{"id":"https://openalex.org/W4226343290","doi":"https://doi.org/10.1093/bioinformatics/btac258","title":"Topsy-Turvy: integrating a global view into sequence-based PPI prediction","display_name":"Topsy-Turvy: integrating a global view into sequence-based PPI prediction","publication_year":2022,"publication_date":"2022-04-14","ids":{"openalex":"https://openalex.org/W4226343290","doi":"https://doi.org/10.1093/bioinformatics/btac258","pmid":"https://pubmed.ncbi.nlm.nih.gov/35758793"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac258","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac258","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/Supplement_1/i264/44269394/btac258.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/Supplement_1/i264/44269394/btac258.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081688191","display_name":"Rohit Singh","orcid":"https://orcid.org/0000-0002-4084-7340"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rohit Singh","raw_affiliation_strings":["Computer Science and Artificial Intelligence Lab., Massachusetts Institute of Technology , Cambridge, MA 02139, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Lab., Massachusetts Institute of Technology , Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036303987","display_name":"Kapil Devkota","orcid":"https://orcid.org/0000-0002-6093-6260"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kapil Devkota","raw_affiliation_strings":["Department of Computer Science, Tufts University , Medford, MA 02155, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Tufts University , Medford, MA 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020346838","display_name":"Samuel Sledzieski","orcid":"https://orcid.org/0000-0002-0170-3029"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel Sledzieski","raw_affiliation_strings":["Computer Science and Artificial Intelligence Lab., Massachusetts Institute of Technology , Cambridge, MA 02139, USA"],"affiliations":[{"raw_affiliation_string":"Computer Science and Artificial Intelligence Lab., Massachusetts Institute of Technology , Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044078921","display_name":"Bonnie Berger","orcid":"https://orcid.org/0000-0002-2724-7228"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bonnie Berger","raw_affiliation_strings":["Department of Mathematics, Massachusetts Institute of Technology , Cambridge, MA 02139, USA","MIT Schwarzman College of Computing Cambridge , MA 02139, USA"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Massachusetts Institute of Technology , Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"MIT Schwarzman College of Computing Cambridge , MA 02139, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026411021","display_name":"Lenore Cowen","orcid":"https://orcid.org/0000-0001-6698-6413"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lenore Cowen","raw_affiliation_strings":["Department of Computer Science, Tufts University , Medford, MA 02155, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Tufts University , Medford, MA 02155, USA","institution_ids":["https://openalex.org/I121934306"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5026411021","https://openalex.org/A5044078921"],"corresponding_institution_ids":["https://openalex.org/I121934306","https://openalex.org/I63966007"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":6.8459,"has_fulltext":false,"cited_by_count":86,"citation_normalized_percentile":{"value":0.98048761,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"38","issue":"Supplement_1","first_page":"i264","last_page":"i272"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9976000189781189,"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":0.9966999888420105,"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":0.806142270565033},{"id":"https://openalex.org/keywords/generalizability-theory","display_name":"Generalizability theory","score":0.5538156628608704},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5278337597846985},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.49826931953430176},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.47086086869239807},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4266059398651123},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3997610807418823},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36620670557022095},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08707642555236816}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.806142270565033},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.5538156628608704},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5278337597846985},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.49826931953430176},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.47086086869239807},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4266059398651123},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3997610807418823},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36620670557022095},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08707642555236816},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac258","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac258","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/Supplement_1/i264/44269394/btac258.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35758793","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35758793","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:pubmedcentral.nih.gov:9235477","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9235477","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac258","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac258","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/Supplement_1/i264/44269394/btac258.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5799999833106995,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G7900601331","display_name":null,"funder_award_id":"CCF-1934553","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8012526549","display_name":null,"funder_award_id":"R35GM141861","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4226343290.pdf","grobid_xml":"https://content.openalex.org/works/W4226343290.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1885254586","https://openalex.org/W1993702356","https://openalex.org/W2007781735","https://openalex.org/W2039473152","https://openalex.org/W2062858001","https://openalex.org/W2064990035","https://openalex.org/W2135197754","https://openalex.org/W2556519015","https://openalex.org/W2624021832","https://openalex.org/W2805679104","https://openalex.org/W2890911678","https://openalex.org/W2907485791","https://openalex.org/W2950742983","https://openalex.org/W2952068915","https://openalex.org/W2957436444","https://openalex.org/W2962756421","https://openalex.org/W2992752586","https://openalex.org/W3015964336","https://openalex.org/W3043771525","https://openalex.org/W3045012301","https://openalex.org/W3107527779","https://openalex.org/W3108458441","https://openalex.org/W3117256259","https://openalex.org/W3166142427","https://openalex.org/W3174753721","https://openalex.org/W3177828909","https://openalex.org/W3199468887","https://openalex.org/W3202105508","https://openalex.org/W4225378695","https://openalex.org/W4319058224","https://openalex.org/W6652023393","https://openalex.org/W6754715044","https://openalex.org/W6787770138","https://openalex.org/W6802033083","https://openalex.org/W6849534884"],"related_works":["https://openalex.org/W2118717649","https://openalex.org/W2413243053","https://openalex.org/W410723623","https://openalex.org/W2015341305","https://openalex.org/W2035068594","https://openalex.org/W4225593417","https://openalex.org/W2573498121","https://openalex.org/W3022298670","https://openalex.org/W3160494304","https://openalex.org/W3006162251"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":28},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":6}],"updated_date":"2026-03-22T08:09:32.410652","created_date":"2025-10-10T00:00:00"}
