{"id":"https://openalex.org/W4417131242","doi":"https://doi.org/10.1109/tse.2025.3641225","title":"Reaching Software Quality for Bioinformatics Applications: How Far Are We?","display_name":"Reaching Software Quality for Bioinformatics Applications: How Far Are We?","publication_year":2025,"publication_date":"2025-12-08","ids":{"openalex":"https://openalex.org/W4417131242","doi":"https://doi.org/10.1109/tse.2025.3641225"},"language":null,"primary_location":{"id":"doi:10.1109/tse.2025.3641225","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tse.2025.3641225","pdf_url":null,"source":{"id":"https://openalex.org/S8351582","display_name":"IEEE Transactions on Software Engineering","issn_l":"0098-5589","issn":["0098-5589","1939-3520","2326-3881"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320439","host_organization_name":"IEEE Computer Society","host_organization_lineage":["https://openalex.org/P4310320439","https://openalex.org/P4310319808"],"host_organization_lineage_names":["IEEE Computer Society","Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Software Engineering","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5100452974","display_name":"Xiaoyan Zhu","orcid":"https://orcid.org/0000-0002-7173-7793"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyan Zhu","raw_affiliation_strings":["School of Computer Science and Technology, Xi&#x02019;an Jiaotong University, Xi&#x02019;an, China","School of Computer Science and Technology, Xi&#x2019;an Jiaotong University, Xi&#x2019;an, China"],"raw_orcid":"https://orcid.org/0000-0002-7173-7793","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi&#x02019;an Jiaotong University, Xi&#x02019;an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi&#x2019;an Jiaotong University, Xi&#x2019;an, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Tianxiang Xu","orcid":"https://orcid.org/0000-0003-0759-6866"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianxiang Xu","raw_affiliation_strings":["School of Computer Science and Technology, Xi&#x02019;an Jiaotong University, Xi&#x02019;an, China","School of Computer Science and Technology, Xi&#x2019;an Jiaotong University, Xi&#x2019;an, China"],"raw_orcid":"https://orcid.org/0000-0003-0759-6866","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi&#x02019;an Jiaotong University, Xi&#x02019;an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi&#x2019;an Jiaotong University, Xi&#x2019;an, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047344339","display_name":"Xin Lai","orcid":"https://orcid.org/0000-0003-3850-5680"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Lai","raw_affiliation_strings":["School of Computer Science and Technology, Xi&#x02019;an Jiaotong University, Xi&#x02019;an, China","School of Computer Science and Technology, Xi&#x2019;an Jiaotong University, Xi&#x2019;an, China"],"raw_orcid":"https://orcid.org/0000-0003-3850-5680","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi&#x02019;an Jiaotong University, Xi&#x02019;an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi&#x2019;an Jiaotong University, Xi&#x2019;an, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079459346","display_name":"Xin Lian","orcid":null},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Lian","raw_affiliation_strings":["School of Computer Science and Technology, Xi&#x02019;an Jiaotong University, Xi&#x02019;an, China","School of Computer Science and Technology, Xi&#x2019;an Jiaotong University, Xi&#x2019;an, China"],"raw_orcid":"https://orcid.org/0009-0003-0425-3646","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi&#x02019;an Jiaotong University, Xi&#x02019;an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi&#x2019;an Jiaotong University, Xi&#x2019;an, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102712132","display_name":"Hangyu Cheng","orcid":"https://orcid.org/0009-0005-1680-5756"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hangyu Cheng","raw_affiliation_strings":["School of Computer Science and Technology, Xi&#x02019;an Jiaotong University, Xi&#x02019;an, China","School of Computer Science and Technology, Xi&#x2019;an Jiaotong University, Xi&#x2019;an, China"],"raw_orcid":"https://orcid.org/0009-0005-1680-5756","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi&#x02019;an