{"id":"https://openalex.org/W4396638317","doi":"https://doi.org/10.1186/s13015-024-00261-7","title":"ESKEMAP: exact sketch-based read mapping","display_name":"ESKEMAP: exact sketch-based read mapping","publication_year":2024,"publication_date":"2024-05-04","ids":{"openalex":"https://openalex.org/W4396638317","doi":"https://doi.org/10.1186/s13015-024-00261-7","pmid":"https://pubmed.ncbi.nlm.nih.gov/38704605"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-024-00261-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-024-00261-7","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-024-00261-7","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-024-00261-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089026356","display_name":"Tizian Schulz","orcid":"https://orcid.org/0000-0003-0744-7078"},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]},{"id":"https://openalex.org/I203082224","display_name":"Hochschule Bielefeld","ror":"https://ror.org/00edvg943","country_code":"DE","type":"education","lineage":["https://openalex.org/I203082224"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Tizian Schulz","raw_affiliation_strings":["Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, Bielefeld, Germany. tizian.schulz@uni-bielefeld.de","Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany. tizian.schulz@uni-bielefeld.de","Graduate School \"Digital Infrastructure for the Life Sciences\" (DILS), Bielefeld University, Bielefeld, Germany. tizian.schulz@uni-bielefeld.de","Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, Bielefeld, Germany. tizian.schulz@uni-bielefeld.de","institution_ids":["https://openalex.org/I20121455"]},{"raw_affiliation_string":"Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany. tizian.schulz@uni-bielefeld.de","institution_ids":["https://openalex.org/I20121455"]},{"raw_affiliation_string":"Graduate School \"Digital Infrastructure for the Life Sciences\" (DILS), Bielefeld University, Bielefeld, Germany. tizian.schulz@uni-bielefeld.de","institution_ids":["https://openalex.org/I20121455","https://openalex.org/I203082224"]},{"raw_affiliation_string":"Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066909672","display_name":"Paul Medvedev","orcid":"https://orcid.org/0000-0003-3143-594X"},"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":"Paul Medvedev","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, USA. pzm11@psu.edu","Department of Computer Science and Engineering, The Pennsylvania State University, University Park, USA. pzm11@psu.edu","Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, USA. pzm11@psu.edu","Department of Computer Science and Engineering, The Pennsylvania State University, University Park, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, USA. pzm11@psu.edu","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, The Pennsylvania State University, University Park, USA. pzm11@psu.edu","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, USA. pzm11@psu.edu","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, The Pennsylvania State University, University Park, USA","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5066909672","https://openalex.org/A5089026356"],"corresponding_institution_ids":["https://openalex.org/I130769515","https://openalex.org/I20121455","https://openalex.org/I203082224"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":1825,"currency":"EUR","value_usd":1968},"fwci":0.4801,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.59751164,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"19","issue":"1","first_page":"19","last_page":"19"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9876000285148621,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.977400004863739,"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/algorithm","display_name":"Algorithm","score":0.639865517616272},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6145519018173218},{"id":"https://openalex.org/keywords/sketch","display_name":"Sketch","score":0.534130334854126},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4558001160621643},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3986937999725342},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.14944902062416077}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.639865517616272},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6145519018173218},{"id":"https://openalex.org/C2779231336","wikidata":"https://www.wikidata.org/wiki/Q7534724","display_name":"Sketch","level":2,"score":0.534130334854126},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4558001160621643},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3986937999725342},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.14944902062416077},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13015-024-00261-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-024-00261-7","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-024-00261-7","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:38704605","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38704605","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11069465","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11069465","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11069465/pdf/13015_2024_Article_261.pdf","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":"Algorithms Mol Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:89c9298a0ec2426a9abe382955ff80f2","is_oa":true,"landing_page_url":"https://doaj.org/article/89c9298a0ec2426a9abe382955ff80f2","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":"Algorithms for Molecular Biology, Vol 19, Iss 1, Pp 1-14 (2024)","raw_type":"article"},{"id":"pmh:oai:pub.uni-bielefeld.de:2989197","is_oa":true,"landing_page_url":"https://pub.uni-bielefeld.de/record/2989197","pdf_url":null,"source":{"id":"https://openalex.org/S4306401671","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"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":"http://purl.org/coar/resource_type/c_6501"}],"best_oa_location":{"id":"doi:10.1186/s13015-024-00261-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-024-00261-7","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/s13015-024-00261-7","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G227648021","display_name":null,"funder_award_id":"031 