{"id":"https://openalex.org/W2564117999","doi":"https://doi.org/10.1093/bioinformatics/btw799","title":"High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE","display_name":"High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE","publication_year":2016,"publication_date":"2016-12-13","ids":{"openalex":"https://openalex.org/W2564117999","doi":"https://doi.org/10.1093/bioinformatics/btw799","mag":"2564117999","pmid":"https://pubmed.ncbi.nlm.nih.gov/28011790"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw799","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw799","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/10/1437/25153124/btw799.pdf","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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/10/1437/25153124/btw799.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087212280","display_name":"William H. Majoros","orcid":"https://orcid.org/0000-0001-7284-9335"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William H Majoros","raw_affiliation_strings":["Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC, USA","Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105348281","display_name":"Michael S. Campbell","orcid":"https://orcid.org/0000-0002-8058-1372"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael S Campbell","raw_affiliation_strings":["Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104027375","display_name":"Carson Holt","orcid":"https://orcid.org/0000-0002-9864-0019"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carson Holt","raw_affiliation_strings":["Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, UT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070105264","display_name":"Erin DeNardo","orcid":null},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erin K DeNardo","raw_affiliation_strings":["Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077105419","display_name":"Doreen Ware","orcid":"https://orcid.org/0000-0002-8125-3821"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]},{"id":"https://openalex.org/I4210142299","display_name":"Robert W. Holley Center for Agriculture & Health","ror":"https://ror.org/050z40a57","country_code":"US","type":"facility","lineage":["https://openalex.org/I1312222531","https://openalex.org/I1336096307","https://openalex.org/I4210138094","https://openalex.org/I4210142299"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Doreen Ware","raw_affiliation_strings":["Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","USDA ARS NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA","institution_ids":["https://openalex.org/I2750212522"]},{"raw_affiliation_string":"USDA ARS NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, USA","institution_ids":["https://openalex.org/I4210142299","https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026198048","display_name":"Andrew S. Allen","orcid":"https://orcid.org/0000-0002-7232-2143"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew S Allen","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, NC, USA","Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, NC, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017968102","display_name":"Mark Yandell","orcid":"https://orcid.org/0000-0002-9497-4505"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]},{"id":"https://openalex.org/I4210159452","display_name":"Star Center","ror":"https://ror.org/04rpkcv59","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210159452"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark Yandell","raw_affiliation_strings":["Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, UT, USA","USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah and School of Medicine, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I223532165"]},{"raw_affiliation_string":"USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA","institution_ids":["https://openalex.org/I4210159452","https://openalex.org/I223532165"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018030255","display_name":"Timothy E. Reddy","orcid":"https://orcid.org/0000-0002-7629-061X"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Timothy E Reddy","raw_affiliation_strings":["Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC, USA","Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, NC, USA","Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, NC, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, USA","institution_ids":["https://openalex.org/I170897317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5017968102","https://openalex.org/A5018030255"],"corresponding_institution_ids":["https://openalex.org/I170897317","https://openalex.org/I223532165","https://openalex.org/I4210159452"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5786,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.79050831,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"33","issue":"10","first_page":"1437","last_page":"1446"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.5672000050544739,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.5672000050544739,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.24459999799728394,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.08709999918937683,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6786587238311768},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6231161952018738},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6200351715087891},{"id":"https://openalex.org/keywords/locus","display_name":"Locus (genetics)","score":0.48780110478401184},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4840785562992096},{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.4759086072444916},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4734755754470825},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.46076393127441406},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.45550796389579773},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.37930765748023987}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6786587238311768},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6231161952018738},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6200351715087891},{"id":"https://openalex.org/C84597430","wikidata":"https://www.wikidata.org/wiki/Q106227","display_name":"Locus (genetics)","level":3,"score":0.48780110478401184},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4840785562992096},{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.4759086072444916},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4734755754470825},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.46076393127441406},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.45550796389579773},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.37930765748023987},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","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":"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011110","descriptor_name":"Polymorphism, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw799","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw799","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/10/1437/25153124/btw799.pdf","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:28011790","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28011790","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:repository.cshl.edu:33949","is_oa":false,"landing_page_url":"http://repository.cshl.edu/id/eprint/33949/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"Paper"},{"id":"pmh:oai:europepmc.org:4867692","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860548","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw799","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw799","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/10/1437/25153124/btw799.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1789552440","display_name":null,"funder_award_id":"R01 GM104390","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2680891385","display_name":null,"funder_award_id":"R01 DK099820","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G3066911417","display_name":"NSF Postdoctoral Fellowship in Biology FY 2015","funder_award_id":"1523793","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3884067589","display_name":null,"funder_award_id":"PRFB-1523793","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4624658857","display_name":"IPGA:  Developing an Effective, Portable Annotation Engine for Plant Genomes","funder_award_id":"1126998","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6178989775","display_name":null,"funder_award_id":"IOS-1126998","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6226231746","display_name":null,"funder_award_id":"T32 GM071340","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G626576221","display_name":null,"funder_award_id":"IOS-1561337","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6498017814","display_name":null,"funder_award_id":"R01 DK097534","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G6858615440","display_name":null,"funder_award_id":"DK097534","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6914837000","display_name":"REU Site: CSHL NSF-REU Bioinformatics and Computational Neuroscience Summer Undergraduate Program","funder_award_id":"1559816","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7168464174","display_name":null,"funder_award_id":"R01 DK097534","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7337391892","display_name":null,"funder_award_id":"DK099820","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7863553252","display_name":null,"funder_award_id":"EAGER IOS-1561337","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8270253415","display_name":null,"funder_award_id":"UL1 TR001067","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G8360567983","display_name":null,"funder_award_id":"R01 DK099820","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8654035160","display_name":null,"funder_award_id":"REU-1559816","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"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"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2564117999.pdf","grobid_xml":"https://content.openalex.org/works/W2564117999.