{"id":"https://openalex.org/W4386694140","doi":"https://doi.org/10.1093/bioinformatics/btad567","title":"ActivePPI: quantifying protein\u2013protein interaction network activity with Markov random fields","display_name":"ActivePPI: quantifying protein\u2013protein interaction network activity with Markov random fields","publication_year":2023,"publication_date":"2023-09-01","ids":{"openalex":"https://openalex.org/W4386694140","doi":"https://doi.org/10.1093/bioinformatics/btad567","pmid":"https://pubmed.ncbi.nlm.nih.gov/37698984"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad567","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad567","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/9/btad567/51724342/btad567.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","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/bioinformatics/article-pdf/39/9/btad567/51724342/btad567.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008268821","display_name":"Chuanyuan Wang","orcid":"https://orcid.org/0000-0002-3206-1372"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chuanyuan Wang","raw_affiliation_strings":["Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University , Jinan, Shandong 250061, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University , Jinan, Shandong 250061, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110630019","display_name":"Shiyu Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiyu Xu","raw_affiliation_strings":["Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University , Jinan, Shandong 250061, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University , Jinan, Shandong 250061, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091130599","display_name":"Duanchen Sun","orcid":"https://orcid.org/0000-0002-2802-6347"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Duanchen Sun","raw_affiliation_strings":["School of Mathematics, Shandong University , Jinan, Shandong 250100, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics, Shandong University , Jinan, Shandong 250100, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109218292","display_name":"Zhi\u2010Ping Liu","orcid":"https://orcid.org/0000-0001-7742-9161"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhi-Ping Liu","raw_affiliation_strings":["Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University , Jinan, Shandong 250061, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University , Jinan, Shandong 250061, China","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5008268821"],"corresponding_institution_ids":["https://openalex.org/I154099455"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.6036,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.70299936,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"39","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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":0.996399998664856,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9825999736785889,"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":0.6697309017181396},{"id":"https://openalex.org/keywords/permutation","display_name":"Permutation (music)","score":0.6332957744598389},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.46499669551849365},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4647255539894104},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.4480401575565338},{"id":"https://openalex.org/keywords/random-permutation","display_name":"Random permutation","score":0.4258449077606201},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39560678601264954},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3879246711730957},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2523233890533447},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24130234122276306},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17237919569015503},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09250405430793762}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6697309017181396},{"id":"https://openalex.org/C21308566","wikidata":"https://www.wikidata.org/wiki/Q7169365","display_name":"Permutation (music)","level":2,"score":0.6332957744598389},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.46499669551849365},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4647255539894104},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.4480401575565338},{"id":"https://openalex.org/C200985842","wikidata":"https://www.wikidata.org/wiki/Q3375503","display_name":"Random permutation","level":3,"score":0.4258449077606201},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39560678601264954},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3879246711730957},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2523233890533447},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24130234122276306},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17237919569015503},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09250405430793762},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011336","descriptor_name":"Probability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","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},{"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/btad567","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad567","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/9/btad567/51724342/btad567.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37698984","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37698984","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:10516639","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10516639","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10516639/pdf/btad567.pdf","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/btad567","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad567","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/9/btad567/51724342/btad567.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1920110554","display_name":null,"funder_award_id":"2022JC008","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2376276132","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G2481619625","display_name":null,"funder_award_id":"61973190","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2484882089","display_name":null,"funder_award_id":"2020YFA0712402","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G2495752485","display_name":null,"funder_award_id":"2022YFA","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G2802911279","display_name":null,"funder_award_id":"Young","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3875336646","display_name":null,"funder_award_id":"62202269","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5248026891","display_name":null,"funder_award_id":"62373216","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8210559533","display_name":null,"funder_award_id":"2022YFA1004801","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8758066315","display_name":null,"funder_award_id":"6197319","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320311026","display_name":"Shandong University","ror":"https://ror.org/0207yh398"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386694140.pdf"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1489950266","https://openalex.org/W1978984420","https://openalex.org/W2020859582","https://openalex.org/W2021613526","https://openalex.org/W2037036397","https://openalex.org/W2041813460","https://openalex.org/W2072099326","https://openalex.org/W2084619201","https://openalex.org/W2098264959","https://openalex.org/W2110687686","https://openalex.org/W2112220625","https://openalex.org/W2113624587","https://openalex.org/W2130410032","https://openalex.org/W2134736660","https://openalex.org/W2135856405","https://openalex.org/W2139036189","https://openalex.org/W2145753039","https://openalex.org/W2148590574","https://openalex.org/W2156737316","https://openalex.org/W2159707944","https://openalex.org/W2315196278","https://openalex.org/W2395887422","https://openalex.org/W2412784379","https://openalex.org/W2519691041","https://openalex.org/W2558534012","https://openalex.org/W2795142864","https://openalex.org/W2900566045","https://openalex.org/W2995684511","https://openalex.org/W3015429854","https://openalex.org/W3024768286","https://openalex.org/W3104755560","https://openalex.org/W3105828785","https://openalex.org/W3120750707","https://openalex.org/W3164046276","https://openalex.org/W3166761727","https://openalex.org/W3187487600","https://openalex.org/W4292261510","https://openalex.org/W4304080474","https://openalex.org/W4308834893","https://openalex.org/W4321851522","https://openalex.org/W6845797936"],"related_works":["https://openalex.org/W2184131469","https://openalex.org/W4321748008","https://openalex.org/W2074196947","https://openalex.org/W2797610470","https://openalex.org/W2120153268","https://openalex.org/W1887300513","https://openalex.org/W4312051210","https://openalex.org/W4297729179","https://openalex.org/W2533058927","https://openalex.org/W102744014"],"abstract_inverted_index":{"All":[0],"source":[1],"code":[2],"and":[3],"data":[4],"are":[5],"freely":[6],"available":[7],"at":[8],"https://github.com/zpliulab/ActivePPI.":[9]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
