{"id":"https://openalex.org/W2277805299","doi":null,"title":"Metagenomic systems biology: frameworks for modeling and characterizing the gut microbiome","display_name":"Metagenomic systems biology: frameworks for modeling and characterizing the gut microbiome","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2277805299","mag":"2277805299"},"language":"en","primary_location":{"id":"pmh:oai:digital.lib.washington.edu:1773/27488","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1773/27488","pdf_url":"https://digital.lib.washington.edu/bitstreams/a6614968-8659-4d09-9eca-9b7c2090318d/download","source":{"id":"https://openalex.org/S4306401128","display_name":"ResearchWorks at the University of Washington (University of Washington)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I201448701","host_organization_name":"University of Washington","host_organization_lineage":["https://openalex.org/I201448701"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://digital.lib.washington.edu/bitstreams/a6614968-8659-4d09-9eca-9b7c2090318d/download","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056199651","display_name":"Sharon I. Greenblum","orcid":"https://orcid.org/0000-0001-6148-3016","observed_orcids":["https://orcid.org/0000-0001-6148-3016"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Sharon Greenblum","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-6148-3016","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5056199651"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"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/T10066","display_name":"Gut microbiota and health","score":0.9945999979972839,"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/T10066","display_name":"Gut microbiota and health","score":0.9945999979972839,"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":0.0012000000569969416,"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":0.000699999975040555,"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/gut-microbiota","display_name":"gut microbiota","score":0.8759999871253967},{"id":"https://openalex.org/keywords/metagenomics","display_name":"metagenomics","score":0.8169999718666077},{"id":"https://openalex.org/keywords/systems-biology","display_name":"systems biology","score":0.8379999995231628},{"id":"https://openalex.org/keywords/microbial-community-metabolism","display_name":"microbial community metabolism","score":0.9399999976158142},{"id":"https://openalex.org/keywords/metabolic-network-topology","display_name":"metabolic network topology","score":0.7870000004768372},{"id":"https://openalex.org/keywords/obesity","display_name":"obesity","score":0.7360000014305115},{"id":"https://openalex.org/keywords/inflammatory-bowel-disease","display_name":"inflammatory bowel disease","score":1.0},{"id":"https://openalex.org/keywords/cross-species-comparison","display_name":"cross-species comparison","score":0.5440000295639038},{"id":"https://openalex.org/keywords/virulence-genes","display_name":"virulence genes","score":0.7369999885559082},{"id":"https://openalex.org/keywords/antibiotic-resistance","display_name":"antibiotic resistance","score":0.8659999966621399},{"id":"https://openalex.org/keywords/nutrient-transport","display_name":"nutrient transport","score":0.875},{"id":"https://openalex.org/keywords/host-microbiome-interactions","display_name":"host-microbiome interactions","score":0.9480000138282776}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.8234362006187439},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.655195951461792},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6228362321853638},{"id":"https://openalex.org/C3019978661","wikidata":"https://www.wikidata.org/wiki/Q739734","display_name":"Gut microbiome","level":3,"score":0.6142351627349854},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5176542401313782},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4720355272293091},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.400585412979126},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3451533615589142},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.33836829662323},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2614767551422119},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14811432361602783},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:digital.lib.washington.edu:1773/27488","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1773/27488","pdf_url":"https://digital.lib.washington.edu/bitstreams/a6614968-8659-4d09-9eca-9b7c2090318d/download","source":{"id":"https://openalex.org/S4306401128","display_name":"ResearchWorks at the University of Washington (University of Washington)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I201448701","host_organization_name":"University of Washington","host_organization_lineage":["https://openalex.org/I201448701"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},{"id":"mag:2277805299","doi":null,"is_oa":false,"landing_page_url":"https://digital.lib.washington.edu:443/researchworks/bitstream/1773/27488/1/Greenblum_washington_0250E_14061.