Jiaotong University, Xi&#x02019;an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi&#x2019;an Jiaotong University, Xi&#x2019;an, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027360778","display_name":"Jiayin Wang","orcid":"https://orcid.org/0000-0002-3862-6557"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiayin Wang","raw_affiliation_strings":["School of Computer Science and Technology, Xi&#x02019;an Jiaotong University, Xi&#x02019;an, China","School of Computer Science and Technology, Xi&#x2019;an Jiaotong University, Xi&#x2019;an, China"],"raw_orcid":"https://orcid.org/0000-0002-3862-6557","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xi&#x02019;an Jiaotong University, Xi&#x02019;an, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Computer Science and Technology, Xi&#x2019;an Jiaotong University, Xi&#x2019;an, China","institution_ids":["https://openalex.org/I87445476"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.34435371,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"52","issue":"2","first_page":"595","last_page":"617"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10743","display_name":"Software Testing and Debugging Techniques","score":0.4756999909877777,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10743","display_name":"Software Testing and Debugging Techniques","score":0.4756999909877777,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"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/T11986","display_name":"Scientific Computing and Data Management","score":0.29660001397132874,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10260","display_name":"Software Engineering Research","score":0.06889999657869339,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/software","display_name":"Software","score":0.5605999827384949},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4587000012397766},{"id":"https://openalex.org/keywords/software-quality","display_name":"Software quality","score":0.45820000767707825},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4544000029563904},{"id":"https://openalex.org/keywords/software-development","display_name":"Software development","score":0.44760000705718994},{"id":"https://openalex.org/keywords/software-analytics","display_name":"Software analytics","score":0.4196000099182129},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.3910999894142151},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.3312999904155731}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7213000059127808},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5605999827384949},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.48510000109672546},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4587000012397766},{"id":"https://openalex.org/C117447612","wikidata":"https://www.wikidata.org/wiki/Q1412670","display_name":"Software quality","level":4,"score":0.45820000767707825},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4544000029563904},{"id":"https://openalex.org/C529173508","wikidata":"https://www.wikidata.org/wiki/Q638608","display_name":"Software development","level":3,"score":0.44760000705718994},{"id":"https://openalex.org/C171981572","wikidata":"https://www.wikidata.org/wiki/Q7554239","display_name":"Software analytics","level":5,"score":0.4196000099182129},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.41940000653266907},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.3910999894142151},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3693000078201294},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.3312999904155731},{"id":"https://openalex.org/C120936955","wikidata":"https://www.wikidata.org/wiki/Q2155640","display_name":"Empirical research","level":2,"score":0.3255999982357025},{"id":"https://openalex.org/C186846655","wikidata":"https://www.wikidata.org/wiki/Q3398377","display_name":"Software construction","level":4,"score":0.3095000088214874},{"id":"https://openalex.org/C149091818","wikidata":"https://www.wikidata.org/wiki/Q2429814","display_name":"Software system","level":3,"score":0.30869999527931213},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.296999990940094},{"id":"https://openalex.org/C48002344","wikidata":"https://www.wikidata.org/wiki/Q2919644","display_name":"Verification