{"id":"https://openalex.org/W2042061300","doi":"https://doi.org/10.1145/1217666.1217672","title":"Modeling protein dependency networks using CoCoA","display_name":"Modeling protein dependency networks using CoCoA","publication_year":2006,"publication_date":"2006-09-01","ids":{"openalex":"https://openalex.org/W2042061300","doi":"https://doi.org/10.1145/1217666.1217672","mag":"2042061300"},"language":"en","primary_location":{"id":"doi:10.1145/1217666.1217672","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1217666.1217672","pdf_url":null,"source":{"id":"https://openalex.org/S4210181451","display_name":"XRDS Crossroads The ACM Magazine for Students","issn_l":"1528-4972","issn":["1528-4972","1528-4980"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"XRDS: Crossroads, The ACM Magazine for Students","raw_type":"journal-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/A5064243391","display_name":"Grey Ballard","orcid":"https://orcid.org/0000-0003-1557-8027"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Grey Ballard","raw_affiliation_strings":[""],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5064243391"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10132318,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"13","issue":"1","first_page":"6","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9988999962806702,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9988999962806702,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987999796867371,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.996399998664856,"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/dependency","display_name":"Dependency (UML)","score":0.77790367603302},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.616684079170227},{"id":"https://openalex.org/keywords/measure","display_name":"Measure (data warehouse)","score":0.5804270505905151},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4683135449886322},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4248952567577362},{"id":"https://openalex.org/keywords/algebraic-number","display_name":"Algebraic number","score":0.4221349358558655},{"id":"https://openalex.org/keywords/voting","display_name":"Voting","score":0.41570913791656494},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3005262315273285},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2905116677284241},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2649635970592499}],"concepts":[{"id":"https://openalex.org/C19768560","wikidata":"https://www.wikidata.org/wiki/Q320727","display_name":"Dependency (UML)","level":2,"score":0.77790367603302},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.616684079170227},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.5804270505905151},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4683135449886322},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4248952567577362},{"id":"https://openalex.org/C9376300","wikidata":"https://www.wikidata.org/wiki/Q168817","display_name":"Algebraic number","level":2,"score":0.4221349358558655},{"id":"https://openalex.org/C520049643","wikidata":"https://www.wikidata.org/wiki/Q189760","display_name":"Voting","level":3,"score":0.41570913791656494},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3005262315273285},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2905116677284241},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2649635970592499},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/1217666.1217672","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1217666.1217672","pdf_url":null,"source":{"id":"https://openalex.org/S4210181451","display_name":"XRDS Crossroads The ACM Magazine for Students","issn_l":"1528-4972","issn":["1528-4972","1528-4980"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"XRDS: Crossroads, The ACM Magazine for Students","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309558","display_name":"Wake Forest University","ror":"https://ror.org/0207ad724"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W1993503466","https://openalex.org/W2007409747","https://openalex.org/W2018615018","https://openalex.org/W2068182415","https://openalex.org/W2090814356","https://openalex.org/W2156841851"],"related_works":["https://openalex.org/W4255837520","https://openalex.org/W2067317451","https://openalex.org/W4211085505","https://openalex.org/W2387011115","https://openalex.org/W2154771632","https://openalex.org/W2084758217","https://openalex.org/W3122478268","https://openalex.org/W408804804","https://openalex.org/W4234808182","https://openalex.org/W3086365953"],"abstract_inverted_index":{"In":[0,160],"an":[1],"interdisciplinary":[2],"effort":[3],"to":[4,31,40,51,66,83,98,123],"model":[5],"protein":[6,33,89],"dependency":[7,34],"networks,":[8],"biologists":[9],"measure":[10,42,99],"signals":[11],"from":[12],"certain":[13],"proteins":[14,46],"within":[15],"cells":[16],"over":[17,47],"a":[18,127],"given":[19,45],"interval":[20],"of":[21,78,80,94,102,106,133,137,172,180],"time.":[22],"Using":[23],"this":[24,150,161],"time":[25,48],"series":[26],"data,":[27],"the":[28,81,91,100,117,121,134,138,145,165,167,170,173,178,181],"goal":[29],"is":[30,39],"deduce":[32],"relationships.":[35,54],"The":[36,108],"mathematical":[37],"challenges":[38],"statistically":[41],"correlations":[43,103],"between":[44,104],"in":[49,64,126,149,175],"order":[50,65],"conjecture":[52],"probable":[53],"Biologists":[55],"can":[56],"then":[57],"consider":[58],"these":[59],"relationships":[60,75],"with":[61,116],"more":[62,128,158],"scrutiny,":[63],"confirm":[67],"their":[68],"conjectures.":[69],"One":[70],"algorithm":[71,109,122,146,174],"for":[72,87],"finding":[73],"such":[74],"makes":[76],"use":[77],"interpolation":[79],"data":[82],"produce":[84],"next-state":[85],"functions":[86],"each":[88],"and":[90,152,177],"Deegan-Packel":[92],"Index":[93],"Power":[95],"voting":[96],"method":[97],"strength":[101],"pairs":[105],"proteins.":[107],"was":[110,147],"previously":[111],"implemented,":[112],"but":[113],"limitations":[114],"associated":[115],"original":[118],"language":[119],"required":[120],"be":[124],"re-implemented":[125,148],"computationally":[129],"efficient":[130],"language.":[131],"Because":[132],"algebraic":[135],"focus":[136],"Computational":[139],"Commutative":[140],"Algebra":[141],"language,":[142,151,169],"or":[143],"CoCoA,":[144,176],"results":[153],"have":[154],"been":[155],"produced":[156],"much":[157],"efficiently.":[159],"paper":[162],"I":[163],"discuss":[164],"algorithm,":[166],"CoCoA":[168],"implementation":[171],"quality":[179],"results.":[182]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
