{"id":"https://openalex.org/W2008952705","doi":"https://doi.org/10.1145/2147805.2147865","title":"Topology aware coloring of gene regulatory networks","display_name":"Topology aware coloring of gene regulatory networks","publication_year":2011,"publication_date":"2011-08-01","ids":{"openalex":"https://openalex.org/W2008952705","doi":"https://doi.org/10.1145/2147805.2147865","mag":"2008952705"},"language":"en","primary_location":{"id":"doi:10.1145/2147805.2147865","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2147805.2147865","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine","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/A5000929673","display_name":"G\u00fcnhan G\u00fclsoy","orcid":"https://orcid.org/0000-0001-8482-2930"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"G\u00fcnhan G\u00fclsoy","raw_affiliation_strings":["University of Florida, Gainesville, Florida"],"affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, Florida","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Bhavik Gandhi","orcid":null},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bhavik Gandhi","raw_affiliation_strings":["University of Florida, Gainesville, Florida"],"affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, Florida","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091769289","display_name":"Tamer Kahveci","orcid":"https://orcid.org/0000-0002-4403-8612"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tamer Kahveci","raw_affiliation_strings":["University of Florida, Gainesville, Florida"],"affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, Florida","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5000929673"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":null,"apc_paid":null,"fwci":0.2668,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.57897786,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"435","last_page":"440"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"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":0.9995999932289124,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9990000128746033,"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":0.9987000226974487,"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/subnetwork","display_name":"Subnetwork","score":0.9310042858123779},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6251567602157593},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.5113775134086609},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5033506751060486},{"id":"https://openalex.org/keywords/upper-and-lower-bounds","display_name":"Upper and lower bounds","score":0.45218178629875183},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.448533833026886},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.35919904708862305},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3583717346191406},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.31568610668182373},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.18162256479263306},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.10432356595993042}],"concepts":[{"id":"https://openalex.org/C2780186347","wikidata":"https://www.wikidata.org/wiki/Q11414","display_name":"Subnetwork","level":2,"score":0.9310042858123779},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6251567602157593},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.5113775134086609},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5033506751060486},{"id":"https://openalex.org/C77553402","wikidata":"https://www.wikidata.org/wiki/Q13222579","display_name":"Upper and lower bounds","level":2,"score":0.45218178629875183},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.448533833026886},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.35919904708862305},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3583717346191406},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.31568610668182373},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.18162256479263306},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.10432356595993042},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2147805.2147865","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2147805.2147865","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1600879148","display_name":null,"funder_award_id":"CCF-0829867IIS-084543","funder_id":"https://openalex.org/F4320337389","funder_display_name":"Division of Information and Intelligent Systems"},{"id":"https://openalex.org/G7017548324","display_name":null,"funder_award_id":"CCF-0829867IIS-084543","funder_id":"https://openalex.org/F4320337387","funder_display_name":"Division of Computing and Communication Foundations"}],"funders":[{"id":"https://openalex.org/F4320337387","display_name":"Division of Computing and Communication Foundations","ror":"https://ror.org/01mng8331"},{"id":"https://openalex.org/F4320337389","display_name":"Division of Information and Intelligent Systems","ror":"https://ror.org/053a2cp42"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W118615843","https://openalex.org/W1598875832","https://openalex.org/W1788277699","https://openalex.org/W1966893452","https://openalex.org/W1994303884","https://openalex.org/W1995070820","https://openalex.org/W2036265926","https://openalex.org/W2055043387","https://openalex.org/W2104009289","https://openalex.org/W2104315543","https://openalex.org/W2110017370","https://openalex.org/W2121773288","https://openalex.org/W2122144032","https://openalex.org/W2148944713","https://openalex.org/W2153929049","https://openalex.org/W2159482845","https://openalex.org/W2167222948","https://openalex.org/W2296148711","https://openalex.org/W3154566661"],"related_works":["https://openalex.org/W2898995567","https://openalex.org/W2905900507","https://openalex.org/W1976893754","https://openalex.org/W2355358221","https://openalex.org/W2092179621","https://openalex.org/W2154096597","https://openalex.org/W4312405462","https://openalex.org/W2016688501","https://openalex.org/W2130341600","https://openalex.org/W2111494768"],"abstract_inverted_index":{"We":[0,27,171],"consider":[1],"the":[2,18,31,35,38,58,68,74,83,128,133,139,168,208,211,214],"problem":[3,56],"of":[4,67,76,124,141,183,204,213],"finding":[5],"a":[6,9,22,43,65,93,102,111,116,121,148,151,192,202],"subnetwork":[7,36],"in":[8,57,120,138,210],"given":[10,23],"biological":[11],"network":[12,85,144,194],"(i.e.,":[13,34],"target":[14,84,143],"network)":[15],"that":[16,72,114,161,177,182],"is":[17,48,97,110,188],"most":[19],"similar":[20],"to":[21,29,54,87,150,164,166],"small":[24,122],"query":[25],"network.":[26],"aim":[28],"find":[30],"optimal":[32,169],"solution":[33,53],"with":[37,42],"largest":[39],"alignment":[40,88,195],"score)":[41],"provable":[44,117],"confidence":[45,96,118,209],"bound.":[46],"There":[47],"no":[49],"known":[50],"polynomial":[51],"time":[52],"this":[55,77],"literature.":[59],"Alon":[60,184],"et":[61,185],"al.":[62,186],"has":[63],"developed":[64],"state":[66],"art":[69],"coloring":[70,104,108,179],"method":[71,80,131,180],"reduces":[73],"cost":[75],"problem.":[78],"This":[79,153],"randomly":[81],"colors":[82],"prior":[86],"for":[89],"many":[90,158],"iterations":[91,125],"until":[92],"user":[94],"supplied":[95],"reached.":[98],"Here":[99],"we":[100],"develop":[101],"novel":[103],"method,":[105],"named":[106],"k-hop":[107],"(k":[109],"positive":[112],"integer),":[113],"achieves":[115],"value":[119],"number":[123,193],"without":[126,206],"sacrificing":[127],"optimality.":[129],"Our":[130],"considers":[132],"color":[134,149,159],"assignments":[135,160],"already":[136],"made":[137],"neighborhood":[140],"each":[142],"node":[145],"while":[146],"assigning":[147],"node.":[152],"way,":[154],"it":[155],"preemptively":[156],"avoids":[157],"are":[162],"guaranteed":[163],"fail":[165],"produce":[167],"alignment.":[170],"demonstrate":[172],"both":[173],"theoretically":[174],"and":[175,199],"experimentally":[176],"our":[178],"outperforms":[181],"which":[187],"also":[189],"used":[190],"by":[191,201],"methods":[196],"including":[197],"QPath":[198],"QNet":[200],"factor":[203],"three":[205],"reducing":[207],"optimality":[212],"result.":[215]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-17T18:11:37.981687","created_date":"2025-10-10T00:00:00"}