{"id":"https://openalex.org/W2891363699","doi":"https://doi.org/10.1093/bioinformatics/bty614","title":"Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations","display_name":"Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations","publication_year":2018,"publication_date":"2018-07-19","ids":{"openalex":"https://openalex.org/W2891363699","doi":"https://doi.org/10.1093/bioinformatics/bty614","mag":"2891363699","pmid":"https://pubmed.ncbi.nlm.nih.gov/30423098"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty614","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty614","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i732/25702522/bty614.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i732/25702522/bty614.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069383911","display_name":"Alex Salazar","orcid":"https://orcid.org/0000-0002-8453-8769"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Alex N Salazar","raw_affiliation_strings":["Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands","Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002088014","display_name":"Thomas Abeel","orcid":"https://orcid.org/0000-0002-7205-7431"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I98358874","display_name":"Delft University of Technology","ror":"https://ror.org/02e2c7k09","country_code":"NL","type":"education","lineage":["https://openalex.org/I98358874"]}],"countries":["NL","US"],"is_corresponding":true,"raw_author_name":"Thomas Abeel","raw_affiliation_strings":["Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands","Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands","institution_ids":["https://openalex.org/I98358874"]},{"raw_affiliation_string":"Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5002088014"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I98358874"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6902,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.75248844,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"34","issue":"17","first_page":"i732","last_page":"i742"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.5630000233650208,"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":0.5630000233650208,"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":0.20990000665187836,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.05620000138878822,"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/genome","display_name":"Genome","score":0.8170816898345947},{"id":"https://openalex.org/keywords/synteny","display_name":"Synteny","score":0.737378716468811},{"id":"https://openalex.org/keywords/ptolemys-table-of-chords","display_name":"Ptolemy's table of chords","score":0.6966722011566162},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4803287088871002},{"id":"https://openalex.org/keywords/bacterial-genome-size","display_name":"Bacterial genome size","score":0.47268158197402954},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44271954894065857},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4165588319301605},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3620017170906067},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3129504323005676},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2689206302165985},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12007588148117065}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.8170816898345947},{"id":"https://openalex.org/C53702515","wikidata":"https://www.wikidata.org/wiki/Q971246","display_name":"Synteny","level":4,"score":0.737378716468811},{"id":"https://openalex.org/C46984397","wikidata":"https://www.wikidata.org/wiki/Q7257100","display_name":"Ptolemy's table of chords","level":2,"score":0.6966722011566162},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4803287088871002},{"id":"https://openalex.org/C3742359","wikidata":"https://www.wikidata.org/wiki/Q4839988","display_name":"Bacterial genome size","level":4,"score":0.47268158197402954},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44271954894065857},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4165588319301605},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3620017170906067},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3129504323005676},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2689206302165985},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12007588148117065},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D026801","descriptor_name":"Synteny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D026801","descriptor_name":"Synteny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D026801","descriptor_name":"Synteny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064349","descriptor_name":"Genome, Microbial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bty614","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty614","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i732/25702522/bty614.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30423098","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30423098","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":null},{"id":"pmh:oai:europepmc.org:5083551","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6129293","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6129293","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6129293","pdf_url":null,"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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:tudelft.nl:uuid:947742c9-840e-4a73-8e27-6b1bd66d5498","is_oa":false,"landing_page_url":"http://resolver.tudelft.nl/uuid:947742c9-840e-4a73-8e27-6b1bd66d5498","pdf_url":null,"source":{"id":"https://openalex.org/S4306400906","display_name":"Research Repository (Delft University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I98358874","host_organization_name":"Delft University of Technology","host_organization_lineage":["https://openalex.org/I98358874"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty614","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty614","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/17/i732/25702522/bty614.