{"id":"https://openalex.org/W2951594653","doi":"https://doi.org/10.1093/bioinformatics/bty567","title":"DREAM-Yara: an exact read mapper for very large databases with short update time","display_name":"DREAM-Yara: an exact read mapper for very large databases with short update time","publication_year":2018,"publication_date":"2018-07-05","ids":{"openalex":"https://openalex.org/W2951594653","doi":"https://doi.org/10.1093/bioinformatics/bty567","mag":"2951594653","pmid":"https://pubmed.ncbi.nlm.nih.gov/30423080"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty567","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty567","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i766/25702473/bty567.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/34/17/i766/25702473/bty567.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060945936","display_name":"Temesgen Hailemariam Dadi","orcid":"https://orcid.org/0000-0002-3701-8461"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Temesgen Hailemariam Dadi","raw_affiliation_strings":["Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Berlin, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053167866","display_name":"Enrico Siragusa","orcid":"https://orcid.org/0000-0002-5943-7544"},"institutions":[{"id":"https://openalex.org/I4210114115","display_name":"IBM Research - Thomas J. Watson Research Center","ror":"https://ror.org/0265w5591","country_code":"US","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Enrico Siragusa","raw_affiliation_strings":["Computational Genomics, IBM Thomas J Watson Research Center, Yorktown Heights, NY, USA"],"affiliations":[{"raw_affiliation_string":"Computational Genomics, IBM Thomas J Watson Research Center, Yorktown Heights, NY, USA","institution_ids":["https://openalex.org/I4210114115"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030335109","display_name":"Vitor C. Piro","orcid":"https://orcid.org/0000-0003-1330-1286"},"institutions":[{"id":"https://openalex.org/I24359323","display_name":"Robert Koch Institute","ror":"https://ror.org/01k5qnb77","country_code":"DE","type":"government","lineage":["https://openalex.org/I24359323"]},{"id":"https://openalex.org/I1293487690","display_name":"Ministry of Education","ror":"https://ror.org/04d0xx942","country_code":"BR","type":"government","lineage":["https://openalex.org/I1293487690","https://openalex.org/I2801200668"]},{"id":"https://openalex.org/I4210097716","display_name":"Coordena\u00e7\u00e3o de Aperfeicoamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614","country_code":"BR","type":"funder","lineage":["https://openalex.org/I1293487690","https://openalex.org/I2801200668","https://openalex.org/I4210097716"]}],"countries":["BR","DE"],"is_corresponding":false,"raw_author_name":"Vitor C Piro","raw_affiliation_strings":["Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany","CAPES Foundation, Ministry of Education of Brazil, Bras\u00edlia DF, Brazil"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany","institution_ids":["https://openalex.org/I24359323"]},{"raw_affiliation_string":"CAPES Foundation, Ministry of Education of Brazil, Bras\u00edlia DF, Brazil","institution_ids":["https://openalex.org/I4210097716","https://openalex.org/I1293487690"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043949227","display_name":"Andreas Andrusch","orcid":null},"institutions":[{"id":"https://openalex.org/I24359323","display_name":"Robert Koch Institute","ror":"https://ror.org/01k5qnb77","country_code":"DE","type":"government","lineage":["https://openalex.org/I24359323"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Andrusch","raw_affiliation_strings":["Centre for Biological Threats and Special Pathogens (ZBS1), Robert Koch Institute, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Centre for Biological Threats and Special Pathogens (ZBS1), Robert Koch Institute, Berlin, Germany","institution_ids":["https://openalex.org/I24359323"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047231982","display_name":"Enrico Seiler","orcid":"https://orcid.org/0000-0003-4270-1086"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Enrico Seiler","raw_affiliation_strings":["Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Berlin, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005996110","display_name":"Bernhard Y. Renard","orcid":"https://orcid.org/0000-0003-4589-9809"},"institutions":[{"id":"https://openalex.org/I24359323","display_name":"Robert Koch Institute","ror":"https://ror.org/01k5qnb77","country_code":"DE","type":"government","lineage":["https://openalex.org/I24359323"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bernhard Y Renard","raw_affiliation_strings":["Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany","institution_ids":["https://openalex.org/I24359323"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078948324","display_name":"Knut Reinert","orcid":"https://orcid.org/0000-0003-3078-8129"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Knut Reinert","raw_affiliation_strings":["Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Algorithmic Bioinformatics, Institute for Bioinformatics, FU Berlin, Berlin, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5060945936"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.5835,"has_fulltext":false,"cited_by_count":52,"citation_normalized_percentile":{"value":0.94395936,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"34","issue":"17","first_page":"i766","last_page":"i772"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9987999796867371,"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":0.9987999796867371,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9914000034332275,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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":0.656692624092102},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5981439352035522},{"id":"https://openalex.org/keywords/dream","display_name":"Dream","score":0.46816393733024597}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.656692624092102},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5981439352035522},{"id":"https://openalex.org/C2781095916","wikidata":"https://www.wikidata.org/wiki/Q36348","display_name":"Dream","level":2,"score":0.46816393733024597},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"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":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty567","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty567","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i766/25702473/bty567.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:30423080","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30423080","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/bty567","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty567","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i766/25702473/bty567.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/G3251340762","display_name":null,"funder_award_id":"BEX 13472/13-5","funder_id":"https://openalex.org/F4320336557","funder_display_name":"Ci\u00eancia sem Fronteiras"}],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320321721","display_name":"Bundesministerium f\u00fcr Gesundheit","ror":"https://ror.org/05vp4ka74"},{"id":"https://openalex.org/F4320327553","display_name":"International Max Planck Research School for Advanced Methods in Process and Systems Engineering","ror":null},{"id":"https://openalex.org/F4320336557","display_name":"Ci\u00eancia sem Fronteiras","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2951594653.pdf","grobid_xml":"https://content.openalex.org/works/W2951594653.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W9498632","https://openalex.org/W1826264422","https://openalex.org/W1986302430","https://openalex.org/W2025648894","https://openalex.org/W2063852444","https://openalex.org/W2103441770","https://openalex.org/W2123845384","https://openalex.org/W2124985265","https://openalex.org/W2129264270","https://openalex.org/W2133687564","https://openalex.org/W2141200343","https://openalex.org/W2142678031","https://openalex.org/W2142759233","https://openalex.org/W2156715753","https://openalex.org/W2158322625","https://openalex.org/W2159682570","https://openalex.org/W2163338240","https://openalex.org/W2170551349","https://openalex.org/W2305300412","https://openalex.org/W2525954034","https://openalex.org/W2753396470","https://openalex.org/W2766648240","https://openalex.org/W2781080143","https://openalex.org/W2952366981","https://openalex.org/W4247053599","https://openalex.org/W6745747970","https://openalex.org/W7055789414"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W1762480892","https://openalex.org/W597599663","https://openalex.org/W3194824274","https://openalex.org/W4205387075","https://openalex.org/W1537165133","https://openalex.org/W2390579330","https://openalex.org/W1578892932"],"abstract_inverted_index":{"https://gitlab.com/pirovc/dream_yara/.":[0]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2025-10-10T00:00:00"}
