{"id":"https://openalex.org/W2048971142","doi":"https://doi.org/10.1145/2389241.2389247","title":"WHAM","display_name":"WHAM","publication_year":2012,"publication_date":"2012-12-01","ids":{"openalex":"https://openalex.org/W2048971142","doi":"https://doi.org/10.1145/2389241.2389247","mag":"2048971142"},"language":"en","primary_location":{"id":"doi:10.1145/2389241.2389247","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2389241.2389247","pdf_url":null,"source":{"id":"https://openalex.org/S90119964","display_name":"ACM Transactions on Database Systems","issn_l":"0362-5915","issn":["0362-5915","1557-4644"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Database Systems","raw_type":"journal-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/A5100599401","display_name":"Yinan Li","orcid":"https://orcid.org/0000-0002-5456-1319"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yinan Li","raw_affiliation_strings":["University of Wisconsin--Madison","University of Wisconsin, Madison"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Wisconsin--Madison","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"University of Wisconsin, Madison","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069237428","display_name":"Jignesh M. Patel","orcid":"https://orcid.org/0000-0003-3653-2538"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jignesh M. Patel","raw_affiliation_strings":["University of Wisconsin--Madison","University of Wisconsin, Madison"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Wisconsin--Madison","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"University of Wisconsin, Madison","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022040349","display_name":"Allison Terrell","orcid":null},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Allison Terrell","raw_affiliation_strings":["University of Wisconsin--Madison","University of Wisconsin, Madison"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Wisconsin--Madison","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"University of Wisconsin, Madison","institution_ids":["https://openalex.org/I135310074"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I135310074"],"apc_list":null,"apc_paid":null,"fwci":4.7843,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.94854727,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"37","issue":"4","first_page":"1","last_page":"39"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9998000264167786,"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/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/T10181","display_name":"Natural Language Processing Techniques","score":0.9779000282287598,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8937812447547913},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.6315503716468811},{"id":"https://openalex.org/keywords/bitwise-operation","display_name":"Bitwise operation","score":0.6267504096031189},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6069658398628235},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5768141150474548},{"id":"https://openalex.org/keywords/hash-function","display_name":"Hash function","score":0.5541976094245911},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5157687664031982},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.48665791749954224},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4686284363269806},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.44097772240638733},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3825948238372803},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3677908182144165},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35893547534942627},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.32337719202041626},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.21601849794387817},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13483762741088867}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8937812447547913},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.6315503716468811},{"id":"https://openalex.org/C134765980","wikidata":"https://www.wikidata.org/wiki/Q879126","display_name":"Bitwise operation","level":2,"score":0.6267504096031189},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6069658398628235},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5768141150474548},{"id":"https://openalex.org/C99138194","wikidata":"https://www.wikidata.org/wiki/Q183427","display_name":"Hash function","level":2,"score":0.5541976094245911},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5157687664031982},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.48665791749954224},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4686284363269806},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.44097772240638733},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3825948238372803},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3677908182144165},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35893547534942627},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.32337719202041626},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.21601849794387817},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13483762741088867},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2389241.2389247","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2389241.2389247","pdf_url":null,"source":{"id":"https://openalex.org/S90119964","display_name":"ACM Transactions on Database Systems","issn_l":"0362-5915","issn":["0362-5915","1557-4644"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Database Systems","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G853943046","display_name":null,"funder_award_id":"IIS-1110948","funder_id":"https://openalex.org/F4320337389","funder_display_name":"Division of Information and Intelligent Systems"}],"funders":[{"id":"https://openalex.org/F4320337389","display_name":"Division of Information and Intelligent Systems","ror":"https://ror.org/053a2cp42"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W22160234","https://openalex.org/W41736568","https://openalex.org/W125979907","https://openalex.org/W1489843519","https://openalex.org/W1974942389","https://openalex.org/W1981409766","https://openalex.org/W1987426253","https://openalex.org/W2001496424","https://openalex.org/W2007239153","https://openalex.org/W2011632873","https://openalex.org/W2016219933","https://openalex.org/W2045821558","https://openalex.org/W2055043387","https://openalex.org/W2074231493","https://openalex.org/W2087064593","https://openalex.org/W2096441981","https://openalex.org/W2096598900","https://openalex.org/W2097341408","https://openalex.org/W2100751585","https://openalex.org/W2103441770","https://openalex.org/W2111306253","https://openalex.org/W2112099725","https://openalex.org/W2112113834","https://openalex.org/W2119057313","https://openalex.org/W2123020735","https://openalex.org/W2124985265","https://openalex.org/W2127230663","https://openalex.org/W2131329986","https://openalex.org/W2139760555","https://openalex.org/W2144990395","https://openalex.org/W2155631901","https://openalex.org/W2161488606","https://openalex.org/W2168459716","https://openalex.org/W2172382511","https://openalex.org/W2752853835"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2041478992","https://openalex.org/W4289949713","https://openalex.org/W2943610686","https://openalex.org/W2112099725","https://openalex.org/W2048971142"],"abstract_inverted_index":{"Over":[0],"the":[1,4,15,59,101,111,119],"last":[2],"decade,":[3],"cost":[5],"of":[6,40,54,64],"producing":[7],"genomic":[8],"sequences":[9,42],"has":[10],"dropped":[11],"dramatically":[12],"due":[13],"to":[14,43,116],"current":[16],"so-called":[17],"next-generation":[18,23],"sequencing":[19,24],"methods.":[20,104],"However,":[21],"these":[22],"methods":[25,35,83],"are":[26],"critically":[27],"dependent":[28],"on":[29,58],"fast":[30],"and":[31,62,84,95],"sophisticated":[32],"data":[33,66],"processing":[34,67],"for":[36,69,87],"aligning":[37],"a":[38,44,65],"set":[39],"query":[41],"reference":[45],"genome":[46],"using":[47],"rich":[48,92],"string":[49],"matching":[50],"models.":[51],"The":[52],"focus":[53],"this":[55,70],"work":[56],"is":[57,97,114],"design,":[60],"development":[61],"evaluation":[63],"system":[68],"crucial":[71],"\u201cshort":[72],"read":[73,123],"alignment\u201d":[74],"problem.":[75],"Our":[76],"system,":[77],"called":[78],"WHAM,":[79],"employs":[80],"hash-based":[81],"indexing":[82],"bitwise":[85],"operations":[86],"sequence":[88,124],"alignments.":[89],"It":[90],"allows":[91],"match":[93],"models":[94],"it":[96],"significantly":[98],"faster":[99],"than":[100],"existing":[102,112],"state-of-the-art":[103],"In":[105],"addition,":[106],"its":[107],"relative":[108],"speedup":[109],"over":[110],"method":[113],"poised":[115],"increase":[117],"in":[118,121],"future":[120],"which":[122],"lengths":[125],"will":[126],"increase.":[127]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":5}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2016-06-24T00:00:00"}