and validation","level":2,"score":0.28690001368522644},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.28360000252723694},{"id":"https://openalex.org/C62913178","wikidata":"https://www.wikidata.org/wiki/Q7554361","display_name":"Software security assurance","level":4,"score":0.2822999954223633},{"id":"https://openalex.org/C82214349","wikidata":"https://www.wikidata.org/wiki/Q657339","display_name":"Software metric","level":5,"score":0.28029999136924744},{"id":"https://openalex.org/C74579156","wikidata":"https://www.wikidata.org/wiki/Q7554342","display_name":"Software peer review","level":5,"score":0.2770000100135803},{"id":"https://openalex.org/C202105479","wikidata":"https://www.wikidata.org/wiki/Q265013","display_name":"Software evolution","level":5,"score":0.26899999380111694},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.267300009727478},{"id":"https://openalex.org/C150292731","wikidata":"https://www.wikidata.org/wiki/Q1342704","display_name":"Code review","level":5,"score":0.265500009059906},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.26330000162124634}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tse.2025.3641225","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tse.2025.3641225","pdf_url":null,"source":{"id":"https://openalex.org/S8351582","display_name":"IEEE Transactions on Software Engineering","issn_l":"0098-5589","issn":["0098-5589","1939-3520","2326-3881"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320439","host_organization_name":"IEEE Computer Society","host_organization_lineage":["https://openalex.org/P4310320439","https://openalex.org/P4310319808"],"host_organization_lineage_names":["IEEE Computer Society","Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Software Engineering","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2715084110","display_name":null,"funder_award_id":"62402376","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3180425335","display_name":null,"funder_award_id":"72293581","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G516663181","display_name":null,"funder_award_id":"72274152","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6671363317","display_name":null,"funder_award_id":"62572389","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":211,"referenced_works":["https://openalex.org/W814172419","https://openalex.org/W1008898928","https://openalex.org/W1510833811","https://openalex.org/W1565378970","https://openalex.org/W1569946922","https://openalex.org/W1835879695","https://openalex.org/W1882772761","https://openalex.org/W1979115864","https://openalex.org/W1979579723","https://openalex.org/W1999574084","https://openalex.org/W2010653277","https://openalex.org/W2041282815","https://openalex.org/W2087527532","https://openalex.org/W2095688269","https://openalex.org/W2101912966","https://openalex.org/W2102619694","https://openalex.org/W2111350087","https://openalex.org/W2111874706","https://openalex.org/W2111947254","https://openalex.org/W2116899182","https://openalex.org/W2119451273","https://openalex.org/W2136102567","https://openalex.org/W2146005104","https://openalex.org/W2149992227","https://openalex.org/W2157253968","https://openalex.org/W2166820820","https://openalex.org/W2167696914","https://openalex.org/W2169456326","https://openalex.org/W2169912638","https://openalex.org/W2170551349","https://openalex.org/W2193667971","https://openalex.org/W2204914826","https://openalex.org/W2227231914","https://openalex.org/W2230465815","https://openalex.org/W2235737683","https://openalex.org/W2236822143","https://openalex.org/W2260037449","https://openalex.org/W2269938998","https://openalex.org/W2276335691","https://openalex.org/W2293946895","https://openalex.org/W2306630387","https://openalex.org/W2315009848","https://openalex.org/W2323326409","https://openalex.org/W2337209831","https://openalex.org/W2338882301","https://openalex.org/W2339819569","https://openalex.org/W2340974016","https://openalex.org/W2342016684","https://openalex.org/W2343956310","https://openalex.org/W2405678927","https://openalex.org/W2410378998","https://openalex.org/W2422879816","https://openalex.org/W2432815617","https://openalex.org/W2467057731","https://openalex.org/W2473818600","https://openalex.org/W2490472517","https://openalex.org/W2512945549","https://openalex.org/W2519794569","https://openalex.org/W2548385112","https://openalex.org/W2561754210","https://openalex.org/W2567940875","https://openalex.org/W2586169357","https://openalex.org/W2586994065","https://openalex.org/W2594807826","https://openalex.org/W2598066557","https://openalex.org/W2599222361","https://openalex.org/W2604944932","https://openalex.org/W2609153336","https://openalex.org/W2610774430","https://openalex.org/W2612550256","https://openalex.org/W2731062088","https://openalex.org/W2733002388","https://openalex.org/W2742478344","https://openalex.org/W2750049634","https://openalex.org/W2757764553","https://openalex.org/W2761803678","https://openalex.org/W2762082538","https://openalex.org/W2762349056","https://openalex.org/W2767943400","https://openalex.org/W2782146634","https://openalex.org/W2784788330","https://openalex.org/W2788194819","https://openalex.org/W2788436468","https://openalex.org/W2790675139","https://openalex.org/W2800392236","https://openalex.org/W2804267743","https://openalex.org/W2809616137","https://openalex.org/W2810110985","https://openalex.org/W2867868648","https://openalex.org/W2885507494","https://openalex.org/W2889664156","https://openalex.org/W2890349324","https://openalex.org/W2894808609","https://openalex.org/W2896872272","https://openalex.org/W2900387735","https://openalex.org/W2900510132","https://openalex.org/W2900576466","https://openalex.org/W2906625258","https://openalex.org/W2907514116","https://openalex.org/W2910366648","https://openalex.org/W2916020270","https://openalex.org/W2925188014","https://openalex.org/W2940982798","https://openalex.org/W2947780575","https://openalex.org/W2949280048","https://openalex.org/W2949465911","https://openalex.org/W2950014930","https://openalex.org/W2950213774","https://openalex.org/W2950814274","https://openalex.org/W2950954328","https://openalex.org/W2951187834","https://openalex.org/W2951217100","https://openalex.org/W2951337536","https://openalex.org/W2951700463","https://openalex.org/W2952027905","https://openalex.org/W2952445740","https://openalex.org/W2952535935","https://openalex.org/W2952766146","https://openalex.org/W2952935243","https://openalex.org/W2953170162","https://openalex.org/W2953251392","https://openalex.org/W2959295202","https://openalex.org/W2962748597","https://openalex.org/W2963132013","https://openalex.org/W2963417953","https://openalex.org/W2969386006","https://openalex.org/W2969707970","https://openalex.org/W2971559821","https://openalex.org/W2979981308","https://openalex.org/W2980284735","https://openalex.org/W2985320478","https://openalex.org/W2986598803","https://openalex.org/W2992446582","https://openalex.org/W2992976869","https://openalex.org/W2994516867","https://openalex.org/W3011486364","https://openalex.org/W3018353191","https://openalex.org/W3018596693","https://openalex.org/W3024992482","https://openalex.org/W3036135788","https://openalex.org/W3037099619","https://openalex.org/W3041129226","https://openalex.org/W3049406222","https://openalex.org/W3091506611","https://openalex.org/W3092327956","https://openalex.org/W3092652421","https://openalex.org/W3106755430","https://openalex.org/W3108941787","https://openalex.org/W3113659825","https://openalex.org/W3114078084","https://openalex.org/W3117398140","https://openalex.org/W3118004748","https://openalex.org/W3118986139","https://openalex.org/W3124819020","https://openalex.org/W3131055609","https://openalex.org/W3140536314","https://openalex.org/W3143063265","https://openalex.org/W3145635506","https://openalex.org/W3146142859","https://openalex.org/W3147574308","https://openalex.org/W3148807116","https://openalex.org/W3155196695","https://openalex.org/W3160770927","https://openalex.org/W3163176492","https://openalex.org/W3185096629","https://openalex.org/W3186404930","https://openalex.org/W3190759848","https://openalex.org/W3198658154","https://openalex.org/W3200315804","https://openalex.org/W3202634790","https://openalex.org/W3209528471","https://openalex.org/W3213886757","https://openalex.org/W3215852532","https://openalex.org/W4205281808","https://openalex.org/W4205835805","https://openalex.org/W4210575300","https://openalex.org/W