Reconstruction of phyletic trees by global alignment of multiple metabolic networks View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-01

AUTHORS

Cheng-Yu Ma, Shu-Hsi Lin, Chi-Ching Lee, Chuan Yi Tang, Bonnie Berger, Chung-Shou Liao

ABSTRACT

BACKGROUND: In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. In contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information. RESULTS: We explored the phylogenetic relationships between microorganisms through global alignment of multiple metabolic networks. The proposed approach integrates sequence homology data with topological information of metabolic networks. In general, compared to recent studies, the resulting trees reflect the living style of organisms as well as classical taxa. Moreover, for phylogenetically closely related organisms, the classification results are consistent with specific metabolic characteristics, such as the light-harvesting systems, fermentation types, and sources of electrons in photosynthesis. CONCLUSIONS: We demonstrate the usefulness of global alignment of multiple metabolic networks to infer phylogenetic relationships between species. In addition, our exhaustive analysis of microbial metabolic pathways reveals differences in metabolic features between phylogenetically closely related organisms. With the ongoing increase in the number of genomic sequences and metabolic annotations, the proposed approach will help identify phenotypic variations that may not be apparent based solely on sequence-based classification. More... »

PAGES

s12

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-14-s2-s12

DOI

http://dx.doi.org/10.1186/1471-2105-14-s2-s12

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1021857270

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/23368411


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0605", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Microbiology", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Algorithms", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Cluster Analysis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Fermentation", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Lactobacillus", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Light-Harvesting Protein Complexes", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Metabolic Networks and Pathways", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Photosynthesis", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Phylogeny", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Prochlorococcus", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sulfur-Reducing Bacteria", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Synechococcus", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "National Tsing Hua University", 
          "id": "https://www.grid.ac/institutes/grid.38348.34", 
          "name": [
            "Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ma", 
        "givenName": "Cheng-Yu", 
        "id": "sg:person.0720476014.77", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0720476014.77"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National Tsing Hua University", 
          "id": "https://www.grid.ac/institutes/grid.38348.34", 
          "name": [
            "Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lin", 
        "givenName": "Shu-Hsi", 
        "id": "sg:person.0705144215.83", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0705144215.83"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Chang Gung University", 
          "id": "https://www.grid.ac/institutes/grid.145695.a", 
          "name": [
            "Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan", 
            "Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lee", 
        "givenName": "Chi-Ching", 
        "id": "sg:person.01157143141.10", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01157143141.10"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Providence University", 
          "id": "https://www.grid.ac/institutes/grid.412550.7", 
          "name": [
            "Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan", 
            "Department of Computer Science and Information Engineering, Providence University, Taichung, Taiwan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Tang", 
        "givenName": "Chuan Yi", 
        "id": "sg:person.01312526135.27", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01312526135.27"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Massachusetts Institute of Technology", 
          "id": "https://www.grid.ac/institutes/grid.116068.8", 
          "name": [
            "Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA", 
            "Department of Mathematics, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Berger", 
        "givenName": "Bonnie", 
        "id": "sg:person.01213307265.33", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01213307265.33"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "National Tsing Hua University", 
          "id": "https://www.grid.ac/institutes/grid.38348.34", 
          "name": [
            "Department of Industrial Engineering and Engineering Management, National Tsing Hua University, Hsinchu, Taiwan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Liao", 
        "givenName": "Chung-Shou", 
        "id": "sg:person.014656677443.53", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014656677443.53"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1016/s0168-1605(96)01233-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000587692"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-12-s1-s27", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003055195", 
          "https://doi.org/10.1186/1471-2105-12-s1-s27"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btl307", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004543138"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-11-s1-s38", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005755094", 
          "https://doi.org/10.1186/1471-2105-11-s1-s38"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0022099", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008922650"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jcm.40.8.2779-2785.2002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009549355"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-252", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009838096", 
          "https://doi.org/10.1186/1471-2105-7-252"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0022-2836(05)80360-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013618994"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1098/rsif.2010.0063", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013784747"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1603", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014262094", 
          "https://doi.org/10.1038/nrg1603"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrg1603", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014262094", 
          "https://doi.org/10.1038/nrg1603"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0607117103", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015929507"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2148-5-23", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016657463", 
