{"id":"https://openalex.org/W2167040870","doi":"https://doi.org/10.1186/1471-2105-11-s11-s4","title":"Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures","display_name":"Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures","publication_year":2010,"publication_date":"2010-12-01","ids":{"openalex":"https://openalex.org/W2167040870","doi":"https://doi.org/10.1186/1471-2105-11-s11-s4","mag":"2167040870","pmid":"https://pubmed.ncbi.nlm.nih.gov/21172054"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-s11-s4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s11-s4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S11-S4","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/10.1186/1471-2105-11-S11-S4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001431051","display_name":"Yang Zhao","orcid":"https://orcid.org/0000-0003-3637-6731"},"institutions":[{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yang Zhao","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan","Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039138118","display_name":"Morihiro Hayashida","orcid":"https://orcid.org/0000-0001-7961-0175"},"institutions":[{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Morihiro Hayashida","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016330265","display_name":"Tatsuya Akutsu","orcid":"https://orcid.org/0000-0001-9763-797X"},"institutions":[{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tatsuya Akutsu","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5001431051"],"corresponding_institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.4663,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.75683234,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"11","issue":"S11","first_page":"S4","last_page":"S4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9997000098228455,"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":0.9997000098228455,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9940999746322632,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9807999730110168,"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/computer-science","display_name":"Computer science","score":0.6185721158981323},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6182498335838318},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.5847035646438599},{"id":"https://openalex.org/keywords/tree-traversal","display_name":"Tree traversal","score":0.5210703611373901},{"id":"https://openalex.org/keywords/search-tree","display_name":"Search tree","score":0.49431800842285156},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.4889196455478668},{"id":"https://openalex.org/keywords/grammar","display_name":"Grammar","score":0.4536239504814148},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4296709895133972},{"id":"https://openalex.org/keywords/context-free-grammar","display_name":"Context-free grammar","score":0.4187600612640381},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.4141119122505188},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38184720277786255},{"id":"https://openalex.org/keywords/rule-based-machine-translation","display_name":"Rule-based machine translation","score":0.3685816824436188},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3613200783729553},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.3316107988357544},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30789244174957275},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.22483834624290466},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1433151662349701}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6185721158981323},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6182498335838318},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.5847035646438599},{"id":"https://openalex.org/C140745168","wikidata":"https://www.wikidata.org/wiki/Q1210082","display_name":"Tree traversal","level":2,"score":0.5210703611373901},{"id":"https://openalex.org/C207024777","wikidata":"https://www.wikidata.org/wiki/Q621673","display_name":"Search tree","level":3,"score":0.49431800842285156},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.4889196455478668},{"id":"https://openalex.org/C26022165","wikidata":"https://www.wikidata.org/wiki/Q8091","display_name":"Grammar","level":2,"score":0.4536239504814148},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4296709895133972},{"id":"https://openalex.org/C97212296","wikidata":"https://www.wikidata.org/wiki/Q338047","display_name":"Context-free grammar","level":3,"score":0.4187600612640381},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.4141119122505188},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38184720277786255},{"id":"https://openalex.org/C53893814","wikidata":"https://www.wikidata.org/wiki/Q7378909","display_name":"Rule-based machine translation","level":2,"score":0.3685816824436188},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3613200783729553},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.3316107988357544},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30789244174957275},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.22483834624290466},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1433151662349701},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D044962","descriptor_name":"Data Compression","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D044962","descriptor_name":"Data Compression","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-11-s11-s4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s11-s4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S11-S4","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:21172054","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21172054","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:irdb.nii.ac.jp:01221:0000098531","is_oa":true,"landing_page_url":"http://hdl.handle.net/2433/134588","pdf_url":null,"source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"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":"journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3024861","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3024861","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-s11-s4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s11-s4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S11-S4","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":[{"id":"https://openalex.org/G7599130655","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G8044579487","display_name":null,"funder_award_id":"Japan","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G8854736479","display_name":null,"funder_award_id":"22240009","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2167040870.pdf","grobid_xml":"https://content.openalex.org/works/W2167040870.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1599548286","https://openalex.org/W1875715385","https://openalex.org/W1966458445","https://openalex.org/W1973608346","https://openalex.org/W1980541971","https://openalex.org/W1987349868","https://openalex.org/W2017555693","https://openalex.org/W2019758562","https://openalex.org/W2036471856","https://openalex.org/W2113004376","https://openalex.org/W2125598538","https://openalex.org/W2148506544"],"related_works":["https://openalex.org/W1557335907","https://openalex.org/W4286266684","https://openalex.org/W1586408085","https://openalex.org/W48124421","https://openalex.org/W1538450113","https://openalex.org/W1656514314","https://openalex.org/W59084530","https://openalex.org/W2293223786","https://openalex.org/W4245826738","https://openalex.org/W3013382169"],"abstract_inverted_index":{"We":[0],"propose":[1],"integer":[2],"programming-based":[3],"methods":[4,22],"that":[5],"find":[6],"the":[7],"minimum":[8],"CFG,":[9],"EOTG,":[10],"and":[11,17],"EUTG":[12],"for":[13,23,27],"given":[14],"strings,":[15],"ordered":[16],"unordered":[18],"trees.":[19],"Our":[20],"proposed":[21],"trees":[24],"are":[25],"useful":[26],"extracting":[28],"patterns":[29],"of":[30],"glycan":[31],"tree":[32],"structures.":[33]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
