{"id":"https://openalex.org/W1552307298","doi":null,"title":"Probabilistic model-based approach to evolutionary analysis of non-coding sequences","display_name":"Probabilistic model-based approach to evolutionary analysis of non-coding sequences","publication_year":2010,"publication_date":"2010-08-31","ids":{"openalex":"https://openalex.org/W1552307298","mag":"1552307298"},"language":"en","primary_location":{"id":"pmh:oai:www.ideals.illinois.edu:2142/16588","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/2142/16588","pdf_url":"http://hdl.handle.net/2142/16588","source":{"id":"https://openalex.org/S4306401358","display_name":"Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801919071","host_organization_name":"University of Illinois System","host_organization_lineage":["https://openalex.org/I2801919071"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2142/16588","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080954876","display_name":"Jaebum Kim","orcid":"https://orcid.org/0000-0002-2287-9760","observed_orcids":["https://orcid.org/0000-0002-2287-9760","https://orcid.org/0009-0001-4141-4723"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Jaebum Kim","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-2287-9760","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5080954876"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06258547,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9951000213623047,"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":0.9951000213623047,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.0017999999690800905,"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/T11269","display_name":"Algorithms and Data Compression","score":0.0006000000284984708,"subfield":{"id":"https://openalex.org/subfields/2614","display_name":"Theoretical Computer Science"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/non-coding-sequences","display_name":"non-coding sequences","score":0.9929999709129333},{"id":"https://openalex.org/keywords/indel-detection","display_name":"indel detection","score":0.5600000023841858},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"multiple sequence alignment","score":0.8659999966621399},{"id":"https://openalex.org/keywords/alignment-benchmarking","display_name":"alignment benchmarking","score":0.5809999704360962},{"id":"https://openalex.org/keywords/drosophila-embryo","display_name":"Drosophila embryo","score":0.7580000162124634},{"id":"https://openalex.org/keywords/body-patterning","display_name":"body patterning","score":0.765999972820282},{"id":"https://openalex.org/keywords/regulatory-elements","display_name":"regulatory elements","score":0.8650000095367432},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"comparative genomics","score":0.722000002861023},{"id":"https://openalex.org/keywords/parsimony","display_name":"parsimony","score":0.5550000071525574}],"concepts":[{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.565159261226654},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.5278998017311096},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5167393088340759},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.4789622128009796},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39397484064102173},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.23553451895713806},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.16155892610549927}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:www.ideals.illinois.edu:2142/16588","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/2142/16588","pdf_url":"http://hdl.handle.net/2142/16588","source":{"id":"https://openalex.org/S4306401358","display_name":"Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801919071","host_organization_name":"University of Illinois System","host_organization_lineage":["https://openalex.org/I2801919071"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:www.ideals.illinois.edu:2142/16981","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/2142/16981","pdf_url":"http://hdl.handle.net/2142/16981","source":{"id":"https://openalex.org/S4306401358","display_name":"Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801919071","host_organization_name":"University of Illinois System","host_organization_lineage":["https://openalex.org/I2801919071"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"mag:1552307298","doi":null,"is_oa":false,"landing_page_url":"https://www.ideals.illinois.edu/handle/2142/16588","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:www.ideals.illinois.edu:2142/16588","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/2142/16588","pdf_url":"http://hdl.handle.net/2142/16588","source":{"id":"https://openalex.org/S4306401358","display_name":"Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801919071","host_organization_name":"University of Illinois