{"id":"https://openalex.org/W2255404115","doi":null,"title":"Comparative and Evolutionary Analysis of Cellular Pathways","display_name":"Comparative and Evolutionary Analysis of Cellular Pathways","publication_year":2007,"publication_date":"2007-01-01","ids":{"openalex":"https://openalex.org/W2255404115","mag":"2255404115"},"language":"en","primary_location":{"id":"pmh:oai:CiteSeerX.psu:10.1.1.318.3265","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.318.3265","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.eecs.berkeley.edu/Pubs/TechRpts/2007/EECS-2007-141.pdf","raw_type":"text"},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"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/A5077782872","display_name":"Manikandan Narayanan","orcid":"https://orcid.org/0000-0002-8490-4087","observed_orcids":["https://orcid.org/0000-0002-8490-4087"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Manikandan Narayanan","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-8490-4087","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5077782872"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.9994999766349792,"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":0.9994999766349792,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0003000000142492354,"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":9.999999747378752e-05,"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/protein-protein-interaction-network","display_name":"protein-protein interaction network","score":0.9570000171661377},{"id":"https://openalex.org/keywords/graph-matching","display_name":"graph matching","score":0.906000018119812},{"id":"https://openalex.org/keywords/function-prediction","display_name":"functional prediction","score":0.7850000262260437},{"id":"https://openalex.org/keywords/tricarboxylic-acid-cycle","display_name":"TCA cycle","score":0.8980000019073486},{"id":"https://openalex.org/keywords/chemotaxis","display_name":"chemotaxis","score":0.949999988079071},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"comparative genomics","score":0.5960000157356262},{"id":"https://openalex.org/keywords/cell-phenotype","display_name":"cell phenotype","score":0.5220000147819519}],"concepts":[{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4570898711681366},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38077512383461},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3434954881668091},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34097662568092346}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:CiteSeerX.psu:10.1.1.318.3265","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.318.3265","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.eecs.berkeley.edu/Pubs/TechRpts/2007/EECS-2007-141.pdf","raw_type":"text"},{"id":"pmh:oai:berkeley.edu:28722-bk0000m3x4r","doi":null,"is_oa":false,"landing_page_url":"http://techreports.lib.berkeley.edu/accessPages/EECS-2007-141.html","pdf_url":null,"source":{"id":"https://openalex.org/S7407050879","display_name":"UC Berkeley","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I95457486","host_organization_name":"University of California, Berkeley","host_organization_lineage":["https://openalex.org/I95457486"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"technical reports"},{"id":"mag:2255404115","doi":null,"is_oa":false,"landing_page_url":"https://www.eecs.berkeley.edu/Pubs/TechRpts/2007/EECS-2007-141.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":126,"referenced_works":["https://openalex.org/W85880394","https://openalex.org/W962305203","https://openalex.org/W1480196627","https://openalex.org/W1480928214","https://openalex.org/W1490937614","https://openalex.org/W1509280691","https://openalex.org/W1509476036","https://openalex.org/W1512943765","https://openalex.org/W1529892973","https://openalex.org/W1568333329","https://openalex.org/W1572663059","https://openalex.org/W1578330309","https://openalex.org/W1581844353","https://openalex.org/W1601296974","https://openalex.org/W1604293137","https://openalex.org/W1604959358","https://openalex.org/W1644749979","https://openalex.org/W1746680969","https://openalex.org/W1759780789","https://openalex.org/W1783384641","https://openalex.org/W1793943890","https://openalex.org/W1814665366","https://openalex.org/W1920973730","https://openalex.org/W1966833356","https://openalex.org/W1967638691","https://openalex.org/W1969857637","https://openalex.org/W1970737407","https://openalex.org/W1971421925","https://openalex.org/W1980397590","https://openalex.org/W1984209790","https://openalex.org/W1984220047","https://openalex.org/W1984249061","https://openalex.org/W1990453950","https://openalex.org/W1993384523","https://openalex.org/W1994803330","https://openalex.org/W2002422491","https://openalex.org/W2003652380","https://openalex.org/W2009570821","https://openalex.org/W2011039300","https://openalex.org/W2013520054","https://openalex.org/W2018041072","https://openalex.org/W2023068097","https://openalex.org/W2027439534","https://openalex.org/W2029230311","https://openalex.org/W2037036397","https://openalex.org/W2041303239","https://openalex.org/W2050137450","https://openalex.org/W2050721857","https://openalex.org/W2053929098","https://openalex.org/W2055033601","https://openalex.org/W2065304353","https://openalex.org/W2068886104","https://openalex.org/W2078969200","https://openalex.org/W2079818352","https://openalex.org/W2081622831","https://openalex.org/W2081931663","https://openalex.org/W2084619201","https://openalex.org/W2087772354","https://openalex.org/W2100585269","https