          "https://doi.org/10.1186/1471-2148-5-23"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/28.1.27", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017305614"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.87.12.4576", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018027137"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s002390010178", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021056177", 
          "https://doi.org/10.1007/s002390010178"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btm630", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023071347"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0902532106", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023253230"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1099/mic.0.29140-0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023276887"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0409522102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026062100"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-13-157", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026416304", 
          "https://doi.org/10.1186/1471-2164-13-157"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1089/cmb.2010.0280", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027225506"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btp203", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031949221"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.jmb.2004.04.059", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034947336"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2148-11-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035841015", 
          "https://doi.org/10.1186/1471-2148-11-1"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-7-284", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038010584", 
          "https://doi.org/10.1186/1471-2105-7-284"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2012-13-1-r6", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038017203", 
          "https://doi.org/10.1186/gb-2012-13-1-r6"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/aem.68.3.1180-1191.2002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040286783"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0806627105", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042725107"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1123061", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043495787"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature04135", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044944309", 
          "https://doi.org/10.1038/nature04135"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature04135", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044944309", 
          "https://doi.org/10.1038/nature04135"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature04135", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044944309", 
          "https://doi.org/10.1038/nature04135"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btn503", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046016888"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btg1018", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046491906"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bti554", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047960379"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-8-460", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050692349", 
          "https://doi.org/10.1186/1471-2105-8-460"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkr1184", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052096621"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.5235706", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052652298"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0806162105", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053143105"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1089/cmb.2009.0099", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1059245831"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1077282387", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2013-01", 
    "datePublishedReg": "2013-01-01", 
    "description": "BACKGROUND: In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. In contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information.\nRESULTS: We explored the phylogenetic relationships between microorganisms through global alignment of multiple metabolic networks. The proposed approach integrates sequence homology data with topological information of metabolic networks. In general, compared to recent studies, the resulting trees reflect the living style of organisms as well as classical taxa. Moreover, for phylogenetically closely related organisms, the classification results are consistent with specific metabolic characteristics, such as the light-harvesting systems, fermentation types, and sources of electrons in photosynthesis.\nCONCLUSIONS: We demonstrate the usefulness of global alignment of multiple metabolic networks to infer phylogenetic relationships between species. In addition, our exhaustive analysis of microbial metabolic pathways reveals differences in metabolic features between phylogenetically closely related organisms. With the ongoing increase in the number of genomic sequences and metabolic annotations, the proposed approach will help identify phenotypic variations that may not be apparent based solely on sequence-based classification.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2105-14-s2-s12", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2519744", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1023786", 
        "issn": [
          "1471-2105"
        ], 
        "name": "BMC Bioinformatics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "Suppl 2", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "14"
      }
    ], 
    "name": "Reconstruction of phyletic trees by global alignment of multiple metabolic networks", 
    "pagination": "s12", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "68224d71f0cfe973ba6325b897be90f6956a094215a08db1982a25b774d6ad58"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "23368411"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965194"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2105-14-s2-s12"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1021857270"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2105-14-s2-s12", 
      "https://app.dimensions.ai/details/publication/pub.1021857270"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T14:03", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8660_00000488.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186/1471-2105-14-S2-S12"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-14-s2-s12'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-14-s2-s12'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-14-s2-s12'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2105-14-s2-s12'


 

This table displays all metadata directly associated to this object as RDF triples.

