{"id":"https://openalex.org/W2904847915","doi":"https://doi.org/10.1186/s12859-018-2453-2","title":"A nearest-neighbors network model for sequence data reveals new insight into genotype distribution of a pathogen","display_name":"A nearest-neighbors network model for sequence data reveals new insight into genotype distribution of a pathogen","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2904847915","doi":"https://doi.org/10.1186/s12859-018-2453-2","mag":"2904847915","pmid":"https://pubmed.ncbi.nlm.nih.gov/30541438"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2453-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2453-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-018-2453-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-018-2453-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086744870","display_name":"Helen N. Catanese","orcid":null},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Helen N. Catanese","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070930919","display_name":"Kelly A. Brayton","orcid":"https://orcid.org/0000-0001-7077-5424"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kelly A. Brayton","raw_affiliation_strings":["Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA","School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA","institution_ids":["https://openalex.org/I72951846"]},{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049685547","display_name":"Assefaw H. Gebremedhin","orcid":"https://orcid.org/0000-0001-5383-8032"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Assefaw H. Gebremedhin","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, USA. assefaw.gebremedhin@wsu.edu","School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, USA. assefaw.gebremedhin@wsu.edu","institution_ids":["https://openalex.org/I72951846"]},{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, USA","institution_ids":["https://openalex.org/I72951846"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5049685547"],"corresponding_institution_ids":["https://openalex.org/I72951846"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.0824,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.44833679,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"19","issue":"1","first_page":"475","last_page":"475"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.967199981212616,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.967199981212616,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.010400000028312206,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.00419999985024333,"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/computer-science","display_name":"Computer science","score":0.6571092009544373},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.554176926612854},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4987328052520752},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4916430115699768},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.489788293838501},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"Nearest neighbor search","score":0.4696855843067169},{"id":"https://openalex.org/keywords/k-nearest-neighbors-algorithm","display_name":"k-nearest neighbors algorithm","score":0.4666326940059662},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.46574389934539795},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.397209107875824},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37845462560653687},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33461132645606995}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6571092009544373},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.554176926612854},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4987328052520752},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4916430115699768},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.489788293838501},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.4696855843067169},{"id":"https://openalex.org/C113238511","wikidata":"https://www.wikidata.org/wiki/Q1071612","display_name":"k-nearest neighbors algorithm","level":2,"score":0.4666326940059662},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.46574389934539795},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.397209107875824},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37845462560653687},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33461132645606995},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000071076","descriptor_name":"Network Meta-Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071076","descriptor_name":"Network Meta-Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000071076","descriptor_name":"Network Meta-Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-018-2453-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2453-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-018-2453-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30541438","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30541438","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:a20336cb93514cbda4ec29eda41dd191","is_oa":false,"landing_page_url":"https://doaj.org/article/a20336cb93514cbda4ec29eda41dd191","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss 1, Pp 1-18 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5265259","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6291930","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6291930","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6291930","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2453-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2453-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-018-2453-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1138953873","display_name":null,"funder_award_id":"IIS-1553528","funder_id":"https://openalex.org/F4320332169","funder_display_name":"Directorate for Computer and Information Science and Engineering"},{"id":"https://openalex.org/G2956472867","display_name":null,"funder_award_id":"IIS-1553528","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4667406367","display_name":"CAREER: Fast and Scalable Combinatorial Algorithms for Data Analytics","funder_award_id":"1553528","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309913","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17"},{"id":"https://openalex.org/F4320332169","display_name":"Directorate for Computer and Information Science and