{"id":"https://openalex.org/W3121391924","doi":"https://doi.org/10.1093/bib/bbaa425","title":"HVIDB: a comprehensive database for human\u2013virus protein\u2013protein interactions","display_name":"HVIDB: a comprehensive database for human\u2013virus protein\u2013protein interactions","publication_year":2020,"publication_date":"2020-12-21","ids":{"openalex":"https://openalex.org/W3121391924","doi":"https://doi.org/10.1093/bib/bbaa425","mag":"3121391924"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa425","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa425","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"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/A5101479635","display_name":"Xiaodi Yang","orcid":"https://orcid.org/0000-0002-3229-5865"},"institutions":[{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaodi Yang","raw_affiliation_strings":["State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China","institution_ids":["https://openalex.org/I52158045"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073838780","display_name":"Xianyi Lian","orcid":"https://orcid.org/0000-0001-7576-2198"},"institutions":[{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xianyi Lian","raw_affiliation_strings":["State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China","institution_ids":["https://openalex.org/I52158045"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011114379","display_name":"Fu Chen","orcid":"https://orcid.org/0000-0001-7226-7554"},"institutions":[{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chen Fu","raw_affiliation_strings":["State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China","institution_ids":["https://openalex.org/I52158045"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076755077","display_name":"Stefan Wuchty","orcid":"https://orcid.org/0000-0001-8916-6522"},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]},{"id":"https://openalex.org/I4210157065","display_name":"Sylvester Comprehensive Cancer Center","ror":"https://ror.org/0552r4b12","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I145608581","https://openalex.org/I4210101935","https://openalex.org/I4210157065"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stefan Wuchty","raw_affiliation_strings":["Dept. of Biology, University of Miami, Miami, FL 33146, USA","Dept. of Computer Science, University of Miami, Miami, FL 33146, USA","Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA"],"affiliations":[{"raw_affiliation_string":"Dept. of Biology, University of Miami, Miami, FL 33146, USA","institution_ids":["https://openalex.org/I145608581"]},{"raw_affiliation_string":"Dept. of Computer Science, University of Miami, Miami, FL 33146, USA","institution_ids":["https://openalex.org/I145608581"]},{"raw_affiliation_string":"Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA","institution_ids":["https://openalex.org/I4210157065","https://openalex.org/I145608581"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006537953","display_name":"Shiping Yang","orcid":"https://orcid.org/0000-0001-5631-3549"},"institutions":[{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shiping Yang","raw_affiliation_strings":["State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China","institution_ids":["https://openalex.org/I52158045"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031348514","display_name":"Ziding Zhang","orcid":"https://orcid.org/0000-0002-9296-571X"},"institutions":[{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ziding Zhang","raw_affiliation_strings":["State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China","institution_ids":["https://openalex.org/I52158045"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5006537953","https://openalex.org/A5031348514"],"corresponding_institution_ids":["https://openalex.org/I52158045"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.3373,"has_fulltext":false,"cited_by_count":94,"citation_normalized_percentile":{"value":0.93533506,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"22","issue":"2","first_page":"832","last_page":"844"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9988999962806702,"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":0.9988999962806702,"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/T11668","display_name":"interferon and immune responses","score":0.9879000186920166,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9828000068664551,"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/virus","display_name":"Virus","score":0.6275888681411743},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.552377462387085},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5321012735366821},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.4452887773513794},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4431111216545105},{"id":"https://openalex.org/keywords/virus-classification","display_name":"Virus classification","score":0.43730318546295166},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4292775094509125},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39140844345092773},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3719349503517151},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.27936863899230957},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.2734995484352112},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.23292112350463867},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16035011410713196}],"concepts":[{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.6275888681411743},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.552377462387085},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5321012735366821},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.4452887773513794},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4431111216545105},{"id":"https://openalex.org/C20850961","wikidata":"https://www.wikidata.org/wiki/Q478216","display_name":"Virus