{"id":"https://openalex.org/W420865124","doi":null,"title":"Causes of Substitution Frequency Variation in Pathogenic Bacteria","display_name":"Causes of Substitution Frequency Variation in Pathogenic Bacteria","publication_year":2005,"publication_date":"2005-01-01","ids":{"openalex":"https://openalex.org/W420865124","mag":"420865124"},"language":"en","primary_location":{"id":"pmh:oai:DiVA.org:uu-4838","doi":null,"is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4838","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I86987016","host_organization_name":"KTH Royal Institute of Technology","host_organization_lineage":["https://openalex.org/I86987016"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/doctoralThesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4838","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049875995","display_name":"Wagied Davids","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Wagied Davids","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5049875995"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.7529000043869019,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.7529000043869019,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.1923000067472458,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.029999999329447746,"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/dn-ds-ratio","display_name":"dN/dS ratio","score":0.9110000133514404},{"id":"https://openalex.org/keywords/rickettsia-prowazekii","display_name":"Rickettsia prowazekii","score":0.9169999957084656},{"id":"https://openalex.org/keywords/helicobacter-pylori","display_name":"Helicobacter pylori","score":0.9549999833106995},{"id":"https://openalex.org/keywords/orphan-genes","display_name":"orphan genes","score":0.9179999828338623},{"id":"https://openalex.org/keywords/pseudogenes","display_name":"pseudogenes","score":0.953000009059906},{"id":"https://openalex.org/keywords/rickettsia-conorii","display_name":"Rickettsia conorii","score":0.8130000233650208},{"id":"https://openalex.org/keywords/split-genes","display_name":"split genes","score":0.8040000200271606},{"id":"https://openalex.org/keywords/protein-evolutionary-rate","display_name":"protein evolutionary rate","score":0.7609999775886536},{"id":"https://openalex.org/keywords/carbamoyl-phosphate-synthetase","display_name":"carbamoyl phosphate synthetase","score":0.9049999713897705},{"id":"https://openalex.org/keywords/protein-protein-interaction","display_name":"protein-protein interaction","score":0.890999972820282},{"id":"https://openalex.org/keywords/gene-essentiality","display_name":"gene essentiality","score":0.9269999861717224},{"id":"https://openalex.org/keywords/chromosome-location","display_name":"chromosomal location","score":0.8169999718666077},{"id":"https://openalex.org/keywords/antigenicity","display_name":"antigenicity","score":0.9580000042915344},{"id":"https://openalex.org/keywords/typhus-group","display_name":"typhus group","score":0.621999979019165},{"id":"https://openalex.org/keywords/spotted-fever-group","display_name":"spotted fever group","score":0.8889999985694885},{"id":"https://openalex.org/keywords/ancestral-sequence-reconstruction","display_name":"ancestral sequence reconstruction","score":0.6859999895095825}],"concepts":[{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.6491708159446716},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.5574110150337219},{"id":"https://openalex.org/C2778883795","wikidata":"https://www.wikidata.org/wiki/Q804517","display_name":"Pathogenic bacteria","level":3,"score":0.4740188717842102},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39542847871780396},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.3924364447593689},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2587718963623047},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21044161915779114},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10425949096679688},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:DiVA.org:uu-4838","doi":null,"is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4838","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I86987016","host_organization_name":"KTH Royal Institute of Technology","host_organization_lineage":["https://openalex.org/I86987016"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/doctoralThesis"},{"id":"mag:420865124","doi":null,"is_oa":false,"landing_page_url":"http://uu.diva-portal.org/smash/get/diva2:165948/FULLTEXT01.