{"id":"https://openalex.org/W2056816080","doi":"https://doi.org/10.1186/1752-0509-6-s2-s5","title":"Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry","display_name":"Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W2056816080","doi":"https://doi.org/10.1186/1752-0509-6-s2-s5","mag":"2056816080","pmid":"https://pubmed.ncbi.nlm.nih.gov/23282116"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-6-s2-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-s2-s5","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-S2-S5","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"conference-abstract","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-S2-S5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100363139","display_name":"Xin Chen","orcid":"https://orcid.org/0009-0004-0966-6025"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Xin Chen","raw_affiliation_strings":["School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore. chenxin@ntu.edu.sg","School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore. chenxin@ntu.edu.sg","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103133463","display_name":"Qiong Wu","orcid":"https://orcid.org/0000-0002-7674-0262"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]},{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["CN","SG"],"is_corresponding":false,"raw_author_name":"Qiong Wu","raw_affiliation_strings":["School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore","The Key Laboratory of Embedded System and Service Computing, Ministry of Education, Tongji University, Shanghai, 200092, China","The Key Laboratory of Embedded System and Service Computing, Ministry of Education, Tongji University, Shanghai, China","School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"The Key Laboratory of Embedded System and Service Computing, Ministry of Education, Tongji University, Shanghai, 200092, China","institution_ids":["https://openalex.org/I116953780"]},{"raw_affiliation_string":"The Key Laboratory of Embedded System and Service Computing, Ministry of Education, Tongji University, Shanghai, China","institution_ids":["https://openalex.org/I116953780"]},{"raw_affiliation_string":"School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore,","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102427520","display_name":"Ruimin Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Ruimin Sun","raw_affiliation_strings":["School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore","School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012300835","display_name":"Louxin Zhang","orcid":"https://orcid.org/0000-0003-0260-824X"},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Louxin Zhang","raw_affiliation_strings":["Department of Mathematics, National University of Singapore, Singapore","(Department of Mathematics, National University of Singapore, Singapore)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"(Department of Mathematics, National University of Singapore, Singapore)","institution_ids":["https://openalex.org/I165932596"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100363139"],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":null,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"6","issue":"Suppl 2","first_page":"S5","last_page":"S5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.1665000021457672,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.1665000021457672,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.09109999984502792,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.08100000023841858,"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/in-silico","display_name":"In silico","score":0.5841432809829712},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.4821050465106964},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47124654054641724},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4445021450519562},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.40921109914779663},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33195626735687256},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23696893453598022},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.08279198408126831},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08264413475990295}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5841432809829712},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.4821050465106964},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47124654054641724},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4445021450519562},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.40921109914779663},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33195626735687256},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23696893453598022},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.08279198408126831},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08264413475990295}],"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1752-0509-6-s2-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-s2-s5","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-S2-S5","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:23282116","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23282116","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 