{"id":"https://openalex.org/W3012361895","doi":"https://doi.org/10.1093/bioinformatics/btaa195","title":"Position-wise binding preference is important for miRNA target site prediction","display_name":"Position-wise binding preference is important for miRNA target site prediction","publication_year":2020,"publication_date":"2020-03-17","ids":{"openalex":"https://openalex.org/W3012361895","doi":"https://doi.org/10.1093/bioinformatics/btaa195","mag":"3012361895","pmid":"https://pubmed.ncbi.nlm.nih.gov/32186709"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa195","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa195","pdf_url":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8453239","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007638508","display_name":"Amlan Talukder","orcid":"https://orcid.org/0000-0001-7457-8268"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Amlan Talukder","raw_affiliation_strings":["Department of Computer Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100669881","display_name":"Xiaoman Li","orcid":"https://orcid.org/0000-0002-9209-458X"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiaoman Li","raw_affiliation_strings":["Burnett School of Biomedical Science , College of Medicine, University of Central Orlando, FL 32816, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Burnett School of Biomedical Science , College of Medicine, University of Central Orlando, FL 32816, USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053178146","display_name":"Haiyan Hu","orcid":"https://orcid.org/0000-0001-9197-3526"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Haiyan Hu","raw_affiliation_strings":["Department of Computer Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5053178146","https://openalex.org/A5100669881"],"corresponding_institution_ids":["https://openalex.org/I106165777"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6373,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.61034741,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"12","first_page":"3680","last_page":"3686"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.9753000140190125,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10062","display_name":"MicroRNA in disease regulation","score":0.9753000140190125,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":"Machine Learning in Bioinformatics","score":0.0017000000225380063,"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/T11765","display_name":"Circular RNAs in diseases","score":0.0015999999595806003,"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/computer-science","display_name":"Computer science","score":0.7273326516151428},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.5959422588348389},{"id":"https://openalex.org/keywords/position","display_name":"Position (finance)","score":0.5268510580062866},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5182669162750244},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4897892475128174},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.45542141795158386},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.448609322309494},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4430014491081238},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4281895160675049},{"id":"https://openalex.org/keywords/pairing","display_name":"Pairing","score":0.4142482280731201},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.30690544843673706}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7273326516151428},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.5959422588348389},{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.5268510580062866},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5182669162750244},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4897892475128174},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.45542141795158386},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.448609322309494},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4430014491081238},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4281895160675049},{"id":"https://openalex.org/C14103023","wikidata":"https://www.wikidata.org/wiki/Q11681459","display_name":"Pairing","level":3,"score":0.4142482280731201},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.30690544843673706},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C54101563","wikidata":"https://www.wikidata.org/wiki/Q124131","display_name":"Superconductivity","level":2,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaa195","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa195","pdf_url":null,"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:32186709","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32186709","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:europepmc.org:7346733","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8453239","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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:8453239","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8453239","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:8453239","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8453239","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":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.4099999964237213,"id":"https://metadata.un.org/sdg/17"},{"display_name":"Industry, innovation