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:DiVA.org:uu-4838","doi":null,"is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4838","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I86987016","host_organization_name":"KTH Royal Institute of Technology","host_organization_lineage":["https://openalex.org/I86987016"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/doctoralThesis"},"sustainable_development_goals":[{"score":0.6240000128746033,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":153,"referenced_works":["https://openalex.org/W104710838","https://openalex.org/W791550880","https://openalex.org/W1489673536","https://openalex.org/W1493831303","https://openalex.org/W1536753671","https://openalex.org/W1546563018","https://openalex.org/W1559644609","https://openalex.org/W1569904835","https://openalex.org/W1617947194","https://openalex.org/W1758410558","https://openalex.org/W1810634920","https://openalex.org/W1881807356","https://openalex.org/W1882986874","https://openalex.org/W1898801155","https://openalex.org/W1907806866","https://openalex.org/W1913751214","https://openalex.org/W1920973730","https://openalex.org/W1931383151","https://openalex.org/W1952540142","https://openalex.org/W1963500218","https://openalex.org/W1966804741","https://openalex.org/W1968508276","https://openalex.org/W1971485638","https://openalex.org/W1974299093","https://openalex.org/W1979824030","https://openalex.org/W1985491754","https://openalex.org/W1986733193","https://openalex.org/W1987510089","https://openalex.org/W1987639630","https://openalex.org/W1988171432","https://openalex.org/W1995117714","https://openalex.org/W1999286199","https://openalex.org/W1999536502","https://openalex.org/W2000486851","https://openalex.org/W2001660787","https://openalex.org/W2003690139","https://openalex.org/W2005122969","https://openalex.org/W2006683038","https://openalex.org/W2008078175","https://openalex.org/W2015292449","https://openalex.org/W2016299826","https://openalex.org/W2016588572","https://openalex.org/W2019591778","https://openalex.org/W2026258231","https://openalex.org/W2029158589","https://openalex.org/W2030136297","https://openalex.org/W2032870665","https://openalex.org/W2034036140","https://openalex.org/W2034229618","https://openalex.org/W2038978937","https://openalex.org/W2040941311","https://openalex.org/W2044128233","https://openalex.org/W2044465665","https://openalex.org/W2044573154","https://openalex.org/W2049469847","https://openalex.org/W2049783361","https://openalex.org/W2050143126","https://openalex.org/W2055043387","https://openalex.org/W2057885377","https://openalex.org/W2062491586","https://openalex.org/W2065304353","https://openalex.org/W2066004232","https://openalex.org/W2066042137","https://openalex.org/W2069511429","https://openalex.org/W2073106255","https://openalex.org/W2081219382","https://openalex.org/W2083788527","https://openalex.org/W2089170463","https://openalex.org/W2093246625","https://openalex.org/W2097805330","https://openalex.org/W2098984028","https://openalex.org/W2101868204","https://openalex.org/W2102122585","https://openalex.org/W2102131597","https://openalex.org/W2102225814","https://openalex.org/W2103601429","https://openalex.org/W2104099887","https://openalex.org/W2104306559","https://openalex.org/W2105585336","https://openalex.org/W2106090237","https://openalex.org/W2106882534","https://openalex.org/W2109278577","https://openalex.org/W2110132014","https://openalex.org/W2111762123","https://openalex.org/W2113824405","https://openalex.org/W2114828923","https://openalex.org/W2115011276","https://openalex.org/W2116088151","https://openalex.org/W2119295056","https://openalex.org/W2120005900","https://openalex.org/W2120122292","https://openalex.org/W2121481633","https://openalex.org/W2122784014","https://openalex.org/W2124037112","https://openalex.org/W2124166542","https://openalex.org/W2125283188","https://openalex.org/W2126161931","https://openalex.org/W2127115092","https://openalex.org/W2128119325","https://openalex.org/W2128514224","https://openalex.org/W2129765241","https://openalex.org/W2130790725","https://openalex.org/W2131351884","https://openalex.org/W2133253129","https://openalex.org/W2133585817","https://openalex.org/W2135123683","https://openalex.org/W2137426528","https://openalex.org/W2138652574","https://openalex.org/W2140494270","https://openalex.org/W2141422242","https://openalex.org/W2142437744","https://openalex.org/W2143011057","https://openalex.org/W2143199763","https://openalex.org/W2143210482","https://openalex.org/W2144885342","https://openalex.org/W2145454207","https://openalex.org/W2146058442","https://openalex.org/W2146245198","https://openalex.org/W2146538795","https://openalex.org/W2146804513","https://openalex.org/W2149824052","https://openalex.org/W2149990334","https