{"id":"https://openalex.org/W2038412002","doi":"https://doi.org/10.1145/1854776.1854804","title":"Enzymatic target identification with dynamic states","display_name":"Enzymatic target identification with dynamic states","publication_year":2010,"publication_date":"2010-08-02","ids":{"openalex":"https://openalex.org/W2038412002","doi":"https://doi.org/10.1145/1854776.1854804","mag":"2038412002"},"language":"en","primary_location":{"id":"doi:10.1145/1854776.1854804","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1854776.1854804","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology","raw_type":"proceedings-article"},"type":"conference-paper","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/A5109856138","display_name":"Bin Song","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":"Bin Song","raw_affiliation_strings":["University of Florida, Gainesville, FL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, FL","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077570468","display_name":"Sanjay Ranka","orcid":"https://orcid.org/0000-0003-4886-1988"},"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":"Sanjay Ranka","raw_affiliation_strings":["University of Florida, Gainesville, FL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, FL","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, FL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Florida, Gainesville, FL","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.14128843,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"180","last_page":"187"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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":0.992900013923645,"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/T10404","display_name":"Enzyme Catalysis and Immobilization","score":0.9922000169754028,"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/euclidean-distance","display_name":"Euclidean distance","score":0.6673483848571777},{"id":"https://openalex.org/keywords/dynamic-time-warping","display_name":"Dynamic time warping","score":0.6557053327560425},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5583074688911438},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.546831488609314},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.5162091851234436},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4822467267513275},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.45088469982147217},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.342600554227829},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.31393715739250183},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1461125910282135}],"concepts":[{"id":"https://openalex.org/C120174047","wikidata":"https://www.wikidata.org/wiki/Q847073","display_name":"Euclidean distance","level":2,"score":0.6673483848571777},{"id":"https://openalex.org/C88516994","wikidata":"https://www.wikidata.org/wiki/Q1268863","display_name":"Dynamic time warping","level":2,"score":0.6557053327560425},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5583074688911438},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.546831488609314},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.5162091851234436},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4822467267513275},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.45088469982147217},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.342600554227829},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.31393715739250183},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1461125910282135},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"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":2,"locations":[{"id":"doi:10.1145/1854776.1854804","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1854776.1854804","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.226.627","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.226.627","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cise.ufl.edu/%7Etamer/papers/bcb2010c.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3587627760","display_name":null,"funder_award_id":"CCF-0829867IIS-0845439","funder_id":"https://openalex.org/F4320337389","funder_display_name":"Division of Information and Intelligent Systems"},{"id":"https://openalex.org/G7598697537","display_name":null,"funder_award_id":"CCF-0829867IIS-0845439","funder_id":"https://openalex.org/F4320337387","funder_display_name":"Division of Computing and Communication Foundations"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"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":22,"referenced_works":["https://openalex.org/W1483118642","https://openalex.org/W1510585142","https://openalex.org/W1529898704","https://openalex.org/W1825789202","https://openalex.org/W2000040887","https://openalex.org/W2006672203","https://openalex.org/W2025399691","https://openalex.org/W2026089579","https://openalex.org/W2037718952","https://openalex.org/W2038012397","https://openalex.org/W2048596643","https://openalex.org/W2049025340","https://openalex.org/W2082948758","https://openalex.org/W2100818174","https://openalex.org/W2122144032","https://openalex.org/W2123027770","https://openalex.org/W2126176298","https://openalex.org/W2128572161","https://openalex.org/W2130364940","https://openalex.org/W2159201347","https://openalex.org/W4290864872","https://openalex.org/W4295816494"],"related_works":["https://openalex.org/W3111157199","https://openalex.org/W3118503757","https://openalex.org/W2760717005","https://openalex.org/W2163118894","https://openalex.org/W58346954","https://openalex.org/W2359638073","https://openalex.org/W3009759344","https://openalex.org/W1545076181","https://openalex.org/W2086226917","https://openalex.org/W4281630436"],"abstract_inverted_index":{"As":[0],"a":[1,6,9,12,67,100,107,122,197,209,230,278],"metabolic":[2,47,82],"network":[3,34],"reaches":[4],"from":[5],"state":[7,40,65,94,124,227,244],"to":[8,36,55,112,126,135,159,189,202,212,233,282],"steady":[10,39,64],"state,":[11,27],"subset":[13],"of":[14,21,77,92,96,106,116,169,183,217,270,280],"its":[15],"fluxes":[16,105],"gradually":[17],"change.":[18],"The":[19],"sequence":[20],"intermediate":[22,51],"states,":[23],"called":[24],"the":[25,29,32,38,50,62,75,89,93,97,104,114,137,145,156,160,170,174,184,192,214,224,234,241,251,268],"dynamic":[26,90,123,141,226,238,243,275],"shows":[28],"pattern":[30,43,102,151,172],"that":[31,119,127,255,263],"underlying":[33],"follows":[35],"reach":[37],"Understanding":[41],"this":[42,71,204],"is":[44,66,245],"crucial":[45],"for":[46,103,167,274],"engineering":[48],"as":[49,59],"states":[52,239,276],"can":[53],"lead":[54],"undesired":[56],"effects":[57],"such":[58],"toxicity":[60],"although":[61],"final":[63],"desired":[68],"one.":[69],"In":[70],"paper,":[72],"we":[73,87,110],"consider":[74,88,131],"problem":[76],"enzymatic":[78],"target":[79],"identification":[80],"in":[81,173,187,191],"networks.":[83,98],"Unlike":[84],"existing":[85],"strategies,":[86],"behavior":[91],"changes":[95],"Given":[99],"goal":[101,128,162,171,185],"given":[108],"network,":[109],"aim":[111],"find":[113],"set":[115],"enzyme":[117],"knockouts":[118],"will":[120],"produce":[121],"similar":[125],"pattern.":[129],"We":[130,195,206],"three":[132],"distance":[133,149,154,165,178,235],"functions":[134],"measure":[136],"difference":[138],"between":[139,236],"two":[140,237],"states.":[142],"These":[143],"are":[144],"Euclidean":[146,153],"distance,":[147],"time-warping":[148],"and":[150,181,199],"distance.":[152],"restricts":[155],"solution":[157],"space":[158],"exact":[161],"state.":[163],"Time-warping":[164],"allows":[166,179],"stretching":[168,190],"time":[175,193,216,271],"domain.":[176,194],"Pattern":[177],"scaling":[180],"shifting":[182],"flux":[186],"addition":[188],"provide":[196],"branch":[198],"bound":[200,232],"method":[201,257],"solve":[203],"problem.":[205],"also":[207,261],"develop":[208],"partitioning":[210,265],"strategy":[211,221,266],"reduce":[213],"running":[215],"our":[218,256,264],"method.":[219],"This":[220],"avoids":[222],"constructing":[223],"entire":[225,242],"by":[228,277],"computing":[229],"lower":[231],"when":[240],"not":[246],"available.":[247],"Our":[248],"experiments":[249],"on":[250],"purine":[252],"metabolism":[253],"show":[254,262],"runs":[258],"accurately.":[259],"They":[260],"reduces":[267],"number":[269],"intervals":[272],"computed":[273],"factor":[279],"2":[281],"6.":[283]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}