{"id":"https://openalex.org/W1564635116","doi":"https://doi.org/10.1093/nar/gkv455","title":"ProtPhylo: identification of protein\u2013phenotype and protein\u2013protein functional associations via phylogenetic profiling","display_name":"ProtPhylo: identification of protein\u2013phenotype and protein\u2013protein functional associations via phylogenetic profiling","publication_year":2015,"publication_date":"2015-05-08","ids":{"openalex":"https://openalex.org/W1564635116","doi":"https://doi.org/10.1093/nar/gkv455","mag":"1564635116","pmid":"https://pubmed.ncbi.nlm.nih.gov/25956654"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkv455","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv455","pdf_url":"https://academic.oup.com/nar/article-pdf/43/W1/W160/7476275/gkv455.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/43/W1/W160/7476275/gkv455.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045669688","display_name":"Yiming Cheng","orcid":"https://orcid.org/0009-0006-4270-7292"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Yiming Cheng","raw_affiliation_strings":["Gene Center, Ludwig-Maximilians-University, Munich, Bavaria 81377, Germany Institute of Human Genetics, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Bavaria 85764, Germany","Gene Center, Ludwig-Maximilians-University, Munich, Bavaria 81377, Germany","Institute of Human Genetics, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Bavaria 85764, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Gene Center, Ludwig-Maximilians-University, Munich, Bavaria 81377, Germany Institute of Human Genetics, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Bavaria 85764, Germany","institution_ids":["https://openalex.org/I3018134672","https://openalex.org/I8204097"]},{"raw_affiliation_string":"Gene Center, Ludwig-Maximilians-University, Munich, Bavaria 81377, Germany","institution_ids":["https://openalex.org/I8204097"]},{"raw_affiliation_string":"Institute of Human Genetics, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Bavaria 85764, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049223262","display_name":"Fabiana Perocchi","orcid":"https://orcid.org/0000-0002-1102-6500"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Fabiana Perocchi","raw_affiliation_strings":["Gene Center, Ludwig-Maximilians-University, Munich, Bavaria 81377, Germany Institute of Human Genetics, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Bavaria 85764, Germany perocchi@genzentrum.lmu.de","Institute of Human Genetics, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Bavaria 85764, Germany","Gene Center, Ludwig-Maximilians-University, Munich, Bavaria 81377, Germany"],"raw_orcid":"https://orcid.org/0000-0002-1102-6500","affiliations":[{"raw_affiliation_string":"Gene Center, Ludwig-Maximilians-University, Munich, Bavaria 81377, Germany Institute of Human Genetics, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Bavaria 85764, Germany perocchi@genzentrum.lmu.de","institution_ids":["https://openalex.org/I3018134672","https://openalex.org/I8204097"]},{"raw_affiliation_string":"Institute of Human Genetics, Helmholtz Zentrum M\u00fcnchen, Neuherberg, Bavaria 85764, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Gene Center, Ludwig-Maximilians-University, Munich, Bavaria 81377, Germany","institution_ids":["https://openalex.org/I8204097"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5049223262"],"corresponding_institution_ids":["https://openalex.org/I3018134672","https://openalex.org/I8204097"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.108,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.86845968,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"43","issue":"W1","first_page":"W160","last_page":"W168"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9983000159263611,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9954000115394592,"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/biology","display_name":"Biology","score":0.8683748841285706},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7468172311782837},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6094501614570618},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.5627559423446655},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5306476950645447},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4858498275279999},{"id":"https://openalex.org/keywords/archaea","display_name":"Archaea","score":0.4461720883846283},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.43715089559555054},{"id":"https://openalex.org/keywords/protein-methods","display_name":"Protein methods","score":0.42826586961746216},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.42236921191215515},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.36190176010131836},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3356130123138428},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.27096468210220337},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.20606762170791626}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8683748841285706},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7468172311782837},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6094501614570618},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.5627559423446655},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5306476950645447},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4858498275279999},{"id":"https://openalex.org/C550995028","wikidata":"https://www.wikidata.org/wiki/Q10872","display_name":"Archaea","level":3,"score":0.4461720883846283},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.43715089559555054},{"id":"https://openalex.org/C111364199","wikidata":"https://www.wikidata.org/wiki/Q2915896","display_name":"Protein methods","level":4,"score":0.42826586961746216},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.42236921191215515},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36190176010131836},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3356130123138428},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.27096468210220337},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.20606762170791626}],"mesh":[{"descriptor_ui":"D000071737","descriptor_name":"Stromal Interaction Molecule 1","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071737","descriptor_name":"Stromal Interaction Molecule 1","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071737","descriptor_name":"Stromal Interaction Molecule 1","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D015220","descriptor_name":"Calcium Channels","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015220","descriptor_name":"Calcium Channels","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015220","descriptor_name":"Calcium Channels","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkv455","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv455","pdf_url":"https://academic.oup.com/nar/article-pdf/43/W1/W160/7476275/gkv455.