{"id":"https://openalex.org/W4400918440","doi":"https://doi.org/10.1093/bib/bbae222","title":"CCPA: cloud-based, self-learning modules for consensus pathway analysis using GO, KEGG and Reactome","display_name":"CCPA: cloud-based, self-learning modules for consensus pathway analysis using GO, KEGG and Reactome","publication_year":2024,"publication_date":"2024-07-01","ids":{"openalex":"https://openalex.org/W4400918440","doi":"https://doi.org/10.1093/bib/bbae222","pmid":"https://pubmed.ncbi.nlm.nih.gov/39041916"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae222","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae222","pdf_url":"https://academic.oup.com/bib/article-pdf/25/Supplement_1/bbae222/58618835/bbae222.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/Supplement_1/bbae222/58618835/bbae222.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007403200","display_name":"Ha Nam Nguyen","orcid":"https://orcid.org/0000-0003-2338-3537"},"institutions":[{"id":"https://openalex.org/I82497590","display_name":"Auburn University","ror":"https://ror.org/02v80fc35","country_code":"US","type":"education","lineage":["https://openalex.org/I82497590"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ha Nguyen","raw_affiliation_strings":["Auburn University Department of Computer Science and Software Engineering, , AL 36849, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auburn University Department of Computer Science and Software Engineering, , AL 36849, USA","institution_ids":["https://openalex.org/I82497590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108959190","display_name":"Van-Dung Pham","orcid":null},"institutions":[{"id":"https://openalex.org/I82497590","display_name":"Auburn University","ror":"https://ror.org/02v80fc35","country_code":"US","type":"education","lineage":["https://openalex.org/I82497590"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Van-Dung Pham","raw_affiliation_strings":["Auburn University Department of Computer Science and Software Engineering, , AL 36849, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auburn University Department of Computer Science and Software Engineering, , AL 36849, USA","institution_ids":["https://openalex.org/I82497590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101704793","display_name":"Hung Nguyen","orcid":"https://orcid.org/0000-0002-4756-1732"},"institutions":[{"id":"https://openalex.org/I82497590","display_name":"Auburn University","ror":"https://ror.org/02v80fc35","country_code":"US","type":"education","lineage":["https://openalex.org/I82497590"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hung Nguyen","raw_affiliation_strings":["Auburn University Department of Computer Science and Software Engineering, , AL 36849, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auburn University Department of Computer Science and Software Engineering, , AL 36849, USA","institution_ids":["https://openalex.org/I82497590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102886561","display_name":"Bang Tran","orcid":"https://orcid.org/0000-0002-4898-8930"},"institutions":[{"id":"https://openalex.org/I43522216","display_name":"California State University, Sacramento","ror":"https://ror.org/03e26wv14","country_code":"US","type":"education","lineage":["https://openalex.org/I43522216"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bang Tran","raw_affiliation_strings":["California State University, Sacramento Department of Computer Science, , CA 95819, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"California State University, Sacramento Department of Computer Science, , CA 95819, USA","institution_ids":["https://openalex.org/I43522216"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057906211","display_name":"Juli Petereit","orcid":"https://orcid.org/0000-0002-8017-3280"},"institutions":[{"id":"https://openalex.org/I134113660","display_name":"University of Nevada, Reno","ror":"https://ror.org/01keh0577","country_code":"US","type":"education","lineage":["https://openalex.org/I134113660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Juli Petereit","raw_affiliation_strings":["University of Nevada, Reno Nevada Bioinformatics Center, , NV 89557, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Nevada, Reno Nevada Bioinformatics Center, , NV 89557, USA","institution_ids":["https://openalex.org/I134113660"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018043372","display_name":"Tin Nguyen","orcid":"https://orcid.org/0000-0001-8001-9470"},"institutions":[{"id":"https://openalex.org/I82497590","display_name":"Auburn University","ror":"https://ror.org/02v80fc35","country_code":"US","type":"education","lineage":["https://openalex.org/I82497590"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tin Nguyen","raw_affiliation_strings":["Auburn University Department of Computer Science and Software Engineering, , AL 36849, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auburn University Department of Computer Science and Software