{"id":"https://openalex.org/W4389207770","doi":"https://doi.org/10.1186/s13015-023-00239-x","title":"New algorithms for structure informed genome rearrangement","display_name":"New algorithms for structure informed genome rearrangement","publication_year":2023,"publication_date":"2023-12-01","ids":{"openalex":"https://openalex.org/W4389207770","doi":"https://doi.org/10.1186/s13015-023-00239-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/38037088"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-023-00239-x","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1186/s13015-023-00239-x","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13015-023-00239-x.pdf","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/s13015-023-00239-x.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093390705","display_name":"Eden Ozeri","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Eden Ozeri","raw_affiliation_strings":["Department of Computer Science, Ben Gurion University of the Negev, Be'er Sheva, Israel. edenozery@gmail.com","Department of Computer Science, Ben Gurion University of the Negev, Be\u2019er Sheva, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben Gurion University of the Negev, Be'er Sheva, Israel. edenozery@gmail.com","institution_ids":["https://openalex.org/I124227911"]},{"raw_affiliation_string":"Department of Computer Science, Ben Gurion University of the Negev, Be\u2019er Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082025487","display_name":"Meirav Zehavi","orcid":"https://orcid.org/0000-0002-3636-5322"},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Meirav Zehavi","raw_affiliation_strings":["Department of Computer Science, Ben Gurion University of the Negev, Be'er Sheva, Israel","Department of Computer Science, Ben Gurion University of the Negev, Be\u2019er Sheva, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben Gurion University of the Negev, Be'er Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]},{"raw_affiliation_string":"Department of Computer Science, Ben Gurion University of the Negev, Be\u2019er Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048383219","display_name":"Michal Ziv-Ukelson","orcid":null},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Michal Ziv-Ukelson","raw_affiliation_strings":["Department of Computer Science, Ben Gurion University of the Negev, Be'er Sheva, Israel","Department of Computer Science, Ben Gurion University of the Negev, Be\u2019er Sheva, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben Gurion University of the Negev, Be'er Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]},{"raw_affiliation_string":"Department of Computer Science, Ben Gurion University of the Negev, Be\u2019er Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5093390705"],"corresponding_institution_ids":["https://openalex.org/I124227911"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.24759077,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"18","issue":"1","first_page":"17","last_page":"17"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9993000030517578,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9993000030517578,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9879999756813049,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.984499990940094,"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/tree","display_name":"Tree (set theory)","score":0.5441932678222656},{"id":"https://openalex.org/keywords/order","display_name":"Order (exchange)","score":0.5272102355957031},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.4823583960533142},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45204973220825195},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.4302385449409485},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37718844413757324},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3735872209072113},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.34001654386520386}],"concepts":[{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5441932678222656},{"id":"https://openalex.org/C182306322","wikidata":"https://www.wikidata.org/wiki/Q1779371","display_name":"Order (exchange)","level":2,"score":0.5272102355957031},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.4823583960533142},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45204973220825195},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.4302385449409485},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37718844413757324},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3735872209072113},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.34001654386520386},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13015-023-00239-x","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1186/s13015-023-00239-x","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13015-023-00239-x.pdf","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:38037088","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38037088","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10691145","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10691145","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10691145/pdf/13015_2023_Article_239.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms Mol Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:00348fcd7c5e4f7c94a97460d61e8250","is_oa":true,"landing_page_url":"https://doaj.org/article/00348fcd7c5e4f7c94a97460d61e8250","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, Vol 18, Iss 1, Pp 1-37 (2023)","raw_type":"article"},{"id":"pmh:oai:drops-oai.dagstuhl.de:17045","is_oa":true,"landing_page_url":"https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.11","pdf_url":null,"source":{"id":"https://openalex.org/S4377196569","display_name":"DROPS (Schloss Dagstuhl \u2013 Leibniz Center for Informatics)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2799853480","host_organization_name":"Schloss Dagstuhl \u2013 Leibniz Center for Informatics","host_organization_lineage":["https://openalex.org/I2799853480"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"InProceedings"},{"id":"doi:10.4230/lipics.wabi.2022.11","is_oa":true,"landing_page_url":"https://doi.org/10.4230/lipics.wabi.2022.11","pdf_url":null,"source":{"id":"https://openalex.org/S7407052059","display_name":"Dagstuhl Research Online Publication Server","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":""}],"best_oa_location":{"id":"doi:10.1186/s13015-023-00239-x","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1186/s13015-023-00239-x","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13015-023-00239-x.pdf","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.550000011920929,"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions"}],"awards":[{"id":"https://openalex.org/G1071907501","display_name":null,"funder_award_id":"939/18","funder_id":"https://openalex.org/F4320322252","funder_display_name":"Israel Science Foundation"},{"id":"https://openalex.org/G7702557058","display_name":null,"funder_award_id":"1176/18","funder_id":"https://openalex.org/F4320322252","funder_display_name":"Israel Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"},{"id":"https://openalex.org/F4320323278","display_name":"Council for Higher Education","ror":"https://ror.org/036mqp197"},{"id":"https://openalex.org/F4320335375","display_name":"Planning and Budgeting Committee of the Council for Higher Education of Israel","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4389207770.pdf","grobid_xml":"https://content.openalex.org/works/W4389207770.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W201898492","https://openalex.org/W1483191758","https://openalex.org/W1486392319","https://openalex.org/W1488696346","https://openalex.org/W1553810969","https://openalex.org/W1563463423","https://openalex.org/W1565130750","https://openalex.org/W1568869859","https://openalex.org/W1986708244","https://openalex.org/W1989978323","https://openalex.org/W1990321397","https://openalex.org/W2007321246","https://openalex.org/W2014444740","https://openalex.org/W2024491681","https://openalex.org/W2032905455","https://openalex.org/W2044007697","https://openalex.org/W2049260160","https://openalex.org/W2053762233","https://openalex.org/W2063731178","https://openalex.org/W2068896404","https://openalex.org/W2072483773","https://openalex.org/W2088316404","https://openalex.org/W2088853706","https://openalex.org/W2095867210","https://openalex.org/W2097103726","https://openalex.org/W2110560983","https://openalex.org/W2120172561","https://openalex.org/W2130849966","https://openalex.org/W2142165164","https://openalex.org/W2144175267","https://openalex.org/W2149628296","https://openalex.org/W2152555393","https://openalex.org/W2153375254","https://openalex.org/W2157