{"id":"https://openalex.org/W2128379289","doi":"https://doi.org/10.1186/1748-7188-8-13","title":"Unrooted unordered homeomorphic subtree alignment of RNA trees","display_name":"Unrooted unordered homeomorphic subtree alignment of RNA trees","publication_year":2013,"publication_date":"2013-04-16","ids":{"openalex":"https://openalex.org/W2128379289","doi":"https://doi.org/10.1186/1748-7188-8-13","mag":"2128379289","pmid":"https://pubmed.ncbi.nlm.nih.gov/23590940"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-8-13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-8-13","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-8-13","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-8-13","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036607839","display_name":"Nimrod Milo","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":"Nimrod Milo","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086253860","display_name":"Shay Zakov","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shay Zakov","raw_affiliation_strings":["Department of Computer Science and Engineering, UC San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, UC San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024329862","display_name":"Erez Katzenelson","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":"Erez Katzenelson","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083255118","display_name":"Eitan Bachmat","orcid":"https://orcid.org/0000-0001-7153-100X"},"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":"Eitan Bachmat","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006177800","display_name":"Yefim Dinitz","orcid":"https://orcid.org/0009-0005-4211-4182"},"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":"Yefim Dinitz","raw_affiliation_strings":["Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University of the Negev, Beer-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, Beer-Sheva, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel","institution_ids":["https://openalex.org/I124227911"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5036607839"],"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":1.0481,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.77026775,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"8","issue":"1","first_page":"13","last_page":"13"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998000264167786,"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":0.9998000264167786,"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/T11482","display_name":"RNA modifications and cancer","score":0.9995999932289124,"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/T10604","display_name":"RNA Research and Splicing","score":0.9979000091552734,"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/computer-science","display_name":"Computer science","score":0.5533426403999329},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37216466665267944},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.35074687004089355},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2189941108226776}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5533426403999329},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37216466665267944},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.35074687004089355},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2189941108226776}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1748-7188-8-13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-8-13","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-8-13","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:23590940","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23590940","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:escholarship.org/ark:/13030/qt7qr8h077","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/7qr8h077","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, vol 8, iss 1","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2760095","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3765143","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:qt7qr8h077","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/7qr8h077","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Milo, Nimrod; Zakov, Shay; Katzenelson, Erez; Bachmat, Eitan; Dinitz, Yefim; & Ziv-Ukelson, Michal. (2013). Unrooted unordered homeomorphic subtree alignment of RNA trees. Algorithms for Molecular Biology, 8(1), 13. doi: http://dx.doi.org/10.1186/1748-7188-8-13. Retrieved from: http://www.escholarship.org/uc/item/7qr8h077","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-8-13","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-8-13","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-8-13","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322252","display_name":"Israel Science Foundation","ror":"https://ror.org/04sazxf24"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2128379289.pdf","grobid_xml":"https://content.openalex.org/works/W2128379289.