{"id":"https://openalex.org/W4384663316","doi":"https://doi.org/10.1186/s12859-023-05390-1","title":"IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods","display_name":"IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods","publication_year":2023,"publication_date":"2023-07-18","ids":{"openalex":"https://openalex.org/W4384663316","doi":"https://doi.org/10.1186/s12859-023-05390-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/37464281"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05390-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05390-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05390-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05390-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103497598","display_name":"Aimin Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210088242","display_name":"ProterixBio (United States)","ror":"https://ror.org/005szp141","country_code":"US","type":"company","lineage":["https://openalex.org/I4210088242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aimin Yan","raw_affiliation_strings":["AVROBIO, Inc., Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AVROBIO, Inc., Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210088242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068939891","display_name":"Cristina Baricordi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210088242","display_name":"ProterixBio (United States)","ror":"https://ror.org/005szp141","country_code":"US","type":"company","lineage":["https://openalex.org/I4210088242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cristina Baricordi","raw_affiliation_strings":["AVROBIO, Inc., Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AVROBIO, Inc., Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210088242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026429049","display_name":"Quoc Nguyen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210088242","display_name":"ProterixBio (United States)","ror":"https://ror.org/005szp141","country_code":"US","type":"company","lineage":["https://openalex.org/I4210088242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Quoc Nguyen","raw_affiliation_strings":["AVROBIO, Inc., Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AVROBIO, Inc., Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210088242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046478648","display_name":"Luigi Barbarossa","orcid":null},"institutions":[{"id":"https://openalex.org/I4210088242","display_name":"ProterixBio (United States)","ror":"https://ror.org/005szp141","country_code":"US","type":"company","lineage":["https://openalex.org/I4210088242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Luigi Barbarossa","raw_affiliation_strings":["AVROBIO, Inc., Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AVROBIO, Inc., Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210088242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067569010","display_name":"Mariana Loperfido","orcid":"https://orcid.org/0000-0001-9365-5388"},"institutions":[{"id":"https://openalex.org/I4210088242","display_name":"ProterixBio (United States)","ror":"https://ror.org/005szp141","country_code":"US","type":"company","lineage":["https://openalex.org/I4210088242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mariana Loperfido","raw_affiliation_strings":["AVROBIO, Inc., Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AVROBIO, Inc., Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210088242"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046553728","display_name":"Luca Biasco","orcid":"https://orcid.org/0000-0003-4022-7640"},"institutions":[{"id":"https://openalex.org/I2800129641","display_name":"Great Ormond Street Hospital","ror":"https://ror.org/00zn2c847","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2800129641","https://openalex.org/I2800349819"]},{"id":"https://openalex.org/I4210145167","display_name":"Consejo de Ciencia y Tecnolog\u00eda del Estado de Tabasco","ror":"https://ror.org/03f2xnj73","country_code":"MX","type":"government","lineage":["https://openalex.org/I4210145167"]},{"id":"https://openalex.org/I4210165024","display_name":"Institute of Infection and Immunity","ror":"https://ror.org/05wdecy17","country_code":"CA","type":"facility","lineage":["https://openalex.org/I176337269","https://openalex.org/I4210165024"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["CA","GB","MX"],"is_corresponding":true,"raw_author_name":"Luca Biasco","raw_affiliation_strings":["AVROBIO, Inc., Cambridge, MA, USA. l.biasco@ucl.ac.uk","Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK. l.biasco@ucl.ac.uk","Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AVROBIO, Inc., Cambridge, MA, USA. l.biasco@ucl.ac.uk","institution_ids":["https://openalex.org/I4210145167"]},{"raw_affiliation_string":"Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK. l.biasco@ucl.ac.uk","institution_ids":["https://openalex.org/I4210165024","https://openalex.org/I45129253"]},{"raw_affiliation_string":"Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK","institution_ids":["https://openalex.org/I2800129641","https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5046553728"],"corresponding_institution_ids":["https://openalex.org/I2800129641","https://openalex.org/I4210145167","https://openalex.org/I4210165024","https://openalex.org/I45129253"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.5172,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.83679685,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"24","issue":"1","first_page":"286","last_page":"286"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10613","display_name":"Virus-based gene therapy research","score":0.8637999892234802,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10613","display_name":"Virus-based gene therapy research","score":0.8637999892234802,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.010700000450015068,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.0066999997943639755,"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/pipeline","display_name":"Pipeline (software)","score":0.7509121894836426},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6875527501106262},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6413078308105469},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5574343204498291},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48906072974205017},{"id":"https://openalex.org/keywords/fragment","display_name":"Fragment (logic)","score":0.45481762290000916},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.45433714985847473},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.45125943422317505},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.44508054852485657},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2179255187511444},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.13730287551879883},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1105145514011383},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.07949239015579224}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7509121894836426},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6875527501106262},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6413078308105469},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5574343204498291},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48906072974205017},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.45481762290000916},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.45433714985847473},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.45125943422317505},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.44508054852485657},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2179255187511444},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.13730287551879883},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1105145514011383},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.07949239015579224},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005822","descriptor_name":"Genetic Vectors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005822","descriptor_name":"Genetic Vectors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005822","descriptor_name":"Genetic Vectors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-023-05390-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05390-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05390-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37464281","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37464281","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10354991","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10354991","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10354991/pdf/12859_2023_Article_5390.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:d7e664d64c5543e5bfcd857847f6fcce","is_oa":true,"landing_page_url":"https://doaj.org/article/d7e664d64c5543e5bfcd857847f6fcce","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-31 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05390-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05390-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05390-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309370","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4384663316.pdf"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W175631674","https://openalex.org/W1801876314","https://openalex.org/W1894850789","https://openalex.org/W1926258489","https://openalex.org/W1990728924","https://openalex.org/W2043248836","https://openalex.org/W2050048256","https://openalex.org/W2060838652","https://openalex.org/W2061639503","https://openalex.org/W2081339067","https://openalex.org/W2089319449","https://openalex.org/W2091324357","https://openalex.org/W2096252688","https://openalex.org/W2098402814","https://openalex.org/W2103441770","https://openalex.org/W2142159826","https://openalex.org/W2152744408","https://openalex.org/W2157539385","https://openalex.org/W2562817659","https://openalex.org/W2563699781","https://openalex.org/W2566544067","https://openalex.org/W2605897695","https://openalex.org/W2763998330","https://openalex.org/W2770876878","https://openalex.org/W2770973768","https://openalex.org/W2787742192","https://openalex.org/W2952109315","https://openalex.org/W2980186137","https://openalex.org/W3011365556","https://openalex.org/W3014093093","https://openalex.org/W3021001696","https://openalex.org/W3023573744","https://openalex.org/W3122109253","https://openalex.org/W4210644165","https://openalex.org/W4281712632"],"related_works":["https://openalex.org/W4380433113","https://openalex.org/W4386072068","https://openalex.org/W252339960","https://openalex.org/W2390529043","https://openalex.org/W2378320433","https://openalex.org/W2358343511","https://openalex.org/W2051877971","https://openalex.org/W1970117064","https://openalex.org/W1787170397","https://openalex.org/W4292347844"],"abstract_inverted_index":{"BACKGROUND:":[0],"Integration":[1],"site":[2],"(IS)":[3],"analysis":[4],"is":[5,97],"a":[6,98,101,130,201,232],"fundamental":[7],"analytical":[8,183],"platform":[9],"for":[10,111,234],"evaluating":[11],"the":[12,55,59,71,156,172,180,187,223],"safety":[13],"and":[14,21,115,148,166,190,200],"efficacy":[15],"of":[16,28,61,100,140,158,174,205],"viral":[17],"vector":[18],"based":[19],"preclinical":[20],"clinical":[22],"Gene":[23],"Therapy":[24],"(GT).":[25],"A":[26],"handful":[27],"groups":[29],"have":[30,67],"developed":[31],"standardized":[32],"bioinformatics":[33,102,131],"pipelines":[34,66,75],"to":[35,40,44],"process":[36,135],"IS":[37,62,79,112,145,151,235],"sequencing":[38,82,85,139],"data,":[39],"generate":[41],"reports,":[42],"and/or":[43],"perform":[45],"comparative":[46],"studies":[47,199],"across":[48],"different":[49,64,159,192],"GT":[50],"trials.":[51],"Keeping":[52],"up":[53],"with":[54],"technological":[56],"advances":[57],"in":[58,121,186,213],"field":[60],"analysis,":[63],"computational":[65],"been":[68],"published":[69],"over":[70],"past":[72],"decade.":[73],"These":[74],"focus":[76],"on":[77],"identifying":[78],"from":[80,137],"single-read":[81],"or":[83,90],"paired-end":[84,138],"data":[86,136],"either":[87],"using":[88,91,191],"read-based":[89],"sonication":[92,228],"fragment-based":[93],"methods,":[94,162],"but":[95],"there":[96],"lack":[99],"tool":[103],"that":[104,133,212],"automatically":[105],"includes":[106],"unique":[107],"molecular":[108],"identifiers":[109],"(UMI)":[110],"abundance":[113,160,236],"estimations":[114],"allows":[116],"comparing":[117],"multiple":[118],"quantification":[119,218],"methods":[120,147],"one":[122],"integrated":[123],"pipeline.":[124],"RESULTS:":[125],"Here":[126],"we":[127,209],"present":[128],"IS-Seq":[129,175,207],"pipeline":[132,208],"can":[134],"both":[141],"old":[142],"restriction":[143],"sites-based":[144],"collection":[146],"new":[149],"sonication-based":[150],"retrieval":[152],"systems":[153],"while":[154],"allowing":[155],"selection":[157],"estimation":[161],"including":[163],"read-based,":[164],"Fragment-based":[165],"UMI-based":[167],"systems.":[168],"CONCLUSIONS:":[169],"We":[170],"validated":[171],"performance":[173],"by":[176,195],"testing":[177],"it":[178],"against":[179],"most":[181,225],"popular":[182],"workflow":[184],"available":[185],"literature":[188],"(INSPIIRED)":[189],"scenarios.":[193],"Lastly,":[194],"performing":[196],"extensive":[197],"simulation":[198],"comprehensive":[202],"wet-lab":[203],"assessment":[204],"our":[206],"could":[210],"show":[211],"clinically":[214],"relevant":[215],"scenarios,":[216],"UMI":[217],"provides":[219],"better":[220],"accuracy":[221],"than":[222],"currently":[224],"widely":[226],"used":[227],"fragment":[229],"counts":[230],"as":[231],"method":[233],"estimation.":[237]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}