{"id":"https://openalex.org/W2054520275","doi":"https://doi.org/10.1371/journal.pcbi.0030176","title":"A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms","display_name":"A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms","publication_year":2007,"publication_date":"2007-09-12","ids":{"openalex":"https://openalex.org/W2054520275","doi":"https://doi.org/10.1371/journal.pcbi.0030176","mag":"2054520275","pmid":"https://pubmed.ncbi.nlm.nih.gov/17941704"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.0030176","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030176","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.0030176","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078595113","display_name":"Erika Kvikstad","orcid":"https://orcid.org/0000-0002-2730-4472"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erika M Kvikstad","raw_affiliation_strings":["Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, USA","Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, United States of America","Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010499534","display_name":"Svitlana Tyekucheva","orcid":"https://orcid.org/0000-0002-3119-6507"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Svitlana Tyekucheva","raw_affiliation_strings":["","Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, United States of America","Department of Statistics, Pennsylvania State University, University Park, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"","institution_ids":[]},{"raw_affiliation_string":"Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Statistics, Pennsylvania State University, University Park, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015561999","display_name":"Francesca Chiaromonte","orcid":"https://orcid.org/0000-0001-5605-9886"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Francesca Chiaromonte","raw_affiliation_strings":["","Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, United States of America","Department of Statistics, Pennsylvania State University, University Park, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"","institution_ids":[]},{"raw_affiliation_string":"Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Statistics, Pennsylvania State University, University Park, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042289737","display_name":"Kateryna D. Makova","orcid":"https://orcid.org/0000-0002-6212-9526"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kateryna D Makova","raw_affiliation_strings":["","Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, United States of America","Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"","institution_ids":[]},{"raw_affiliation_string":"Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5042289737"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":7.3714,"has_fulltext":false,"cited_by_count":60,"citation_normalized_percentile":{"value":0.96600346,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"3","issue":"9","first_page":"e176","last_page":"e176"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9986000061035156,"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/indel","display_name":"Indel","score":0.8350334167480469},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7882540225982666},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6997799873352051},{"id":"https://openalex.org/keywords/indel-mutation","display_name":"INDEL Mutation","score":0.6920817494392395},{"id":"https://openalex.org/keywords/recombination","display_name":"Recombination","score":0.6092011332511902},{"id":"https://openalex.org/keywords/macaque","display_name":"Macaque","score":0.5460997223854065},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5445847511291504},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.52077716588974},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.43278712034225464},{"id":"https://openalex.org/keywords/homologous-recombination","display_name":"Homologous recombination","score":0.4277874827384949},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.41915658116340637},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3997926712036133},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2581283450126648},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.0747169554233551}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.8350334167480469},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7882540225982666},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6997799873352051},{"id":"https://openalex.org/C2910714999","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"INDEL Mutation","level":5,"score":0.6920817494392395},{"id":"https://openalex.org/C156695909","wikidata":"https://www.wikidata.org/wiki/Q3373825","display_name":"Recombination","level":3,"score":0.6092011332511902},{"id":"https://openalex.org/C2778950215","wikidata":"https://www.wikidata.org/wiki/Q177601","display_name":"Macaque","level":2,"score":0.5460997223854065},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5445847511291504},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.52077716588974},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.43278712034225464},{"id":"https://openalex.org/C102744134","wikidata":"https://www.wikidata.org/wiki/Q22280388","display_name":"Homologous recombination","level":3,"score":0.4277874827384949},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.41915658116340637},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3997926712036133},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2581283450126648},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.0747169554233551},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","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":"D008251","descriptor_name":"Macaca","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008251","descriptor_name":"Macaca","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008251","descriptor_name":"Macaca","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.0030176","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030176","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:17941704","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17941704","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.276.1309","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.276.1309","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/19/6a/PLoS_Comput_Biol_2007_Sep_14_3(9)_e176.tar.gz","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.279.3659","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.279.3659","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/19/6a/PLoS_Comput_Biol_2007_Sep_14_3(9)_e176.tar.gz","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:0acf197cabbd47388c5c50acb9a0c7cc","is_oa":true,"landing_page_url":"https://doaj.org/article/0acf197cabbd47388c5c50acb9a0c7cc","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":"PLoS