{"id":"https://openalex.org/W3204538020","doi":null,"title":"Evolutionary dynamics under a stability-constrained model","display_name":"Evolutionary dynamics under a stability-constrained model","publication_year":2021,"publication_date":"2021-08-17","ids":{"openalex":"https://openalex.org/W3204538020","mag":"3204538020"},"language":"en","primary_location":{"id":"pmh:oai:dal.scholaris.ca:10222/80681","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/10222/80681","pdf_url":null,"source":{"id":"https://openalex.org/S7407064432","display_name":"DalSpace (Dalhousie University)","issn_l":"2041-2096","issn":["2041-2096"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":["dongbi-a","poland-140","russia-white-list-1"],"host_organization":"https://openalex.org/I129902397","host_organization_name":"Dalhousie University","host_organization_lineage":["https://openalex.org/I129902397"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084588085","display_name":"Noor Youssef","orcid":"https://orcid.org/0000-0002-7708-982X","observed_orcids":["https://orcid.org/0000-0002-7708-982X"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Noor Youssef","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5084588085"],"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":0.9746000170707703,"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":0.9746000170707703,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.018400000408291817,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.0031999999191612005,"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-evolution","display_name":"protein evolution","score":0.9079999923706055},{"id":"https://openalex.org/keywords/epistasis","display_name":"epistasis","score":0.9079999923706055},{"id":"https://openalex.org/keywords/substitution-rate","display_name":"substitution rate","score":0.6370000243186951},{"id":"https://openalex.org/keywords/amino-acid-propensities","display_name":"amino acid propensities","score":0.8190000057220459},{"id":"https://openalex.org/keywords/protein-stability","display_name":"protein stability","score":0.5619999766349792},{"id":"https://openalex.org/keywords/buried-residues","display_name":"buried residues","score":0.7379999756813049},{"id":"https://openalex.org/keywords/protein-sequence-evolution","display_name":"protein sequence evolution","score":0.37700000405311584},{"id":"https://openalex.org/keywords/population-genetics","display_name":"population genetics","score":0.4699999988079071},{"id":"https://openalex.org/keywords/protein-folding-thermodynamics","display_name":"protein folding thermodynamics","score":0.6420000195503235}],"concepts":[{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.6032134890556335},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.573276698589325},{"id":"https://openalex.org/C171578705","wikidata":"https://www.wikidata.org/wiki/Q5418700","display_name":"Evolutionary dynamics","level":3,"score":0.43595123291015625},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32338282465934753},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.1834123134613037},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.1695822775363922},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.12208086252212524},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.11007627844810486},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0},{"id":"https://openalex.org/C19417346","wikidata":"https://www.wikidata.org/wiki/Q7922","display_name":"Pedagogy","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:dal.scholaris.ca:10222/80681","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/10222/80681","pdf_url":null,"source":{"id":"https://openalex.org/S7407064432","display_name":"DalSpace (Dalhousie University)","issn_l":"2041-2096","issn":["2041-2096"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":["dongbi-a","poland-140","russia-white-list-1"],"host_organization":"https://openalex.org/I129902397","host_organization_name":"Dalhousie