{"id":"https://openalex.org/W2463615102","doi":"https://doi.org/10.1093/bioinformatics/btw402","title":"The SMAL web server: global multiple network alignment from pairwise alignments","display_name":"The SMAL web server: global multiple network alignment from pairwise alignments","publication_year":2016,"publication_date":"2016-07-04","ids":{"openalex":"https://openalex.org/W2463615102","doi":"https://doi.org/10.1093/bioinformatics/btw402","mag":"2463615102","pmid":"https://pubmed.ncbi.nlm.nih.gov/27378297"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw402","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3330/7889664/btw402.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3330/7889664/btw402.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003533446","display_name":"Jakob Dohrmann","orcid":null},"institutions":[{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jakob Dohrmann","raw_affiliation_strings":["1 Department of Computer Science, San Francisco State University, San Francisco, CA 94132, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, San Francisco State University, San Francisco, CA 94132, USA","institution_ids":["https://openalex.org/I71838634"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073550054","display_name":"Rahul Singh","orcid":"https://orcid.org/0000-0003-3900-4298"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210157321","display_name":"Center for Discovery","ror":"https://ror.org/04jna0a58","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210157321"]},{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rahul Singh","raw_affiliation_strings":["1 Department of Computer Science, San Francisco State University, San Francisco, CA 94132, USA","2 Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, CA 92093, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, San Francisco State University, San Francisco, CA 94132, USA","institution_ids":["https://openalex.org/I71838634"]},{"raw_affiliation_string":"2 Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, CA 92093, USA","institution_ids":["https://openalex.org/I4210157321","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5073550054"],"corresponding_institution_ids":["https://openalex.org/I36258959","https://openalex.org/I4210157321","https://openalex.org/I71838634"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3335,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.67217799,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"32","issue":"21","first_page":"3330","last_page":"3332"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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":0.9997000098228455,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9843000173568726,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9836000204086304,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.6899359226226807},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6610894203186035},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6426692605018616},{"id":"https://openalex.org/keywords/interactome","display_name":"Interactome","score":0.43404752016067505},{"id":"https://openalex.org/keywords/graph-layout","display_name":"Graph Layout","score":0.4126339554786682},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.3687586188316345},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33358699083328247},{"id":"https://openalex.org/keywords/graph-drawing","display_name":"Graph drawing","score":0.299662709236145},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2758856415748596},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.26340749859809875},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1973719298839569},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16136980056762695}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6899359226226807},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6610894203186035},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6426692605018616},{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.43404752016067505},{"id":"https://openalex.org/C2911174283","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph Layout","level":4,"score":0.4126339554786682},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.3687586188316345},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33358699083328247},{"id":"https://openalex.org/C112953755","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph drawing","level":3,"score":0.299662709236145},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2758856415748596},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26340749859809875},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1973719298839569},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16136980056762695},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw402","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3330/7889664/btw402.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27378297","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27378297","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/21/3330","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/21/3330","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw402","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3330/7889664/btw402.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.5099999904632568}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2463615102.pdf","grobid_xml":"https://content.openalex.org/works/W2463615102.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W2039616005","https://openalex.org/W2096173332","https://openalex.org/W2097624459","https://openalex.org/W2134189979","https://openalex.org/W2136845897","https://openalex.org/W2153929049","https://openalex.org/W2155834877","https://openalex.org/W2179127114","https://openalex.org/W6674655209"],"related_works":["https://openalex.org/W4292634579","https://openalex.org/W2964314049","https://openalex.org/W2022326234","https://openalex.org/W1531941329","https://openalex.org/W4388694323","https://openalex.org/W3215098729","https://openalex.org/W2616505514","https://openalex.org/W2547723202","https://openalex.org/W2294734161","https://openalex.org/W4388097011"],"abstract_inverted_index":{"SMAL":[0,48,63,93,138,153],"(Scaffold-Based":[1],"Multiple":[2],"Network":[3],"Aligner)":[4],"is":[5,49,139,159],"a":[6,57,101,140],"public,":[7],"open-source,":[8],"web-based":[9],"application":[10],"for":[11],"determining":[12],"MNAs":[13,94],"from":[14],"existing":[15,69],"PNAs":[16,25],"that":[17,68,124],"addresses":[18],"all":[19,121],"the":[20,107,118,131],"aforementioned":[21],"challenges.":[22],"With":[23],"SMAL,":[24],"can":[26],"be":[27,98,146],"combined":[28],"rapidly":[29],"to":[30,42,56,97,130,148],"obtain":[31],"an":[32],"MNA.":[33],"The":[34,152],"software":[35],"also":[36],"supports":[37],"visualization":[38],"and":[39,46,113,144,156],"user-data":[40],"interactions":[41],"facilitate":[43],"exploratory":[44],"analysis":[45],"sensemaking.":[47],"especially":[50],"useful":[51],"when":[52],"multiple":[53],"alignments":[54,64],"relative":[55],"particular":[58],"PPIN":[59],"are":[60,65,78,84,125,168],"required;":[61],"furthermore,":[62],"persistent":[66],"in":[67],"correspondences":[70,123],"between":[71],"networks":[72,83],"(obtained":[73],"during":[74],"PNA":[75],"or":[76,128],"MNA)":[77],"not":[79],"lost":[80],"as":[81,106,115,117],"new":[82],"added.":[85],"In":[86],"comparative":[87],"studies":[88],"alongside":[89],"existent":[90],"MNA":[91],"techniques,":[92],"were":[95],"found":[96],"superior":[99],"per":[100],"number":[102,109],"of":[103,110,120],"measures,":[104],"such":[105],"total":[108],"identified":[111,122],"homologs":[112],"interologs":[114],"well":[116],"fraction":[119],"functionally":[126],"similar":[127],"homologous":[129],"scaffold.":[132],"While":[133],"directed":[134],"primarily":[135],"at":[136,170],"PPIN-alignment,":[137],"generic":[141],"network":[142],"aligner":[143],"may":[145],"applied":[147],"arbitrary":[149],"networks.Availability":[150],"information:":[151,165],"web":[154],"server":[155],"source":[157],"code":[158],"available":[160,169],"at:":[161],"http://haddock6.sfsu.edu/smal/":[162],"CONTACT:":[163],"rahul@sfsu.eduSupplementary":[164],"Supplementary":[166],"data":[167],"Bioinformatics":[171],"online.":[172]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