295 TRIPLES      21 PREDICATES      80 URIs      33 LITERALS      21 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2105-14-s2-s12 schema:about N258a18f5b7534309a242e687852075ae
2 N49344b1b7e0b46759613a5e1da5b59d7
3 N51e882833bdf4beeb856571646c0b5ba
4 N62d928f077084da6af07ed77aa19aa03
5 N6f43657500e44b7a979c5f998f9d46c5
6 N7850a5d5c0434bed82e806e6bd1d3dcf
7 N90714b54183348539c7988a9ca6618e2
8 Na600417f11614cbc9b192738280a85c4
9 Na818ada49abe4e8ba3fc9672f1f4c788
10 Nb23d41f04aa44cbf802d62ba8b36320d
11 Nc0463602b00b4eda9280ac64844351da
12 Nd5104f1b5aa9452080c41e6447704fda
13 anzsrc-for:06
14 anzsrc-for:0605
15 schema:author N3797c87f3c274a818b30bc40ae080502
16 schema:citation sg:pub.10.1007/s002390010178
17 sg:pub.10.1038/nature04135
18 sg:pub.10.1038/nrg1603
19 sg:pub.10.1186/1471-2105-11-s1-s38
20 sg:pub.10.1186/1471-2105-12-s1-s27
21 sg:pub.10.1186/1471-2105-7-252
22 sg:pub.10.1186/1471-2105-7-284
23 sg:pub.10.1186/1471-2105-8-460
24 sg:pub.10.1186/1471-2148-11-1
25 sg:pub.10.1186/1471-2148-5-23
26 sg:pub.10.1186/1471-2164-13-157
27 sg:pub.10.1186/gb-2012-13-1-r6
28 https://app.dimensions.ai/details/publication/pub.1077282387
29 https://doi.org/10.1016/j.jmb.2004.04.059
30 https://doi.org/10.1016/s0022-2836(05)80360-2
31 https://doi.org/10.1016/s0168-1605(96)01233-0
32 https://doi.org/10.1073/pnas.0409522102
33 https://doi.org/10.1073/pnas.0607117103
34 https://doi.org/10.1073/pnas.0806162105
35 https://doi.org/10.1073/pnas.0806627105
36 https://doi.org/10.1073/pnas.0902532106
37 https://doi.org/10.1073/pnas.87.12.4576
38 https://doi.org/10.1089/cmb.2009.0099
39 https://doi.org/10.1089/cmb.2010.0280
40 https://doi.org/10.1093/bioinformatics/btg1018
41 https://doi.org/10.1093/bioinformatics/bti554
42 https://doi.org/10.1093/bioinformatics/btl307
43 https://doi.org/10.1093/bioinformatics/btm630
44 https://doi.org/10.1093/bioinformatics/btn503
45 https://doi.org/10.1093/bioinformatics/btp203
46 https://doi.org/10.1093/nar/28.1.27
47 https://doi.org/10.1093/nar/gkr1184
48 https://doi.org/10.1098/rsif.2010.0063
49 https://doi.org/10.1099/mic.0.29140-0
50 https://doi.org/10.1101/gr.5235706
51 https://doi.org/10.1126/science.1123061
52 https://doi.org/10.1128/aem.68.3.1180-1191.2002
53 https://doi.org/10.1128/jcm.40.8.2779-2785.2002
54 https://doi.org/10.1371/journal.pone.0022099
55 schema:datePublished 2013-01
56 schema:datePublishedReg 2013-01-01
57 schema:description BACKGROUND: In the last decade, a considerable amount of research has been devoted to investigating the phylogenetic properties of organisms from a systems-level perspective. Most studies have focused on the classification of organisms based on structural comparison and local alignment of metabolic pathways. In contrast, global alignment of multiple metabolic networks complements sequence-based phylogenetic analyses and provides more comprehensive information. RESULTS: We explored the phylogenetic relationships between microorganisms through global alignment of multiple metabolic networks. The proposed approach integrates sequence homology data with topological information of metabolic networks. In general, compared to recent studies, the resulting trees reflect the living style of organisms as well as classical taxa. Moreover, for phylogenetically closely related organisms, the classification results are consistent with specific metabolic characteristics, such as the light-harvesting systems, fermentation types, and sources of electrons in photosynthesis. CONCLUSIONS: We demonstrate the usefulness of global alignment of multiple metabolic networks to infer phylogenetic relationships between species. In addition, our exhaustive analysis of microbial metabolic pathways reveals differences in metabolic features between phylogenetically closely related organisms. With the ongoing increase in the number of genomic sequences and metabolic annotations, the proposed approach will help identify phenotypic variations that may not be apparent based solely on sequence-based classification.
58 schema:genre research_article
59 schema:inLanguage en
60 schema:isAccessibleForFree true
61 schema:isPartOf N3f18bd9325a44936a532d080c9b0ab78
62 Nda4e64d0ea884b19a8068469d483f84c
63 sg:journal.1023786
64 schema:name Reconstruction of phyletic trees by global alignment of multiple metabolic networks
65 schema:pagination s12
66 schema:productId N2c853544933d4420bac8ca476feedb04
