{"id":"https://openalex.org/W2100923859","doi":"https://doi.org/10.1093/bioinformatics/bti060","title":"ParIS Genome Rearrangement server","display_name":"ParIS Genome Rearrangement server","publication_year":2004,"publication_date":"2004-10-12","ids":{"openalex":"https://openalex.org/W2100923859","doi":"https://doi.org/10.1093/bioinformatics/bti060","mag":"2100923859","pmid":"https://pubmed.ncbi.nlm.nih.gov/15479709"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti060","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/6/817/48962401/bioinformatics_21_6_817.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/6/817/48962401/bioinformatics_21_6_817.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015015590","display_name":"Ida Mikl\u00f3s","orcid":"https://orcid.org/0000-0002-7074-4019"},"institutions":[{"id":"https://openalex.org/I106118109","display_name":"E\u00f6tv\u00f6s Lor\u00e1nd University","ror":"https://ror.org/01jsq2704","country_code":"HU","type":"education","lineage":["https://openalex.org/I106118109"]},{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"government","lineage":["https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"I. Mikl\u00f3s","raw_affiliation_strings":["Theoretical Biology and Ecology Modelling Group, Hungarian Academy of Sciences and E\u00f6tv\u00f6s Lor\u00e1nd University, P\u00e1zm\u00e1ny P\u00e9ter S\u00e9t\u00e1ny 1/c. H-1117 Budapest, Hungary. miklosi@ramet.elte.hu","Theoretical Biology and Ecology Modelling Group, Hungarian Academy of Sciences and E\u00f6tv\u00f6s Lor\u00e1nd University P\u00e1zm\u00e1ny P\u00e9ter S\u00e9t\u00e1ny 1/c. H-1117 Budapest, Hunga ...#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Ecology Modelling Group, Hungarian Academy of Sciences and E\u00f6tv\u00f6s Lor\u00e1nd University, P\u00e1zm\u00e1ny P\u00e9ter S\u00e9t\u00e1ny 1/c. H-1117 Budapest, Hungary. miklosi@ramet.elte.hu","institution_ids":["https://openalex.org/I106118109","https://openalex.org/I7597260"]},{"raw_affiliation_string":"Theoretical Biology and Ecology Modelling Group, Hungarian Academy of Sciences and E\u00f6tv\u00f6s Lor\u00e1nd University P\u00e1zm\u00e1ny P\u00e9ter S\u00e9t\u00e1ny 1/c. H-1117 Budapest, Hunga ...#TAB#","institution_ids":["https://openalex.org/I106118109","https://openalex.org/I7597260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091869721","display_name":"P\u00e9ter Ittz\u00e9s","orcid":null},"institutions":[{"id":"https://openalex.org/I4210099710","display_name":"Collegium Budapest","ror":"https://ror.org/00j39nx61","country_code":"HU","type":"other","lineage":["https://openalex.org/I4210099710"]},{"id":"https://openalex.org/I4210161853","display_name":"Budapest Institute","ror":"https://ror.org/050hvq478","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210161853"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"P. Ittz\u00e9s","raw_affiliation_strings":["Collegium Budapest, Institute for Advanced Study Szenth\u00e1roms\u00e1g u. 2. H-1014 Budapest, Hungary#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Collegium Budapest, Institute for Advanced Study Szenth\u00e1roms\u00e1g u. 2. H-1014 Budapest, Hungary#TAB#","institution_ids":["https://openalex.org/I4210099710","https://openalex.org/I4210161853"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079496228","display_name":"Jotun Hein","orcid":"https://orcid.org/0000-0002-8100-0824"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"J. Hein","raw_affiliation_strings":["Genome Analysis and Bioinformatics Group, Oxford Centre for Gene Function, Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK","Genome Analysis and Bioinformatics Group, Oxford Centre for Gene Function, Department of Statistics, Oxford University 1 South Parks Road, Oxford OX1 3TG, UK#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Analysis and Bioinformatics Group, Oxford Centre for Gene Function, Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Genome Analysis and Bioinformatics Group, Oxford Centre for Gene Function, Department of Statistics, Oxford University 1 South Parks Road, Oxford OX1 3TG, UK#TAB#","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5015015590"],"corresponding_institution_ids":["https://openalex.org/I106118109","https://openalex.org/I7597260"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.037,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.77443804,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"21","issue":"6","first_page":"817","last_page":"820"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9973999857902527,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9925000071525574,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.609184741973877},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5947468876838684},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5780711770057678},{"id":"https://openalex.org/keywords/unix","display_name":"Unix","score":0.4637930989265442},{"id":"https://openalex.org/keywords/ensembl","display_name":"Ensembl","score":0.4283674359321594},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.416763037443161},