{"id":"https://openalex.org/W2146067967","doi":"https://doi.org/10.1093/database/bau057","title":"A novel multi-alignment pipeline for high-throughput sequencing data","display_name":"A novel multi-alignment pipeline for high-throughput sequencing data","publication_year":2014,"publication_date":"2014-06-18","ids":{"openalex":"https://openalex.org/W2146067967","doi":"https://doi.org/10.1093/database/bau057","mag":"2146067967","pmid":"https://pubmed.ncbi.nlm.nih.gov/24948510"},"language":"en","primary_location":{"id":"doi:10.1093/database/bau057","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau057","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau057/8246344/bau057.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau057/8246344/bau057.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051466839","display_name":"Shun\u2010Ping Huang","orcid":"https://orcid.org/0000-0002-6060-3095"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Huang","raw_affiliation_strings":["Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, Department of Computer Science, University of California, Los Angeles, CA 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, Department of Computer Science, University of California, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071742303","display_name":"James Holt","orcid":"https://orcid.org/0000-0001-6411-9236"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Holt","raw_affiliation_strings":["Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, Department of Computer Science, University of California, Los Angeles, CA 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, Department of Computer Science, University of California, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011172653","display_name":"C.-Y. Kao","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C.-Y. Kao","raw_affiliation_strings":["Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, Department of Computer Science, University of California, Los Angeles, CA 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, Department of Computer Science, University of California, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042463953","display_name":"Leonard McMillan","orcid":"https://orcid.org/0000-0002-8453-0847"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"L. McMillan","raw_affiliation_strings":["Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, Department of Computer Science, University of California, Los Angeles, CA 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, Department of Computer Science, University of California, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100392089","display_name":"Wei Wang","orcid":"https://orcid.org/0000-0002-8180-2886"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"W. Wang","raw_affiliation_strings":["Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, Department of Computer Science, University of California, Los Angeles, CA 90095, USA weiwang@cs.ucla.edu","Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, Department of Computer Science, University of California, Los Angeles, CA 90095, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, Department of Computer Science, University of California, Los Angeles, CA 90095, USA weiwang@cs.ucla.edu","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, Department of Computer Science, University of California, Los Angeles, CA 90095, USA","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100392089"],"corresponding_institution_ids":["https://openalex.org/I114027177"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":1.6916,"has_fulltext":true,"cited_by_count":51,"citation_normalized_percentile":{"value":0.84178374,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2014","issue":"0","first_page":"bau057","last_page":"bau057"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.991599977016449,"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/T11482","display_name":"RNA modifications and cancer","score":0.9887999892234802,"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":0.8030292987823486},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.7521487474441528},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6686356067657471},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4921116232872009},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.47943538427352905},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4599892199039459},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4353160560131073},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3807013928890228},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.2574329376220703},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21927642822265625},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2088037133216858},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20493704080581665},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07900342345237732}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8030292987823486},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.7521487474441528},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6686356067657471},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4921116232872009},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.47943538427352905},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4599892199039459},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4353160560131073},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3807013928890228},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2574329376220703},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21927642822265625},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2088037133216858},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20493704080581665},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07900342345237732},{"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/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000483","descriptor_name":"Alleles","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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003433","descriptor_name":"Crosses, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003433","descriptor_name":"Crosses, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003433","descriptor_name":"Crosses, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006824","descriptor_name":"Hybridization, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006824","descriptor_name":"Hybridization, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006824","descriptor_name":"Hybridization, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011544","descriptor_name":"Pseudogenes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011544","descriptor_name":"Pseudogenes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011544","descriptor_name":"Pseudogenes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D033481","descriptor_name":"Chromosomes, Mammalian","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D033481","descriptor_name":"Chromosomes, Mammalian","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D033481","descriptor_name":"Chromosomes, Mammalian","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"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":5,"locations":[{"id":"doi:10.1093/database/bau057","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau057","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau057/8246344/bau057.