Engineering, , AL 36849, USA","institution_ids":["https://openalex.org/I82497590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":4.6946,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.95820263,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"25","issue":"Supplement_1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9891999959945679,"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/sandbox","display_name":"Sandbox (software development)","score":0.7868428230285645},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7708767056465149},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.6917194724082947},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4620012938976288},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4381347894668579},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3457478880882263},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32455289363861084},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.16632547974586487},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12847083806991577}],"concepts":[{"id":"https://openalex.org/C167981075","wikidata":"https://www.wikidata.org/wiki/Q2667186","display_name":"Sandbox (software development)","level":2,"score":0.7868428230285645},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7708767056465149},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.6917194724082947},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4620012938976288},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4381347894668579},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3457478880882263},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32455289363861084},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.16632547974586487},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12847083806991577},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","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":"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":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae222","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae222","pdf_url":"https://academic.oup.com/bib/article-pdf/25/Supplement_1/bbae222/58618835/bbae222.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39041916","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39041916","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11264295","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11264295","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11264295/pdf/bbae222.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae222","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae222","pdf_url":"https://academic.oup.com/bib/article-pdf/25/Supplement_1/bbae222/58618835/bbae222.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3797595049","display_name":null,"funder_award_id":"2343019 and 2203236","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5242985691","display_name":null,"funder_award_id":"GM103440 and 1R44GM152152-01","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G568089319","display_name":null,"funder_award_id":"1U01CA274573-01A1","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G926880157","display_name":null,"funder_award_id":"80NSSC22M0255","funder_id":"https://openalex.org/F4320306101","funder_display_name":"National Aeronautics and Space Administration"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306101","display_name":"National Aeronautics and Space Administration","ror":"https://ror.org/027ka1x80"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4400918440.pdf","grobid_xml":"https://content.openalex.org/works/W4400918440.grobid-xml"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W34846693","https://openalex.org/W1583341569","https://openalex.org/W1998902445","https://openalex.org/W1999895438","https://openalex.org/W2020541351","https://openalex.org/W2020859582","https://openalex.org/W2027895157","https://openalex.org/W2040957831","https://openalex.org/W2094953050","https://openalex.org/W2100239923","https://openalex.org/W2100471807","https://openalex.org/W2100980426","https://openalex.org/W2103017472","https://openalex.org/W2112220625","https://openalex.org/W2114104545","https://openalex.org/W2121169932","https://openalex.org/W2129099812","https://openalex.org/W2139036189","https://openalex.org/W2146026944","https://openalex.org/W2158323345","https://openalex.org/W2159482845","https://openalex.org/W2167980479","https://openalex.org/W2179438025","https://openalex.org/W2255394077","https://openalex.org/W2330406605","https://openalex.org/W2466314544","https://openalex.org/W2521492299","https://openalex.org/W2559588208","https://openalex.org/W2758934854","https://openalex.org/W2785694006","https://openalex.org/W2946173685","https://openalex.org/W2963367647","https://openalex.org/W2975424845","https://openalex.org/W2979832776","https://openalex.org/W2995336440","https://openalex.org/W3004890574","https://openalex.org/W3089451699","https://openalex.org/