System","host_organization_lineage":["https://openalex.org/I2801919071"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1552307298.pdf","grobid_xml":"https://content.openalex.org/works/W1552307298.grobid-xml"},"referenced_works_count":179,"referenced_works":["https://openalex.org/W10219220","https://openalex.org/W614012683","https://openalex.org/W1505838730","https://openalex.org/W1506197483","https://openalex.org/W1510739935","https://openalex.org/W1525734744","https://openalex.org/W1553325587","https://openalex.org/W1595688369","https://openalex.org/W1596576919","https://openalex.org/W1608071358","https://openalex.org/W1634746048","https://openalex.org/W1646393397","https://openalex.org/W1664003695","https://openalex.org/W1665731021","https://openalex.org/W1863643864","https://openalex.org/W1866488244","https://openalex.org/W1866859902","https://openalex.org/W1872483787","https://openalex.org/W1899949781","https://openalex.org/W1922163769","https://openalex.org/W1963590211","https://openalex.org/W1966875588","https://openalex.org/W1968256798","https://openalex.org/W1969153299","https://openalex.org/W1969770714","https://openalex.org/W1973310573","https://openalex.org/W1976521104","https://openalex.org/W1980397590","https://openalex.org/W1983792126","https://openalex.org/W1986014242","https://openalex.org/W1991439294","https://openalex.org/W1991770658","https://openalex.org/W1994190548","https://openalex.org/W1994990680","https://openalex.org/W1997631042","https://openalex.org/W1999707793","https://openalex.org/W2001167864","https://openalex.org/W2001706442","https://openalex.org/W2004178884","https://openalex.org/W2007278061","https://openalex.org/W2007939821","https://openalex.org/W2009596137","https://openalex.org/W2011289056","https://openalex.org/W2012354488","https://openalex.org/W2013298312","https://openalex.org/W2016223901","https://openalex.org/W2017777683","https://openalex.org/W2018248334","https://openalex.org/W2020749481","https://openalex.org/W2021839440","https://openalex.org/W2024665422","https://openalex.org/W2025665146","https://openalex.org/W2026074998","https://openalex.org/W2026551295","https://openalex.org/W2030816054","https://openalex.org/W2031830181","https://openalex.org/W2032548898","https://openalex.org/W2032558547","https://openalex.org/W2033339460","https://openalex.org/W2033785622","https://openalex.org/W2034536549","https://openalex.org/W2035343693","https://openalex.org/W2036799822","https://openalex.org/W2041966847","https://openalex.org/W2045219458","https://openalex.org/W2045391589","https://openalex.org/W2046233233","https://openalex.org/W2046374070","https://openalex.org/W2049173972","https://openalex.org/W2049633694","https://openalex.org/W2061149284","https://openalex.org/W2061408624","https://openalex.org/W2065400176","https://openalex.org/W2065461553","https://openalex.org/W2066077768","https://openalex.org/W2066502527","https://openalex.org/W2068469513","https://openalex.org/W2068473194","https://openalex.org/W2069787595","https://openalex.org/W2070340804","https://openalex.org/W2073234837","https://openalex.org/W2074231493","https://openalex.org/W2085442947","https://openalex.org/W2085950579","https://openalex.org/W2088930530","https://openalex.org/W2089611415","https://openalex.org/W2089956843","https://openalex.org/W2090044421","https://openalex.org/W2091913260","https://openalex.org/W2092979861","https://openalex.org/W2095824228","https://openalex.org/W2096118921","https://openalex.org/W2097020631","https://openalex.org/W2097311877","https://openalex.org/W2097386339","https://openalex.org/W2099762535","https://openalex.org/W2100261113","https://openalex.org/W2100990361","https://openalex.org/W2102159699","https://openalex.org/W2102424972","https://openalex.org/W2102502076","https://openalex.org/W2106882534","https://openalex.org/W2108187446","https://openalex.org/W2109314645","https://openalex.org/W2109618648","https://openalex.org/W2110335151","https://openalex.org/W2112132489","https://openalex.org/W2112717966","https://openalex.org/W2114019432","https://openalex.org/W2114122189","https://openalex.org/W2115918447","https://openalex.org/W2117502535","https://openalex.org/W2118533197","https://openalex.org/W2119295056","https://openalex.org/W2119362018","https://openalex.org/W2120248467","https://openalex.org/W2120958393","https://openalex.org/W2121691652","https://openalex.org/W2124495196","https://openalex.org/W2125359798","https://openalex.org/W2125427437","https://openalex.org/W2125838338","https://openalex.org/W2126257080","https://openalex.org/W2127164334","https://openalex.org/W2127556561","https://openalex.org/W2127688908","https://openalex.org/W2127860913","https://openalex.org/W2128613007","https://openalex.org/W2131510900","https://openalex.org/W2134941776","https://openalex.org/W2137502130","https://openalex.org/W2138629076","https://openalex.org/W2139659560","https://openalex.org/W2140872496","https://openalex.org/W2141411672","https://openalex.org/W2142987298","https://openalex.org/W2143249831","https://openalex.org/W2143292980","https://openalex.org/W2143357251","https://openalex.org/W2145396697","https://openalex.org/W2146222452","https://openalex.org/W2146310648","https