{"id":"https://openalex.org/W2147849085","doi":"https://doi.org/10.1093/bioinformatics/btu755","title":"SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP","display_name":"SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP","publication_year":2014,"publication_date":"2014-11-13","ids":{"openalex":"https://openalex.org/W2147849085","doi":"https://doi.org/10.1093/bioinformatics/btu755","mag":"2147849085","pmid":"https://pubmed.ncbi.nlm.nih.gov/25398608"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu755","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu755","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/7/1133/50306182/bioinformatics_31_7_1133.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/31/7/1133/50306182/bioinformatics_31_7_1133.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069222769","display_name":"Karen E. van Rens","orcid":null},"institutions":[{"id":"https://openalex.org/I103855431","display_name":"HAN University of Applied Sciences","ror":"https://ror.org/0500gea42","country_code":"NL","type":"education","lineage":["https://openalex.org/I103855431"]},{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]}],"countries":["FI","NL"],"is_corresponding":false,"raw_author_name":"Karen E. van Rens","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and 2HAN University of Applied Sciences, Nijmegen, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and 2HAN University of Applied Sciences, Nijmegen, The Netherlands","institution_ids":["https://openalex.org/I103855431","https://openalex.org/I133731052","https://openalex.org/I32943570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043558409","display_name":"Veli M\u00e4kinen","orcid":"https://orcid.org/0000-0003-4454-1493"},"institutions":[{"id":"https://openalex.org/I103855431","display_name":"HAN University of Applied Sciences","ror":"https://ror.org/0500gea42","country_code":"NL","type":"education","lineage":["https://openalex.org/I103855431"]},{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]}],"countries":["FI","NL"],"is_corresponding":false,"raw_author_name":"Veli M\u00e4kinen","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and 2HAN University of Applied Sciences, Nijmegen, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and 2HAN University of Applied Sciences, Nijmegen, The Netherlands","institution_ids":["https://openalex.org/I103855431","https://openalex.org/I133731052","https://openalex.org/I32943570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063897224","display_name":"Alexandru I. Tomescu","orcid":"https://orcid.org/0000-0002-5747-8350"},"institutions":[{"id":"https://openalex.org/I103855431","display_name":"HAN University of Applied Sciences","ror":"https://ror.org/0500gea42","country_code":"NL","type":"education","lineage":["https://openalex.org/I103855431"]},{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]}],"countries":["FI","NL"],"is_corresponding":true,"raw_author_name":"Alexandru I. Tomescu","raw_affiliation_strings":["1 Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and 2HAN University of Applied Sciences, Nijmegen, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland and 2HAN University of Applied Sciences, Nijmegen, The Netherlands","institution_ids":["https://openalex.org/I103855431","https://openalex.org/I133731052","https://openalex.org/I32943570"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5063897224"],"corresponding_institution_ids":["https://openalex.org/I103855431","https://openalex.org/I133731052","https://openalex.org/I32943570"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.697,"has_fulltext":true,"cited_by_count":42,"citation_normalized_percentile":{"value":0.68236431,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"31","issue":"7","first_page":"1133","last_page":"1135"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.22210000455379486,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.22210000455379486,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.21969999372959137,"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":0.19429999589920044,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5593739748001099},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5154184103012085},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4119737148284912},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3971705138683319}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5593739748001099},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5154184103012085},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4119737148284912},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3971705138683319}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011382","descriptor_name":"Programming, Linear","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btu755","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu755","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/7/1133/50306182/bioinformatics_31_7_1133.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:25398608","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25398608","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},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1016.2130","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1016.2130","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2014/11/13/bioinformatics.btu755.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu755","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu755","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/7/1133/50306182/bioinformatics_31_7_1133.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":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.800000011920929}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2147849085.pdf","grobid_xml":"https://content.openalex.org/works/W2147849085.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1994815346","https://openalex.org/W2065076110","https://openalex.org/W2103441770","https://openalex.org/W2112997276","https://openalex.org/W2119180969","https://openalex.org/W2150575159","https://openalex.org/W2161055995","https://openalex.org/W6666744536"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869"],"abstract_inverted_index":{"MOTIVATION:":[0],"Recent":[1],"studies":[2],"sequenced":[3],"tumor":[4],"samples":[5,71],"from":[6],"the":[7,21,95,104,129],"same":[8],"progenitor":[9],"at":[10,121,140],"different":[11],"development":[12],"stages":[13],"and":[14,57,92,127],"showed":[15],"that":[16],"by":[17],"taking":[18],"into":[19],"account":[20],"phylogeny":[22,97],"of":[23,43,87,94,106],"this":[24],"development,":[25],"single-nucleotide":[26],"variant":[27],"(SNV)":[28],"calling":[29],"can":[30,36],"be":[31],"improved.":[32],"Accurate":[33],"SNV":[34,67],"calls":[35],"better":[37],"reveal":[38],"early-stage":[39],"tumors,":[40],"identify":[41],"mechanisms":[42],"cancer":[44],"progression":[45],"or":[46,102],"help":[47],"in":[48,125],"drug":[49],"targeting.":[50],"RESULTS:":[51],"We":[52,77,99],"present":[53],"SNV-PPILP,":[54,119],"a":[55,75,84,109],"fast":[56],"easy":[58],"to":[59,73],"use":[60],"tool":[61],"for":[62,69],"refining":[63],"GATK's":[64],"Unified":[65],"Genotyper":[66],"calls,":[68],"multiple":[70],"assumed":[72],"form":[74],"phylogeny.":[76],"tested":[78],"SNV-PPILP":[79],"on":[80,112],"simulated":[81],"data,":[82],"with":[83,108],"varying":[85],"number":[86],"samples,":[88],"SNVs,":[89],"read":[90,114],"coverage":[91],"violations":[93],"perfect":[96],"assumption.":[98],"always":[100],"match":[101],"improve":[103],"accuracy":[105],"GATK,":[107],"significant":[110],"improvement":[111],"low":[113],"coverage.":[115],"AVAILABILITY":[116],"AND":[117],"IMPLEMENTATION:":[118],"available":[120,139],"cs.helsinki.fi/gsa/snv-ppilp/,":[122],"is":[123],"written":[124],"Python":[126],"requires":[128],"free":[130],"ILP":[131],"solver":[132],"lp_solve.":[133],"SUPPLEMENTARY":[134],"INFORMATION:":[135],"Supplementary":[136],"data":[137],"are":[138],"Bioinformatics":[141],"online.":[142]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":33},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