University","host_organization_lineage":["https://openalex.org/I129902397"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"},{"id":"mag:3204538020","doi":null,"is_oa":false,"landing_page_url":"https://dalspace.library.dal.ca/handle/10222/80681","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":138,"referenced_works":["https://openalex.org/W1512750650","https://openalex.org/W1525734744","https://openalex.org/W1548178570","https://openalex.org/W1575333721","https://openalex.org/W1587026990","https://openalex.org/W1675572849","https://openalex.org/W1801345324","https://openalex.org/W1851602452","https://openalex.org/W1881807356","https://openalex.org/W1920973730","https://openalex.org/W1964145455","https://openalex.org/W1964529071","https://openalex.org/W1967055944","https://openalex.org/W1972464683","https://openalex.org/W1975017420","https://openalex.org/W1977890263","https://openalex.org/W1983102293","https://openalex.org/W1983528535","https://openalex.org/W1989297730","https://openalex.org/W1990823383","https://openalex.org/W1992579032","https://openalex.org/W1992613346","https://openalex.org/W1992860213","https://openalex.org/W1993351732","https://openalex.org/W1997816460","https://openalex.org/W2002651564","https://openalex.org/W2003235560","https://openalex.org/W2003890287","https://openalex.org/W2004778468","https://openalex.org/W2004875842","https://openalex.org/W2007339420","https://openalex.org/W2008708467","https://openalex.org/W2016185554","https://openalex.org/W2020680099","https://openalex.org/W2022449400","https://openalex.org/W2023553163","https://openalex.org/W2024291508","https://openalex.org/W2029377901","https://openalex.org/W2029549914","https://openalex.org/W2031818329","https://openalex.org/W2031900710","https://openalex.org/W2038898901","https://openalex.org/W2039817196","https://openalex.org/W2042997873","https://openalex.org/W2046793790","https://openalex.org/W2051603200","https://openalex.org/W2054017637","https://openalex.org/W2055968189","https://openalex.org/W2058212562","https://openalex.org/W2060588922","https://openalex.org/W2062018285","https://openalex.org/W2063216803","https://openalex.org/W2066609402","https://openalex.org/W2071461674","https://openalex.org/W2075597546","https://openalex.org/W2080473579","https://openalex.org/W2090336802","https://openalex.org/W2092189458","https://openalex.org/W2092387745","https://openalex.org/W2096413602","https://openalex.org/W2097356092","https://openalex.org/W2097977090","https://openalex.org/W2106756635","https://openalex.org/W2111485477","https://openalex.org/W2111647009","https://openalex.org/W2115148114","https://openalex.org/W2116303244","https://openalex.org/W2118261180","https://openalex.org/W2118982822","https://openalex.org/W2119326915","https://openalex.org/W2119904585","https://openalex.org/W2120442255","https://openalex.org/W2124795824","https://openalex.org/W2127322768","https://openalex.org/W2133204396","https://openalex.org/W2134761488","https://openalex.org/W2135753651","https://openalex.org/W2136847298","https://openalex.org/W2139135174","https://openalex.org/W2141555161","https://openalex.org/W2142942973","https://openalex.org/W2143499154","https://openalex.org/W2145250129","https://openalex.org/W2145317354","https://openalex.org/W2150842476","https://openalex.org/W2152824619","https://openalex.org/W2153811962","https://openalex.org/W2154188431","https://openalex.org/W2155418451","https://openalex.org/W2159368933","https://openalex.org/W2160364329","https://openalex.org/W2161726503","https://openalex.org/W2162430545","https://openalex.org/W2164494468","https://openalex.org/W2164889035","https://openalex.org/W2168749685","https://openalex.org/W2170565120","https://openalex.org/W2171463101","https://openalex.org/W2176711441","https://openalex.org/W2182926188","https://openalex.org/W2217362286","https://openalex.org/W2259165058","https://openalex.org/W2266201493","https://openalex.org/W2266439690","https://openalex.org/W2312494234","https://openalex.org/W2401346147","https://openalex.org/W2471654536","https://openalex.org/W2518754795","https://openalex.org/W2531095031","https://openalex.org/W2547075996","https://openalex.org/W2549224827","https://openalex.org/W2553352972","https://openalex.org/W2593070627","https://openalex.org/W2612196455","https://openalex.org/W2743493305","https://openalex.org/W2766677998","https://openalex.org/W2766925510","https://openalex.org/W2767078712","https://openalex.org/W2777797644","https://openalex.org/W2782613909","https://openalex.org/W2794656815","https://openalex.org/W2798952779","https://openalex.org/W2890223884","https://openalex.org/W2950672524","https://openalex.org/W2951184823","https://openalex.org/W2951667064","https://openalex.org/W2953298003","https://openalex.org/W2964915524","https://openalex.org/W2987941611","