://openalex.org/W2146663379","https://openalex.org/W2147789429","https://openalex.org/W2147847662","https://openalex.org/W2150687466","https://openalex.org/W2151120398","https://openalex.org/W2151233592","https://openalex.org/W2152688507","https://openalex.org/W2155320525","https://openalex.org/W2155717510","https://openalex.org/W2155940790","https://openalex.org/W2156521045","https://openalex.org/W2157552136","https://openalex.org/W2157674573","https://openalex.org/W2159480618","https://openalex.org/W2160659074","https://openalex.org/W2161387979","https://openalex.org/W2163860567","https://openalex.org/W2165322293","https://openalex.org/W2165378709","https://openalex.org/W2165686834","https://openalex.org/W2165890696","https://openalex.org/W2167300924","https://openalex.org/W2167359290","https://openalex.org/W2167698733","https://openalex.org/W2168783124","https://openalex.org/W2170628952","https://openalex.org/W2170702273","https://openalex.org/W2740984310","https://openalex.org/W4237033704","https://openalex.org/W4242342141","https://openalex.org/W7009952664","https://openalex.org/W7073839493","https://openalex.org/W7096884946","https://openalex.org/W7097764011","https://openalex.org/W7098600529","https://openalex.org/W7099311627","https://openalex.org/W7099666281"],"related_works":["https://openalex.org/W2145958666","https://openalex.org/W7096884946","https://openalex.org/W2061641880","https://openalex.org/W7097109659","https://openalex.org/W4402559352","https://openalex.org/W73353026","https://openalex.org/W2145396697","https://openalex.org/W1584129042","https://openalex.org/W2125310048","https://openalex.org/W7099453251"],"abstract_inverted_index":{"Non-coding":[0],"sequences,":[1,94,198],"constituting":[2],"a":[3,106,119,133,173,218,238,255,293],"large":[4],"fraction":[5],"of":[6,10,25,36,43,46,66,80,101,113,140,146,158,185,243,250,271,284,308],"genomic":[7,68],"DNA,":[8],"are":[9,20,31,96,202],"great":[11],"importance":[12],"because":[13],"(i)":[14],"they":[15,30],"harbor":[16],"functional":[17],"elements":[18,165],"that":[19,74,130,225,265],"involved":[21,142],"in":[22,118,143,149,156,282,296],"the":[23,34,76,111,138,144,150,183,241,247,258,266],"regulation":[24,145],"gene":[26],"expression":[27],"and":[28,39,78,86,115,166,199,208,246,301,311],"(ii)":[29],"essential":[32],"for":[33,109,177,182,195,204,221,240,257],"study":[35,137],"genome":[37,44,81],"structure":[38],"evolution.":[40,103,312],"The":[41,64,286],"availability":[42],"sequences":[45,56,141,245],"closely":[47],"related":[48,162],"species":[49],"has":[50],"provided":[51],"opportunities":[52],"to":[53,90,126,163,192,304],"analyze":[54,92],"non-coding":[55,93,186,197],"by":[57,132,230],"comparing":[58],"multiple":[59,120,206,222],"genomes":[60],"from":[61],"different":[62],"species.":[63],"success":[65],"comparative":[67],"studies":[69],"relies":[70],"on":[71,98,168,212,237],"bioinformatics":[72],"tools":[73,89,211,288],"aid":[75],"comparison":[77],"analysis":[79],"sequences.":[82,187],"Here,":[83],"we":[84,216],"propose":[85,172],"develop":[87,217],"computational":[88,287],"evolutionarily":[91],"which":[95],"based":[97,236],"probabilistic":[99,107,219],"models":[100],"sequence":[102,223],"We":[104,136,170,263],"present":[105],"framework":[108,220,268],"finding":[110],"locations":[112],"insertions":[114],"deletions":[116],"(indels)":[117],"alignment.":[121],"Its":[122],"performance":[123],"is":[124,190],"found":[125],"be":[127],"better":[128],"than":[129,275],"obtained":[131],"parsimony-based":[134],"method.":[135],"evolution":[139,242],"body":[147],"patterning":[148],"Drosophila":[151,196],"embryo,":[152],"reporting":[153],"statistical":[154],"evidence":[155],"favor":[157],"key":[159],"evolutionary":[160],"hypotheses":[161],"regulatory":[164],"constraints":[167],"indels.":[169],"also":[171],"new":[174,267],"simulation":[175],"scheme":[176,189],"generating":[178],"biologically":[179],"realistic":[180],"benchmarks":[181,194],"alignments":[184,270],"This":[188],"used":[191,260],"construct":[193],"evaluation":[200],"results":[201],"shown":[203],"several":[205],"alignment":[207,224,229,234,252],"indel":[209],"annotation":[210],"those":[213],"benchmarks.":[214],"Finally,":[215],"finds":[226],"an":[227,251],"optimal":[228],"incrementally":[231],"building":[232],"up":[233],"columns,":[235],"model":[239],"three":[244],"joint":[248],"probability":[249],"column":[253],"as":[254],"substitute":[256],"traditionally":[259],"sum-of-pairs":[261],"score.":[262],"find":[264],"produces":[269],"much":[272,281],"greater":[273],"specificity":[274],"state-of-the-art":[276],"methods,":[277],"without":[278],"compromising":[279],"too":[280],"terms":[283],"sensitivity.":[285],"developed":[289],"here":[290],"will":[291],"play":[292],"significant":[294],"role":[295],"solving":[297],"many":[298],"biological":[299],"problems":[300],"further":[302],"contribute":[303],"broaden":[305],"our":[306],"understanding":[307],"organismal":[309],"diversity":[310]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2016-06-24T00:00:00"}