11,50],"on":[12,51,58,190],"other":[13,55,130,173],"positions":[14],"of":[15,28,37,54,61,70,99,117,148],"the":[16,43,52,59,115],"sequence,":[17],"but":[18],"this":[19,134],"is":[20,202],"not":[21],"accounted":[22],"for":[23,84,97],"by":[24],"commonly":[25],"used":[26],"models":[27,83],"evolution.":[30],"Here":[31],"we":[32,110,136],"introduce":[33],"a":[34,48,67,94,106,139,149,153],"Markov":[35],"model":[36,65],"nucleotide":[38,150,171],"in":[41,182],"which":[42,188],"instantaneous":[44],"substitution":[45],"rate":[46],"at":[47,204],"site":[49],"states":[53],"sites.":[56,75],"Based":[57],"concept":[60],"neighbourhood":[62],"systems,":[63,196],"our":[64,91,162,180],"represents":[66],"universal":[68],"description":[69],"arbitrarily":[71],"complex":[72,82,168],"dependencies":[73],"among":[74,170],"Results:":[76],"We":[77,178],"show":[78],"how":[79],"to":[80,113,165],"define":[81],"some":[85],"illustrative":[86],"examples":[87],"and":[88,129,172,193],"demonstrate":[89],"that":[90,145],"method":[92,163,181],"provides":[93],"versatile":[95],"resource":[96],"simulations":[98],"with":[102],"site-specific":[103,159],"interactions":[104,169],"along":[105,152],"tree.":[107],"For":[108],"example,":[109],"are":[111],"able":[112],"simulate":[114,166],"RNA":[118],"taking":[119],"into":[120],"account":[121],"both":[122],"secondary":[123],"structure":[124],"as":[125,127],"well":[126],"pseudoknots":[128],"tertiary":[131],"interactions.":[132,160],"To":[133],"end,":[135],"have":[137],"developed":[138],"program":[140,186],"Simulating":[141],"Site-Specific":[142],"Interactions":[143],"(SISSI)":[144],"simulates":[146],"phylogenetic":[154],"tree":[155],"incorporating":[156],"user":[157],"defined":[158],"Furthermore,":[161],"allows":[164],"more":[167],"character":[174],"based":[175],"sequences.":[176],"Availability:":[177],"implemented":[179],"an":[183],"ANSI":[184],"C":[185],"SISSI":[187,201],"runs":[189],"UNIX/Linux,":[191],"Windows":[192],"Mac":[194,198],"OS":[195,199],"including":[197],"X.":[200],"available":[203],"Contact:":[205],"sissi@cs.uni-duesseldorf.de":[206]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2104504949","counts_by_year":[{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2024-02-22T20:24:18.312418","created_date":"2016-06-24"}