https://openalex.org/W3036039277","https://openalex.org/W3038248848","https://openalex.org/W3046703180","https://openalex.org/W3086163014","https://openalex.org/W3111146891","https://openalex.org/W3140369281","https://openalex.org/W3156458251","https://openalex.org/W4231286578","https://openalex.org/W4299702438"],"related_works":["https://openalex.org/W2897701522","https://openalex.org/W3036039277","https://openalex.org/W4210402083","https://openalex.org/W3109016049","https://openalex.org/W2910699203","https://openalex.org/W2766677998","https://openalex.org/W3151741762","https://openalex.org/W6929619133","https://openalex.org/W4360807713","https://openalex.org/W2778423532"],"abstract_inverted_index":{"The":[0],"space":[1],"of":[2,15,20,29,52,60,76,89,105,117,128,138,188,199,224,319],"possible":[3],"proteins":[4,39,129],"is":[5,72,203],"vast.":[6],"For":[7],"all":[8],"but":[9],"the":[10,13,18,23,27,50,68,90,103,115,136,177,186,197,206,211,222,276,301,313,317],"smallest":[11],"proteins,":[12],"number":[14,19],"sequences":[16],"exceeds":[17],"atoms":[21],"in":[22,48,93,135,156,233,271],"observable":[24],"universe.":[25],"Evolution\u2014through":[26],"forces":[28],"natural":[30,157],"selection,":[31],"drift,":[32],"and":[33,43,62,140,175,229,283,324],"mutation\u2014samples":[34],"this":[35,121,181],"space,":[36],"leading":[37],"to":[38,81,164,167,172,238,266,279,303],"with":[40,86,210],"diverse":[41],"structures":[42],"functions.":[44],"Evolutionary":[45],"biologists":[46],"interested":[47],"understanding":[49],"history":[51],"a":[53,131,244,255,297],"protein":[54,77,285,322],"must":[55,246],"identify":[56],"signals":[57],"from":[58,191],"patterns":[59,154],"substitutions":[61,281,291],"decipher":[63],"their":[64],"likely":[65],"causes.":[66],"However,":[67],"true":[69],"evolutionary":[70,277],"process":[71,116],"often":[73,204,295],"unknown.":[74],"Simulations":[75],"evolution":[78,151,174,323],"allow":[79],"us":[80],"investigate":[82,185,275],"various":[83,153],"emergent":[84],"phenomena":[85,260],"complete":[87],"knowledge":[88],"generating":[91],"parameters":[92],"hand.":[94],"Additionally,":[95,183],"using":[96,130],"plausible":[97],"simulating":[98],"models,":[99],"we":[100],"can":[101,235],"assess":[102],"accuracy":[104,187],"inference":[106,190,194],"procedures":[107],"which,":[108],"by":[109,315],"necessity,":[110],"make":[111],"simplifying":[112],"assumptions":[113],"about":[114],"sequence":[118],"evolution.":[119],"In":[120,144,217,250],"dissertation,":[122],"I":[123,147,159,184,220,253,274,287,311],"focus":[124],"on":[125,258,321],"stability":[126,165],"constraints":[127],"modelling":[132],"framework":[133],"grounded":[134],"formalisms":[137],"thermodynamics":[139],"population":[141],"genetics":[142],"theory.":[143],"Chapter":[145,218,251,272],"2,":[146],"show":[148,230],"that":[149,161,231,242,261,289],"stability-constrained":[150],"recapitulates":[152],"present":[155],"alignments.":[158],"demonstrate":[160],"epistasis":[162,320],"due":[163,237],"leads":[166],"elevated":[168],"substitution":[169],"rates":[170,208,214],"compared":[171],"site-independent":[173],"discuss":[176],"underlying":[178],"mechanisms":[179],"causing":[180],"increase.":[182],"rate":[189,201],"commonly":[192],"used":[193],"models.":[195],"While":[196],"amount":[198],"among-site":[200],"variability":[202],"underestimated,":[205],"inferred":[207],"correlated":[209],"most":[212],"common":[213],"across":[215,282],"sites.":[216,310],"3,":[219],"explore":[221],"dynamics":[223],"resident":[225],"amino":[226,263],"acid":[227,264],"propensities":[228,234],"decreases":[232],"occur":[236],"epistasis,":[239],"challenging":[240],"claims":[241],"such":[243],"trend":[245],"have":[247],"adaptive":[248],"origins.":[249],"4,":[252],"conduct":[254],"literature":[256],"review":[257],"nonadaptive":[259],"lead":[262],"preferences":[265],"change":[267],"over":[268],"time.":[269],"Finally,":[270],"5,":[273],"response":[278],"destabilizing":[280,290],"within":[284],"structures.":[286],"find":[288],"at":[292,308],"buried":[293],"residues":[294],"require":[296],"longer":[298],"time":[299],"for":[300],"effects":[302],"be":[304],"mitigated":[305],"than":[306],"destabilizations":[307],"exposed":[309],"end":[312],"dissertation":[314],"discussing":[316],"implications":[318],"future":[325],"research":[326],"directions.":[327]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2021-10-11T00:00:00"}