{"id":"https://openalex.org/W4406261591","doi":"https://doi.org/10.1109/bibm62325.2024.10822458","title":"Applying the DeepSeqDock Harmonization Framework on Pseudomonas Aeruginosa Bacterial Biofilm Data","display_name":"Applying the DeepSeqDock Harmonization Framework on Pseudomonas Aeruginosa Bacterial Biofilm Data","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406261591","doi":"https://doi.org/10.1109/bibm62325.2024.10822458"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822458","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822458","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-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/A5101293705","display_name":"Corey Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I4210143528","display_name":"Lexington City Schools","ror":"https://ror.org/043f52r95","country_code":"US","type":"education","lineage":["https://openalex.org/I4210143528"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Corey Zhao","raw_affiliation_strings":["Lexington High School,Lexington,MA,USA"],"affiliations":[{"raw_affiliation_string":"Lexington High School,Lexington,MA,USA","institution_ids":["https://openalex.org/I4210143528"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091622645","display_name":"Bichar Dip Shrestha Gurung","orcid":"https://orcid.org/0000-0002-9818-5108"},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bichar Dip Shrestha Gurung","raw_affiliation_strings":["University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA"],"affiliations":[{"raw_affiliation_string":"University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093414899","display_name":"Tim Hartman","orcid":null},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tim Hartman","raw_affiliation_strings":["University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA"],"affiliations":[{"raw_affiliation_string":"University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036103687","display_name":"Tuyen Do","orcid":"https://orcid.org/0000-0002-1817-4565"},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tuyen Do","raw_affiliation_strings":["University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA"],"affiliations":[{"raw_affiliation_string":"University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA","institution_ids":["https://openalex.org/I189957204"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048065612","display_name":"Mariah Hoffman","orcid":"https://orcid.org/0000-0002-0509-3408"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mariah Hoffman","raw_affiliation_strings":["Vanderbilt University Medical Center,Nashville,TN,USA"],"affiliations":[{"raw_affiliation_string":"Vanderbilt University Medical Center,Nashville,TN,USA","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003549657","display_name":"Etienne Z. Gnimpi\u00e9ba","orcid":"https://orcid.org/0000-0002-5338-084X"},"institutions":[{"id":"https://openalex.org/I189957204","display_name":"University of South Dakota","ror":"https://ror.org/0043h8f16","country_code":"US","type":"education","lineage":["https://openalex.org/I189957204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Etienne Z. Gnimpieba","raw_affiliation_strings":["University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA"],"affiliations":[{"raw_affiliation_string":"University of South Dakota,Dept. of Biomedical Engineering,Vermillion,SD,USA","institution_ids":["https://openalex.org/I189957204"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101293705"],"corresponding_institution_ids":["https://openalex.org/I4210143528"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.22077424,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"6896","last_page":"6898"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9487000107765198,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9487000107765198,"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":0.9142000079154968,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9118000268936157,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/pseudomonas-aeruginosa","display_name":"Pseudomonas aeruginosa","score":0.8018499612808228},{"id":"https://openalex.org/keywords/biofilm","display_name":"Biofilm","score":0.7711420655250549},{"id":"https://openalex.org/keywords/harmonization","display_name":"Harmonization","score":0.6034104824066162},{"id":"https://openalex.org/keywords/microbiology","display_name":"Microbiology","score":0.5537649989128113},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3328224718570709},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23002687096595764},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.2132757008075714},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.044855475425720215}],"concepts":[{"id":"https://openalex.org/C2777637488","wikidata":"https://www.wikidata.org/wiki/Q31856","display_name":"Pseudomonas aeruginosa","level":3,"score":0.8018499612808228},{"id":"https://openalex.org/C58123911","wikidata":"https://www.wikidata.org/wiki/Q467410","display_name":"Biofilm","level":3,"score":0.7711420655250549},{"id":"https://openalex.org/C2779962950","wikidata":"https://www.wikidata.org/wiki/Q5659376","display_name":"Harmonization","level":2,"score":0.6034104824066162},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.5537649989128113},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3328224718570709},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23002687096595764},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.2132757008075714},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.044855475425720215},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822458","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822458","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320338440","display_name":"HORIZON EUROPE Health","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W2064397275","https://openalex.org/W2107665951","https://openalex.org/W2161036742","https://openalex.org/W2949216109","https://openalex.org/W2953067954","https://openalex.org/W3216421094","https://openalex.org/W4214621647"],"related_works":["https://openalex.org/W2377024769","https://openalex.org/W2365912673","https://openalex.org/W2984106036","https://openalex.org/W4396580402","https://openalex.org/W2896567050","https://openalex.org/W1641596209","https://openalex.org/W2091185511","https://openalex.org/W3131527100","https://openalex.org/W2336024593","https://openalex.org/W4388202013"],"abstract_inverted_index":{"In":[0,86],"the":[1,16,18,34,46,61,84,95,110,116],"modern":[2],"era,":[3],"data":[4,38,40,52,66,82,113],"availability":[5],"has":[6],"exponentially":[7],"increased.":[8],"From":[9],"different":[10],"universities,":[11],"institutions,":[12],"and":[13,26,71,76,115],"laboratories":[14],"across":[15],"globe,":[17],"wealth":[19],"of":[20,36,94,112,125],"information":[21],"brings":[22],"potential":[23],"for":[24,99,105,118,127],"integration":[25,35],"downstream":[27,128],"analysis.":[28,129],"This":[29],"paper":[30],"focuses":[31],"specifically":[32],"on":[33,79],"RNA-sequencing":[37],"using":[39],"harmonization,":[41],"a":[42],"technique":[43],"that":[44,50],"reduces":[45],"inter-institutional":[47],"batch":[48],"effects":[49],"confound":[51],"quality":[53],"with":[54],"non-biological":[55],"factors.":[56],"One":[57],"such":[58],"framework":[59,98],"is":[60,77],"DeepSeqDock":[62,97,117],"framework,":[63],"which":[64],"creates":[65],"harmonization":[67,114],"pipelines":[68],"through":[69],"training":[70],"tuning":[72],"in":[73,121],"specific":[74,122],"domains":[75,124],"evaluated":[78],"human":[80],"RNA":[81],"from":[83],"SEQC.":[85],"this":[87],"study,":[88],"we":[89,108],"present":[90],"an":[91],"alternate":[92],"application":[93],"adjusted":[96],"bacterial":[100,123],"biofilm":[101],"data.":[102],"By":[103],"adjusting":[104],"non-human":[106],"data,":[107],"show":[109],"generalization":[111],"its":[119],"applications":[120],"interest":[126]},"counts_by_year":[],"updated_date":"2025-12-27T23:08:20.325037","created_date":"2025-10-10T00:00:00"}