{"id":"https://openalex.org/W2103734240","doi":"https://doi.org/10.1109/csb.2003.1227430","title":"A contradiction-based framework for testing gene regulation hypotheses","display_name":"A contradiction-based framework for testing gene regulation hypotheses","publication_year":2004,"publication_date":"2004-03-30","ids":{"openalex":"https://openalex.org/W2103734240","doi":"https://doi.org/10.1109/csb.2003.1227430","mag":"2103734240"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2003.1227430","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227430","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046262641","display_name":"Stephen Racunas","orcid":null},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"S. Racunas","raw_affiliation_strings":["Pennsylvania State University, USA","Pennsylvania State University, University Park, PA, USA"],"affiliations":[{"raw_affiliation_string":"Pennsylvania State University, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Pennsylvania State University, University Park, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041175834","display_name":"Nigam H. Shah","orcid":"https://orcid.org/0000-0001-9385-7158"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"N. Shah","raw_affiliation_strings":["Pennsylvania State University, USA","Pennsylvania State University, University Park, PA, USA"],"affiliations":[{"raw_affiliation_string":"Pennsylvania State University, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Pennsylvania State University, University Park, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042977462","display_name":"Nina V. Fedoroff","orcid":"https://orcid.org/0000-0002-9028-1701"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"N.V. Fedoroff","raw_affiliation_strings":["Pennsylvania State University, USA","Pennsylvania State University, University Park, PA, USA"],"affiliations":[{"raw_affiliation_string":"Pennsylvania State University, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Pennsylvania State University, University Park, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5046262641"],"corresponding_institution_ids":["https://openalex.org/I130769515"],"apc_list":null,"apc_paid":null,"fwci":0.3508,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.57790079,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"9","issue":null,"first_page":"634","last_page":"638"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9962999820709229,"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":0.9962999820709229,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9962000250816345,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9958999752998352,"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/contradiction","display_name":"Contradiction","score":0.7328565120697021},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7135785818099976},{"id":"https://openalex.org/keywords/formalism","display_name":"Formalism (music)","score":0.5467754602432251},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5192853808403015},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.48696908354759216},{"id":"https://openalex.org/keywords/convergence","display_name":"Convergence (economics)","score":0.42964038252830505},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3802562952041626},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35006222128868103},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3471652567386627},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18107718229293823}],"concepts":[{"id":"https://openalex.org/C2776728590","wikidata":"https://www.wikidata.org/wiki/Q363948","display_name":"Contradiction","level":2,"score":0.7328565120697021},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7135785818099976},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.5467754602432251},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5192853808403015},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.48696908354759216},{"id":"https://openalex.org/C2777303404","wikidata":"https://www.wikidata.org/wiki/Q759757","display_name":"Convergence (economics)","level":2,"score":0.42964038252830505},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3802562952041626},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35006222128868103},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3471652567386627},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18107718229293823},{"id":"https://openalex.org/C50522688","wikidata":"https://www.wikidata.org/wiki/Q189833","display_name":"Economic growth","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C558565934","wikidata":"https://www.wikidata.org/wiki/Q2743","display_name":"Musical","level":2,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/csb.2003.1227430","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2003.1227430","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1763161027","https://openalex.org/W2004975621","https://openalex.org/W2059057465","https://openalex.org/W2101011890","https://openalex.org/W2103017472","https://openalex.org/W2116027790","https://openalex.org/W2121775312","https://openalex.org/W2160948978","https://openalex.org/W2161036175","https://openalex.org/W2798619248","https://openalex.org/W6750398542"],"related_works":["https://openalex.org/W2381825231","https://openalex.org/W2377933838","https://openalex.org/W2348916262","https://openalex.org/W4210310594","https://openalex.org/W2330422317","https://openalex.org/W2354224618","https://openalex.org/W2354172502","https://openalex.org/W2391836570","https://openalex.org/W2361796009","https://openalex.org/W2392027916"],"abstract_inverted_index":{"We":[0,48,77],"have":[1,49,78],"developed":[2,50,79],"a":[3,20,39,80,100],"mathematical":[4,107],"framework":[5],"for":[6,55],"representing":[7],"and":[8,14,24,36,69,93,118],"testing":[9],"hypotheses":[10],"about":[11,90,116],"gene,":[12],"protein,":[13],"signaling":[15],"molecule":[16],"interactions.":[17],"It":[18],"takes":[19],"hierarchical,":[21],"contradiction-based":[22],"approach,":[23],"can":[25],"make":[26,87,113],"use":[27],"of":[28,46,58,96,99],"multiple":[29],"data":[30],"sources":[31],"to":[32,37,74,86,112],"assess":[33],"hypothesis":[34,91],"viability":[35,40],"generate":[38],"partial":[41],"order":[42],"over":[43],"the":[44,56,94],"space":[45],"hypotheses.":[47,60],"an":[51],"event-based":[52],"formal":[53],"language":[54,62],"expression":[57],"such":[59],"This":[61],"seamlessly":[63],"integrates":[64],"regulatory":[65],"diagrams":[66],"(graphical":[67],"inputs)":[68],"structured":[70],"English":[71],"(text":[72],"input)":[73],"maximize":[75],"flexibility.":[76],"pre-topological":[81],"formalism":[82],"that":[83,109],"allows":[84,110],"us":[85,111],"precise":[88,114],"statements":[89,115],"similarity":[92],"convergence":[95],"iterative":[97],"refinements":[98],"base":[101],"hypothesis.":[102],"To":[103],"this,":[104],"we":[105],"add":[106],"machinery":[108],"control":[117],"regulation.":[119]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}