{"id":"https://openalex.org/W2558103361","doi":"https://doi.org/10.1145/2975167.2985653","title":"Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection","display_name":"Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection","publication_year":2016,"publication_date":"2016-10-02","ids":{"openalex":"https://openalex.org/W2558103361","doi":"https://doi.org/10.1145/2975167.2985653","mag":"2558103361"},"language":"en","primary_location":{"id":"doi:10.1145/2975167.2985653","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2975167.2985653","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015039171","display_name":"Amelia Bateman","orcid":null},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Amelia Bateman","raw_affiliation_strings":["Department of Computer Science, University of Maryland, College Park"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Maryland, College Park","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054369332","display_name":"Todd J. Treangen","orcid":"https://orcid.org/0000-0002-3760-564X"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Todd J. Treangen","raw_affiliation_strings":["Department of Computer Science, University of Maryland, College Park"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Maryland, College Park","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064979917","display_name":"Mihai Pop","orcid":"https://orcid.org/0000-0001-9617-5304"},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mihai Pop","raw_affiliation_strings":["Department of Computer Science, University of Maryland, College Park"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Maryland, College Park","institution_ids":["https://openalex.org/I66946132"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5015039171"],"corresponding_institution_ids":["https://openalex.org/I66946132"],"apc_list":null,"apc_paid":null,"fwci":0.3335,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.68520888,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"499","last_page":"500"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9994999766349792,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9984999895095825,"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":0.9933000206947327,"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/computer-science","display_name":"Computer science","score":0.737718403339386},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.7363752126693726},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5152685642242432},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.4384026825428009},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4207801818847656},{"id":"https://openalex.org/keywords/graph-theory","display_name":"Graph theory","score":0.41037893295288086},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.40716880559921265},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3431931734085083},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33436739444732666},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32991456985473633},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14676615595817566},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.136610209941864},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10743626952171326},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09094750881195068}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.737718403339386},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7363752126693726},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5152685642242432},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.4384026825428009},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4207801818847656},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.41037893295288086},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.40716880559921265},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3431931734085083},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33436739444732666},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32991456985473633},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14676615595817566},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.136610209941864},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10743626952171326},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09094750881195068},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2975167.2985653","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2975167.2985653","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2010361633","https://openalex.org/W2096981901","https://openalex.org/W2150859566","https://openalex.org/W2151752966","https://openalex.org/W2157905021","https://openalex.org/W2160969485"],"related_works":["https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W2359440920","https://openalex.org/W4242417330","https://openalex.org/W2889550857","https://openalex.org/W3013372948","https://openalex.org/W3135997498","https://openalex.org/W3198631238","https://openalex.org/W2968048207","https://openalex.org/W2762831627"],"abstract_inverted_index":{"Detection":[0],"of":[1,5,11,25],"variants":[2],"via":[3],"examination":[4],"sequence":[6],"graphs":[7],"enables":[8],"fast":[9],"analysis":[10],"non-model":[12],"organisms,":[13],"metagenomic":[14],"samples,":[15],"and":[16],"individual":[17],"human":[18],"genomes.":[19],"Here,":[20],"we":[21],"analyze":[22],"the":[23],"shortcomings":[24],"existing":[26],"algorithms":[27],"for":[28,36],"reference-free":[29],"variant":[30],"detection,":[31],"then":[32],"provide":[33],"algorithmic":[34],"recommendations":[35],"their":[37],"improvement.":[38]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
