{"id":"https://openalex.org/W2950813571","doi":"https://doi.org/10.1142/s0219720019500252","title":"Protein function prediction from dynamic protein interaction network using gene expression data","display_name":"Protein function prediction from dynamic protein interaction network using gene expression data","publication_year":2019,"publication_date":"2019-06-11","ids":{"openalex":"https://openalex.org/W2950813571","doi":"https://doi.org/10.1142/s0219720019500252","mag":"2950813571","pmid":"https://pubmed.ncbi.nlm.nih.gov/31617461"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720019500252","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019500252","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080194488","display_name":"Sovan Saha","orcid":"https://orcid.org/0000-0001-9251-8656"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Sovan Saha","raw_affiliation_strings":["Department of Computer Science & Engineering, Dr. Sudhir Chandra Sur Degree Engineering College, 540, Dum Dum Road, Near Dum Dum Jn. Station, Surermath, Kolkata 700074, India"],"raw_orcid":"https://orcid.org/0000-0001-9251-8656","affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, Dr. Sudhir Chandra Sur Degree Engineering College, 540, Dum Dum Road, Near Dum Dum Jn. Station, Surermath, Kolkata 700074, India","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083748306","display_name":"Abhimanyu Prasad","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Abhimanyu Prasad","raw_affiliation_strings":["Department of Computer Science & Engineering, Dr. Sudhir Chandra Sur Degree Engineering College, 540, Dum Dum Road, Near Dum Dum Jn. Station, Surermath, Kolkata 700074, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, Dr. Sudhir Chandra Sur Degree Engineering College, 540, Dum Dum Road, Near Dum Dum Jn. Station, Surermath, Kolkata 700074, India","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018474833","display_name":"Piyali Chatterjee","orcid":"https://orcid.org/0000-0002-7655-0485"},"institutions":[{"id":"https://openalex.org/I36090812","display_name":"Netaji Subhas University of Technology","ror":"https://ror.org/01fczmh85","country_code":"IN","type":"education","lineage":["https://openalex.org/I36090812"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Piyali Chatterjee","raw_affiliation_strings":["Department of Computer Science & Engineering, Netaji Subhash Engineering College, Techno City, Panchpota, Garia, Kolkata 700152, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, Netaji Subhash Engineering College, Techno City, Panchpota, Garia, Kolkata 700152, India","institution_ids":["https://openalex.org/I36090812"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043105133","display_name":"Subhadip Basu","orcid":"https://orcid.org/0000-0003-1780-0461"},"institutions":[{"id":"https://openalex.org/I170979836","display_name":"Jadavpur University","ror":"https://ror.org/02af4h012","country_code":"IN","type":"education","lineage":["https://openalex.org/I170979836"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Subhadip Basu","raw_affiliation_strings":["Department of Computer Science & Engineering, Jadavpur University, 188, Raja S.C.\u00a0Mallick Road, Kolkata 700032, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, Jadavpur University, 188, Raja S.C.\u00a0Mallick Road, Kolkata 700032, India","institution_ids":["https://openalex.org/I170979836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000210772","display_name":"Mita Nasipuri","orcid":"https://orcid.org/0000-0002-3906-5309"},"institutions":[{"id":"https://openalex.org/I36090812","display_name":"Netaji Subhas University of Technology","ror":"https://ror.org/01fczmh85","country_code":"IN","type":"education","lineage":["https://openalex.org/I36090812"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Mita Nasipuri","raw_affiliation_strings":["Department of Computer Science & Engineering, Netaji Subhash Engineering College, Techno City, Panchpota, Garia, Kolkata 700152, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Engineering, Netaji Subhash Engineering College, Techno City, Panchpota, Garia, Kolkata 700152, India","institution_ids":["https://openalex.org/I36090812"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5080194488"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.2822,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.79949972,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"17","issue":"04","first_page":"1950025","last_page":"1950025"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9975000023841858,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.991599977016449,"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/function","display_name":"Function (biology)","score":0.5868454575538635},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5104626417160034},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.49324411153793335},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4619283080101013},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4536617696285248},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.442963570356369},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4414644241333008},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.39550304412841797},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36588186025619507},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.32846885919570923},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32257765531539917}],"concepts":[{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5868454575538635},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5104626417160034},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.49324411153793335},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4619283080101013},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4536617696285248},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.442963570356369},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4414644241333008},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.39550304412841797},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36588186025619507},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32846885919570923},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32257765531539917},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015003","descriptor_name":"Yeasts","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720019500252","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019500252","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:31617461","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31617461","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1485582261","https://openalex.org/W1486817521","https://openalex.org/W1506427777","https://openalex.org/W1663797894","https://openalex.org/W1969412499","https://openalex.org/W1981267648","https://openalex.org/W2011986160","https://openalex.org/W2029588446","https://openalex.org/W2045131140","https://openalex.org/W2090766471","https://openalex.org/W2102814386","https://openalex.org/W2103453943","https://openalex.org/W2107710781","https://openalex.org/W2108735638","https://openalex.org/W2111805188","https://openalex.org/W2123854512","https://openalex.org/W2131456688","https://openalex.org/W2138003801","https://openalex.org/W2138582694","https://openalex.org/W2144393227","https://openalex.org/W2152495216","https://openalex.org/W2163844901","https://openalex.org/W2171403830","https://openalex.org/W2171692650","https://openalex.org/W2293572535","https://openalex.org/W2318899560","https://openalex.org/W2615066396","https://openalex.org/W2754675281","https://openalex.org/W2757974612","https://openalex.org/W2889660853","https://openalex.org/W4236956086"],"related_works":["https://openalex.org/W2094822546","https://openalex.org/W4388708026","https://openalex.org/W1969080446","https://openalex.org/W3108941781","https://openalex.org/W1578069856","https://openalex.org/W2084200259","https://openalex.org/W2134206588","https://openalex.org/W2065993463","https://openalex.org/W2401071219","https://openalex.org/W2554237979"],"abstract_inverted_index":{"Computational":[0],"prediction":[1,96],"of":[2,5,20,25,36,50,58,97,100,104,136,167,185,216],"functional":[3,18,98,183],"annotation":[4,99],"proteins":[6,59,117,141,188,197],"is":[7,12,39,43,70,223],"an":[8,13,168,210],"uphill":[9],"task.":[10],"There":[11],"ever":[14],"increasing":[15],"gap":[16],"between":[17,155],"characterization":[19,57],"protein":[21,26,37,92,157],"sequences":[22,27,158],"and":[23,91,138,159,194,214,219],"deluge":[24],"generated":[28],"by":[29,46,147],"large-scale":[30],"sequencing":[31],"projects.":[32],"The":[33],"dynamic":[34,71,81,133,177],"nature":[35],"interactions":[38,65],"frequently":[40],"observed":[41,112],"which":[42,69,222],"mostly":[44],"influenced":[45],"any":[47],"new":[48],"change":[49,53],"state":[51],"or":[52],"in":[54,72,170],"stimuli.":[55],"Functional":[56],"can":[60],"be":[61],"inferred":[62],"from":[63,174],"their":[64],"with":[66],"each":[67,180],"other,":[68],"nature.":[73],"In":[74],"this":[75],"work,":[76],"we":[77],"have":[78],"used":[79],"a":[80,105,171,203],"protein\u2013protein":[82],"interaction":[83],"network":[84],"(PPIN),":[85],"time":[86,122,144,181],"course":[87],"gene":[88],"expression":[89],"data":[90],"sequence":[93],"information":[94],"for":[95],"proteins.":[101],"During":[102],"progression":[103],"particular":[106],"function,":[107],"it":[108],"has":[109],"also":[110],"been":[111],"that":[113],"not":[114],"all":[115,121],"the":[116,132,153,165,175,186,192,199,227],"are":[118,189],"active":[119,126,196],"at":[120,142,179],"points.":[123],"For":[124],"unannotated":[125,195],"proteins,":[127],"our":[128],"proposed":[129,207],"methodology":[130,208],"explores":[131],"PPIN":[134],"consisting":[135],"level-1":[137,200],"level-2":[139,187],"neighboring":[140],"different":[143],"points,":[145],"filtered":[146,176],"Damerau\u2013Levenshtein":[148],"edit":[149],"distance":[150],"to":[151,163,191],"estimate":[152],"similarity":[154],"two":[156],"coefficient":[160],"variation":[161],"methods":[162],"assess":[164],"strength":[166],"edge":[169],"network.":[172],"Finally,":[173],"PPIN,":[178],"point,":[182],"annotations":[184],"assigned":[190],"unknown":[193],"through":[198],"neighbor,":[201],"following":[202],"bottom-up":[204],"strategy.":[205],"Our":[206],"achieves":[209],"average":[211],"precision,":[212],"recall":[213],"F-Score":[215],"0.59,":[217],"0.76":[218],"0.61":[220],"respectively,":[221],"significantly":[224],"higher":[225],"than":[226],"reported":[228],"state-of-the-art":[229],"methods.":[230]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":3}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}