{"id":"https://openalex.org/W2949074212","doi":"https://doi.org/10.1093/bioinformatics/btx636","title":"Squeakr: an exact and approximate <i>k</i> -mer counting system","display_name":"Squeakr: an exact and approximate <i>k</i> -mer counting system","publication_year":2017,"publication_date":"2017-10-06","ids":{"openalex":"https://openalex.org/W2949074212","doi":"https://doi.org/10.1093/bioinformatics/btx636","mag":"2949074212","pmid":"https://pubmed.ncbi.nlm.nih.gov/29444235"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx636","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx636","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/4/568/25117209/btx636.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/4/568/25117209/btx636.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014159929","display_name":"Prashant Pandey","orcid":"https://orcid.org/0000-0001-5576-0320"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Prashant Pandey","raw_affiliation_strings":["Department of Computer Science, Stony Brook University, Stony Brook, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Stony Brook University, Stony Brook, NY, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068761590","display_name":"Michael A. Bender","orcid":"https://orcid.org/0000-0001-7639-530X"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael A Bender","raw_affiliation_strings":["Department of Computer Science, Stony Brook University, Stony Brook, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Stony Brook University, Stony Brook, NY, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101626826","display_name":"Rob Johnson","orcid":"https://orcid.org/0000-0002-0784-7410"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rob Johnson","raw_affiliation_strings":["Department of Computer Science, Stony Brook University, Stony Brook, NY, USA","VMware Research, Palo Alto, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Stony Brook University, Stony Brook, NY, USA","institution_ids":["https://openalex.org/I59553526"]},{"raw_affiliation_string":"VMware Research, Palo Alto, CA, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014584023","display_name":"Rob Patro","orcid":"https://orcid.org/0000-0001-8463-1675"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rob Patro","raw_affiliation_strings":["Department of Computer Science, Stony Brook University, Stony Brook, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Stony Brook University, Stony Brook, NY, USA","institution_ids":["https://openalex.org/I59553526"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5014159929"],"corresponding_institution_ids":["https://openalex.org/I59553526"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.0427,"has_fulltext":false,"cited_by_count":96,"citation_normalized_percentile":{"value":0.94878243,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"34","issue":"4","first_page":"568","last_page":"575"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9915000200271606,"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/multiset","display_name":"Multiset","score":0.8705305457115173},{"id":"https://openalex.org/keywords/de-bruijn-sequence","display_name":"De Bruijn sequence","score":0.7890670299530029},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6142498254776001},{"id":"https://openalex.org/keywords/quotient","display_name":"Quotient","score":0.6045085787773132},{"id":"https://openalex.org/keywords/k-mer","display_name":"k-mer","score":0.5854824185371399},{"id":"https://openalex.org/keywords/tree-traversal","display_name":"Tree traversal","score":0.5436129570007324},{"id":"https://openalex.org/keywords/de-bruijn-graph","display_name":"De Bruijn graph","score":0.5183199644088745},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.515489399433136},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.5052881836891174},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4992849826812744},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4728914797306061},{"id":"https://openalex.org/keywords/filter","display_name":"Filter (signal processing)","score":0.44916659593582153},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.3310331702232361},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.26362699270248413},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.24196818470954895}],"concepts":[{"id":"https://openalex.org/C2779623528","wikidata":"https://www.wikidata.org/wiki/Q864377","display_name":"Multiset","level":2,"score":0.8705305457115173},{"id":"https://openalex.org/C170320093","wikidata":"https://www.wikidata.org/wiki/Q1953457","display_name":"De Bruijn sequence","level":2,"score":0.7890670299530029},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6142498254776001},{"id":"https://openalex.org/C199422724","wikidata":"https://www.wikidata.org/wiki/Q41118","display_name":"Quotient","level":2,"score":0.6045085787773132},{"id":"https://openalex.org/C2279292","wikidata":"https://www.wikidata.org/wiki/Q6322851","display_name":"k-mer","level":4,"score":0.5854824185371399},{"id":"https://openalex.org/C140745168","wikidata":"https://www.wikidata.org/wiki/Q1210082","display_name":"Tree traversal","level":2,"score":0.5436129570007324},{"id":"https://openalex.org/C20218877","wikidata":"https://www.wikidata.org/wiki/Q3066095","display_name":"De Bruijn graph","level":3,"score":0.5183199644088745},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.515489399433136},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.5052881836891174},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4992849826812744},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4728914797306061},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.44916659593582153},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.3310331702232361},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.26362699270248413},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.24196818470954895},{"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/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"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":"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":"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":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"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":2,"locations":[{"id":"doi:10.1093/bioinformatics/btx636","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx636","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/4/568/25117209/btx636.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29444235","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29444235","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx636","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx636","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/4/568/25117209/btx636.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5383279761","display_name":null,"funder_award_id":"BBSRC-NSF/BIO-1564917, IIS-1247726, IIS-1251137, CNS-1408695, CCF-1439084, and CCF-1617618","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320338291","display_name":"Sandia National Laboratories","ror":"https://ror.org/01apwpt12"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2949074212.pdf","grobid_xml":"https://content.openalex.org/works/W2949074212.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1509816035","https://openalex.org/W1579534339","https://openalex.org/W1966822396","https://openalex.org/W2001079689","https://openalex.org/W2003347102","https://openalex.org/W2014099509","https://openalex.org/W2064803799","https://openalex.org/W2065128082","https://openalex.org/W2080234606","https://openalex.org/W2096128575","https://openalex.org/W2105656684","https://openalex.org/W2115546424","https://openalex.org/W2116435146","https://openalex.org/W2120902911","https://openalex.org/W2121873871","https://openalex.org/W2123845384","https://openalex.org/W2125266506","https://openalex.org/W2126300961","https://openalex.org/W2126419817","https://openalex.org/W2126540423","https://openalex.org/W2135966669","https://openalex.org/W2136651963","https://openalex.org/W2144560237","https://openalex.org/W2152809196","https://openalex.org/W2156841387","https://openalex.org/W2159433569","https://openalex.org/W2159954944","https://openalex.org/W2160969485","https://openalex.org/W2163584430","https://openalex.org/W2163830511","https://openalex.org/W2171963266","https://openalex.org/W2914482275","https://openalex.org/W2950150251"],"related_works":["https://openalex.org/W2120956621","https://openalex.org/W2915362964","https://openalex.org/W3215786367","https://openalex.org/W2953339515","https://openalex.org/W3205360317","https://openalex.org/W4214573178","https://openalex.org/W2562683361","https://openalex.org/W3200242814","https://openalex.org/W4200364103","https://openalex.org/W4282946044"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":17},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":1}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2019-06-27T00:00:00"}