://openalex.org/W2101181377","https://openalex.org/W2101499441","https://openalex.org/W2103546861","https://openalex.org/W2104315543","https://openalex.org/W2104891575","https://openalex.org/W2106202847","https://openalex.org/W2107705503","https://openalex.org/W2112200469","https://openalex.org/W2113019448","https://openalex.org/W2113654464","https://openalex.org/W2115682970","https://openalex.org/W2116117181","https://openalex.org/W2116503869","https://openalex.org/W2119634475","https://openalex.org/W2121773288","https://openalex.org/W2123435633","https://openalex.org/W2124354935","https://openalex.org/W2124463526","https://openalex.org/W2124681451","https://openalex.org/W2124790653","https://openalex.org/W2125179362","https://openalex.org/W2125489655","https://openalex.org/W2126922170","https://openalex.org/W2127320825","https://openalex.org/W2127874029","https://openalex.org/W2130687290","https://openalex.org/W2132926880","https://openalex.org/W2133147430","https://openalex.org/W2135445920","https://openalex.org/W2136316164","https://openalex.org/W2136850043","https://openalex.org/W2137188869","https://openalex.org/W2138003801","https://openalex.org/W2140412523","https://openalex.org/W2142510328","https://openalex.org/W2146243727","https://openalex.org/W2146804513","https://openalex.org/W2150681269","https://openalex.org/W2151296292","https://openalex.org/W2152495216","https://openalex.org/W2154139219","https://openalex.org/W2155534524","https://openalex.org/W2159482845","https://openalex.org/W2159675211","https://openalex.org/W2160167256","https://openalex.org/W2162142896","https://openalex.org/W2162551958","https://openalex.org/W2164228620","https://openalex.org/W2164813401","https://openalex.org/W2165937624","https://openalex.org/W2166444569","https://openalex.org/W2166468869","https://openalex.org/W2166574880","https://openalex.org/W2167869241","https://openalex.org/W2168147993","https://openalex.org/W2171081680","https://openalex.org/W2296148711","https://openalex.org/W2432517183","https://openalex.org/W2484870474","https://openalex.org/W2491142891","https://openalex.org/W2913066018","https://openalex.org/W2981264952","https://openalex.org/W3094133439","https://openalex.org/W3147056755","https://openalex.org/W3199943451","https://openalex.org/W3216731846","https://openalex.org/W7099253376"],"related_works":["https://openalex.org/W1963597472","https://openalex.org/W1507669248","https://openalex.org/W2106202847","https://openalex.org/W2339207854","https://openalex.org/W1480196627","https://openalex.org/W194554374","https://openalex.org/W1984249061","https://openalex.org/W2104009289","https://openalex.org/W4405427575","https://openalex.org/W2541237469"],"abstract_inverted_index":{"Various":[0],"pathways":[1,76,100,151,167,247],"maintain":[2],"the":[3,48,65,78,111,122,131,135,139,148,169,191,200,214,218,242],"structure,":[4],"function":[5,161],"and":[6,11,38,57,67,118,143,157,176,259],"health":[7],"of":[8,51,69,75,80,83,125,166,171,174,245],"a":[9,27,90,94,182,222],"cell,":[10],"intricate":[12],"molecular":[13],"mechanisms":[14,22],"underlie":[15],"these":[16],"cellular":[17,40,70,261],"pathways.":[18,71,178],"Inquiring":[19],"how":[20],"such":[21,224,246],"could":[23],"have":[24],"evolved":[25,231],"is":[26,107,119],"basic":[28],"question":[29],"in":[30,77,115,121,168,197,249],"evolutionary":[31],"biology":[32],"with":[33,138],"wide-ranging":[34],"implications":[35],"for":[36,60,186],"predicting":[37],"altering":[39],"phenotypes.":[41],"This":[42],"dissertation":[43],"presents":[44],"our":[45],"work":[46],"on":[47,93],"computational":[49],"analysis":[50,82,173],"genome-level":[52],"data":[53],"(on":[54],"biomolecular":[55],"sequences":[56],"interactions)":[58],"available":[59],"many":[61],"organisms":[62],"to":[63,97,133,160,199,216,237],"study":[64,73,164],"conservation":[66,74],"evolution":[68,165,188,195],"We":[72,87,129,163,179,211,240],"context":[79,170],"comparative":[81],"protein":[84,103,155],"interaction":[85],"networks.":[86,104],"specifically":[88,180],"present":[89,181],"method":[91,132],"based":[92,209],"graph-matching":[95,126],"algorithm":[96,106],"detect":[98],"conserved":[99,150],"between":[101],"two":[102],"Our":[105],"provably":[108],"efficient":[109],"unlike":[110],"search":[112],"heuristics":[113],"used":[114],"previous":[116],"methods,":[117],"novel":[120],"broader":[123],"field":[124],"as":[127,225],"well.":[128],"apply":[130,213],"compare":[134],"yeast":[136,154],"network":[137],"human,":[140],"fruit":[141],"fly":[142],"nematode":[144],"worm":[145],"networks,":[146],"evaluate":[147],"detected":[149],"using":[152,255],"known":[153,256],"complexes,":[156],"demonstrate":[158],"applications":[159],"prediction.":[162],"phylogenetic":[172],"bacterial":[175],"archaeal":[177],"tractable":[183],"probabilistic":[184],"model":[185,215],"pathway":[187,194,207,223],"that":[189,204],"makes":[190],"assumptions":[192],"about":[193],"explicit,":[196],"contrast":[198],"few":[201],"past":[202],"studies":[203],"use":[205],"discrete":[206],"similarity":[208],"models.":[210],"then":[212],"estimate":[217],"phylogeny":[219],"along":[220],"which":[221],"citric":[226],"acid":[227],"cycle":[228],"or":[229,252],"chemotaxis":[230],"from":[232],"its":[233],"unknown":[234],"ancestral":[235],"forms":[236],"extant":[238],"forms.":[239],"interpret":[241],"estimated":[243],"phylogenies":[244,258],"involved":[248],"essential":[250],"metabolisms":[251],"stress":[253],"responses":[254],"species":[257],"published":[260],"phenotypes":[262]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