A 534A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2414046978","display_name":null,"funder_award_id":"031A533A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2431772652","display_name":null,"funder_award_id":"031 A538A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G300121295","display_name":null,"funder_award_id":"# 031A537C","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G318861138","display_name":"Leveraging k-mer sketching statistics to enhance metagenomic methods and alignment algorithms","funder_award_id":"5r01gm146462-02","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3603598162","display_name":null,"funder_award_id":"031 A535A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G4848351824","display_name":null,"funder_award_id":"#031A537B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5128364324","display_name":null,"funder_award_id":"31A532B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5157400669","display_name":null,"funder_award_id":"031A537A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5870080920","display_name":null,"funder_award_id":"031A537D","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G6697205189","display_name":"Pan-genome Graph Algorithms and Data Integration","funder_award_id":"872539","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8387372653","display_name":null,"funder_award_id":"031A533B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320323389","display_name":"Universit\u00e4t Bielefeld","ror":"https://ror.org/02hpadn98"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4396638317.pdf"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W2046601740","https://openalex.org/W2055043387","https://openalex.org/W2111295912","https://openalex.org/W2139747296","https://openalex.org/W2144560237","https://openalex.org/W2789843538","https://openalex.org/W2953174564","https://openalex.org/W3088711112","https://openalex.org/W3090950993","https://openalex.org/W3098495126","https://openalex.org/W3128964673","https://openalex.org/W4206102744","https://openalex.org/W4206761915","https://openalex.org/W4220999759","https://openalex.org/W4221104280","https://openalex.org/W4225293672","https://openalex.org/W4226289813","https://openalex.org/W4379054112","https://openalex.org/W4381489623","https://openalex.org/W4399326752"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2378994405","https://openalex.org/W2385974820","https://openalex.org/W2373478030","https://openalex.org/W2378679551","https://openalex.org/W3149739944","https://openalex.org/W2392363776","https://openalex.org/W2063051341","https://openalex.org/W2591066345"],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"Given":[2],"a":[3,23,33,57,85,88,121],"sequencing":[4],"read,":[5],"the":[6,15,18,98,104,181,191,194,200,210,220,232,237,240,252,279],"broad":[7],"goal":[8],"of":[9,100,106,183,193,202,222,239,255,275,281,290],"read":[10,38,86,101],"mapping":[11,67,82,102,248,269],"is":[12,73,180,199,219,284],"to":[13,45,60,251,265,287],"find":[14,79,266],"location(s)":[16],"in":[17,127,236,247],"reference":[19],"genome":[20],"that":[21,77,116,224],"have":[22],"\u201csimilar":[24,27],"sequence\u201d.":[25],"Traditionally,":[26],"sequence\u201d":[28],"was":[29],"defined":[30],"as":[31,42,277],"having":[32],"high":[34],"alignment":[35],"score":[36,90],"and":[37,157,213],"mappers":[39],"were":[40],"viewed":[41],"heuristic":[43],"solutions":[44],"this":[46,94],"well-defined":[47],"problem.":[48],"For":[49,271],"sketch-based":[50,66,75],"mappers,":[51],"however,":[52],"there":[53,72],"has":[54],"not":[55],"been":[56],"problem":[58,63,99],"formulation":[59],"capture":[61],"what":[62],"an":[64,111,272],"exact":[65,112],"algorithm":[68,115,283],"should":[69],"solve.":[70],"Moreover,":[71],"no":[74],"method":[76],"can":[78],"all":[80,118,267],"possible":[81],"positions":[83],"for":[84],"above":[87,120],"certain":[89],"threshold.":[91,124],"Results":[92],"In":[93],"paper,":[95],"we":[96],"formulate":[97],"at":[103],"level":[105,274],"sequence":[107],"sketches.":[108],"We":[109,242],"give":[110],"dynamic":[113],"programming":[114],"finds":[117],"hits":[119],"given":[122],"similarity":[123],"It":[125],"runs":[126],"$$\\mathcal":[128,158],"{O}":[129,159],"(|t|":[130],"+":[131,133],"|p|":[132],"\\ell":[134,162],"^2)$$":[135],"<mml:math":[136,164,185,204,215,226],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\">":[137,165,186,205,216,227],"<mml:mrow>":[138,166],"<mml:mi>O</mml:mi>":[139,167],"<mml:mo>(</mml:mo>":[140,168],"<mml:mo>|</mml:mo>":[141,143,145,147],"<mml:mi>t</mml:mi>":[142],"<mml:mo>+</mml:mo>":[144,148],"<mml:mi>p</mml:mi>":[146],"<mml:msup>":[149],"<mml:mi>\u2113</mml:mi>":[150,169,171,217],"<mml:mn>2</mml:mn>":[151],"</mml:msup>":[152],"<mml:mo>)</mml:mo>":[153,172],"</mml:mrow>":[154,173],"</mml:math>":[155,174,188,207,218,229],"time":[156],"(\\ell":[160],"\\log":[161],")$$":[163],"<mml:mo>log</mml:mo>":[170],"space,":[175],"where":[176,259],"|":[177,179,196,198],"t":[178],"number":[182,201,221],"$$k$$":[184,203,225],"<mml:mi>k</mml:mi>":[187,206,228],"-mers":[189,208,230],"inside":[190,209],"sketch":[192,212,234,238],"reference,":[195],"p":[197],"read\u2019s":[211],"$$\\ell$$":[214],"times":[223],"from":[231],"pattern":[233],"occur":[235],"text.":[241],"evaluate":[243],"our":[244,282],"algorithm\u2019s":[245],"performance":[246],"long":[249],"reads":[250],"T2T":[253],"assembly":[254],"human":[256],"chromosome":[257],"Y,":[258],"ampliconic":[260],"regions":[261],"make":[262],"it":[263],"desirable":[264],"good":[268],"positions.":[270],"equivalent":[273],"precision":[276],"minimap2,":[278],"recall":[280],"0.88,":[285],"compared":[286],"only":[288],"0.76":[289],"minimap2.":[291]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
