{"id":"https://openalex.org/W4281261566","doi":"https://doi.org/10.1109/tcbb.2022.3175908","title":"Problem of Domain/Building Block Preservation in the Evolution of Biological Macromolecules and Evolutionary Computation","display_name":"Problem of Domain/Building Block Preservation in the Evolution of Biological Macromolecules and Evolutionary Computation","publication_year":2022,"publication_date":"2022-05-20","ids":{"openalex":"https://openalex.org/W4281261566","doi":"https://doi.org/10.1109/tcbb.2022.3175908","pmid":"https://pubmed.ncbi.nlm.nih.gov/35594219"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3175908","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3175908","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5002399513","display_name":"Alexander V. Spirov","orcid":"https://orcid.org/0000-0002-0509-6203"},"institutions":[{"id":"https://openalex.org/I163234304","display_name":"Institute of Evolutionary Physiology and Biochemistry","ror":"https://ror.org/02vf4sk45","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I163234304","https://openalex.org/I4210115279"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Alexander V. Spirov","raw_affiliation_strings":["I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Saint Petersburg, Russia"],"affiliations":[{"raw_affiliation_string":"I. M. Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Saint Petersburg, Russia","institution_ids":["https://openalex.org/I163234304"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048711176","display_name":"Ekaterina Myasnikova","orcid":"https://orcid.org/0000-0001-6301-1012"},"institutions":[{"id":"https://openalex.org/I212220629","display_name":"Peter the Great St. Petersburg Polytechnic University","ror":"https://ror.org/02x91aj62","country_code":"RU","type":"education","lineage":["https://openalex.org/I212220629"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ekaterina M. Myasnikova","raw_affiliation_strings":["Peter the Great St. Petersburg Polytechnical University, St. Petersburg, Russia"],"affiliations":[{"raw_affiliation_string":"Peter the Great St. Petersburg Polytechnical University, St. Petersburg, Russia","institution_ids":["https://openalex.org/I212220629"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5002399513"],"corresponding_institution_ids":["https://openalex.org/I163234304"],"apc_list":null,"apc_paid":null,"fwci":0.3431,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.54386798,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"20","issue":"2","first_page":"1345","last_page":"1362"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9984999895095825,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9984999895095825,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9973999857902527,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9940999746322632,"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/shuffling","display_name":"Shuffling","score":0.6687057018280029},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.566655158996582},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.5305139422416687},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5247105360031128},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5157976150512695},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5053744912147522},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.49945068359375},{"id":"https://openalex.org/keywords/evolutionary-computation","display_name":"Evolutionary computation","score":0.48284679651260376},{"id":"https://openalex.org/keywords/evolutionary-algorithm","display_name":"Evolutionary algorithm","score":0.45705294609069824},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.42827731370925903},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.41521376371383667},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3481599688529968},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33985331654548645},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16309002041816711}],"concepts":[{"id":"https://openalex.org/C167927819","wikidata":"https://www.wikidata.org/wiki/Q1930567","display_name":"Shuffling","level":2,"score":0.6687057018280029},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.566655158996582},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.5305139422416687},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5247105360031128},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5157976150512695},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5053744912147522},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.49945068359375},{"id":"https://openalex.org/C105902424","wikidata":"https://www.wikidata.org/wiki/Q1197129","display_name":"Evolutionary