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":{"id":"pmh:oai:digital.lib.washington.edu:1773/27488","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1773/27488","pdf_url":"https://digital.lib.washington.edu/bitstreams/a6614968-8659-4d09-9eca-9b7c2090318d/download","source":{"id":"https://openalex.org/S4306401128","display_name":"ResearchWorks at the University of Washington (University of Washington)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I201448701","host_organization_name":"University of Washington","host_organization_lineage":["https://openalex.org/I201448701"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2277805299.pdf","grobid_xml":"https://content.openalex.org/works/W2277805299.grobid-xml"},"referenced_works_count":99,"referenced_works":["https://openalex.org/W1497287772","https://openalex.org/W1571319209","https://openalex.org/W1909953453","https://openalex.org/W1915617735","https://openalex.org/W1968105193","https://openalex.org/W1969346416","https://openalex.org/W1972740086","https://openalex.org/W1978486653","https://openalex.org/W1978852892","https://openalex.org/W1982388837","https://openalex.org/W1989348205","https://openalex.org/W1989433663","https://openalex.org/W1991260321","https://openalex.org/W1995393174","https://openalex.org/W1996529795","https://openalex.org/W1996718064","https://openalex.org/W1998077837","https://openalex.org/W2002368733","https://openalex.org/W2002574233","https://openalex.org/W2007707048","https://openalex.org/W2008194879","https://openalex.org/W2017802408","https://openalex.org/W2021950980","https://openalex.org/W2024471867","https://openalex.org/W2024704006","https://openalex.org/W2028561804","https://openalex.org/W2028582941","https://openalex.org/W2034082915","https://openalex.org/W2036410122","https://openalex.org/W2037701117","https://openalex.org/W2039751833","https://openalex.org/W2041136224","https://openalex.org/W2041579725","https://openalex.org/W2045506688","https://openalex.org/W2046594601","https://openalex.org/W2046846930","https://openalex.org/W2049094395","https://openalex.org/W2051163560","https://openalex.org/W2057710367","https://openalex.org/W2061156796","https://openalex.org/W2063361228","https://openalex.org/W2071841602","https://openalex.org/W2073141486","https://openalex.org/W2073332363","https://openalex.org/W2074668828","https://openalex.org/W2076962784","https://openalex.org/W2077072558","https://openalex.org/W2080461503","https://openalex.org/W2087300928","https://openalex.org/W2088110146","https://openalex.org/W2089616676","https://openalex.org/W2090925778","https://openalex.org/W2094399313","https://openalex.org/W2095040140","https://openalex.org/W2097826371","https://openalex.org/W2097875133","https://openalex.org/W2098824895","https://openalex.org/W2101181144","https://openalex.org/W2108859156","https://openalex.org/W2108959333","https://openalex.org/W2110300022","https://openalex.org/W2111381495","https://openalex.org/W2112705721","https://openalex.org/W2112874908","https://openalex.org/W2113883363","https://openalex.org/W2115137666","https://openalex.org/W2115944543","https://openalex.org/W2121062713","https://openalex.org/W2124821727","https://openalex.org/W2124927293","https://openalex.org/W2125826054","https://openalex.org/W2126809954","https://openalex.org/W2127013413","https://openalex.org/W2127059753","https://openalex.org/W2127415562","https://openalex.org/W2133885724","https://openalex.org/W2135250036","https://openalex.org/W2140145798","https://openalex.org/W2141125135","https://openalex.org/W2144568881","https://openalex.org/W2144656637","https://openalex.org/W2144885342","https://openalex.org/W2145336165","https://openalex.org/W2145537580","https://openalex.org/W2149001103","https://openalex.org/W2149960646","https://openalex.org/W2151372451","https://openalex.org/W2152495216","https://openalex.org/W2152538010","https://openalex.org/W2153624566","https://openalex.org/W2156434996","https://openalex.org/W2159649357","https://openalex.org/W2159675211","https://openalex.org/W2166691283","https://openalex.org/W2167458075","https://openalex.org/W2167566687","https://openalex.org/W2168330282","https://openalex.org/W2168405980","https://openalex.org/W2171998389"],"related_works":["https://openalex.org/W7126712337","https://openalex.org/W6992797834","https://openalex.org/W7126293536","https://openalex.org/W2340868256","https://openalex.org/W7126948247","https://openalex.org/W7126912372","https://openalex.org/W2979097929