systems biology","raw_type":null},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/104406","is_oa":false,"landing_page_url":"http://scholarbank.nus.edu.sg/handle/10635/104406","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus","raw_type":"Article"},{"id":"pmh:oai:dr.ntu.edu.sg:10356/105219","is_oa":true,"landing_page_url":"https://hdl.handle.net/10356/105219","pdf_url":null,"source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"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":"Journal Article"},{"id":"pmh:oai:europepmc.org:2521560","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3521188","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"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-6-s2-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-s2-s5","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-S2-S5","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life below water","id":"https://metadata.un.org/sdg/14","score":0.7200000286102295}],"awards":[{"id":"https://openalex.org/G4944503469","display_name":null,"funder_award_id":"AcRF Tier 2","funder_id":"https://openalex.org/F4320334737","funder_display_name":"National Medical Research Council"},{"id":"https://openalex.org/G5302130745","display_name":null,"funder_award_id":"CBRG11nov091","funder_id":"https://openalex.org/F4320334737","funder_display_name":"National Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320322724","display_name":"Ministry of Education, India","ror":"https://ror.org/048xjjh50"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334737","display_name":"National Medical Research Council","ror":"https://ror.org/04x3cxs03"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2056816080.pdf","grobid_xml":"https://content.openalex.org/works/W2056816080.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W2010296522","https://openalex.org/W2014966027","https://openalex.org/W2025888918","https://openalex.org/W2029047779","https://openalex.org/W2050404755","https://openalex.org/W2095381673","https://openalex.org/W2136651963","https://openalex.org/W2139476567","https://openalex.org/W2797195473"],"related_works":["https://openalex.org/W2164855536","https://openalex.org/W1997352593","https://openalex.org/W2143489661","https://openalex.org/W2070581548","https://openalex.org/W4281711902","https://openalex.org/W3206555169","https://openalex.org/W3016573916","https://openalex.org/W3157359833","https://openalex.org/W3024317680","https://openalex.org/W1511048503"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,89],"discovery":[2,28,51],"of":[3,13,48,80,144,181,201,213],"single-nucleotide":[4],"polymorphisms":[5],"(SNPs)":[6],"has":[7],"important":[8],"implications":[9],"in":[10,103,113,134,203],"a":[11,175,178,198],"variety":[12],"genetic":[14],"studies":[15],"on":[16,31],"human":[17],"diseases":[18],"and":[19,34,163,219],"biological":[20],"functions.":[21],"One":[22],"valuable":[23],"approach":[24],"proposed":[25],"for":[26,156,217],"SNP":[27,50,94,125,159,168,221],"is":[29,39,172],"based":[30],"base-specific":[32,206],"cleavage":[33,207],"mass":[35,106,116,137,147],"spectrometry.":[36],"However,":[37],"it":[38],"still":[40],"very":[41],"challenging":[42],"to":[43,100,131,192],"achieve":[44],"the":[45,71,77,114,120,142,145,158,167,182,211,214],"full":[46],"potential":[47],"this":[49,55],"approach.":[52],"RESULTS:":[53],"In":[54,118],"study,":[56],"we":[57],"formulate":[58],"two":[59],"new":[60],"combinatorial":[61],"optimization":[62],"problems.":[63],"While":[64],"both":[65],"problems":[66],"are":[67],"aimed":[68],"at":[69],"reconstructing":[70],"sample":[72],"sequence":[73,87],"that":[74,166,188],"would":[75],"attain":[76],"minimum":[78],"number":[79],"SNPs,":[81],"they":[82],"search":[83,99,130],"over":[84],"different":[85],"candidate":[86],"spaces.":[88],"first":[90],"problem,":[91,122],"denoted":[92,123],"as":[93,124],"-":[95,126,160,169],"MSP,":[96],"limits":[97,128],"its":[98,129],"sequences":[101,132],"whose":[102,133],"silico":[104,135],"predicted":[105,136],"spectra":[107,138],"have":[108],"all":[109,141],"their":[110],"signals":[111,143],"contained":[112],"measured":[115,146],"spectra.":[117,148],"contrast,":[119],"second":[121],"MSQ,":[127],"instead":[139],"contain":[140],"We":[149,186],"present":[150],"an":[151,189],"exact":[152],"dynamic":[153],"programming":[154],"algorithm":[155],"solving":[157],"MSP":[161],"problem":[162,171,194],"also":[164],"show":[165],"MSQ":[170],"NP-hard":[173],"by":[174],"reduction":[176],"from":[177],"restricted":[179],"variation":[180],"3-partition":[183],"problem.":[184],"CONCLUSIONS:":[185],"believe":[187],"efficient":[190],"solution":[191],"either":[193],"above":[195],"could":[196],"offer":[197],"seamless":[199],"integration":[200],"information":[202],"four":[204],"complementary":[205],"reactions,":[208],"thereby":[209],"improving":[210],"capability":[212],"underlying":[215],"biotechnology":[216],"sensitive":[218],"accurate":[220],"discovery.":[222]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2015,"cited_by_count":2}],"updated_date":"2026-07-26T07:53:14.480251","created_date":"2025-10-10T00:00:00"}
