{"id":"https://openalex.org/W7171512377","doi":"https://doi.org/10.1145/3807503.3819462","title":"MetabOmics: Metabolism-Oriented Omics Data Integration","display_name":"MetabOmics: Metabolism-Oriented Omics Data Integration","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171512377","doi":"https://doi.org/10.1145/3807503.3819462"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3819462","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819462","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3807503.3819462","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5143819249","display_name":"Aycan \u015eahin","orcid":"https://orcid.org/0000-0001-7849-9882"},"institutions":[{"id":"https://openalex.org/I48912391","display_name":"Istanbul Technical University","ror":"https://ror.org/059636586","country_code":"TR","type":"education","lineage":["https://openalex.org/I48912391"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Aycan \u015eahin","raw_affiliation_strings":["Istanbul Technical University, Istanbul, Turkiye"],"raw_orcid":"https://orcid.org/0000-0001-7849-9882","affiliations":[{"raw_affiliation_string":"Istanbul Technical University, Istanbul, Turkiye","institution_ids":["https://openalex.org/I48912391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5141014593","display_name":"Mehmet Ali Erdogan","orcid":null},"institutions":[{"id":"https://openalex.org/I48912391","display_name":"Istanbul Technical University","ror":"https://ror.org/059636586","country_code":"TR","type":"education","lineage":["https://openalex.org/I48912391"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Mehmet Ali Erdo\u011fan","raw_affiliation_strings":["Istanbul Technical University, Istanbul, Turkiye"],"raw_orcid":"https://orcid.org/0009-0009-3092-7978","affiliations":[{"raw_affiliation_string":"Istanbul Technical University, Istanbul, Turkiye","institution_ids":["https://openalex.org/I48912391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5143761133","display_name":"Utku Sabri Kaya","orcid":"https://orcid.org/0009-0009-0000-5059"},"institutions":[{"id":"https://openalex.org/I48912391","display_name":"Istanbul Technical University","ror":"https://ror.org/059636586","country_code":"TR","type":"education","lineage":["https://openalex.org/I48912391"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Utku Sabri Kaya","raw_affiliation_strings":["Istanbul Technical University, Istanbul, Turkiye"],"raw_orcid":"https://orcid.org/0009-0009-0000-5059","affiliations":[{"raw_affiliation_string":"Istanbul Technical University, Istanbul, Turkiye","institution_ids":["https://openalex.org/I48912391"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035836413","display_name":"Ali Cakmak","orcid":"https://orcid.org/0000-0002-1382-6130"},"institutions":[{"id":"https://openalex.org/I48912391","display_name":"Istanbul Technical University","ror":"https://ror.org/059636586","country_code":"TR","type":"education","lineage":["https://openalex.org/I48912391"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ali \u00c7akmak","raw_affiliation_strings":["Istanbul Technical University, Istanbul, Turkiye"],"raw_orcid":"https://orcid.org/0000-0002-1382-6130","affiliations":[{"raw_affiliation_string":"Istanbul Technical University, Istanbul, Turkiye","institution_ids":["https://openalex.org/I48912391"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I48912391"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.6097999811172485},{"id":"https://openalex.org/keywords/system-integration","display_name":"System integration","score":0.2687000036239624},{"id":"https://openalex.org/keywords/information-integration","display_name":"Information integration","score":0.2635999917984009},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.24410000443458557},{"id":"https://openalex.org/keywords/big-data","display_name":"Big data","score":0.2337999939918518}],"concepts":[{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.6097999811172485},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5878000259399414},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33379998803138733},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2838999927043915},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.26930001378059387},{"id":"https://openalex.org/C19527686","wikidata":"https://www.wikidata.org/wiki/Q1665453","display_name":"System integration","level":2,"score":0.2687000036239624},{"id":"https://openalex.org/C33326189","wikidata":"https://www.wikidata.org/wiki/Q17092450","display_name":"Information integration","level":2,"score":0.2635999917984009},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.24410000443458557},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.2337999939918518},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.22609999775886536}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3819462","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819462","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3807503.3819462","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819462","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1567112601","https://openalex.org/W2014988241","https://openalex.org/W2032691440","https://openalex.org/W2050140657","https://openalex.org/W2057793636","https://openalex.org/W2069269337","https://openalex.org/W2074490119","https://openalex.org/W2088891952","https://openalex.org/W2090406819","https://openalex.org/W2132623845","https://openalex.org/W2344089340","https://openalex.org/W2493103841","https://openalex.org/W2531904292","https://openalex.org/W2698350175","https://openalex.org/W2789128799","https://openalex.org/W2900616886","https://openalex.org/W3041823559","https://openalex.org/W4225696671","https://openalex.org/W4295898550","https://openalex.org/W4319597824","https://openalex.org/W4377233107","https://openalex.org/W4380987157","https://openalex.org/W4381248780","https://openalex.org/W4393142382","https://openalex.org/W4393157019","https://openalex.org/W4407390690","https://openalex.org/W4413816496","https://openalex.org/W4413852195","https://openalex.org/W4414753568"],"related_works":[],"abstract_inverted_index":{"Biological":[0],"processes":[1],"arise":[2],"from":[3],"complex":[4],"interactions":[5],"across":[6],"multiple":[7],"molecular":[8,82],"layers,":[9],"yet":[10],"bridging":[11],"the":[12,48,78,106,116],"gap":[13],"between":[14],"disparate":[15],"omics":[16],"data":[17],"types":[18],"remains":[19],"a":[20,27,58,125,130],"significant":[21],"challenge.":[22],"This":[23],"paper":[24],"introduces":[25],"MetabOmics,":[26],"comprehensive":[28],"metabolism-oriented":[29],"integrated":[30,52],"multi-omics":[31],"analysis":[32,140],"method":[33],"structurally":[34],"designed":[35],"to":[36,102,114,142],"accommodate":[37],"genomics,":[38],"transcriptomics,":[39],"proteomics,":[40],"and":[41,71,92,118,145],"metabolomics":[42],"datasets.":[43],"Our":[44],"methodology":[45],"centers":[46],"on":[47],"construction":[49],"of":[50,61,81,121],"an":[51,136],"multi-omic":[53],"interaction":[54],"network":[55,91],"that":[56],"incorporates":[57],"wide":[59],"range":[60],"biological":[62,87],"interactions,":[63],"including":[64],"gene":[65],"expression,":[66],"translation,":[67],"transcription":[68],"factor":[69],"activity,":[70],"post-transcriptional":[72],"regulation":[73],"via":[74],"microRNAs.":[75],"To":[76],"capture":[77],"cascading":[79],"effects":[80],"changes,":[83],"we":[84,134],"map":[85],"measured":[86],"entities":[88],"onto":[89],"this":[90],"utilize":[93],"information":[94],"diffusion":[95],"models,":[96],"such":[97],"as":[98],"Linear":[99],"Threshold":[100],"Diffusion,":[101],"propagate":[103],"fold-changes":[104],"throughout":[105],"system.":[107],"These":[108],"propagated":[109],"measurements":[110],"are":[111],"then":[112],"used":[113],"update":[115],"lower":[117],"upper":[119],"bounds":[120],"metabolic":[122,127,138],"reactions":[123],"within":[124],"genome-scale":[126],"model":[128],"in":[129],"personalized":[131],"manner.":[132],"Finally,":[133],"apply":[135],"extended":[137],"flux":[139],"algorithm":[141],"compute":[143],"reaction":[144],"pathway":[146],"differentiation":[147],"scores.":[148]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}