67 Nd52e1363ecf54800abfdfe49049bf1c6
68 Ne6ba704a4eef4064952b777d3e23e8fb
69 Nf72b125e4a2641d799f739b6f9e15cd0
70 Nfbcc7175d0db46208573123fee1d1f32
71 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021857270
72 https://doi.org/10.1186/1471-2105-14-s2-s12
73 schema:sdDatePublished 2019-04-10T14:03
74 schema:sdLicense https://scigraph.springernature.com/explorer/license/
75 schema:sdPublisher N82e10d51cf344e6790470ca49a611807
76 schema:url http://link.springer.com/10.1186/1471-2105-14-S2-S12
77 sgo:license sg:explorer/license/
78 sgo:sdDataset articles
79 rdf:type schema:ScholarlyArticle
80 N006a08b20c7f43b0850e930ff7cb0e6b rdf:first sg:person.0705144215.83
81 rdf:rest Nd75943a939704054ab1f4ccd30633749
82 N258a18f5b7534309a242e687852075ae schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
83 schema:name Algorithms
84 rdf:type schema:DefinedTerm
85 N2c853544933d4420bac8ca476feedb04 schema:name doi
86 schema:value 10.1186/1471-2105-14-s2-s12
87 rdf:type schema:PropertyValue
88 N3797c87f3c274a818b30bc40ae080502 rdf:first sg:person.0720476014.77
89 rdf:rest N006a08b20c7f43b0850e930ff7cb0e6b
90 N3f18bd9325a44936a532d080c9b0ab78 schema:issueNumber Suppl 2
91 rdf:type schema:PublicationIssue
92 N49344b1b7e0b46759613a5e1da5b59d7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
93 schema:name Prochlorococcus
94 rdf:type schema:DefinedTerm
95 N51e882833bdf4beeb856571646c0b5ba schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
96 schema:name Light-Harvesting Protein Complexes
97 rdf:type schema:DefinedTerm
98 N62d928f077084da6af07ed77aa19aa03 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
99 schema:name Photosynthesis
100 rdf:type schema:DefinedTerm
101 N6df79538e4464d5fb76814352e07e378 rdf:first sg:person.01312526135.27
102 rdf:rest N8400a79829fa47dc99dda0d6e3a6c29b
103 N6f43657500e44b7a979c5f998f9d46c5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
104 schema:name Lactobacillus
105 rdf:type schema:DefinedTerm
106 N7850a5d5c0434bed82e806e6bd1d3dcf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
107 schema:name Fermentation
108 rdf:type schema:DefinedTerm
109 N82e10d51cf344e6790470ca49a611807 schema:name Springer Nature - SN SciGraph project
110 rdf:type schema:Organization
111 N8400a79829fa47dc99dda0d6e3a6c29b rdf:first sg:person.01213307265.33
112 rdf:rest N8c9792655df94fdfaa6e2474895f56bd
113 N8c9792655df94fdfaa6e2474895f56bd rdf:first sg:person.014656677443.53
114 rdf:rest rdf:nil
115 N90714b54183348539c7988a9ca6618e2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
116 schema:name Genomics
117 rdf:type schema:DefinedTerm
118 Na600417f11614cbc9b192738280a85c4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
119 schema:name Cluster Analysis
120 rdf:type schema:DefinedTerm
121 Na818ada49abe4e8ba3fc9672f1f4c788 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
122 schema:name Metabolic Networks and Pathways
123 rdf:type schema:DefinedTerm
124 Nb23d41f04aa44cbf802d62ba8b36320d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
125 schema:name Phylogeny
126 rdf:type schema:DefinedTerm
127 Nc0463602b00b4eda9280ac64844351da schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
128 schema:name Synechococcus
129 rdf:type schema:DefinedTerm
130 Nd5104f1b5aa9452080c41e6447704fda schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
131 schema:name Sulfur-Reducing Bacteria
132 rdf:type schema:DefinedTerm
133 Nd52e1363ecf54800abfdfe49049bf1c6 schema:name pubmed_id
134 schema:value 23368411
135 rdf:type schema:PropertyValue
136 Nd75943a939704054ab1f4ccd30633749 rdf:first sg:person.01157143141.10
137 rdf:rest N6df79538e4464d5fb76814352e07e378
138 Nda4e64d0ea884b19a8068469d483f84c schema:volumeNumber 14
139 rdf:type schema:PublicationVolume
140 Ne6ba704a4eef4064952b777d3e23e8fb schema:name dimensions_id
141 schema:value pub.1021857270
142 rdf:type schema:PropertyValue
143 Nf72b125e4a2641d799f739b6f9e15cd0 schema:name readcube_id
144 schema:value 68224d71f0cfe973ba6325b897be90f6956a094215a08db1982a25b774d6ad58
145 rdf:type schema:PropertyValue
146 Nfbcc7175d0db46208573123fee1d1f32 schema:name nlm_unique_id
147 schema:value 100965194
148 rdf:type schema:PropertyValue
149 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
150 schema:name Biological Sciences
151 rdf:type schema:DefinedTerm
152 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
153 schema:name Microbiology
154 rdf:type schema:DefinedTerm