4210587306","https://openalex.org/W4211233231","https://openalex.org/W4221030787","https://openalex.org/W4224470052","https://openalex.org/W4225587613","https://openalex.org/W4226096338","https://openalex.org/W4226258670","https://openalex.org/W4282935730","https://openalex.org/W4287958635","https://openalex.org/W4291950457","https://openalex.org/W4295530758","https://openalex.org/W4304959451","https://openalex.org/W4309321042","https://openalex.org/W4309944312","https://openalex.org/W4319334382","https://openalex.org/W4375863320","https://openalex.org/W4378212544","https://openalex.org/W4378942602","https://openalex.org/W4385759320","https://openalex.org/W4387088549","https://openalex.org/W4389332145","https://openalex.org/W4390500910","https://openalex.org/W4391738165","https://openalex.org/W4391759634","https://openalex.org/W4392111189","https://openalex.org/W4392868006","https://openalex.org/W4396803203","https://openalex.org/W4400579932","https://openalex.org/W4401464022","https://openalex.org/W4401545624","https://openalex.org/W4402684050","https://openalex.org/W4403288742","https://openalex.org/W4404952942","https://openalex.org/W4407514551","https://openalex.org/W4408273382"],"related_works":[],"abstract_inverted_index":{"With":[0],"the":[1,17,68,88,111,194,209,231],"rapid":[2],"advancements":[3],"in":[4,171,230],"medicine,":[5],"biology,":[6],"and":[7,31,53,63,73,102,118,124,196,215,234,240],"information":[8],"technology,":[9],"their":[10],"deep":[11],"integration":[12],"has":[13,85],"given":[14],"rise":[15],"to":[16,66,80,128,176,183],"emerging":[18],"field":[19],"of":[20,37,43,70,90,142,158,169,198],"bioinformatics.":[21],"In":[22],"this":[23],"process,":[24],"high\u2013throughput":[25],"technologies":[26],"such":[27],"as":[28],"genomics,":[29],"transcriptomics,":[30],"proteomics":[32],"have":[33],"generated":[34],"massive":[35],"volumes":[36],"biological":[38,41],"data.":[39],"The":[40,140],"significance":[42],"these":[44,204],"data":[45,127],"heavily":[46],"relies":[47],"on":[48,203,227],"bioinformatics":[49,71,91,107,143,172,213,232],"software":[50,72,108,144,164,173,214,228],"for":[51,59,115,224,238],"analysis":[52,135],"processing.":[54],"Therefore,":[55],"it":[56],"is":[57],"crucial":[58],"both":[60],"scientific":[61],"research":[62,131,226],"clinical":[64],"applications":[65],"ensure":[67],"quality":[69,89,141,229],"avoiding":[74],"errors":[75],"or":[76,188],"hidden":[77],"defects.":[78],"However,":[79],"date,":[81],"no":[82],"dedicated":[83],"study":[84,98],"systematically":[86],"analyzed":[87],"software.":[92,160],"we":[93,122,206],"conduct":[94],"a":[95,166,222],"comprehensive":[96],"empirical":[97],"that":[99,157],"aggregates,":[100],"synthesizes,":[101],"analyzes":[103],"findings":[104],"from":[105],"167":[106],"projects.":[109],"Following":[110],"Preferred":[112],"Reporting":[113],"Items":[114],"Systematic":[116],"Review":[117],"Meta\u2013Analysis":[119],"(PRISMA)":[120],"protocol,":[121],"extract":[123],"evaluate":[125],"quality\u2013related":[126],"answer":[129],"our":[130],"questions":[132],"(RQs).":[133],"Our":[134],"reveals":[136],"several":[137],"key":[138],"findings.":[139],"requires":[145],"significant":[146],"improvement,":[147],"with":[148],"an":[149],"average":[150],"defect":[151],"density":[152],"approximately":[153],"11.8\u00d7":[154],"higher":[155],"than":[156],"general-purpose":[159],"Additionally,":[161],"unlike":[162],"traditional":[163],"domains,":[165],"considerable":[167],"proportion":[168],"defects":[170],"are":[174],"related":[175],"annotations.":[177],"These":[178],"issues":[179],"can":[180],"lead":[181],"developers":[182],"overlook":[184],"potential":[185,217],"security":[186],"vulnerabilities":[187],"make":[189],"incorrect":[190],"fixes,":[191],"thereby":[192],"increasing":[193],"cost":[195],"complexity":[197],"subsequent":[199],"code":[200],"maintenance.":[201],"Based":[202],"findings,":[205],"further":[207,225],"discuss":[208],"challenges":[210],"faced":[211],"by":[212],"propose":[216],"solutions.":[218],"This":[219],"paper":[220],"lays":[221],"foundation":[223],"domain":[233],"offers":[235],"actionable":[236],"insights":[237],"researchers":[239],"practitioners":[241],"alike.":[242]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-12-08T00:00:00"}
