{"id":"https://openalex.org/W2989651145","doi":"https://doi.org/10.1109/tcbb.2019.2954315","title":"ERINS: Novel Sequence Insertion Detection by Constructing an Extended Reference","display_name":"ERINS: Novel Sequence Insertion Detection by Constructing an Extended Reference","publication_year":2019,"publication_date":"2019-11-19","ids":{"openalex":"https://openalex.org/W2989651145","doi":"https://doi.org/10.1109/tcbb.2019.2954315","mag":"2989651145","pmid":"https://pubmed.ncbi.nlm.nih.gov/31751246"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2954315","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2954315","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017698164","display_name":"Xiguo Yuan","orcid":"https://orcid.org/0000-0002-0822-5189"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiguo Yuan","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xi'an, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi'an, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103528982","display_name":"Xiangyan Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangyan Xu","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xi'an, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi'an, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101808940","display_name":"Haiyong Zhao","orcid":"https://orcid.org/0000-0002-0380-9134"},"institutions":[{"id":"https://openalex.org/I196934937","display_name":"Liaocheng University","ror":"https://ror.org/03yh0n709","country_code":"CN","type":"education","lineage":["https://openalex.org/I196934937"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haiyong Zhao","raw_affiliation_strings":["School of Computer Science and Technology, Liaocheng University, Liaocheng, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Liaocheng University, Liaocheng, China","institution_ids":["https://openalex.org/I196934937"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023726254","display_name":"Junbo Duan","orcid":"https://orcid.org/0000-0001-7170-3772"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junbo Duan","raw_affiliation_strings":["Key Laboratory of Biomedical Information Engineering of Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Biomedical Information Engineering of Ministry of Education, Department of Biomedical Engineering, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China","institution_ids":["https://openalex.org/I87445476"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5017698164"],"corresponding_institution_ids":["https://openalex.org/I149594827"],"apc_list":null,"apc_paid":null,"fwci":0.341,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.5978629,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":96},"biblio":{"volume":"18","issue":"5","first_page":"1893","last_page":"1901"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9950000047683716,"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":0.7404964566230774},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5662809014320374},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5264880657196045},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.4894801378250122},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.474005788564682},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.4567524194717407},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.41206198930740356},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3699406385421753},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.24214476346969604},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11994516849517822},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07772189378738403},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07432812452316284}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7404964566230774},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5662809014320374},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5264880657196045},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.4894801378250122},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.474005788564682},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.4567524194717407},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.41206198930740356},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3699406385421753},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.24214476346969604},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11994516849517822},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07772189378738403},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07432812452316284},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2019.2954315","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2954315","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31751246","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31751246","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7623042354","display_name":null,"funder_award_id":"61571341","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1997417518","https://openalex.org/W1998120162","https://openalex.org/W2000823432","https://openalex.org/W2024789434","https://openalex.org/W2032247293","https://openalex.org/W2033409266","https://openalex.org/W2038840669","https://openalex.org/W2083870688","https://openalex.org/W2084981198","https://openalex.org/W2092203068","https://openalex.org/W2095680943","https://openalex.org/W2105656684","https://openalex.org/W2108234281","https://openalex.org/W2117716708","https://openalex.org/W2121679244","https://openalex.org/W2125341668","https://openalex.org/W2139993758","https://openalex.org/W2146472631","https://openalex.org/W2150506261","https://openalex.org/W2152036878","https://openalex.org/W2154397429","https://openalex.org/W2160969485","https://openalex.org/W2162212014","https://openalex.org/W2165963439","https://openalex.org/W2315196278","https://openalex.org/W2330697475","https://openalex.org/W2469322050","https://openalex.org/W2491124495","https://openalex.org/W2515914883","https://openalex.org/W2592622428","https://openalex.org/W2593315535","https://openalex.org/W2602431927","https://openalex.org/W2734575741","https://openalex.org/W2734886065","https://openalex.org/W2775698023","https://openalex.org/W2796126220","https://openalex.org/W2885815722","https://openalex.org/W2901613208","https://openalex.org/W2902308587","https://openalex.org/W2942487723","https://openalex.org/W2950833487","https://openalex.org/W4388295307","https://openalex.org/W4394666350","https://openalex.org/W6674561012","https://openalex.org/W6750166546"],"related_works":["https://openalex.org/W2378757965","https://openalex.org/W4224903346","https://openalex.org/W1593262897","https://openalex.org/W2372869593","https://openalex.org/W2384194537","https://openalex.org/W2031011156","https://openalex.org/W1991935520","https://openalex.org/W2368745429","https://openalex.org/W2067940999","https://openalex.org/W2369984616"],"abstract_inverted_index":{"Next":[0],"generation":[1],"sequencing":[2,131],"technology":[3],"has":[4],"led":[5],"to":[6,27,52,76,87,105,146,187],"the":[7,12,38,65,94,106,123],"development":[8],"of":[9,14,34,58,67,73,125,163],"methods":[10,143,176],"for":[11,196],"detection":[13,30],"novel":[15],"sequence":[16],"insertions":[17],"(nsINS).":[18],"Multiple":[19],"signatures":[20],"from":[21],"short":[22],"reads":[23,75,104],"are":[24],"usually":[25],"extracted":[26],"improve":[28],"nsINS":[29,54,78,89,111],"performance.":[31],"However,":[32],"characterization":[33],"nsINSs":[35,168],"larger":[36],"than":[37],"mean":[39],"insert":[40],"size":[41],"is":[42],"still":[43],"challenging.":[44],"This":[45],"article":[46],"presents":[47],"a":[48,83,185,193],"new":[49],"method,":[50],"ERINS,":[51],"detect":[53],"contents":[55],"and":[56,70,80,109,121,129,148,166,190],"genotypes":[57,112],"full":[59],"spectrum":[60],"range":[61],"size.":[62],"It":[63],"integrates":[64],"features":[66],"structural":[68],"variations":[69],"mapping":[71,85],"states":[72],"split":[74],"find":[77],"breakpoints,":[79],"then":[81],"adopts":[82],"left-most":[84],"strategy":[86],"infer":[88],"content":[90],"by":[91],"iteratively":[92],"extending":[93],"standard":[95],"reference":[96,108],"at":[97],"each":[98],"breakpoint.":[99],"Finally,":[100],"it":[101,139],"realigns":[102],"all":[103],"extended":[107],"infers":[110],"through":[113],"statistical":[114],"testing":[115],"on":[116,127],"read":[117],"counts.":[118],"We":[119],"test":[120],"validate":[122],"performance":[124],"ERINS":[126,156,180],"simulation":[128,134],"real":[130,151],"datasets.":[132],"The":[133,150],"experimental":[135],"results":[136,160],"demonstrate":[137],"that":[138,155,173],"outperforms":[140],"several":[141],"peer":[142],"with":[144,161],"respect":[145],"sensitivity":[147],"precision.":[149],"data":[152],"application":[153],"indicates":[154],"obtains":[157],"high":[158],"consistent":[159],"those":[162],"previously":[164],"reported":[165],"detects":[167],"over":[169],"200":[170],"base":[171],"pairs":[172],"many":[174],"other":[175],"fail.":[177],"In":[178],"conclusion,":[179],"can":[181],"be":[182],"used":[183],"as":[184],"supplement":[186],"existing":[188],"tools":[189],"will":[191],"become":[192],"routine":[194],"approach":[195],"characterizing":[197],"nsINSs.":[198]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}