155 sg:grant.2519744 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2105-14-s2-s12
156 rdf:type schema:MonetaryGrant
157 sg:journal.1023786 schema:issn 1471-2105
158 schema:name BMC Bioinformatics
159 rdf:type schema:Periodical
160 sg:person.01157143141.10 schema:affiliation https://www.grid.ac/institutes/grid.145695.a
161 schema:familyName Lee
162 schema:givenName Chi-Ching
163 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01157143141.10
164 rdf:type schema:Person
165 sg:person.01213307265.33 schema:affiliation https://www.grid.ac/institutes/grid.116068.8
166 schema:familyName Berger
167 schema:givenName Bonnie
168 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01213307265.33
169 rdf:type schema:Person
170 sg:person.01312526135.27 schema:affiliation https://www.grid.ac/institutes/grid.412550.7
171 schema:familyName Tang
172 schema:givenName Chuan Yi
173 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01312526135.27
174 rdf:type schema:Person
175 sg:person.014656677443.53 schema:affiliation https://www.grid.ac/institutes/grid.38348.34
176 schema:familyName Liao
177 schema:givenName Chung-Shou
178 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014656677443.53
179 rdf:type schema:Person
180 sg:person.0705144215.83 schema:affiliation https://www.grid.ac/institutes/grid.38348.34
181 schema:familyName Lin
182 schema:givenName Shu-Hsi
183 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0705144215.83
184 rdf:type schema:Person
185 sg:person.0720476014.77 schema:affiliation https://www.grid.ac/institutes/grid.38348.34
186 schema:familyName Ma
187 schema:givenName Cheng-Yu
188 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0720476014.77
189 rdf:type schema:Person
190 sg:pub.10.1007/s002390010178 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021056177
191 https://doi.org/10.1007/s002390010178
192 rdf:type schema:CreativeWork
193 sg:pub.10.1038/nature04135 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044944309
194 https://doi.org/10.1038/nature04135
195 rdf:type schema:CreativeWork
196 sg:pub.10.1038/nrg1603 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014262094
197 https://doi.org/10.1038/nrg1603
198 rdf:type schema:CreativeWork
199 sg:pub.10.1186/1471-2105-11-s1-s38 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005755094
200 https://doi.org/10.1186/1471-2105-11-s1-s38
201 rdf:type schema:CreativeWork
202 sg:pub.10.1186/1471-2105-12-s1-s27 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003055195
203 https://doi.org/10.1186/1471-2105-12-s1-s27
204 rdf:type schema:CreativeWork
205 sg:pub.10.1186/1471-2105-7-252 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009838096
206 https://doi.org/10.1186/1471-2105-7-252
207 rdf:type schema:CreativeWork
208 sg:pub.10.1186/1471-2105-7-284 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038010584
209 https://doi.org/10.1186/1471-2105-7-284
210 rdf:type schema:CreativeWork
211 sg:pub.10.1186/1471-2105-8-460 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050692349
212 https://doi.org/10.1186/1471-2105-8-460
213 rdf:type schema:CreativeWork
214 sg:pub.10.1186/1471-2148-11-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035841015
215 https://doi.org/10.1186/1471-2148-11-1
216 rdf:type schema:CreativeWork
217 sg:pub.10.1186/1471-2148-5-23 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016657463
218 https://doi.org/10.1186/1471-2148-5-23
219 rdf:type schema:CreativeWork
220 sg:pub.10.1186/1471-2164-13-157 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026416304
221 https://doi.org/10.1186/1471-2164-13-157
222 rdf:type schema:CreativeWork
223 sg:pub.10.1186/gb-2012-13-1-r6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038017203
224 https://doi.org/10.1186/gb-2012-13-1-r6
225 rdf:type schema:CreativeWork
226 https://app.dimensions.ai/details/publication/pub.1077282387 schema:CreativeWork
227 https://doi.org/10.1016/j.jmb.2004.04.059 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034947336
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1016/s0022-2836(05)80360-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013618994
230 rdf:type schema:CreativeWork
231 https://doi.org/10.1016/s0168-1605(96)01233-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000587692
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1073/pnas.0409522102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026062100
