Publicação
GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
| Resumo: | Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens. |
|---|---|
| Autores principais: | Zhou, Zhemin |
| Outros Autores: | Alikhan, Nabil-Fareed; Sergeant, Martin; Luhmann, Nina; Vaz, Cátia; Francisco, Alexandre; Carrico, Joao; Achtman, Mark |
| Assunto: | Bacterial genome GrapeTree Genoma bacteriano |
| Ano: | 2018 |
| País: | Portugal |
| Tipo de documento: | artigo |
| Tipo de acesso: | acesso restrito |
| Instituição associada: | Instituto Politécnico de Lisboa |
| Idioma: | inglês |
| Origem: | Repositório Científico do Instituto Politécnico de Lisboa |
| _version_ | 1866887514255523840 |
|---|---|
| author | Zhou, Zhemin |
| author2 | Alikhan, Nabil-Fareed Sergeant, Martin Luhmann, Nina Vaz, Cátia Francisco, Alexandre Carrico, Joao Achtman, Mark |
| author2_role | author author author author author author author |
| author_facet | Zhou, Zhemin Alikhan, Nabil-Fareed Sergeant, Martin Luhmann, Nina Vaz, Cátia Francisco, Alexandre Carrico, Joao Achtman, Mark |
| author_role | author |
| contributor_name_str_mv | RCIPL |
| country_str | PT |
| creators_json_txt | [{\"Person.name\":\"Zhou, Zhemin\",\"Person.identifier.orcid\":\"0000-0001-9783-0366\"},{\"Person.name\":\"Alikhan, Nabil-Fareed\",\"Person.identifier.orcid\":\"0000-0002-1243-0767\"},{\"Person.name\":\"Sergeant, Martin\",\"Person.identifier.orcid\":\"0000-0001-7264-2668\"},{\"Person.name\":\"Luhmann, Nina\",\"Person.identifier.orcid\":\"0000-0001-8112-7027\"},{\"Person.name\":\"Vaz, Cátia\",\"Person.identifier.orcid\":\"0000-0001-6074-3074\"},{\"Person.name\":\"Francisco, Alexandre\",\"Person.identifier.orcid\":\"0000-0003-4852-1641\"},{\"Person.name\":\"Carrico, Joao\",\"Person.identifier.orcid\":\"0000-0002-5274-2722\"},{\"Person.name\":\"Achtman, Mark\",\"Person.identifier.orcid\":\"0000-0001-6815-0070\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | RCIPL |
| datacite.creators.creator.creatorName.fl_str_mv | Zhou, Zhemin Alikhan, Nabil-Fareed Sergeant, Martin Luhmann, Nina Vaz, Cátia Francisco, Alexandre Carrico, Joao Achtman, Mark |
| datacite.date.Accepted.fl_str_mv | 2018-09-01T00:00:00Z |
| datacite.date.available.fl_str_mv | 2018-11-28T11:56:44Z |
| datacite.date.embargoed.fl_str_mv | 2018-11-28T11:56:44Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_16ec |
| datacite.subjects.subject.fl_str_mv | Bacterial genome GrapeTree Genoma bacteriano |
| datacite.titles.title.fl_str_mv | GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens |
| dc.contributor.none.fl_str_mv | RCIPL |
| dc.creator.none.fl_str_mv | Zhou, Zhemin Alikhan, Nabil-Fareed Sergeant, Martin Luhmann, Nina Vaz, Cátia Francisco, Alexandre Carrico, Joao Achtman, Mark |
| dc.date.Accepted.fl_str_mv | 2018-09-01T00:00:00Z |
| dc.date.available.fl_str_mv | 2018-11-28T11:56:44Z |
| dc.date.embargoed.fl_str_mv | 2018-11-28T11:56:44Z |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | http://hdl.handle.net/10400.21/9099 |
| dc.language.none.fl_str_mv | eng |
| dc.publisher.none.fl_str_mv | Cold Spring Harbor Laboratory Press |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_16ec |
| dc.subject.none.fl_str_mv | Bacterial genome GrapeTree Genoma bacteriano |
| dc.title.fl_str_mv | GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_6501 |
| description | Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens. |
| dirty | 0 |
| eu_rights_str_mv | restrictedAccess |
| format | article |
| fulltext.url.fl_str_mv | https://repositorio.ipl.pt/bitstreams/0e745261-eae8-4ea1-ad67-35330075f169/download |
| id | ripl_efef9d86ec558dd08ce13f7faebb0149 |
| identifier.url.fl_str_mv | http://hdl.handle.net/10400.21/9099 |
| instacron_str | ipl |
| institution | Instituto Politécnico de Lisboa |
| instname_str | Instituto Politécnico de Lisboa |
| language | eng |
| network_acronym_str | ripl |
| network_name_str | Repositório Científico do Instituto Politécnico de Lisboa |
| oai_identifier_str | oai:repositorio.ipl.pt:10400.21/9099 |
| organization_str_mv | urn:organizationAcronym:ipl |
| person_str_mv | Zhou, Zhemin Zhou, Zhemin http://orcid.org/0000-0001-9783-0366 0000-0001-9783-0366 Alikhan, Nabil-Fareed Alikhan, Nabil-Fareed http://orcid.org/0000-0002-1243-0767 0000-0002-1243-0767 Sergeant, Martin Sergeant, Martin http://orcid.org/0000-0001-7264-2668 0000-0001-7264-2668 Luhmann, Nina Luhmann, Nina http://orcid.org/0000-0001-8112-7027 0000-0001-8112-7027 Vaz, Cátia Vaz, Cátia https://www.ciencia-id.pt/8718-741E-BBD9 8718-741E-BBD9 http://orcid.org/0000-0001-6074-3074 0000-0001-6074-3074 Francisco, Alexandre Francisco, Alexandre http://orcid.org/0000-0003-4852-1641 0000-0003-4852-1641 Carrico, Joao Carrico, Joao http://orcid.org/0000-0002-5274-2722 0000-0002-5274-2722 Achtman, Mark Achtman, Mark http://orcid.org/0000-0001-6815-0070 0000-0001-6815-0070 |