computation","level":2,"score":0.48284679651260376},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.45705294609069824},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42827731370925903},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.41521376371383667},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3481599688529968},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33985331654548645},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16309002041816711},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058615","descriptor_name":"Synthetic Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2022.3175908","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3175908","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35594219","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35594219","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5199999809265137,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G6009502696","display_name":null,"funder_award_id":"16.8549.2017/8.9","funder_id":"https://openalex.org/F4320321912","funder_display_name":"Ministry of Education and Science of the Russian Federation"},{"id":"https://openalex.org/G7256041567","display_name":null,"funder_award_id":"17-18-01536","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320321912","display_name":"Ministry of Education and Science of the Russian Federation","ror":"https://ror.org/00ghqgy32"},{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":158,"referenced_works":["https://openalex.org/W13915400","https://openalex.org/W48038378","https://openalex.org/W59428951","https://openalex.org/W76498526","https://openalex.org/W139482607","https://openalex.org/W1248084178","https://openalex.org/W1507582389","https://openalex.org/W1508543123","https://openalex.org/W1533873536","https://openalex.org/W1540016209","https://openalex.org/W1540706608","https://openalex.org/W1542173035","https://openalex.org/W1550474463","https://openalex.org/W1552716706","https://openalex.org/W1568364087","https://openalex.org/W1581075644","https://openalex.org/W1607539085","https://openalex.org/W1639694146","https://openalex.org/W1659842140","https://openalex.org/W1692958259","https://openalex.org/W1826803447","https://openalex.org/W1853318555","https://openalex.org/W1884986037","https://openalex.org/W1905590028","https://openalex.org/W1914267757","https://openalex.org/W1937288783","https://openalex.org/W1954202239","https://openalex.org/W1957053378","https://openalex.org/W1966355747","https://openalex.org/W1971237725","https://openalex.org/W1971309542","https://openalex.org/W1972073962","https://openalex.org/W1972277434","https://openalex.org/W1972837291","https://openalex.org/W1976410590","https://openalex.org/W1977516605","https://openalex.org/W1981482533","https://openalex.org/W1984164188","https://openalex.org/W1986799612","https://openalex.org/W1994258343","https://openalex.org/W1998424052","https://openalex.org/W1999104032","https://openalex.org/W2003621391","https://openalex.org/W2011235285","https://openalex.org/W2011513747","https://openalex.org/W2011698647","https://openalex.org/W2020925359","https://openalex.org/W2024377181","https://openalex.org/W2027945080","https://openalex.org/W2030948359","https://openalex.org/W2035278976","https://openalex.org/W2036165008","https://openalex.org/W2038836884","https://openalex.org/W2041589571","https://openalex.org/W2042521440","https://openalex.org/W2045396155","https://openalex.org/W2048602141","https://openalex.org/W2050110866","https://openalex.org/W2051036957","https://openalex.org/W2053410797","https://openalex.org/W2053671774","https://openalex.org/W2054621971","https://openalex.org/W2055118532","https://openalex.org/W2056151032","https://openalex.org/W2056679161","https://openalex.org/W2064809769","https://openalex.org/W2066790509","https://openalex.org/W2068687506","https://openalex.org/W2068796656","https://openalex.org/W2070136856","https://openalex.org/W2071086763","https://openalex.org/W2072879379","https://openalex.org/W2074580034","https://openalex.org/W2074959648","https://openalex.org/W2081574196","https://openalex.org/W2088252348","https://openalex.org/W2091535033","https://openalex.org/W2092006899","https://openalex.org/W2092495304","https://openalex.org/W2093111452","https://openalex.org/W2097973361","https://openalex.org/W2099299706","https://openalex.org/W2099346664","https://openalex.org/W2099560117","https://openalex.org/W2100303812","https://openalex.org/W2101783996","https://openalex.org/W2101903625","https://openalex.org/W2103385859","https://openalex.org/W2106522957","https://openalex.org/W2106595865","https://openalex.org/W2107197669","https://openalex.org/W2108703244","https://openalex.org/W2113403117","https://openalex.org