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:25956654","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25956654","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:epub.ub.uni-muenchen.de:34201","is_oa":false,"landing_page_url":"http://nbn-resolving.de/urn:nbn:de:bvb:19-epub-34201-1","pdf_url":null,"source":{"id":"https://openalex.org/S4306401845","display_name":"Open access LMU (Ludwid Maxmilian's Universitat Munchen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I8204097","host_organization_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","host_organization_lineage":["https://openalex.org/I8204097"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research","raw_type":"doc-type:article"},{"id":"pmh:oai:europepmc.org:3458189","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4489284","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:opus-zb.helmholtz-muenchen.de:44813","is_oa":true,"landing_page_url":"https://push-zb.helmholtz-muenchen.de/frontdoor.php?source_opus=44813","pdf_url":null,"source":{"id":"https://openalex.org/S4377196115","display_name":"Site cant be reached","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"Nucleic Acids Res. 41, W160-W168 (2015)","raw_type":"article"},{"id":"pmh:oai:push-zb.helmholtz-munich.de:44813","is_oa":true,"landing_page_url":"https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=44813","pdf_url":null,"source":{"id":"https://openalex.org/S7407055352","display_name":"PuSH - Publication Server of Helmholtz Zentrum M\u00fcnchen","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"Nucleic Acids Res. 41, W160-W168 (2015)","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkv455","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv455","pdf_url":"https://academic.oup.com/nar/article-pdf/43/W1/W160/7476275/gkv455.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4553965039","display_name":null,"funder_award_id":"PE 2053/1-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W1564635116.pdf"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1490161904","https://openalex.org/W1616183675","https://openalex.org/W1978593035","https://openalex.org/W1980633311","https://openalex.org/W1986213783","https://openalex.org/W1991055482","https://openalex.org/W1997272729","https://openalex.org/W1998767819","https://openalex.org/W2008856488","https://openalex.org/W2010572143","https://openalex.org/W2030317329","https://openalex.org/W2043764521","https://openalex.org/W2048692507","https://openalex.org/W2053501576","https://openalex.org/W2057885377","https://openalex.org/W2059803549","https://openalex.org/W2067841051","https://openalex.org/W2085111073","https://openalex.org/W2089563539","https://openalex.org/W2098905232","https://openalex.org/W2101117598","https://openalex.org/W2101586949","https://openalex.org/W2103132055","https://openalex.org/W2105924489","https://openalex.org/W2111582408","https://openalex.org/W2117486996","https://openalex.org/W2117602634","https://openalex.org/W2118988881","https://openalex.org/W2127660113","https://openalex.org/W2130253098","https://openalex.org/W2131412555","https://openalex.org/W2137424160","https://openalex.org/W2139118683","https://openalex.org/W2143197938","https://openalex.org/W2143250705","https://openalex.org/W2143335572","https://openalex.org/W2143592941","https://openalex.org/W2144171388","https://openalex.org/W2146341872","https://openalex.org/W2147526198","https://openalex.org/W2148043260","https://openalex.org/W2152458080","https://openalex.org/W2152770371","https://openalex.org/W2158742931","https://openalex.org/W2163789582","https://openalex.org/W2168048337","https://openalex.org/W4252706339","https://openalex.org/W6681010238"],"related_works":["https://openalex.org/W2054124141","https://openalex.org/W1986155816","https://openalex.org/W2938453170","https://openalex.org/W2037556998","https://openalex.org/W3135130381","https://openalex.org/W4306831161","https://openalex.org/W2008510935","https://openalex.org/W1559328993","https://openalex.org/W2118290743","https://openalex.org/W4317911177"],"abstract_inverted_index":{"ProtPhylo":[0,24,74,115,178],"is":[1,179],"a":[2,14,17,76,130,171],"web-based":[3],"tool":[4],"to":[5,12,75],"identify":[6],"proteins":[7,107,121],"that":[8],"are":[9],"functionally":[10],"linked":[11],"either":[13,91],"phenotype":[15],"or":[16,103,122],"protein":[18,30,44,160,164],"of":[19,35,50,56,79,105,119,132,136],"interest":[20],"based":[21,90],"on":[22,92,150],"co-evolution.":[23],"infers":[25],"functional":[26],"associations":[27],"by":[28,82,147],"comparing":[29],"phylogenetic":[31,117,137],"profiles":[32],"(co-occurrence":[33],"patterns":[34],"orthology":[36,87],"relationships)":[37],"for":[38,175],"more":[39],"than":[40],"9.7":[41],"million":[42],"non-redundant":[43],"sequences":[45],"from":[46],"all":[47],"three":[48],"domains":[49],"life.":[51],"Users":[52],"can":[53,72,141,166],"query":[54,120],"any":[55],"2048":[57],"fully":[58],"sequenced":[59],"organisms,":[60],"including":[61],"1678":[62],"bacteria,":[63],"255":[64],"eukaryotes":[65],"and":[66,99,112,144,159],"115":[67],"archaea.":[68],"In":[69],"addition,":[70],"they":[71],"tailor":[73],"particular":[77],"kind":[78],"biological":[80],"question":[81],"choosing":[83],"among":[84],"four":[85],"main":[86],"inference":[88],"methods":[89],"pair-wise":[93],"sequence":[94],"comparisons":[95],"(One-way":[96],"Best":[97,100],"Hits":[98],"Reciprocal":[101],"Hits)":[102],"clustering":[104],"orthologous":[106],"across":[108],"multiple":[109],"species":[110],"(OrthoMCL":[111],"eggNOG).":[113],"Next,":[114],"ranks":[116],"neighbors":[118],"phenotypic":[123],"properties":[124],"using":[125],"the":[126],"Hamming":[127],"distance":[128],"as":[129],"measure":[131],"similarity":[133],"between":[134],"pairs":[135],"profiles.":[138],"Candidate":[139],"hits":[140],"be":[142,167],"easily":[143],"flexibly":[145],"prioritized":[146],"complementary":[148],"clues":[149],"subcellular":[151],"localization,":[152],"known":[153],"protein-protein":[154],"interactions,":[155],"membrane":[156],"spanning":[157],"regions":[158],"domains.":[161],"The":[162],"resulting":[163],"list":[165],"quickly":[168],"exported":[169],"into":[170],"csv":[172],"text":[173],"file":[174],"further":[176],"analyses.":[177],"freely":[180],"available":[181],"at":[182],"http://www.protphylo.org.":[183]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3}],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2025-10-10T00:00:00"}