{"id":"https://openalex.org/W4412454199","doi":"https://doi.org/10.1093/bioinformatics/btaf244","title":"LYCEUM: learning to call copy number variants on low-coverage ancient genomes","display_name":"LYCEUM: learning to call copy number variants on low-coverage ancient genomes","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412454199","doi":"https://doi.org/10.1093/bioinformatics/btaf244","pmid":"https://pubmed.ncbi.nlm.nih.gov/40662803"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf244","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i285/63745472/btaf244.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i285/63745472/btaf244.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102781182","display_name":"Mehmet Alper Y\u0131lmaz","orcid":"https://orcid.org/0009-0001-8933-823X"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Mehmet Alper Y\u0131lmaz","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University , Ankara 06800, T\u00fcrkiye"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University , Ankara 06800, T\u00fcrkiye","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037883358","display_name":"Ahmet Ceylan","orcid":"https://orcid.org/0000-0001-5878-8775"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ahmet Arda Ceylan","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University , Ankara 06800, T\u00fcrkiye"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University , Ankara 06800, T\u00fcrkiye","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087896157","display_name":"G\u00fcn Kaynar","orcid":"https://orcid.org/0009-0006-6764-7716"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gun Kaynar","raw_affiliation_strings":["Computational Biology Department, School of Computer Science, Carnegie Mellon University , Pittsburgh, PA 06800,"],"affiliations":[{"raw_affiliation_string":"Computational Biology Department, School of Computer Science, Carnegie Mellon University , Pittsburgh, PA 06800,","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090836372","display_name":"A. Erc\u00fcment \u00c7i\u00e7ek","orcid":"https://orcid.org/0000-0001-8613-6619"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"A Erc\u00fcment \u00c7i\u00e7ek","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University , Ankara 06800, T\u00fcrkiye"],"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University , Ankara 06800, T\u00fcrkiye","institution_ids":["https://openalex.org/I168864056"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5102781182"],"corresponding_institution_ids":["https://openalex.org/I168864056"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.9,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.86457687,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"41","issue":"Supplement_1","first_page":"i285","last_page":"i293"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9998000264167786,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9998000264167786,"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":0.9987000226974487,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9966999888420105,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/ancient-dna","display_name":"Ancient DNA","score":0.8046129941940308},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.731545627117157},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6728071570396423},{"id":"https://openalex.org/keywords/adaptation","display_name":"Adaptation (eye)","score":0.5642457604408264},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5243033170700073},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.515882134437561},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4748568534851074},{"id":"https://openalex.org/keywords/1000-genomes-project","display_name":"1000 Genomes Project","score":0.44694870710372925},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.43919551372528076},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4364648759365082},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.43047723174095154},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42549145221710205},{"id":"https://openalex.org/keywords/deep-sequencing","display_name":"Deep sequencing","score":0.4147006869316101},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3963451385498047},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.2828730344772339},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.233035147190094},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22926613688468933},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.13972917199134827},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1064457893371582},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.08390063047409058}],"concepts":[{"id":"https://openalex.org/C189338579","wikidata":"https://www.wikidata.org/wiki/Q290447","display_name":"Ancient DNA","level":3,"score":0.8046129941940308},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.731545627117157},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6728071570396423},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.5642457604408264},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5243033170700073},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.515882134437561},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4748568534851074},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.44694870710372925},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.43919551372528076},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4364648759365082},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.43047723174095154},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42549145221710205},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.4147006869316101},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3963451385498047},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2828730344772339},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.233035147190094},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22926613688468933},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.13972917199134827},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1064457893371582},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.08390063047409058},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","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},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D000072441","descriptor_name":"DNA, Ancient","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf244","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i285/63745472/btaf244.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40662803","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40662803","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:pubmedcentral.nih.gov:12261418","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12261418","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf244","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i285/63745472/btaf244.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.6399999856948853,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412454199.pdf","grobid_xml":"https://content.openalex.org/works/W4412454199.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1976555450","https://openalex.org/W1981734114","https://openalex.org/W1983194657","https://openalex.org/W1987975628","https://openalex.org/W1997031801","https://openalex.org/W2002438422","https://openalex.org/W2050161506","https://openalex.org/W2119180969","https://openalex.org/W2121743948","https://openalex.org/W2150506261","https://openalex.org/W2156330112","https://openalex.org/W2162927194","https://openalex.org/W2165765309","https://openalex.org/W2798064943","https://openalex.org/W2919564569","https://openalex.org/W2950121474","https://openalex.org/W2970150218","https://openalex.org/W3015850611","https://openalex.org/W3041611157","https://openalex.org/W3129075539","https://openalex.org/W3131055609","https://openalex.org/W3162783973","https://openalex.org/W3193581299","https://openalex.org/W4220897484","https://openalex.org/W4225379371","https://openalex.org/W4282840811","https://openalex.org/W4294012180","https://openalex.org/W4311438734","https://openalex.org/W4381248205","https://openalex.org/W4390500957","https://openalex.org/W4390655821","https://openalex.org/W4390694263","https://openalex.org/W4390707638","https://openalex.org/W4402532521","https://openalex.org/W4403770348","https://openalex.org/W4404923153","https://openalex.org/W6873111560"],"related_works":["https://openalex.org/W2086381437","https://openalex.org/W4391340216","https://openalex.org/W4389452249","https://openalex.org/W2619166255","https://openalex.org/W2905822234","https://openalex.org/W2989944812","https://openalex.org/W3132115146","https://openalex.org/W2793353350","https://openalex.org/W1969673184","https://openalex.org/W2741663684"],"abstract_inverted_index":{"LYCEUM":[0],"is":[1],"available":[2],"at":[3],"https://github.com/ciceklab/LYCEUM.":[4]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}