| publishDate | 2018 |
| publisher.none.fl_str_mv | Cold Spring Harbor Laboratory Press |
| reponame_str | Repositório Científico do Instituto Politécnico de Lisboa |
| repository_id_str | urn:repositoryAcronym:ripl |
| service_str_mv | urn:repositoryAcronym:ripl |
| spelling | engCold Spring Harbor Laboratory Presspt_PTCurrent methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. GrapeTree also implements a novel minimum spanning tree algorithm (MSTree V2) to reconstruct genetic relationships despite high levels of missing data. GrapeTree is a stand-alone package for investigating phylogenetic trees plus associated metadata and is also integrated into EnteroBase to facilitate cutting edge navigation of genomic relationships among bacterial pathogens.application/pdfpt_PTGrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogensPersonalZhou, ZheminDSpacehttp://dspace.org/items/5b25736a-a5a2-4ce9-8d9d-43ca1dc07001DSpacehttp://dspace.org/items/5b25736a-a5a2-4ce9-8d9d-43ca1dc07001ZhouZheminORCIDhttp://orcid.org0000-0001-9783-0366PersonalAlikhan, Nabil-FareedDSpacehttp://dspace.org/items/3a6d3309-b0ea-4ab8-b063-7116e51413dcDSpacehttp://dspace.org/items/3a6d3309-b0ea-4ab8-b063-7116e51413dcAlikhanNabil-FareedORCIDhttp://orcid.org0000-0002-1243-0767Researcher IDhttps://www.researcherid.comB-7824-2017Scopus Author IDhttps://www.scopus.com6504136193PersonalSergeant, MartinDSpacehttp://dspace.org/items/9d9e33f6-77d6-4d4a-9cb6-ddc862e0521aDSpacehttp://dspace.org/items/9d9e33f6-77d6-4d4a-9cb6-ddc862e0521aSergeantMartinORCIDhttp://orcid.org0000-0001-7264-2668Scopus Author IDhttps://www.scopus.com6602649951PersonalLuhmann, NinaDSpacehttp://dspace.org/items/580d6565-9063-4938-bcbc-08dcbfda2fc8DSpacehttp://dspace.org/items/580d6565-9063-4938-bcbc-08dcbfda2fc8LuhmannNinaORCIDhttp://orcid.org0000-0001-8112-7027PersonalVaz, CátiaDSpacehttp://dspace.org/items/0c5cb0fd-7cd7-4a16-86a8-7a68188e53ffDSpacehttp://dspace.org/items/0c5cb0fd-7cd7-4a16-86a8-7a68188e53ffVazCátiaCiência IDhttps://www.ciencia-id.pt8718-741E-BBD9ORCIDhttp://orcid.org0000-0001-6074-3074Researcher IDhttps://www.researcherid.comADC-1473-2022Scopus Author IDhttps://www.scopus.com27267941600PersonalFrancisco, AlexandreDSpacehttp://dspace.org/items/c151b29d-016d-448b-82e7-4c012e300ee2DSpacehttp://dspace.org/items/c151b29d-016d-448b-82e7-4c012e300ee2FranciscoAlexandreORCIDhttp://orcid.org0000-0003-4852-1641PersonalCarrico, JoaoDSpacehttp://dspace.org/items/5f4ad9ce-0a68-496f-a0d6-2062d39f4702DSpacehttp://dspace.org/items/5f4ad9ce-0a68-496f-a0d6-2062d39f4702CarricoJoaoORCIDhttp://orcid.org0000-0002-5274-2722Researcher IDhttps://www.researcherid.comA-7367-2008Scopus Author IDhttps://www.scopus.com8266333200PersonalAchtman, MarkDSpacehttp://dspace.org/items/d034cdfd-9237-47ff-8e09-fce9109daea3DSpacehttp://dspace.org/items/d034cdfd-9237-47ff-8e09-fce9109daea3AchtmanMarkORCIDhttp://orcid.org0000-0001-6815-0070HostingInstitutionOrganizationalRCIPLe-mailmailto:rcaap@sp.ipl.ptrcaap@sp.ipl.ptISSNIsPartOf1088-9051ISSNIsPartOf1549-5469DOIIsPartOf10.1101/gr.232397.1172018-11-28T11:56:44Z2018-092018-09-01T00:00:00ZHandlehttp://hdl.handle.net/10400.21/9099http://purl.org/coar/access_right/c_16ecrestricted accessBacterial genomeGrapeTreeGenoma bacteriano3711843 bytesliteraturehttp://purl.org/coar/resource_type/c_6501journal articlehttp://purl.org/coar/access_right/c_16ecapplication/pdffulltexthttps://repositorio.ipl.pt/bitstreams/0e745261-eae8-4ea1-ad67-35330075f169/downloadGenome Research28913951404 |
| spellingShingle | GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens Zhou, Zhemin Bacterial genome GrapeTree Genoma bacteriano |
| status | SINGLETON |
| subject.fl_str_mv | Bacterial genome GrapeTree Genoma bacteriano |
| title | GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens |
| title_full | GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens |
| title_fullStr | GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens |
| title_full_unstemmed | GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens |
| title_short | GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens |
| title_sort | GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens |
| topic | Bacterial genome GrapeTree Genoma bacteriano |
| topic_facet | Bacterial genome GrapeTree Genoma bacteriano |
| url | http://hdl.handle.net/10400.21/9099 |
| visible | 1 |