/W2115001850","https://openalex.org/W2119565467","https://openalex.org/W2119861865","https://openalex.org/W2125725328","https://openalex.org/W2127379360","https://openalex.org/W2128151276","https://openalex.org/W2139413955","https://openalex.org/W2141346454","https://openalex.org/W2149230251","https://openalex.org/W2152958427","https://openalex.org/W2154277781","https://openalex.org/W2160373945","https://openalex.org/W2161792971","https://openalex.org/W2162060940","https://openalex.org/W2162320743","https://openalex.org/W2164701497","https://openalex.org/W2166603077","https://openalex.org/W2170174907","https://openalex.org/W2170757973","https://openalex.org/W2224056471","https://openalex.org/W2289283401","https://openalex.org/W2313102193","https://openalex.org/W2339374701","https://openalex.org/W2346626577","https://openalex.org/W2346667626","https://openalex.org/W2376557535","https://openalex.org/W2501818914","https://openalex.org/W2502620487","https://openalex.org/W2502979484","https://openalex.org/W2554436331","https://openalex.org/W2594505635","https://openalex.org/W2607155480","https://openalex.org/W2729598826","https://openalex.org/W2731963663","https://openalex.org/W2806228718","https://openalex.org/W2884402573","https://openalex.org/W2903758591","https://openalex.org/W2911724974","https://openalex.org/W2949706399","https://openalex.org/W2955232493","https://openalex.org/W2960223991","https://openalex.org/W2977063126","https://openalex.org/W3023540311","https://openalex.org/W3092040603","https://openalex.org/W3101738797","https://openalex.org/W3110415374","https://openalex.org/W3129830773","https://openalex.org/W3139510258","https://openalex.org/W3142736544","https://openalex.org/W3154803405","https://openalex.org/W3156428263","https://openalex.org/W3163970098","https://openalex.org/W3178295718","https://openalex.org/W3210789049","https://openalex.org/W4210380092","https://openalex.org/W4213261160","https://openalex.org/W4229487902","https://openalex.org/W4229809574","https://openalex.org/W4239615332","https://openalex.org/W4292640182","https://openalex.org/W4312782672","https://openalex.org/W6601013398","https://openalex.org/W6603326361","https://openalex.org/W6631792174","https://openalex.org/W6632891469"],"related_works":["https://openalex.org/W2057769265","https://openalex.org/W2338895903","https://openalex.org/W2024161258","https://openalex.org/W1911418903","https://openalex.org/W3044523069","https://openalex.org/W2136248167","https://openalex.org/W2126646394","https://openalex.org/W2211443823","https://openalex.org/W1987445442","https://openalex.org/W4211049090"],"abstract_inverted_index":{"Structurally":[0],"and":[1,11,42,54,59,67,86,149,153,159],"functionally":[2],"isolated":[3],"domains":[4,36,71,98],"in":[5,21,29,45,50,83,90,99,105,114,123,136,161,187],"biological":[6],"macromolecular":[7],"evolution,":[8],"both":[9],"natural":[10],"artificial,":[12],"are":[13,56,102],"largely":[14],"similar":[15],"to":[16,65,94,118,128,140],"\"schemata\",":[17],"building":[18],"blocks":[19],"(BBs),":[20],"evolutionary":[22,31,129,156],"computation":[23],"(EC).":[24],"The":[25],"problem":[26],"of":[27,62,79,97,144,147,151,169,175,181,186],"preserving":[28,68],"subsequent":[30],"searches":[32],"the":[33,77,142,173],"already":[34],"found":[35],"/":[37,72],"BBs":[38],"is":[39,172],"well":[40,48],"known":[41],"quite":[43],"relevant":[44],"biology":[46,53,85,106,124,158],"as":[47,49],"EC.":[51,91,115,137],"Both":[52],"EC":[55,160],"seeing":[57],"parallel":[58],"independent":[60],"development":[61],"several":[63],"approaches":[64,93,117,154],"identifying":[66],"previously":[69],"identified":[70],"BBs.":[73],"First,":[74],"we":[75],"notice":[76],"similarity":[78],"DNA":[80],"shuffling":[81],"methods":[82,113,131],"synthetic":[84],"multi-parent":[87],"recombination":[88],"algorithms":[89,152],"Furthermore,":[92],"computer":[95],"identification":[96,112],"proteins":[100],"that":[101],"being":[103],"developed":[104],"can":[107,125],"be":[108,126],"aligned":[109],"with":[110],"BB":[111],"Finally,":[116],"chimeric":[119],"protein":[120],"libraries":[121],"optimization":[122],"compared":[127],"search":[130],"based":[132],"on":[133],"probabilistic":[134],"models":[135],"We":[138],"propose":[139],"validate":[141],"prospects":[143],"mutual":[145],"exchange":[146],"ideas":[148],"transfer":[150,171],"between":[155],"systems":[157],"these":[162],"three":[163],"principal":[164],"directions.":[165],"A":[166],"crucial":[167],"aim":[168],"this":[170],"design":[174],"new":[176],"advanced":[177],"experimental":[178],"techniques":[179],"capable":[180],"solving":[182],"more":[183],"complex":[184],"problems":[185],"vitro":[188],"evolution.":[189]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