://openalex.org/W2150044006","https://openalex.org/W2151831732","https://openalex.org/W2152193238","https://openalex.org/W2152873040","https://openalex.org/W2153232310","https://openalex.org/W2154406573","https://openalex.org/W2154478075","https://openalex.org/W2156745542","https://openalex.org/W2158714788","https://openalex.org/W2159595936","https://openalex.org/W2159656294","https://openalex.org/W2160323890","https://openalex.org/W2160364329","https://openalex.org/W2160500073","https://openalex.org/W2160582562","https://openalex.org/W2162888916","https://openalex.org/W2164217177","https://openalex.org/W2165979915","https://openalex.org/W2167222948","https://openalex.org/W2167680767","https://openalex.org/W2167869241","https://openalex.org/W2168491690","https://openalex.org/W2169153685","https://openalex.org/W2169395813","https://openalex.org/W2169748335","https://openalex.org/W2329196066","https://openalex.org/W2424052232","https://openalex.org/W2601913882","https://openalex.org/W2743633116","https://openalex.org/W4236580199","https://openalex.org/W7096321448"],"related_works":["https://openalex.org/W649505133","https://openalex.org/W597891297","https://openalex.org/W2020836030","https://openalex.org/W2091838190","https://openalex.org/W2055864549","https://openalex.org/W7096833514","https://openalex.org/W2076481630","https://openalex.org/W2035583520","https://openalex.org/W6940589096","https://openalex.org/W2651679602"],"abstract_inverted_index":{"Estimating":[0],"substitution":[1,52],"frequencies":[2],"at":[3],"sites":[4],"that":[5,31,126,139,157,181],"influence":[6,11],"(Ka)":[7],"and":[8,27,66,97,119,138,222,237,274,282],"do":[9],"not":[10],"(Ks)":[12],"the":[13,21,28,48,60,86,130,136,142,151,184,193,243,265],"amino":[14],"acid":[15],"sequence":[16,25,95,110,258],"is":[17,267],"important":[18,269],"for":[19,279],"understanding":[20,46],"dynamics":[22],"of":[23,38,47,51,63,88,112,168,174,183,192,234,276],"molecular":[24,272],"evolution":[26,87,96,259,273],"selective":[29],"pressures":[30],"have":[32],"shaped":[33],"genetic":[34],"variation.":[35],"The":[36,108,153,172],"aim":[37],"this":[39],"work":[40],"was":[41,84],"to":[42,133,145,202],"gain":[43],"a":[44,208],"deeper":[45],"driving":[49],"forces":[50],"frequency":[53],"variation":[54],"in":[55,73,91,103,129,135,141,150,177,229,251,271],"human":[56,252],"pathogens.":[57],"Rickettsia":[58],"prowazekii,":[59],"causative":[61],"agent":[62],"epidemic":[64],"typhus":[65],"Helicobacter":[67],"pylori,":[68],"which":[69,235],"has":[70],"been":[71],"implicated":[72],"gastric":[74],"diseases":[75],"were":[76,106,232,240],"used":[77],"as":[78,215,242],"model":[79],"systems.":[80],"A":[81],"specific":[82],"focus":[83],"on":[85,207,225],"orphan":[89,113,127],"genes":[90,114,128,176],"Rickettsia.":[92],"Additionally,":[93],"adaptive":[94,211,257],"factors":[98],"influencing":[99],"protein":[100,209,226],"evolutionary":[101,227],"rates":[102,228],"H.":[104,194,230],"pylori":[105,195,231],"studied.":[107],"comparative":[109],"analyses":[111],"using":[115],"Typhus":[116],"Group":[117,122],"(TG)":[118],"Spotted":[120],"Fever":[121],"(SFG)":[123],"Rickettsia,":[124],"indicate":[125,180],"SFG":[131,143],"correspond":[132,144],"pseudogenes":[134,140],"TG":[137],"extensively":[146],"degraded":[147],"gene":[148,159,166,220,238,261],"remnants":[149,167],"TG.":[152],"analysis":[154],"also":[155,275],"showed":[156],"ancestral":[158],"sequences":[160],"could":[161],"be":[162],"reconstructed":[163],"from":[164],"extant":[165],"closely":[169],"related":[170],"species.":[171],"studies":[173],"split":[175],"R.":[178],"conorii":[179],"many":[182],"small":[185],"fragmented":[186],"ORFs":[187],"are":[188],"probably":[189],"pseudogenes.":[190],"Analysis":[191],"carbamoyl":[196],"phosphate":[197],"synthetase":[198],"provided":[199],"an":[200,268],"opportunity":[201],"understand":[203],"natural":[204],"selection":[205],"acting":[206],"undergoing":[210],"evolution.":[212],"Factors":[213],"such":[214],"network":[216],"properties,":[217],"protein-protein":[218],"interactions,":[219],"essentiality":[221],"chromosomal":[223],"position":[224],"studied,":[233],"antigenicity":[236],"location":[239],"identified":[241],"strongest":[244],"factors.":[245],"In":[246],"conclusion,":[247],"high":[248],"Ka/Ks":[249],"ratios":[250],"pathogens":[253],"may":[254],"reflect":[255],"either":[256],"or":[260],"deterioration.":[262],"Distinguishing":[263],"between":[264],"two":[266],"task":[270],"great":[277],"relevance":[278],"medical":[280],"microbiology":[281],"functional":[283],"genomics":[284],"research.":[285]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}