Engineering","ror":"https://ror.org/025kzpk63"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2904847915.pdf","grobid_xml":"https://content.openalex.org/works/W2904847915.grobid-xml"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W112627137","https://openalex.org/W140325011","https://openalex.org/W186067300","https://openalex.org/W206566442","https://openalex.org/W229097380","https://openalex.org/W247241571","https://openalex.org/W1496508106","https://openalex.org/W1527356121","https://openalex.org/W1550211845","https://openalex.org/W1554174647","https://openalex.org/W1558365920","https://openalex.org/W1976937534","https://openalex.org/W1980073965","https://openalex.org/W1983067644","https://openalex.org/W1993216012","https://openalex.org/W1998926649","https://openalex.org/W2001781153","https://openalex.org/W2022012334","https://openalex.org/W2037275405","https://openalex.org/W2058244017","https://openalex.org/W2065678066","https://openalex.org/W2072596762","https://openalex.org/W2074231493","https://openalex.org/W2077720176","https://openalex.org/W2082042699","https://openalex.org/W2086504823","https://openalex.org/W2089499735","https://openalex.org/W2096598900","https://openalex.org/W2097921974","https://openalex.org/W2099629766","https://openalex.org/W2101999582","https://openalex.org/W2110026675","https://openalex.org/W2113561798","https://openalex.org/W2128557693","https://openalex.org/W2128703518","https://openalex.org/W2130219916","https://openalex.org/W2131681506","https://openalex.org/W2132863465","https://openalex.org/W2133075481","https://openalex.org/W2135152200","https://openalex.org/W2135326109","https://openalex.org/W2137999759","https://openalex.org/W2142678478","https://openalex.org/W2143516113","https://openalex.org/W2158266834","https://openalex.org/W2158627511","https://openalex.org/W2161008043","https://openalex.org/W2161855013","https://openalex.org/W2162142896","https://openalex.org/W2167482691","https://openalex.org/W2169911158","https://openalex.org/W2170630035","https://openalex.org/W2342204193","https://openalex.org/W2417798154","https://openalex.org/W2427881153","https://openalex.org/W2597608265","https://openalex.org/W2911762832","https://openalex.org/W2914482275","https://openalex.org/W2945262074","https://openalex.org/W2946317780","https://openalex.org/W2956131382","https://openalex.org/W2964164193","https://openalex.org/W3099768174","https://openalex.org/W4245252159","https://openalex.org/W4300382868"],"related_works":["https://openalex.org/W2148008870","https://openalex.org/W2381195555","https://openalex.org/W2368606575","https://openalex.org/W4246757943","https://openalex.org/W2132753198","https://openalex.org/W2369874856","https://openalex.org/W2182477562","https://openalex.org/W2792185758","https://openalex.org/W2787484455","https://openalex.org/W2119808169"],"abstract_inverted_index":{"BACKGROUND:":[0],"Sequence":[1],"similarity":[2,16,40,266,295],"networks":[3,41,146,296,327],"are":[4,23],"useful":[5,48],"for":[6,58,174,334],"classifying":[7],"and":[8,28,87,132,152,168,204,276,311,331],"characterizing":[9],"biologically":[10],"important":[11],"proteins.":[12],"Threshold-based":[13],"approaches":[14],"to":[15,26,94,124,147,165,195,250,292,299,351],"network":[17,56,122,178,189,237,251,267,307,318,337],"construction":[18,238],"using":[19,215,288,338],"exact":[20,221,339],"distance":[21,45,213,290,340],"measures":[22,291,341],"prohibitively":[24],"slow":[25],"compute":[27],"rely":[29],"on":[30,43],"the":[31,72,96,102,107,134,138,142,154,157,162,187,234,259,303,322,336,346],"difficult":[32],"task":[33],"of":[34,61,104,137,182,201,220,228,261,268,305,325,345],"selecting":[35],"an":[36,54,118,171,269,332],"appropriate":[37],"threshold,":[38],"while":[39,198,328],"based":[42,248],"approximate":[44,212,289],"calculations":[46],"compromise":[47],"structural":[49,135,229,323],"information.":[50,230],"RESULTS:":[51],"We":[52,184,231,253,285,314],"present":[53,315],"alternative":[55],"representation":[57,190,319],"a":[59,85,91,176,180,241,245,256,262,265,316,343,353],"set":[60,181],"sequence":[62,81,126,263,273,280],"data":[63,127],"that":[64,186,211,233,279,287,306,320],"overcomes":[65],"these":[66],"drawbacks.":[67],"In":[68],"our":[69],"model,":[70],"called":[71],"Directed":[73],"Weighted":[74],"All":[75],"Nearest":[76],"Neighbors":[77],"(DiWANN)":[78],"network,":[79],"each":[80],"is":[82,88,281],"represented":[83],"by":[84],"node":[86],"connected":[89],"via":[90],"directed":[92],"edge":[93],"only":[95],"closest":[97],"sequence,":[98],"or":[99],"sequences":[100],"in":[101,106,218,264,302,308,342],"case":[103],"ties,":[105],"dataset.":[108],"Our":[109],"contributions":[110],"span":[111],"several":[112],"aspects.":[113],"Specifically,":[114],"we:":[115],"(i)":[116],"Apply":[117],"all":[119],"nearest":[120],"neighbors":[121],"model":[123,143,158],"protein":[125],"from":[128,179],"three":[129],"different":[130],"applications":[131],"examine":[133],"properties":[136,194],"networks;":[139],"(ii)":[140],"Compare":[141],"against":[144],"threshold-based":[145,196,326,354],"validate":[148],"their":[149],"semantic":[150,193],"equivalence,":[151],"demonstrate":[153,286],"relative":[155],"advantages":[156],"offers;":[159],"(iii)":[160],"Demonstrate":[161],"model's":[163],"resilience":[164],"missing":[166],"sequences;":[167],"(iv)":[169],"Develop":[170],"efficient":[172],"algorithm":[173,239,333],"constructing":[175,335],"DiWANN":[177,188,236],"sequences.":[183],"find":[185,210],"attains":[191],"similar":[192],"graphs,":[197],"avoiding":[199],"weaknesses":[200],"both":[202],"high":[203],"low":[205],"threshold":[206,247],"graphs.":[207],"Additionally,":[208],"we":[209],"networks,":[214],"BLAST":[216],"bitscores":[217],"place":[219],"edit":[222],"distances,":[223],"can":[224],"cause":[225],"significant":[226,300],"loss":[227],"show":[232],"proposed":[235],"provides":[240],"fourfold":[242],"speedup":[243],"over":[244],"standard":[246],"approach":[249],"construction.":[252],"also":[254],"identify":[255],"relationship":[257],"between":[258],"centrality":[260,310],"Anaplasma":[270],"marginale":[271],"short":[272],"repeat":[274],"dataset":[275],"how":[277],"broadly":[278],"dispersed":[282],"geographically.":[283],"CONCLUSION:":[284],"rapidly":[293],"construct":[294],"may":[297],"lead":[298],"deficiencies":[301],"structure":[304],"terms":[309],"clustering":[312],"analyses.":[313],"new":[317],"maintains":[321],"semantics":[324],"increasing":[329],"connectedness,":[330],"fraction":[344],"time":[347],"it":[348],"would":[349],"take":[350],"build":[352],"equivalent.":[355]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