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:24948510","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24948510","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4062837","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4062837","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"},{"id":"pmh:ark:/13030/qt7zb7c0v9","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org/ark:/13030/qt7zb7c0v9","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/7zb7c0v9","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database : the journal of biological databases and curation, vol 2014, iss 0","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/database/bau057","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau057","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau057/8246344/bau057.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2404817244","display_name":"An Interdisciplinary program for systems genomics of complex behaviors","funder_award_id":"5p50mh090338-02","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4564641823","display_name":null,"funder_award_id":"P50-MH090338","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G5025366415","display_name":"III-Core: Discovering and Exploring Patterns in Subspaces","funder_award_id":"0812464","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6758428026","display_name":"III: Medium: Collaborative Research: Toward Robust and Scalable Discovering of Significant Associations in Massive Genetic Data","funder_award_id":"1313606","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6781161026","display_name":null,"funder_award_id":"NIH P50","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320314997","display_name":"Strong","ror":"https://ror.org/041vyzr56"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2146067967.pdf","grobid_xml":"https://content.openalex.org/works/W2146067967.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W170592302","https://openalex.org/W1570564798","https://openalex.org/W1988939568","https://openalex.org/W1990061958","https://openalex.org/W2005501593","https://openalex.org/W2047022068","https://openalex.org/W2053782598","https://openalex.org/W2086323500","https://openalex.org/W2087984565","https://openalex.org/W2097065948","https://openalex.org/W2099642610","https://openalex.org/W2108234281","https://openalex.org/W2113312463","https://openalex.org/W2124985265","https://openalex.org/W2125369849","https://openalex.org/W2129916363","https://openalex.org/W2134199796","https://openalex.org/W2137779717","https://openalex.org/W2148264969","https://openalex.org/W2149992227","https://openalex.org/W2170551349"],"related_works":["https://openalex.org/W2136583354","https://openalex.org/W2111238207","https://openalex.org/W3037187668","https://openalex.org/W2760721665","https://openalex.org/W2380685755","https://openalex.org/W4205762803","https://openalex.org/W330130819","https://openalex.org/W2288610023","https://openalex.org/W2375218795","https://openalex.org/W2393010557"],"abstract_inverted_index":{"Mapping":[0],"reads":[1,142,157,223,229],"to":[2,37,49,72,102,104,137,143,154,190],"a":[3,7,38,113,165,185,205,225],"reference":[4,21,41,75,132,145],"sequence":[5,29],"is":[6,22,31,44,176],"common":[8,45,167],"step":[9],"when":[10],"analyzing":[11],"allele":[12,196],"effects":[13],"in":[14,93],"high-throughput":[15],"sequencing":[16],"data.":[17],"The":[18],"choice":[19],"of":[20,58,99,173,188,204,220,228],"critical":[23],"because":[24],"its":[25],"effect":[26],"on":[27,54],"quantitative":[28],"analysis":[30],"non-negligible.":[32],"Recent":[33],"studies":[34],"suggest":[35],"aligning":[36],"single":[39,166],"standard":[40],"sequence,":[42],"as":[43],"practice,":[46],"can":[47],"lead":[48],"an":[50],"underlying":[51],"bias":[52,161],"depending":[53],"the":[55,59,63,97,122,160,170,181,213],"genetic":[56],"distances":[57],"target":[60],"sequences":[61,133,146],"from":[62,125],"reference.":[64,168],"To":[65,107],"avoid":[66],"this":[67,79],"bias,":[68],"researchers":[69],"have":[70],"resorted":[71],"using":[73,164],"modified":[74],"sequences.":[76],"Even":[77],"with":[78,212,230],"improvement,":[80],"various":[81],"limitations":[82],"and":[83,96,115,134,147,158,178,216,224],"problems":[84],"remain":[85],"unsolved,":[86],"which":[87,100],"include":[88,103],"reduced":[89],"mapping":[90,141],"ratios,":[91],"shifts":[92],"read":[94,175],"mappings":[95],"selection":[98],"variants":[101],"remove":[105],"biases.":[106],"address":[108],"these":[109],"issues,":[110],"we":[111,151,208],"propose":[112],"novel":[114],"generic":[116],"multi-alignment":[117],"pipeline.":[118],"Our":[119],"pipeline":[120,211,215],"integrates":[121],"genomic":[123,171],"variations":[124],"known":[126,199],"or":[127],"suspected":[128],"founders":[129],"into":[130],"separate":[131],"performs":[135],"alignments":[136],"each":[138,174],"one.":[139],"By":[140],"multiple":[144],"merging":[148,182],"them":[149],"afterward,":[150],"are":[152],"able":[153],"rescue":[155],"more":[156,221],"diminish":[159],"caused":[162],"by":[163],"Moreover,":[169],"origin":[172],"determined":[177],"annotated":[179],"during":[180],"process,":[183],"providing":[184],"better":[186],"source":[187],"information":[189],"assess":[191],"differential":[192],"expression":[193],"than":[194],"simple":[195],"queries":[197],"at":[198],"variant":[200],"positions.":[201],"Using":[202],"RNA-seq":[203],"diallel":[206],"cross,":[207],"compare":[209],"our":[210,218],"single-reference":[214],"demonstrate":[217],"advantages":[219],"aligned":[222],"higher":[226],"percentage":[227],"assigned":[231],"origins.":[232],"Database":[233],"URL:":[234],"http://csbio.unc.edu/CCstatus/index.py?run=Pseudo.":[235]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":5},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
