{"id":"https://openalex.org/W1657324220","doi":"https://doi.org/10.1186/1471-2105-16-s7-s10","title":"MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)","display_name":"MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC)","publication_year":2015,"publication_date":"2015-04-23","ids":{"openalex":"https://openalex.org/W1657324220","doi":"https://doi.org/10.1186/1471-2105-16-s7-s10","mag":"1657324220","pmid":"https://pubmed.ncbi.nlm.nih.gov/25952019"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-16-s7-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s7-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S7-S10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S7-S10","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027440970","display_name":"Ruibang Luo","orcid":"https://orcid.org/0000-0001-9711-6533"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Ruibang Luo","raw_affiliation_strings":["HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014858101","display_name":"Jeanno Cheung","orcid":null},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jeanno Cheung","raw_affiliation_strings":["HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055937002","display_name":"Edward Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Edward Wu","raw_affiliation_strings":["HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100453950","display_name":"Heng Wang","orcid":"https://orcid.org/0000-0002-1727-9226"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Heng Wang","raw_affiliation_strings":["HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","School of Computer Science, National University of Defense Technology, 410073, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology, 410073, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111962182","display_name":"Sze-Hang Chan","orcid":null},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Sze-Hang Chan","raw_affiliation_strings":["HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014359173","display_name":"Wai-Chun Law","orcid":null},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Wai-Chun Law","raw_affiliation_strings":["HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042788000","display_name":"Guangzhu He","orcid":null},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Guangzhu He","raw_affiliation_strings":["HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015191834","display_name":"Chang Yu","orcid":"https://orcid.org/0000-0002-6132-6085"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Chang Yu","raw_affiliation_strings":["HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036140304","display_name":"Chi-Man Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Chi-Man Liu","raw_affiliation_strings":["HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010034230","display_name":"Dazong Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Dazong Zhou","raw_affiliation_strings":["HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064592001","display_name":"Yingrui Li","orcid":"https://orcid.org/0000-0001-6630-1277"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Yingrui Li","raw_affiliation_strings":["BGI-Shenzhen, Shenzhen, 518083, China","HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038736219","display_name":"Ruiqiang Li","orcid":"https://orcid.org/0000-0003-4760-1535"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Ruiqiang Li","raw_affiliation_strings":["Department of Computer Science, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111964102","display_name":"Jun Wang","orcid":"https://orcid.org/0009-0008-8475-2934"},"institutions":[{"id":"https://openalex.org/I100135526","display_name":"BGI Group (China)","ror":"https://ror.org/045pn2j94","country_code":"CN","type":"company","lineage":["https://openalex.org/I100135526"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Jun Wang","raw_affiliation_strings":["BGI-Shenzhen, Shenzhen, 518083, China","HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BGI-Shenzhen, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I100135526"]},{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101024277","display_name":"Xiaoqian Zhu","orcid":"https://orcid.org/0000-0003-0861-2362"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoqian Zhu","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology, 410073, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology, 410073, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108008219","display_name":"Shaoliang Peng","orcid":"https://orcid.org/0000-0002-4647-2615"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaoliang Peng","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology, 410073, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology, 410073, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077116003","display_name":"Tak\u2010Wah Lam","orcid":"https://orcid.org/0000-0003-4676-8587"},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Tak-Wah Lam","raw_affiliation_strings":["Department of Computer Science, The University of Hong Kong, Hong Kong","HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]},{"raw_affiliation_string":"HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, The University of Hong Kong, Hong Kong","institution_ids":["https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":16,"corresponding_author_ids":["https://openalex.org/A5077116003"],"corresponding_institution_ids":["https://openalex.org/I889458895"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":9.5545,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.98333477,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"16","issue":"S7","first_page":"S10","last_page":"S10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.4426000118255615,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.4426000118255615,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T12613","display_name":"X-ray Diffraction in Crystallography","score":0.18770000338554382,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.06350000202655792,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials 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":0.7411662936210632},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6432108879089355},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.636012077331543},{"id":"https://openalex.org/keywords/xeon-phi","display_name":"Xeon