","https://openalex.org/W7039523101","https://openalex.org/W3174010238","https://openalex.org/W7128980948"],"abstract_inverted_index":{"Though":[0],"invisible":[1],"to":[2,9,27,90,124,157,175,294,315,417],"the":[3,61,71,82,111,138,180,225,249,276,343,350,377,412],"naked":[4],"eye,":[5],"microbes":[6,41,59],"are":[7,19,337],"crucial":[8],"life":[10],"as":[11,149,354],"we":[12],"know":[13],"it.":[14],"These":[15],"tiny":[16],"single-celled":[17],"organisms":[18,304],"found":[20],"in":[21,81,108,165,232,290,368,385,404,415],"almost":[22],"every":[23],"known":[24],"environment,":[25,345],"helping":[26],"maintain":[28],"balance":[29],"across":[30,248,261,303,327],"a":[31,159,184,192,229,306,312,322],"vast":[32],"array":[33],"of":[34,48,58,70,76,84,110,114,183,201,256,279,324,349,388,411],"ecological":[35],"niches":[36],"plays.":[37],"Within":[38],"each":[39],"site,":[40],"may":[42,129,361,382,407],"form":[43],"intricate":[44],"multi-species":[45],"communities":[46,178,214,244],"capable":[47],"carrying":[49],"out":[50],"diverse":[51],"and":[52,73,79,128,146,179,196,205,218,253,270,282,320,346,358,396,400],"complex":[53],"metabolic":[54],"processes.":[55],"The":[56,221],"set":[57],"inhabiting":[60],"human":[62,65,212,329],"gut":[63,66,106,213,226,243,330,344],"(the":[64],"microbiome)":[67],"comprises":[68],"one":[69],"richest":[72],"most":[74,351],"well-studied":[75],"these":[77,265,317],"communities,":[78,390],"shifts":[80],"composition":[83],"this":[85,405],"microbiome":[86,234,280],"have":[87,91,362],"been":[88],"shown":[89],"significant":[92],"implications":[93],"for":[94,135,144,162,194,274,364],"host":[95,246],"health.":[96],"However,":[97],"while":[98],"current":[99,173],"comparative":[100],"studies":[101,387],"mostly":[102],"focus":[103],"on":[104,137,299,375],"characterizing":[105,145,197],"microbiomes":[107,148],"terms":[109],"relative":[112],"abundance":[113],"individual":[115,295],"species":[116,247,308,340],"or":[117,236],"genes,":[118],"such":[119,353],"profiles":[120],"offer":[121,131,372],"limited":[122,132],"translation":[123],"overall":[125],"community":[126,166,203,291],"capabilities,":[127],"thus":[130],"predictive":[133],"capacity":[134],"effect":[136],"host.":[139],"Here,":[140],"I":[141,171,190,241,263,287,332,371],"develop":[142],"frameworks":[143,379],"comparing":[147],"integrated":[150],"systems,":[151],"leveraging":[152],"concepts":[153],"from":[154,215,245],"systems":[155],"biology":[156],"provide":[158],"deeper":[160],"context":[161],"interpreting":[163],"differences":[164,210,289],"composition.":[167],"In":[168,187,238,284],"chapter":[169,188,239,285,369],"1,":[170],"describe":[172],"efforts":[174],"characterize":[176],"microbial":[177,202,296,389,413],"potential":[181],"advantages":[182],"systems-level":[185,378],"perspective.":[186],"2,":[189],"present":[191],"method":[193],"constructing":[195],"topological":[198,209],"network":[199],"models":[200],"metabolism,":[204],"then":[206],"identify":[207,254],"specific":[208],"between":[211],"healthy,":[216],"obese,":[217],"IBD-afflicted":[219],"individuals.":[220],"results":[222],"suggest":[223],"that":[224,259,334,347],"environment":[227],"plays":[228],"critical":[230],"role":[231],"shaping":[233],"topology,":[235],"structure.":[237],"3,":[240],"examine":[242],"mammalian":[250],"phylogenetic":[251],"tree":[252],"groups":[255,267],"functionally-related":[257],"genes":[258],"co-occur":[260],"hosts.":[262],"term":[264],"gene":[266],"`assembly":[268],"modules',":[269],"demonstrate":[271],"their":[272,325],"value":[273],"understanding":[275,410],"functional":[277],"units":[278],"assembly":[281],"adaptation.":[283],"4,":[286],"relate":[288],"function":[292],"back":[293],"strains,":[297],"focusing":[298],"functions":[300,336],"whose":[301],"representation":[302],"within":[305],"given":[307],"is":[309],"community-dependent.":[310],"Establishing":[311],"computational":[313],"pipeline":[314],"detect":[316],"strain-specific":[318,335],"functions,":[319],"generating":[321],"database":[323],"frequency":[326],"109":[328],"microbiomes,":[331],"show":[333],"widespread":[338],"among":[339],"associated":[341],"with":[342],"some":[348,373],"prominent,":[352],"virulence,":[355],"antibiotic":[356],"resistance,":[357],"nutrient":[359],"transport,":[360],"significance":[363],"host-microbiome":[365],"stability.":[366],"Finally,":[367],"5,":[370],"perspective":[374],"how":[376,401],"presented":[380],"here":[381],"be":[383],"used":[384],"future":[386],"potentially":[391],"incorporating":[392],"burgeoning":[393],"new":[394],"technologies":[395],"growing":[397],"data":[398],"resources,":[399],"continued":[402],"work":[403],"vein":[406],"advance":[408],"our":[409,418],"world":[414],"relation":[416],"own.":[419]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2016-06-24T00:00:00"}