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1073/pnas.0607117103 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015929507
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1073/pnas.0806162105 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053143105
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1073/pnas.0806627105 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042725107
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1073/pnas.0902532106 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023253230
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1073/pnas.87.12.4576 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018027137
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1089/cmb.2009.0099 schema:sameAs https://app.dimensions.ai/details/publication/pub.1059245831
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1089/cmb.2010.0280 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027225506
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1093/bioinformatics/btg1018 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046491906
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1093/bioinformatics/bti554 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047960379
252 rdf:type schema:CreativeWork
253 https://doi.org/10.1093/bioinformatics/btl307 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004543138
254 rdf:type schema:CreativeWork
255 https://doi.org/10.1093/bioinformatics/btm630 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023071347
256 rdf:type schema:CreativeWork
257 https://doi.org/10.1093/bioinformatics/btn503 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046016888
258 rdf:type schema:CreativeWork
259 https://doi.org/10.1093/bioinformatics/btp203 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031949221
260 rdf:type schema:CreativeWork
261 https://doi.org/10.1093/nar/28.1.27 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017305614
262 rdf:type schema:CreativeWork
263 https://doi.org/10.1093/nar/gkr1184 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052096621
264 rdf:type schema:CreativeWork
265 https://doi.org/10.1098/rsif.2010.0063 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013784747
266 rdf:type schema:CreativeWork
267 https://doi.org/10.1099/mic.0.29140-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023276887
268 rdf:type schema:CreativeWork
269 https://doi.org/10.1101/gr.5235706 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052652298
270 rdf:type schema:CreativeWork
271 https://doi.org/10.1126/science.1123061 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043495787
272 rdf:type schema:CreativeWork
273 https://doi.org/10.1128/aem.68.3.1180-1191.2002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040286783
274 rdf:type schema:CreativeWork
275 https://doi.org/10.1128/jcm.40.8.2779-2785.2002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009549355
276 rdf:type schema:CreativeWork
277 https://doi.org/10.1371/journal.pone.0022099 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008922650
278 rdf:type schema:CreativeWork
279 https://www.grid.ac/institutes/grid.116068.8 schema:alternateName Massachusetts Institute of Technology
280 schema:name Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA
281 Department of Mathematics, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA
282 rdf:type schema:Organization
283 https://www.grid.ac/institutes/grid.145695.a schema:alternateName Chang Gung University
284 schema:name Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan
285 Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
286 rdf:type schema:Organization
287 https://www.grid.ac/institutes/grid.38348.34 schema:alternateName National Tsing Hua University
288 schema:name Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
289 Department of Industrial Engineering and Engineering Management, National Tsing Hua University, Hsinchu, Taiwan
290 Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
291 rdf:type schema:Organization
292 https://www.grid.ac/institutes/grid.412550.7 schema:alternateName Providence University
293 schema:name Department of Computer Science and Information Engineering, Providence University, Taichung, Taiwan
294 Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan
295 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...