Phi","score":0.6198945045471191},{"id":"https://openalex.org/keywords/mica","display_name":"Mica","score":0.48691046237945557},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4723043441772461},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3315727710723877},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.24558895826339722},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.09868934750556946}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7411662936210632},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6432108879089355},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.636012077331543},{"id":"https://openalex.org/C96972482","wikidata":"https://www.wikidata.org/wiki/Q1049168","display_name":"Xeon Phi","level":2,"score":0.6198945045471191},{"id":"https://openalex.org/C2781038479","wikidata":"https://www.wikidata.org/wiki/Q114675","display_name":"Mica","level":2,"score":0.48691046237945557},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4723043441772461},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3315727710723877},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.24558895826339722},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.09868934750556946},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"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":"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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-16-s7-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s7-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S7-S10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25952019","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25952019","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3389588","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4423751","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:hub.hku.hk:10722/215514","is_oa":true,"landing_page_url":"http://hdl.handle.net/10722/215514","pdf_url":null,"source":{"id":"https://openalex.org/S4377196271","display_name":"The HKU Scholars Hub (University of Hong Kong)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I889458895","host_organization_name":"University of Hong Kong","host_organization_lineage":["https://openalex.org/I889458895"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:hub.hku.hk:10722/251167","is_oa":false,"landing_page_url":"http://hdl.handle.net/10722/251167","pdf_url":null,"source":{"id":"https://openalex.org/S4377196271","display_name":"The HKU Scholars Hub (University of Hong Kong)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I889458895","host_organization_name":"University of Hong Kong","host_organization_lineage":["https://openalex.org/I889458895"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-16-s7-s10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-16-s7-s10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-16-S7-S10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1657324220.pdf","grobid_xml":"https://content.openalex.org/works/W1657324220.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W2015831381","https://openalex.org/W2025648894","https://openalex.org/W2037748100","https://openalex.org/W2068448872","https://openalex.org/W2075996757","https://openalex.org/W2087064593","https://openalex.org/W2095680943","https://openalex.org/W2098291606","https://openalex.org/W2107824361","https://openalex.org/W2112113834","https://openalex.org/W2119279650","https://openalex.org/W2124985265","https://openalex.org/W2129933858","https://openalex.org/W2139523073"],"related_works":["https://openalex.org/W2317245370","https://openalex.org/W4249323025","https://openalex.org/W2981664121","https://openalex.org/W2526069705","https://openalex.org/W198851386","https://openalex.org/W1980160788","https://openalex.org/W2030310580","https://openalex.org/W2148915962","https://openalex.org/W4313433561","https://openalex.org/W947442053"],"abstract_inverted_index":{"BACKGROUND:":[0],"Short-read":[1],"aligners":[2],"have":[3,201],"recently":[4],"gained":[5],"a":[6,72,78,93,125,153,162,178,183],"lot":[7],"of":[8,15,30,45,103,152,235],"speed":[9],"by":[10,194],"exploiting":[11],"the":[12,55,107,116,121],"massive":[13],"parallelism":[14,109],"GPU.":[16],"An":[17],"uprising":[18],"alterative":[19],"to":[20,38,50,60],"GPU":[21,61,73],"is":[22,32,57,99,143,229,243,255],"Intel":[23],"MIC;":[24],"supercomputers":[25,196],"like":[26],"Tianhe-2,":[27],"currently":[28],"top":[29],"TOP500,":[31],"built":[33],"with":[34,206],"48,000":[35],"MIC":[36,46,65,112,122,141,173,228],"boards":[37],"offer":[39],"~55":[40],"PFLOPS.":[41],"The":[42],"CPU-like":[43],"architecture":[44],"allows":[47,167],"CPU-based":[48],"software":[49],"be":[51,191,214],"parallelized":[52],"easily;":[53],"however,":[54],"performance":[56,225],"often":[58],"inferior":[59],"counterparts":[62],"as":[63,257],"an":[64,217],"card":[66,74,142],"contains":[67],"only":[68,230],"~60":[69],"cores":[70,151],"(while":[71],"typically":[75],"has":[76,223],"over":[77,186],"thousand":[79],"cores).":[80],"RESULTS:":[81],"To":[82],"better":[83],"utilize":[84],"MIC-enabled":[85,195],"computers":[86],"for":[87,197],"NGS":[88],"data":[89],"analysis,":[90],"we":[91],"developed":[92],"new":[94,126],"short-read":[95],"aligner":[96],"MICA":[97,138,189,203,222],"that":[98,137],"optimized":[100],"in":[101,120,177,216,231],"view":[102],"MIC's":[104],"limitation":[105],"and":[106,123,156],"extra":[108],"inside":[110],"each":[111],"core.":[113],"By":[114],"utilizing":[115],"512-bit":[117],"vector":[118],"units":[119],"implementing":[124],"seeding":[127],"strategy,":[128],"experiments":[129],"on":[130,204],"aligning":[131],"150":[132],"bp":[133],"paired-end":[134],"reads":[135],"show":[136],"using":[139,219],"one":[140],"4.9":[144],"times":[145],"faster":[146,158],"than":[147,159],"BWA-MEM":[148],"(using":[149,161],"6":[150],"top-end":[154],"CPU),":[155],"slightly":[157],"SOAP3-dp":[160],"GPU).":[163],"Furthermore,":[164],"MICA's":[165,240],"simplicity":[166],"very":[168],"efficient":[169],"scale-up":[170],"when":[171],"multiple":[172],"cards":[174,181],"are":[175,262],"used":[176,193],"node":[179],"(3":[180],"give":[182],"14.1-fold":[184],"speedup":[185],"BWA-MEM).":[187],"SUMMARY:":[188],"can":[190,213],"readily":[192],"production":[198],"purpose.":[199],"We":[200],"tested":[202],"Tianhe-2":[205],"90":[207],"WGS":[208],"samples":[209],"(17.47":[210],"Tera-bases),":[211],"which":[212],"aligned":[215],"hour":[218],"400":[220],"nodes.":[221],"impressive":[224],"even":[226],"though":[227],"its":[232],"initial":[233],"stage":[234],"development.":[236],"AVAILABILITY":[237],"AND":[238],"IMPLEMENTATION:":[239],"source":[241],"code":[242],"freely":[244],"available":[245,256,263],"at":[246,264],"http://sourceforge.net/projects/mica-aligner":[247],"under":[248],"GPL":[249],"v3.":[250],"SUPPLEMENTARY":[251],"INFORMATION:":[252],"Supplementary":[253],"information":[254],"\"Additional":[258],"File":[259],"1\".":[260],"Datasets":[261],"www.bio8.cs.hku.hk/dataset/mica.":[265]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