761435","https://openalex.org/W2167034750","https://openalex.org/W2223524248","https://openalex.org/W2265278721","https://openalex.org/W2527473185","https://openalex.org/W2801774617","https://openalex.org/W2963396431","https://openalex.org/W2980510672","https://openalex.org/W3042408110","https://openalex.org/W3081786092","https://openalex.org/W3095538133","https://openalex.org/W4205982804","https://openalex.org/W4213205621"],"related_works":["https://openalex.org/W2980963558","https://openalex.org/W1882246857","https://openalex.org/W3103304230","https://openalex.org/W2185360082","https://openalex.org/W1992365905","https://openalex.org/W4287664878","https://openalex.org/W3212023493","https://openalex.org/W1991411408","https://openalex.org/W2066456778","https://openalex.org/W4288278856"],"abstract_inverted_index":{"We":[0],"define":[1,59],"two":[2],"new":[3],"computational":[4],"problems":[5,26],"in":[6,202,237,255,274,291,327,344,401],"the":[7,25,40,49,60,69,74,79,88,95,109,122,126,144,153,180,186,191,217,227,230,233,238,249,256,262,271,306,316,319,323,328,338,345,357,367,376,380,388,393,424],"domain":[8],"of":[9,73,97,108,220,222,229,235,251,261,264,309,311,318,325,340,379,387,392,395,429,438],"perfect":[10],"genome":[11,116],"rearrangements,":[12],"and":[13,29,33,43,125,152,168,174,207,232,240,244,253,279,296,333,342,348,359,406,421,426],"propose":[14],"three":[15],"algorithms":[16],"to":[17,38,44,106,160,164,190,351,361,374,423],"solve":[18],"them.":[19],"The":[20,85,130,195,284,369,411],"rearrangement":[21,63,117,156],"scenarios":[22],"modeled":[23],"by":[24,101],"consider":[27,162],"Reversal":[28],"Block":[30],"Interchange":[31],"operations,":[32,176],"a":[34,114,223,312,385,416,436],"PQ-tree":[35,80,86,124,181],"is":[36,81,91,104,119,158,216,226,268,305,315,322,372,399,413],"utilized":[37],"guide":[39],"allowed":[41],"operations":[42],"compute":[45],"their":[46],"weights.":[47],"In":[48],"first":[50,196],"problem,":[51,132],"[Formula:":[52,133,140,165,169,199,203,208,213,241,245,265,275,280,288,292,297,302,330,334,352,362,396,402,407],"see":[53,56,134,137,141,166,170,200,204,209,214,242,246,266,276,281,289,293,298,303,331,335,353,363,397,403,408],"text]":[54,135,167,171,201,205,210,215,243,247,267,277,282,290,294,299,304,332,336,354,364,398,404,409],"([Formula:":[55,136],"text]),":[57,138],"we":[58,66],"basic":[61],"structure-informed":[62,115],"measure.":[64],"Here,":[65],"assume":[67],"that":[68,94,107],"gene":[70,75,89,98,111,128,145,172,188,193,432],"order":[71,146,189],"members":[72,147],"cluster":[76,90],"from":[77,185,356,366,435],"which":[78],"constructed":[82],"are":[83,148,248,337],"permutations.":[84],"representing":[87],"ordered":[92,123],"such":[93],"series":[96],"IDs":[99],"spelled":[100],"its":[102],"leaves":[103,236,326],"equivalent":[105],"reference":[110,187],"order.":[112,129,194],"Then,":[113],"distance":[118],"computed":[120],"between":[121],"target":[127,192],"second":[131,285,381],"generalizes":[139],"text],":[142],"where":[143,212,301],"not":[149],"necessarily":[150],"permutations":[151],"structure":[154],"informed":[155,182],"measure":[157],"extended":[159],"also":[161],"up":[163,350,360],"insertion":[173],"deletion":[175],"respectively,":[177,347],"when":[178],"modelling":[179],"divergence":[183],"process":[184],"algorithm":[197,272,286,371,412],"solves":[198,287,384],"time":[206,278,295,405],"space,":[211,300],"maximum":[218,307],"number":[219,234,250,308,324,339],"children":[221,310],"node,":[224,313],"n":[225,314],"length":[228,317],"string":[231],"tree,":[239,257,329,346],"P-nodes":[252,341],"Q-nodes":[254,343],"respectively.":[258],"If":[259],"one":[260,391],"penalties":[263,394],"0,":[269],"then":[270],"runs":[273],"space.":[283,410],"string,":[320],"m":[321],"allowing":[349],"deletions":[355,365],"tree":[358],"string.":[368],"third":[370],"intended":[373],"reduce":[375],"space":[377],"complexity":[378],"algorithm.":[382],"It":[383],"variant":[386],"problem":[389],"(where":[390],"0)":[400],"implemented":[414],"as":[415],"software":[417],"tool,":[418],"denoted":[419],"MEM-Rearrange,":[420],"applied":[422],"comparative":[425],"evolutionary":[427],"analysis":[428],"59":[430],"chromosomal":[431],"clusters":[433],"extracted":[434],"dataset":[437],"1487":[439],"prokaryotic":[440],"genomes.":[441]},"counts_by_year":[],"updated_date":"2026-06-13T06:13:01.061226","created_date":"2025-10-10T00:00:00"}