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W108777047","https://openalex.org/W139823962","https://openalex.org/W1481362230","https://openalex.org/W1484020851","https://openalex.org/W1495524224","https://openalex.org/W1495979635","https://openalex.org/W1513400187","https://openalex.org/W1541543831","https://openalex.org/W1543796220","https://openalex.org/W1557536303","https://openalex.org/W1630774304","https://openalex.org/W1902180264","https://openalex.org/W1950410402","https://openalex.org/W1964119857","https://openalex.org/W1969357318","https://openalex.org/W1969781519","https://openalex.org/W1977545325","https://openalex.org/W1978036746","https://openalex.org/W1978478796","https://openalex.org/W1980532649","https://openalex.org/W1983955493","https://openalex.org/W1996641400","https://openalex.org/W2008288996","https://openalex.org/W2011975945","https://openalex.org/W2017372245","https://openalex.org/W2018414460","https://openalex.org/W2020556510","https://openalex.org/W2021202955","https://openalex.org/W2044485666","https://openalex.org/W2046953300","https://openalex.org/W2054104509","https://openalex.org/W2056708848","https://openalex.org/W2060296641","https://openalex.org/W2072851563","https://openalex.org/W2074231493","https://openalex.org/W2076963640","https://openalex.org/W2082317627","https://openalex.org/W2084224084","https://openalex.org/W2085899914","https://openalex.org/W2086974119","https://openalex.org/W2090010485","https://openalex.org/W2091828646","https://openalex.org/W2102225325","https://openalex.org/W2103250001","https://openalex.org/W2106184136","https://openalex.org/W2125690626","https://openalex.org/W2128356721","https://openalex.org/W2128695242","https://openalex.org/W2134861301","https://openalex.org/W2136735223","https://openalex.org/W2138007734","https://openalex.org/W2147828873","https://openalex.org/W2149342630","https://openalex.org/W2162224067","https://openalex.org/W2166481425","https://openalex.org/W2169528473","https://openalex.org/W2171881599","https://openalex.org/W2397172274","https://openalex.org/W4212877087","https://openalex.org/W4236207470","https://openalex.org/W4251866352","https://openalex.org/W4255375128"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{":":[0],"We":[1,24],"generalize":[2],"some":[3,340],"current":[4],"approaches":[5],"for":[6,90,134,152,165,171,242,356],"RNA":[7,284,308],"tree":[8,53,142],"alignment,":[9],"which":[10,37,275,296,314],"are":[11,109,214],"traditionally":[12],"confined":[13],"to":[14,18,39,72,140,160,185,291,335],"ordered":[15,46,76,323,349],"rooted":[16,50,74,322,348],"mappings,":[17],"also":[19],"consider":[20],"unordered":[21,85],"unrooted":[22,52,84],"mappings.":[23],"define":[25],"the":[26,63,73,81,110,114,119,141,146,157,176,222,237,246,255,263,320,346],"Homeomorphic":[27],"Subtree":[28],"Alignment":[29],"problem":[30,64,180],"(HSA),":[31],"and":[32,49,94,107,118,132,136,193,202,209,244,251,277,288,306,354],"present":[33],"a":[34,172,271,292],"new":[35,169,312],"algorithm":[36,56,97,241,264],"applies":[38],"several":[40],"modes,":[41],"combining":[42],"global":[43],"or":[44,47,51,69,230],"local,":[45],"unordered,":[48],"alignments.":[54],"Our":[55],"generalizes":[57],"previous":[58,150],"algorithms":[59,151,170],"that":[60,89,329],"either":[61],"solved":[62,215],"in":[65,123,216,254,295,362],"an":[66,99],"asymmetric":[67],"manner,":[68],"were":[70],"restricted":[71],"and/or":[75],"cases.":[77],"Focusing":[78],"here":[79],"on":[80],"most":[82],"general":[83,154],"case,":[86],"we":[87,167,297],"show":[88],"input":[91,197],"trees":[92],"T":[93],"S,":[95],"our":[96,330,357],"has":[98],"O(nTnS":[100],"+":[101,218],"min(dT,dS)LTLS)":[102],"time":[103,147,163,240],"complexity,":[104],"where":[105,204,258],"nT,LT":[106],"dT":[108,127],"number":[111,115],"of":[112,116,149,156,175,188,199,224,249,283,303],"nodes,":[113],"leaves,":[117],"maximum":[120],"node":[121],"degree":[122],"T,":[124],"respectively":[125],"(satisfying":[126],"\u2264":[128,130,206],"LT":[129],"nT),":[131],"similarly":[133],"nS,LS":[135],"dS":[137],"with":[138,342],"respect":[139],"S.":[143],"This":[144,235],"improves":[145,245],"complexity":[148],"less":[153],"variants":[155],"problem.In":[158],"order":[159],"obtain":[161],"this":[162,189],"bound":[164],"HSA,":[166],"developed":[168],"generalized":[173],"variant":[174],"Min-Cost":[177],"Bipartite":[178],"Matching":[179],"(MCM),":[181],"as":[182,184,270,286],"well":[183],"two":[186,196],"derivatives":[187,213],"problem,":[190],"entitled":[191],"All-Cavity-MCM":[192,252],"All-Pairs-Cavity-MCM.":[194],"For":[195],"sets":[198],"size":[200],"n":[201,205,259],"m,":[203,207],"MCM":[208,250],"both":[210],"its":[211],"cavity":[212],"O(n3":[217],"nm)":[219],"time,":[220],"without":[221],"usage":[223],"priority":[225],"queues":[226],"(e.g.":[227],"Fibonacci":[228],"heaps)":[229],"other":[231],"complex":[232],"data":[233],"structures.":[234],"gives":[236],"first":[238],"cubic":[239],"All-Pairs-Cavity-MCM,":[243],"running":[247],"times":[248],"problems":[253],"unbalanced":[256],"case":[257],"\u226a":[260],"m.We":[261],"implemented":[262],"(in":[265],"all":[266],"modes":[267],"mentioned":[268],"above)":[269],"graphical":[272],"software":[273],"tool":[274,358],"computes":[276],"displays":[278],"similarities":[279,313],"between":[280,339],"secondary":[281],"structures":[282],"given":[285],"input,":[287],"employed":[289],"it":[290],"preliminary":[293],"experiment":[294],"ran":[298],"all-against-all":[299],"inter-family":[300],"pairwise":[301],"alignments":[302],"RNAse":[304],"P":[305],"Hammerhead":[307],"family":[309],"members,":[310],"exposing":[311],"could":[315],"not":[316],"be":[317,333,360],"detected":[318],"by":[319],"traditional":[321,347],"alignment":[324,350],"approaches.":[325,351],"The":[326],"results":[327],"demonstrate":[328],"approach":[331],"can":[332,359],"used":[334],"expose":[336],"structural":[337],"similarity":[338],"RNAs":[341],"higher":[343],"sensitivity":[344],"than":[345],"Source":[352],"code":[353],"web-interface":[355],"found":[361],"http://www.cs.bgu.ac.il/\\~negevcb/FRUUT.":[363]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}