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320312414","display_name":"Oxford Nanopore Technologies","ror":"https://ror.org/04hyfx005"},{"id":"https://openalex.org/F4320328178","display_name":"BE-Basic Foundation","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2891363699.pdf"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W206171377","https://openalex.org/W319819633","https://openalex.org/W1519765314","https://openalex.org/W1868469711","https://openalex.org/W2002833133","https://openalex.org/W2003111456","https://openalex.org/W2005203688","https://openalex.org/W2012473911","https://openalex.org/W2013447902","https://openalex.org/W2019505357","https://openalex.org/W2024116008","https://openalex.org/W2041257508","https://openalex.org/W2058417246","https://openalex.org/W2064452752","https://openalex.org/W2070517644","https://openalex.org/W2074556793","https://openalex.org/W2079497788","https://openalex.org/W2106208020","https://openalex.org/W2107282968","https://openalex.org/W2114674713","https://openalex.org/W2126423997","https://openalex.org/W2131180151","https://openalex.org/W2138445042","https://openalex.org/W2143398242","https://openalex.org/W2143592941","https://openalex.org/W2153325555","https://openalex.org/W2158023121","https://openalex.org/W2161493476","https://openalex.org/W2164786886","https://openalex.org/W2165686834","https://openalex.org/W2166825456","https://openalex.org/W2179444328","https://openalex.org/W2194172909","https://openalex.org/W2397891977","https://openalex.org/W2416395093","https://openalex.org/W2547528004","https://openalex.org/W2606086658","https://openalex.org/W2607669908","https://openalex.org/W2760599003","https://openalex.org/W2767958753","https://openalex.org/W2776539412","https://openalex.org/W2781129742","https://openalex.org/W2950122868","https://openalex.org/W2950150251","https://openalex.org/W2952366981","https://openalex.org/W2953342537","https://openalex.org/W2963071637","https://openalex.org/W4210689220","https://openalex.org/W4211155627","https://openalex.org/W4230096730","https://openalex.org/W6639228707","https://openalex.org/W6729335427","https://openalex.org/W6744479686","https://openalex.org/W6745505986","https://openalex.org/W6746807042"],"related_works":["https://openalex.org/W2131180151","https://openalex.org/W2037172645","https://openalex.org/W4243565069","https://openalex.org/W2119233950","https://openalex.org/W2889029343","https://openalex.org/W2079327011","https://openalex.org/W2056973287","https://openalex.org/W3111025641","https://openalex.org/W2061340009","https://openalex.org/W2106726141"],"abstract_inverted_index":{"Motivation:":[0],"A":[1],"long-standing":[2],"limitation":[3],"in":[4,35,146,216],"comparative":[5],"genomic":[6],"studies":[7],"is":[8,32,46,102,188,201],"the":[9,17,36,57,80,96,157,170],"dependency":[10],"on":[11],"a":[12,27,48,66,75,90,99,103,124,147,208],"reference":[13],"genome,":[14],"which":[15],"hinders":[16],"spectrum":[18],"of":[19,29,59,82,92,98,143,163,172,176,225],"genetic":[20],"diversity":[21,81],"that":[22,53,186],"can":[23,42,54,191],"be":[24],"identified":[25],"across":[26,153],"population":[28],"organisms.":[30],"This":[31],"especially":[33],"true":[34],"microbial":[37,93],"world":[38],"where":[39],"genome":[40,83,109,198],"architectures":[41,58],"significantly":[43],"vary.":[44],"There":[45],"therefore":[47],"need":[49,97],"for":[50,78],"computational":[51],"methods":[52],"simultaneously":[55],"analyze":[56],"multiple":[60],"genomes":[61,145,215],"without":[62,95],"introducing":[63],"bias":[64],"from":[65],"reference.":[67,100],"Results:":[68],"In":[69],"this":[70],"article,":[71],"we":[72],"present":[73],"Ptolemy:":[74],"novel":[76],"method":[77],"studying":[79],"architectures-such":[84],"as":[85,114,118],"structural":[86,141,151,167],"variation":[87,152,168],"and":[88,169,180,190,195,222,228],"pan-genomes-across":[89],"collection":[91,149],"assemblies":[94],"Ptolemy":[101,164,187,200],"'top-down'":[104],"approach":[105],"to":[106],"compare":[107],"whole":[108],"assemblies.":[110],"Genomes":[111],"are":[112,120,236],"represented":[113],"labeled":[115],"multi-directed":[116],"graphs-known":[117],"quivers-which":[119],"then":[121],"merged":[122],"into":[123],"single,":[125],"canonical":[126,136],"quiver":[127,137],"by":[128,165],"identifying":[129],"'gene":[130],"anchors'":[131],"via":[132],"synteny":[133],"analysis.":[134],"The":[135],"represents":[138],"an":[139],"approximate,":[140],"alignment":[142],"all":[144],"given":[148],"encoding":[150],"(sub-)":[154],"populations":[155],"within":[156],"collection.":[158],"We":[159],"highlight":[160],"various":[161],"applications":[162],"analyzing":[166],"pan-genomes":[171],"different":[173],"datasets":[174],"composing":[175],"Mycobacterium,":[177],"Saccharomyces,":[178],"Escherichia":[179],"Shigella":[181],"species.":[182],"Our":[183],"results":[184],"show":[185],"flexible":[189],"handle":[192],"both":[193],"conserved":[194],"highly":[196],"dynamic":[197],"architectures.":[199],"user-friendly-requires":[202],"only":[203],"FASTA-formatted":[204],"assembly":[205],"along":[206],"with":[207,219],"corresponding":[209],"GFF-formatted":[210],"file-and":[211],"resource-friendly-can":[212],"align":[213],"24":[214],"\u223c10":[217],"mins":[218],"four":[220],"CPUs":[221],"<2":[223],"GB":[224],"RAM.":[226],"Availability":[227],"implementation:":[229],"Github:":[230],"https://github.com/AbeelLab/ptolemy.":[231],"Supplementary":[232,234],"information:":[233],"data":[235],"available":[237],"at":[238],"Bioinformatics":[239],"online.":[240]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2025-10-10T00:00:00"}