W3093535455","https://openalex.org/W3099862724","https://openalex.org/W3112600195","https://openalex.org/W3121573178","https://openalex.org/W3139511935","https://openalex.org/W3165022492","https://openalex.org/W3192940627","https://openalex.org/W4220973174","https://openalex.org/W4241872665","https://openalex.org/W4252684946","https://openalex.org/W4253759977","https://openalex.org/W4255375128","https://openalex.org/W4288070228","https://openalex.org/W4293109331","https://openalex.org/W4294216483","https://openalex.org/W4306640162","https://openalex.org/W4388034160","https://openalex.org/W4388539829","https://openalex.org/W4394819521","https://openalex.org/W4403240373","https://openalex.org/W6719957963","https://openalex.org/W6768074067","https://openalex.org/W6771384282","https://openalex.org/W6785161123","https://openalex.org/W6865076397","https://openalex.org/W6873209535"],"related_works":["https://openalex.org/W2033352828","https://openalex.org/W2355810117","https://openalex.org/W3098313552","https://openalex.org/W70177500","https://openalex.org/W2546418048","https://openalex.org/W2076427967","https://openalex.org/W3212184609","https://openalex.org/W2499283203","https://openalex.org/W2795849205","https://openalex.org/W2111618996"],"abstract_inverted_index":{"This":[0,275,318],"manuscript":[1,276],"describes":[2,277],"the":[3,64,71,77,173,187,253,278,302,307,313,324],"development":[4,279],"of":[5,12,66,73,79,107,164,230,280,287,301,315,326],"a":[6,13,84,105,135,281,288],"resource":[7,282],"module":[8,24,138,162,251,269,283,319],"that":[9,37,109,139,168,284,336],"is":[10,49,104,270,285,304],"part":[11,286],"learning":[14,26,289,321],"platform":[15,290],"named":[16,291],"'NIGMS":[17],"Sandbox":[18,293,303,310],"for":[19,42,92,172,243,255,294,341],"Cloud-based":[20,29,295],"Learning'":[21],"(https://github.com/NIGMS/NIGMS-Sandbox).":[22],"The":[23,160,250,268,298],"delivers":[25,320],"materials":[27,322],"on":[28,82,323],"Consensus":[30],"Pathway":[31,47],"Analysis":[32],"in":[33,306,332],"an":[34,333],"interactive":[35,334],"format":[36,335],"uses":[38,337],"appropriate":[39,338],"cloud":[40,339],"resources":[41,340],"data":[43,331,342],"access":[44,343],"and":[45,76,97,120,152,157,185,206,224,226,240,265,328,344],"analyses.":[46,232,345],"analysis":[48,69,100,114,122,147,193,211,254,325],"important":[50],"because":[51],"it":[52,89],"allows":[53],"us":[54],"to":[55,95,112,124,149,245],"gain":[56],"insights":[57],"into":[58],"biological":[59],"mechanisms":[60],"underlying":[61],"conditions.":[62],"But":[63],"availability":[65],"many":[67,256],"pathway":[68,99,146,202,210],"methods,":[70],"requirement":[72],"coding":[74],"skills,":[75],"focus":[78],"current":[80],"tools":[81,108],"only":[83],"few":[85],"species":[86],"all":[87],"make":[88],"very":[90],"difficult":[91],"biomedical":[93],"researchers":[94,111,153],"self-learn":[96],"perform":[98,181,209],"efficiently.":[101],"Furthermore,":[102],"there":[103],"lack":[106],"allow":[110],"compare":[113,186],"results":[115,142,188,229],"obtained":[116,189],"from":[117,190],"different":[118,121],"experiments":[119],"methods":[123,194,214],"find":[125],"consensus":[126,141],"results.":[127],"To":[128],"address":[129],"these":[130],"challenges,":[131],"we":[132],"have":[133],"designed":[134],"cloud-based,":[136],"self-learning":[137],"provides":[140],"among":[143],"established,":[144],"state-of-the-art":[145],"techniques":[148],"provide":[150,169,235],"students":[151],"with":[154],"necessary":[155],"training":[156,161],"example":[158],"materials.":[159],"consists":[163],"five":[165],"Jupyter":[166,248],"Notebooks":[167],"complete":[170,246],"tutorials":[171],"following":[174],"tasks:":[175],"(i)":[176],"process":[177,200],"expression":[178],"data,":[179],"(ii)":[180],"differential":[182,192],"analysis,":[183],"visualize":[184],"four":[191],"(limma,":[195],"t-test,":[196],"edgeR,":[197],"DESeq2),":[198],"(iii)":[199],"three":[201],"databases":[203],"(GO,":[204],"KEGG":[205],"Reactome),":[207],"(iv)":[208],"using":[212],"eight":[213],"(ORA,":[215],"CAMERA,":[216],"KS":[217],"test,":[218,220],"Wilcoxon":[219],"FGSEA,":[221],"GSA,":[222],"SAFE":[223],"PADOG)":[225],"(v)":[227],"combine":[228],"multiple":[231],"We":[233],"also":[234],"examples,":[236],"source":[237],"code,":[238],"explanations":[239],"instructional":[241],"videos":[242],"trainees":[244],"each":[247],"Notebook.":[249],"supports":[252],"model":[257],"(e.g.":[258],"human,":[259],"mouse,":[260],"fruit":[261],"fly,":[262],"zebra":[263],"fish)":[264],"non-model":[266],"species.":[267],"publicly":[271],"available":[272],"at":[273,312],"https://github.com/NIGMS/Consensus-Pathway-Analysis-in-the-Cloud.":[274],"``NIGMS":[292],"Learning''":[296],"https://github.com/NIGMS/NIGMS-Sandbox.":[297],"overall":[299],"genesis":[300],"described":[305],"editorial":[308],"NIGMS":[309],"[1]":[311],"beginning":[314],"this":[316],"Supplement.":[317],"bulk":[327],"single-cell":[329],"ATAC-seq":[330]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