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36397644877433777},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3369837999343872},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2828689217567444},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2713642716407776},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.18171781301498413},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.16431233286857605},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.15590384602546692}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.609184741973877},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5947468876838684},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5780711770057678},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.4637930989265442},{"id":"https://openalex.org/C141674004","wikidata":"https://www.wikidata.org/wiki/Q1344256","display_name":"Ensembl","level":5,"score":0.4283674359321594},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.416763037443161},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36397644877433777},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3369837999343872},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2828689217567444},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2713642716407776},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.18171781301498413},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.16431233286857605},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.15590384602546692}],"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":"D002869","descriptor_name":"Chromosome Aberrations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002869","descriptor_name":"Chromosome Aberrations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002869","descriptor_name":"Chromosome Aberrations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004252","descriptor_name":"DNA Mutational Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bti060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti060","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/6/817/48962401/bioinformatics_21_6_817.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15479709","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15479709","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:a75b6817-3e9a-4237-adf9-4cbfd6d30de4","is_oa":false,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:a75b6817-3e9a-4237-adf9-4cbfd6d30de4","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PubMed (http://www.ncbi.nlm.nih.gov/pubmed/)","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti060","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti060","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/6/817/48962401/bioinformatics_21_6_817.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10","score":0.7699999809265137}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2100923859.pdf","grobid_xml":"https://content.openalex.org/works/W2100923859.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W48572399","https://openalex.org/W1971383554","https://openalex.org/W1975922463","https://openalex.org/W1988577833","https://openalex.org/W1989978323","https://openalex.org/W1993361911","https://openalex.org/W2068426944","https://openalex.org/W2143420603","https://openalex.org/W2167792089"],"related_works":["https://openalex.org/W2321656188","https://openalex.org/W4233194547","https://openalex.org/W2002128513","https://openalex.org/W2165640100","https://openalex.org/W2462807523","https://openalex.org/W4205546893","https://openalex.org/W2092874662","https://openalex.org/W1965942136","https://openalex.org/W2078545882","https://openalex.org/W4200520333"],"abstract_inverted_index":{"SUMMARY:":[0],"ParIS":[1],"Genome":[2],"Rearrangement":[3],"is":[4],"a":[5,9,28,32,79,91,94,109],"web":[6],"server":[7,26,97],"for":[8],"Bayesian":[10],"analysis":[11],"of":[12,40,57,59,70,73,111],"unichromosomal":[13],"genome":[14,65],"pairs.":[15],"The":[16,25,45],"underlying":[17],"model":[18],"allows":[19],"inversions,":[20],"transpositions":[21],"and":[22,37,84,108],"inverted":[23],"transpositions.":[24],"generates":[27],"Markov":[29],"chain":[30],"using":[31],"Partial":[33],"Importance":[34],"Sampler":[35],"technique,":[36],"samples":[38],"trajectories":[39],"mutations":[41,60,74],"from":[42],"this":[43],"chain.":[44],"user":[46],"can":[47,99],"specify":[48],"several":[49],"marginalizations":[50],"to":[51,62],"the":[52,54],"posterior:":[53],"posterior":[55],"distribution":[56,69],"number":[58,72],"needed":[61],"transform":[63],"one":[64],"into":[66],"another,":[67],"length":[68],"mutations,":[71],"that":[75,98],"have":[76],"occurred":[77],"at":[78],"given":[80],"site.":[81],"Both":[82],"text":[83],"graphical":[85],"outputs":[86],"are":[87],"available.":[88],"We":[89],"provide":[90],"limited":[92],"server,":[93],"downloadable":[95],"unlimited":[96],"be":[100],"installed":[101],"locally":[102],"on":[103],"any":[104],"linux/Unix":[105],"operating":[106],"system,":[107],"database":[110],"mitochondrial":[112],"gene":[113],"orders.":[114]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