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W626356915","https://openalex.org/W1482244404","https://openalex.org/W1484347389","https://openalex.org/W1487554690","https://openalex.org/W1713135633","https://openalex.org/W1846422913","https://openalex.org/W1861628010","https://openalex.org/W1963905877","https://openalex.org/W1964426200","https://openalex.org/W1980740976","https://openalex.org/W1984068087","https://openalex.org/W1990103381","https://openalex.org/W2024371767","https://openalex.org/W2025943989","https://openalex.org/W2036056816","https://openalex.org/W2047173662","https://openalex.org/W2047710235","https://openalex.org/W2047717735","https://openalex.org/W2049110540","https://openalex.org/W2059145105","https://openalex.org/W2080327186","https://openalex.org/W2095859808","https://openalex.org/W2096465161","https://openalex.org/W2099753867","https://openalex.org/W2101786683","https://openalex.org/W2103534177","https://openalex.org/W2104005232","https://openalex.org/W2104549677","https://openalex.org/W2106352274","https://openalex.org/W2106578986","https://openalex.org/W2108108770","https://openalex.org/W2108996658","https://openalex.org/W2112001822","https://openalex.org/W2115941316","https://openalex.org/W2115954594","https://openalex.org/W2116929369","https://openalex.org/W2119338364","https://openalex.org/W2126927919","https://openalex.org/W2127230663","https://openalex.org/W2129857098","https://openalex.org/W2136101247","https://openalex.org/W2136826997","https://openalex.org/W2140729960","https://openalex.org/W2141327598","https://openalex.org/W2141652419","https://openalex.org/W2142386149","https://openalex.org/W2142418779","https://openalex.org/W2143602768","https://openalex.org/W2143801061","https://openalex.org/W2145809383","https://openalex.org/W2146450575","https://openalex.org/W2157115023","https://openalex.org/W2160053034","https://openalex.org/W2160591072","https://openalex.org/W2166187656","https://openalex.org/W2168909179","https://openalex.org/W2256016639","https://openalex.org/W2258553021","https://openalex.org/W2303542186","https://openalex.org/W2323326409","https://openalex.org/W2417483443","https://openalex.org/W4210267605","https://openalex.org/W4252232449","https://openalex.org/W6662686041"],"related_works":["https://openalex.org/W3146762847","https://openalex.org/W2398263405","https://openalex.org/W2056886854","https://openalex.org/W2025446304","https://openalex.org/W2166354960","https://openalex.org/W1888102361","https://openalex.org/W2131321814","https://openalex.org/W2171251480","https://openalex.org/W1492100763","https://openalex.org/W4237549798"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"accurate":[2,27],"interpretation":[3,46],"of":[4,16,54,73,102,122,125,174,189,228],"genetic":[5,17],"variants":[6,18,35,230],"is":[7,155,238,247,259],"critical":[8],"for":[9,59,76,215,223],"characterizing":[10],"genotype-phenotype":[11],"associations.":[12],"Because":[13],"the":[14,37,52,171,194,225],"effects":[15,173],"can":[19,140,198],"depend":[20],"strongly":[21],"on":[22],"their":[23,115],"local":[24],"genomic":[25],"context,":[26],"genome":[28,153],"annotations":[29,56,108],"are":[30,132,184],"essential.":[31],"Furthermore,":[32],"as":[33],"some":[34],"have":[36],"potential":[38],"to":[39,49,93,99,143,191,202],"disrupt":[40],"or":[41,66,253],"alter":[42],"gene":[43,62,82],"structure,":[44],"variant":[45],"efforts":[47],"stand":[48],"gain":[50],"from":[51,87,249],"use":[53,216],"individualized":[55],"that":[57,84,164,180],"account":[58],"differences":[60],"in":[61,81,217,240],"structure":[63,83],"between":[64],"individuals":[65],"strains.":[67],"RESULTS:":[68],"We":[69],"describe":[70],"a":[71,100,211,232],"suite":[72],"software":[74],"tools":[75],"identifying":[77],"possible":[78,116,123],"functional":[79],"changes":[80,113],"may":[85],"result":[86],"sequence":[88,154],"variants.":[89],"ACE":[90,131,165,197,237],"('Assessing":[91],"Changes":[92],"Exons')":[94],"converts":[95],"phased":[96],"genotype":[97],"calls":[98],"collection":[101],"explicit":[103],"haplotype":[104],"sequences,":[105],"maps":[106],"transcript":[107,148],"onto":[109],"them,":[110],"detects":[111],"gene-structure":[112],"and":[114,118,139,147,177,207,244,246],"repercussions,":[117],"identifies":[119],"several":[120],"classes":[121],"loss":[124],"function.":[126],"Novel":[127],"transcripts":[128],"predicted":[129,181],"by":[130,135],"commonly":[133],"supported":[134],"spliced":[136],"RNA-seq":[137,160],"reads,":[138],"be":[141,199],"used":[142],"improve":[144],"read":[145],"alignment":[146],"quantification":[149],"when":[150],"an":[151],"individual-specific":[152],"available.":[156],"Using":[157],"publicly":[158],"available":[159,248,260],"data,":[161],"we":[162,178],"show":[163,179],"predictions":[166],"confirm":[167],"earlier":[168],"results":[169],"regarding":[170],"quantitative":[172],"nonsense-mediated":[175],"decay,":[176],"loss-of-function":[182],"events":[183],"highly":[185],"concordant":[186],"with":[187],"patterns":[188],"intolerance":[190],"mutations":[192],"across":[193],"human":[195],"population.":[196],"readily":[200],"applied":[201],"diverse":[203],"species":[204],"including":[205],"animals":[206],"plants,":[208],"making":[209],"it":[210],"broadly":[212],"useful":[213],"tool":[214],"eukaryotic":[218],"population-based":[219],"resequencing":[220],"projects,":[221],"particularly":[222],"assessing":[224],"joint":[226],"impact":[227],"all":[229],"at":[231,261],"locus.":[233],"AVAILABILITY":[234],"AND":[235],"IMPLEMENTATION:":[236],"written":[239],"open-source":[241],"C":[242],"++":[243],"Perl":[245],"geneprediction.org/ACE.":[250],"CONTACT:":[251],"myandell@genetics.utah.edu":[252],"tim.reddy@duke.edu.":[254],"SUPPLEMENTARY":[255],"INFORMATION:":[256],"Supplementary":[257],"information":[258],"Bioinformatics":[262],"online.":[263]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