and infrastructure","score":0.4099999964237213,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G180596448","display_name":null,"funder_award_id":"R15 GM123407","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1970121668","https://openalex.org/W1993799748","https://openalex.org/W2014845588","https://openalex.org/W2026570544","https://openalex.org/W2033724104","https://openalex.org/W2041509376","https://openalex.org/W2053003053","https://openalex.org/W2059073003","https://openalex.org/W2088930981","https://openalex.org/W2102874238","https://openalex.org/W2104806799","https://openalex.org/W2109608461","https://openalex.org/W2120456037","https://openalex.org/W2134629862","https://openalex.org/W2149785901","https://openalex.org/W2150395782","https://openalex.org/W2154085311","https://openalex.org/W2156154309","https://openalex.org/W2159793493","https://openalex.org/W2163199119","https://openalex.org/W2174734928","https://openalex.org/W2180388440","https://openalex.org/W2337379458","https://openalex.org/W2407848977","https://openalex.org/W2501277993","https://openalex.org/W2727545883","https://openalex.org/W2757425689","https://openalex.org/W2937979402","https://openalex.org/W3004097159","https://openalex.org/W4237142329","https://openalex.org/W6740516218","https://openalex.org/W6773627796"],"related_works":["https://openalex.org/W3015473028","https://openalex.org/W3201176751","https://openalex.org/W1993094293","https://openalex.org/W2029180842","https://openalex.org/W2024971119","https://openalex.org/W2057898405","https://openalex.org/W2953807518","https://openalex.org/W2258335979","https://openalex.org/W2890366349","https://openalex.org/W3119345543"],"abstract_inverted_index":{"MOTIVATION:":[0],"It":[1],"is":[2,59,257],"a":[3,45,56,104,121,126,192],"fundamental":[4],"task":[5],"to":[6,40,44,54,79,107,191,235,253],"identify":[7],"microRNAs":[8],"(miRNAs)":[9],"targets":[10],"and":[11,34,124,166,180,251],"accurately":[12],"locate":[13],"their":[14,209,220,226],"target":[15,21,66,88,98,139,146,198,210,237],"sites.":[16],"Genome-scale":[17],"experiments":[18],"for":[19,137],"miRNA":[20,97,138,194],"site":[22,140],"detection":[23],"are":[24,36,265],"still":[25],"costly.":[26],"The":[27,71,151,248],"prediction":[28,99,238],"accuracies":[29],"of":[30,48,62,64,69,83,87,112,148,162],"existing":[31,216,242],"computational":[32],"algorithms":[33],"tools":[35],"often":[37],"not":[38],"up":[39],"the":[41,60,65,160,167,173,186,233],"expectation":[42],"due":[43],"large":[46],"number":[47],"false":[49],"positives.":[50],"One":[51],"major":[52],"obstacle":[53],"achieve":[55],"higher":[57],"accuracy":[58],"lack":[61],"knowledge":[63],"binding":[67,188,211],"features":[68],"miRNAs.":[70],"published":[72],"high-throughput":[73],"experimental":[74],"data":[75,264],"provide":[76],"an":[77,93],"opportunity":[78],"analyze":[80],"position-wise":[81,109,187,229],"preference":[82],"miRNAs":[84,204],"in":[85,96,208],"terms":[86],"binding,":[89],"which":[90],"can":[91,143,155],"be":[92],"important":[94],"feature":[95],"algorithms.":[100],"RESULTS:":[101],"We":[102,115,200],"developed":[103,125],"Markov":[105,175],"model":[106,119],"characterize":[108],"pairing":[110,164,169,230],"patterns":[111,231],"miRNA-target":[113,149],"interactions.":[114],"further":[116],"integrated":[117],"this":[118],"as":[120],"scoring":[122],"method":[123],"dynamic":[127],"programming":[128],"(DP)":[129],"algorithm,":[130],"MDPS":[131,152,214,255],"(Markov":[132],"model-scored":[133],"Dynamic":[134],"Programming":[135],"algorithm":[136,153],"Selection)":[141],"that":[142,185,203],"screen":[144],"putative":[145],"sites":[147],"binding.":[150],"thus":[154],"take":[156],"into":[157,241],"account":[158],"both":[159,178],"dependency":[161],"neighboring":[163],"positions":[165],"global":[168],"information.":[170],"Based":[171],"on":[172],"trained":[174],"models":[176],"from":[177],"miRNA-specific":[179],"general":[181],"datasets,":[182],"we":[183],"discovered":[184],"information":[189],"specific":[190],"given":[193],"would":[195],"benefit":[196],"its":[197],"prediction.":[199],"also":[201],"found":[202],"maintain":[205],"region-wise":[206],"similarity":[207],"patterns.":[212],"Combining":[213],"with":[215],"methods":[217],"significantly":[218],"improves":[219],"precision":[221],"while":[222],"only":[223],"slightly":[224],"reduces":[225],"recall.":[227],"Therefore,":[228],"have":[232],"promise":[234],"improve":[236],"if":[239],"incorporated":[240],"software":[243],"tools.":[244],"AVAILABILITY":[245],"AND":[246],"IMPLEMENTATION:":[247],"source":[249],"code":[250],"tool":[252],"calculate":[254],"score":[256],"available":[258,266],"at":[259,267],"http://hulab.ucf.edu/research/projects/MDPS/index.html.":[260],"SUPPLEMENTARY":[261],"INFORMATION:":[262],"Supplementary":[263],"Bioinformatics":[268],"online.":[269]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":7}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