Computational Biology, Vol 3, Iss 9, Pp 1772-1782 (2007)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2622424","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC1976337","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/152085","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/A_Macaque_s_Eye_View_of_Human_Insertions_and_Deletions_Differences_in_Mechanisms/152085","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:1976337","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1976337","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.0030176","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0030176","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W791550880","https://openalex.org/W1646393397","https://openalex.org/W1689369637","https://openalex.org/W1963590211","https://openalex.org/W1964773414","https://openalex.org/W1966875588","https://openalex.org/W1971118090","https://openalex.org/W1983844625","https://openalex.org/W1984104678","https://openalex.org/W1985520143","https://openalex.org/W1987882116","https://openalex.org/W1996942642","https://openalex.org/W1998120162","https://openalex.org/W1998646180","https://openalex.org/W2001085484","https://openalex.org/W2001103208","https://openalex.org/W2010595044","https://openalex.org/W2010872048","https://openalex.org/W2036729517","https://openalex.org/W2042903453","https://openalex.org/W2043419192","https://openalex.org/W2050014875","https://openalex.org/W2053276922","https://openalex.org/W2058306877","https://openalex.org/W2061008984","https://openalex.org/W2061149284","https://openalex.org/W2062098224","https://openalex.org/W2072398298","https://openalex.org/W2075168304","https://openalex.org/W2076032878","https://openalex.org/W2080434054","https://openalex.org/W2081989648","https://openalex.org/W2083033591","https://openalex.org/W2085494643","https://openalex.org/W2102514909","https://openalex.org/W2104743461","https://openalex.org/W2110973918","https://openalex.org/W2112132489","https://openalex.org/W2113565103","https://openalex.org/W2115457188","https://openalex.org/W2119632499","https://openalex.org/W2124696903","https://openalex.org/W2125548284","https://openalex.org/W2126084304","https://openalex.org/W2127150942","https://openalex.org/W2131669390","https://openalex.org/W2136961040","https://openalex.org/W2145191876","https://openalex.org/W2145958666","https://openalex.org/W2147631681","https://openalex.org/W2149414420","https://openalex.org/W2152775760","https://openalex.org/W2154243124","https://openalex.org/W2155452725","https://openalex.org/W2157314679","https://openalex.org/W2160708989","https://openalex.org/W2168783599","https://openalex.org/W2168909179","https://openalex.org/W2612812586","https://openalex.org/W3146425672"],"related_works":["https://openalex.org/W1971376828","https://openalex.org/W2046457574","https://openalex.org/W2135846417","https://openalex.org/W4206406917","https://openalex.org/W2080028493","https://openalex.org/W2167094946","https://openalex.org/W3103976079","https://openalex.org/W4387460329","https://openalex.org/W2147536515","https://openalex.org/W2996849075"],"abstract_inverted_index":{"Insertions":[0],"and":[1,8,58,78,85,117,210,221],"deletions":[2,145],"(indels)":[3],"cause":[4],"numerous":[5],"genetic":[6],"diseases":[7],"lead":[9,223],"to":[10,22,61,83,142,196,204,224],"pronounced":[11],"evolutionary":[12],"differences":[13],"among":[14],"genomes.":[15],"The":[16],"macaque":[17],"sequences":[18],"provide":[19],"an":[20,63,184,192],"opportunity":[21],"gain":[23],"insights":[24,207],"into":[25,208],"the":[26,37,43,50,101,107,120,158,176],"mechanisms":[27],"generating":[28],"these":[29,213],"mutations":[30,124,162],"on":[31,167],"a":[32,154,168,180,187],"genome-wide":[33],"scale":[34],"by":[35,130,164],"establishing":[36],"polarity":[38],"of":[39,103,110,123,161,179,191,200],"indels":[40],"occurring":[41],"in":[42,73,128,217],"human":[44],"lineage":[45],"since":[46],"its":[47,198],"divergence":[48],"from":[49,70],"chimpanzee.":[51],"Here":[52],"we":[53,173],"apply":[54],"novel":[55,206],"regression":[56],"techniques":[57],"multiscale":[59],"analyses":[60],"demonstrate":[62],"extensive":[64],"regional":[65],"indel":[66],"rate":[67],"variation":[68],"stemming":[69],"local":[71],"fluctuations":[72],"divergence,":[74],"GC":[75],"content,":[76],"male":[77],"female":[79],"recombination":[80,96,113],"rates,":[81],"proximity":[82],"telomeres,":[84],"other":[86],"genomic":[87,227],"factors.":[88],"We":[89],"find":[90],"that":[91,175],"both":[92],"replication":[93,111],"and,":[94],"surprisingly,":[95],"are":[97,125,135,146],"significantly":[98],"associated":[99,138,148],"with":[100,139,149],"occurrence":[102],"small":[104,181],"indels.":[105],"Intriguingly,":[106],"relative":[108],"inputs":[109],"versus":[112],"differ":[114],"between":[115],"insertions":[116,134],"deletions,":[118],"thus":[119],"two":[121,159],"types":[122,160],"likely":[126],"guided":[127],"part":[129],"distinct":[131],"mechanisms.":[132],"Namely,":[133],"more":[136,225],"strongly":[137],"factors":[140],"linked":[141],"recombination,":[143],"while":[144],"mostly":[147],"replication-related":[150],"features.":[151],"Indel":[152],"as":[153,183],"term":[155],"misleadingly":[156],"groups":[157],"together":[163],"their":[165],"effect":[166],"sequence":[169],"alignment.":[170],"However,":[171],"here":[172],"establish":[174],"correct":[177],"identification":[178],"gap":[182,218],"insertion":[185,209],"or":[186],"deletion":[188,211],"(by":[189],"use":[190],"outgroup)":[193],"is":[194],"crucial":[195],"determining":[197],"mechanism":[199],"origin.":[201],"In":[202],"addition":[203],"providing":[205],"mutagenesis,":[212],"results":[214],"will":[215],"assist":[216],"penalty":[219],"modeling":[220],"eventually":[222],"reliable":[226],"alignments.":[228]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":5}],"updated_date":"2026-05-07T13:39:58.223016","created_date":"2025-10-10T00:00:00"}