classification","level":4,"score":0.43730318546295166},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4292775094509125},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39140844345092773},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3719349503517151},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.27936863899230957},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.2734995484352112},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.23292112350463867},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16035011410713196}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bib/bbaa425","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa425","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1449101145","display_name":null,"funder_award_id":"2017YFC1200205","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W1983079600","https://openalex.org/W2004051391","https://openalex.org/W2011226251","https://openalex.org/W2011340259","https://openalex.org/W2012034410","https://openalex.org/W2028491236","https://openalex.org/W2033727482","https://openalex.org/W2039473152","https://openalex.org/W2043764521","https://openalex.org/W2048299923","https://openalex.org/W2065283382","https://openalex.org/W2069152576","https://openalex.org/W2079277579","https://openalex.org/W2095867585","https://openalex.org/W2097217326","https://openalex.org/W2102278945","https://openalex.org/W2104005232","https://openalex.org/W2116041602","https://openalex.org/W2116988471","https://openalex.org/W2118258530","https://openalex.org/W2124249167","https://openalex.org/W2130687290","https://openalex.org/W2131271579","https://openalex.org/W2131858707","https://openalex.org/W2138875004","https://openalex.org/W2146512944","https://openalex.org/W2147526198","https://openalex.org/W2148043260","https://openalex.org/W2156269526","https://openalex.org/W2156564520","https://openalex.org/W2159126118","https://openalex.org/W2159482845","https://openalex.org/W2163038531","https://openalex.org/W2164353258","https://openalex.org/W2164813401","https://openalex.org/W2168637722","https://openalex.org/W2179127114","https://openalex.org/W2179438025","https://openalex.org/W2272509401","https://openalex.org/W2360131028","https://openalex.org/W2465613542","https://openalex.org/W2472798369","https://openalex.org/W2519110432","https://openalex.org/W2537623931","https://openalex.org/W2544136853","https://openalex.org/W2594569350","https://openalex.org/W2621037640","https://openalex.org/W2624282460","https://openalex.org/W2749136581","https://openalex.org/W2758437023","https://openalex.org/W2763483475","https://openalex.org/W2893748874","https://openalex.org/W2898598946","https://openalex.org/W2904824676","https://openalex.org/W2915536738","https://openalex.org/W2918063357","https://openalex.org/W2936781144","https://openalex.org/W2950595506","https://openalex.org/W2951679282","https://openalex.org/W2970491619","https://openalex.org/W2998220730","https://openalex.org/W3007643904","https://openalex.org/W3009335299","https://openalex.org/W3011537081","https://openalex.org/W3012858620","https://openalex.org/W3015190630","https://openalex.org/W3020695284","https://openalex.org/W3021100201","https://openalex.org/W3022285953","https://openalex.org/W4243979784","https://openalex.org/W4294216483","https://openalex.org/W6787121867","https://openalex.org/W7075630220"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W2251519152"],"abstract_inverted_index":{"Abstract":[0],"While":[1],"leading":[2],"to":[3,45,78,183,213,250,256],"millions":[4],"of":[5,12,25,42,52,57,139,150,165,190,199],"people\u2019s":[6],"deaths":[7],"every":[8],"year":[9],"the":[10,31,50,76,86,181,217],"treatment":[11],"viral":[13,53,221],"infectious":[14],"diseases":[15],"remains":[16],"a":[17,35,246],"huge":[18],"public":[19],"health":[20],"challenge.Therefore,":[21],"an":[22,196],"in-depth":[23,197],"understanding":[24],"human\u2013virus":[26,63,81,96,115,140,258],"protein\u2013protein":[27],"interactions":[28,215],"(PPIs)":[29],"as":[30,99,101,130,132,245],"molecular":[32],"interface":[33],"between":[34,216],"virus":[36,119],"and":[37,55,71,159,175,194,220,234],"its":[38],"host":[39,124,127,219],"cell":[40],"is":[41],"paramount":[43],"importance":[44],"obtain":[46,185],"new":[47],"insights":[48],"into":[49],"pathogenesis":[51],"infections":[54],"development":[56],"antiviral":[58],"therapeutic":[59],"treatments.":[60],"However,":[61],"current":[62],"PPI":[64,97,105],"database":[65,144,179],"resources":[66],"are":[67,155,224],"incomplete,":[68],"lack":[69],"annotation":[70],"usually":[72],"do":[73],"not":[74],"provide":[75],"opportunity":[77],"computationally":[79],"predict":[80,214],"PPIs.":[82,141],"Here,":[83],"we":[84],"present":[85],"Human\u2013Virus":[87],"Interaction":[88],"DataBase":[89],"(HVIDB,":[90],"http://zzdlab.com/hvidb/)":[91],"that":[92,154,223,241],"provides":[93,146],"comprehensively":[94],"annotated":[95,176],"data":[98],"well":[100,131],"seamlessly":[102],"integrates":[103,208],"online":[104],"prediction":[106],"tools.":[107],"Currently,":[108],"HVIDB":[109,206,242],"highlights":[110],"48":[111],"643":[112],"experimentally":[113,134],"verified":[114],"PPIs":[116,189],"covering":[117],"35":[118],"families,":[120],"6633":[121],"virally":[122],"targeted":[123,156],"complexes,":[125],"3572":[126],"dependency/restriction":[128],"factors":[129],"911":[133],"verified/predicted":[135],"3D":[136],"complex":[137],"structures":[138],"Furthermore,":[142],"our":[143,178],"resource":[145],"tissue-specific":[147],"expression":[148],"profiles":[149],"6790":[151],"human":[152,192,218],"genes":[153,168],"by":[157],"viruses":[158,193],"129":[160],"Gene":[161],"Expression":[162],"Omnibus":[163],"series":[164],"differentially":[166],"expressed":[167],"post-viral":[169],"infections.":[170],"Based":[171],"on":[172,226],"these":[173],"multifaceted":[174],"data,":[177],"allows":[180],"users":[182],"easily":[184],"reliable":[186],"information":[187],"about":[188],"various":[191],"conduct":[195],"analysis":[198],"their":[200],"inherent":[201],"biological":[202],"significance.":[203],"In":[204],"particular,":[205],"also":[207],"well-performing":[209],"machine":[210],"learning":[211],"models":[212],"proteins":[222],"based":[225],"(i)":[227],"sequence":[228],"embedding":[229],"techniques,":[230],"(ii)":[231],"interolog":[232],"mapping":[233],"(iii)":[235],"domain\u2013domain":[236],"interaction":[237],"inference.":[238],"We":[239],"anticipate":[240],"will":[243],"serve":[244],"one-stop":[247],"knowledge":[248],"base":[249],"further":[251],"guide":[252],"hypothesis-driven":[253],"experimental":[254],"efforts":[255],"investigate":[257],"relationships.":[259]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":23},{"year":2024,"cited_by_count":26},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":6}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2021-02-01T00:00:00"}
