{"id":"https://openalex.org/W2795345500","doi":"https://doi.org/10.1093/bioinformatics/bty186","title":"pyNBS: a Python implementation for network-based stratification of tumor mutations","display_name":"pyNBS: a Python implementation for network-based stratification of tumor mutations","publication_year":2018,"publication_date":"2018-03-28","ids":{"openalex":"https://openalex.org/W2795345500","doi":"https://doi.org/10.1093/bioinformatics/bty186","mag":"2795345500","pmid":"https://pubmed.ncbi.nlm.nih.gov/29608663"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty186","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty186","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/16/2859/25441865/bty186.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/16/2859/25441865/bty186.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026087488","display_name":"Justin K. Huang","orcid":"https://orcid.org/0000-0002-9150-8533"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210133661","display_name":"La Jolla Bioengineering Institute","ror":"https://ror.org/03sgbh608","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210133661"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Justin K Huang","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, Bioengineering Department, UC San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, Bioengineering Department, UC San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I4210133661","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031571167","display_name":"Tongqiu Jia","orcid":"https://orcid.org/0000-0002-6012-6436"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tongqiu Jia","raw_affiliation_strings":["Department of Medicine, UC San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, UC San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076514426","display_name":"Daniel E. Carlin","orcid":"https://orcid.org/0000-0001-5075-9486"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel E Carlin","raw_affiliation_strings":["Department of Medicine, UC San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, UC San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089373684","display_name":"Trey Ideker","orcid":"https://orcid.org/0000-0002-1708-8454"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210133661","display_name":"La Jolla Bioengineering Institute","ror":"https://ror.org/03sgbh608","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210133661"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Trey Ideker","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, Bioengineering Department, UC San Diego, La Jolla, CA, USA","Department of Medicine, UC San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, Bioengineering Department, UC San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I4210133661","https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, UC San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5026087488"],"corresponding_institution_ids":["https://openalex.org/I36258959","https://openalex.org/I4210133661"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1929,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.7476952,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"34","issue":"16","first_page":"2859","last_page":"2861"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":1.0,"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":1.0,"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/T10417","display_name":"Lung Cancer Treatments and Mutations","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11369","display_name":"Genetic factors in colorectal cancer","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.9448592662811279},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7455617785453796},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5263924598693848},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.49615344405174255},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.47732052206993103},{"id":"https://openalex.org/keywords/stratification","display_name":"Stratification (seeds)","score":0.45946431159973145},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4448954164981842},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4321151077747345},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36433905363082886},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.29242873191833496},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1382671296596527}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9448592662811279},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7455617785453796},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5263924598693848},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.49615344405174255},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.47732052206993103},{"id":"https://openalex.org/C192943249","wikidata":"https://www.wikidata.org/wiki/Q1893382","display_name":"Stratification (seeds)","level":5,"score":0.45946431159973145},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4448954164981842},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4321151077747345},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36433905363082886},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.29242873191833496},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1382671296596527},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C3527866","wikidata":"https://www.wikidata.org/wiki/Q162267","display_name":"Dormancy","level":3,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C88548481","wikidata":"https://www.wikidata.org/wiki/Q2397491","display_name":"Seed dormancy","level":4,"score":0.0},{"id":"https://openalex.org/C100701293","wikidata":"https://www.wikidata.org/wiki/Q193838","display_name":"Germination","level":2,"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty186","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty186","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/16/2859/25441865/bty186.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29608663","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29608663","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:europepmc.org:5640757","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6084608","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty186","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty186","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/16/2859/25441865/bty186.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/17","display_name":"Partnerships for the goals","score":0.49000000953674316}],"awards":[{"id":"https://openalex.org/G1605731393","display_name":null,"funder_award_id":"CA209891","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1863333649","display_name":null,"funder_award_id":"CA184427","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2423745062","display_name":null,"funder_award_id":"W911-NF-14-1-0397","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4412323338","display_name":null,"funder_award_id":"GM103504","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4628589723","display_name":null,"funder_award_id":"W911-NF-14-1-0397","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"},{"id":"https://openalex.org/G5180836318","display_name":null,"funder_award_id":"GM10350","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5214182589","display_name":null,"funder_award_id":"T32 GM008806","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5298496832","display_name":null,"funder_award_id":"P41 GM103504","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6332831770","display_name":null,"funder_award_id":"T32 GM008","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6913339659","display_name":null,"funder_award_id":"U24 CA184427","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8841462186","display_name":null,"funder_award_id":"U54CA209891","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2795345500.pdf","grobid_xml":"https://content.openalex.org/works/W2795345500.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1966331733","https://openalex.org/W2038122249","https://openalex.org/W2042851051","https://openalex.org/W2044433401","https://openalex.org/W2088891952","https://openalex.org/W2095319945","https://openalex.org/W2096766502","https://openalex.org/W2100714130","https://openalex.org/W2108119513","https://openalex.org/W2117692326","https://openalex.org/W2121443461","https://openalex.org/W2132623845","https://openalex.org/W2144940507","https://openalex.org/W2160981405","https://openalex.org/W2171504383","https://openalex.org/W2461427403","https://openalex.org/W2494960642","https://openalex.org/W2558715006","https://openalex.org/W2794479004","https://openalex.org/W4230962320"],"related_works":["https://openalex.org/W2768092088","https://openalex.org/W270927586","https://openalex.org/W4297632510","https://openalex.org/W2080797126","https://openalex.org/W4312312709","https://openalex.org/W2020328473","https://openalex.org/W4309804142","https://openalex.org/W3101523611","https://openalex.org/W2900707193","https://openalex.org/W4290719030"],"abstract_inverted_index":{"The":[0],"package,":[1],"along":[2],"with":[3],"examples":[4],"and":[5,10],"data,":[6],"can":[7],"be":[8],"downloaded":[9],"installed":[11],"from":[12],"the":[13],"URL":[14],"https://github.com/idekerlab/pyNBS.":[15]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
