{"id":"https://openalex.org/W4392568117","doi":"https://doi.org/10.1145/3638569.3638574","title":"A Wavelet-Based Approach Reveals Host-Cell-Type-Specific Multi-omics Networks in Inflammatory Bowel Disease","display_name":"A Wavelet-Based Approach Reveals Host-Cell-Type-Specific Multi-omics Networks in Inflammatory Bowel Disease","publication_year":2023,"publication_date":"2023-12-11","ids":{"openalex":"https://openalex.org/W4392568117","doi":"https://doi.org/10.1145/3638569.3638574"},"language":"en","primary_location":{"id":"doi:10.1145/3638569.3638574","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3638569.3638574","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3638569.3638574","source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2023 7th International Conference on Computational Biology and Bioinformatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3638569.3638574","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023624658","display_name":"Stephanie Chang","orcid":"https://orcid.org/0009-0005-6809-7552"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephanie Chang","raw_affiliation_strings":["Massachusetts Instititute of Technology, USA"],"raw_orcid":"https://orcid.org/0009-0005-6809-7552","affiliations":[{"raw_affiliation_string":"Massachusetts Instititute of Technology, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067920802","display_name":"Adeethyia Shankar","orcid":"https://orcid.org/0000-0003-4298-2797"},"institutions":[{"id":"https://openalex.org/I175594653","display_name":"John Brown University","ror":"https://ror.org/02ct41q97","country_code":"US","type":"education","lineage":["https://openalex.org/I175594653"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adeethyia Shankar","raw_affiliation_strings":["Brown University, USA"],"raw_orcid":"https://orcid.org/0000-0003-4298-2797","affiliations":[{"raw_affiliation_string":"Brown University, USA","institution_ids":["https://openalex.org/I175594653"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052600103","display_name":"Yongzhong Zhao","orcid":"https://orcid.org/0000-0002-4046-2117"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yongzhong Zhao","raw_affiliation_strings":["Frontage Labs, USA"],"raw_orcid":"https://orcid.org/0000-0002-4046-2117","affiliations":[{"raw_affiliation_string":"Frontage Labs, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101926262","display_name":"Tong Liu","orcid":"https://orcid.org/0000-0003-1880-6590"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tong Liu","raw_affiliation_strings":["Department of Mathematical Sciences, Tsinghua University, China"],"raw_orcid":"https://orcid.org/0000-0003-1880-6590","affiliations":[{"raw_affiliation_string":"Department of Mathematical Sciences, Tsinghua University, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083928205","display_name":"Xiaodi Wang","orcid":"https://orcid.org/0000-0003-3150-9574"},"institutions":[{"id":"https://openalex.org/I204366597","display_name":"Western Connecticut State University","ror":"https://ror.org/01565p617","country_code":"US","type":"education","lineage":["https://openalex.org/I204366597","https://openalex.org/I4210132746"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaodi Wang","raw_affiliation_strings":["Department of Mathematics, Western Connecticut State University, USA"],"raw_orcid":"https://orcid.org/0000-0003-3150-9574","affiliations":[{"raw_affiliation_string":"Department of Mathematics, Western Connecticut State University, USA","institution_ids":["https://openalex.org/I204366597"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"31","last_page":"37"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994000196456909,"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":0.9994000196456909,"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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9866999983787537,"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/inflammatory-bowel-disease","display_name":"Inflammatory bowel disease","score":0.7268632054328918},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.6493037343025208},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.6145256757736206},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.5795491337776184},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5221750736236572},{"id":"https://openalex.org/keywords/wavelet","display_name":"Wavelet","score":0.5157973766326904},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5104590654373169},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3361471891403198},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.31548652052879333},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2788771986961365},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.25993475317955017},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.14464262127876282},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07898768782615662}],"concepts":[{"id":"https://openalex.org/C2778260677","wikidata":"https://www.wikidata.org/wiki/Q917447","display_name":"Inflammatory bowel disease","level":3,"score":0.7268632054328918},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.6493037343025208},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.6145256757736206},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.5795491337776184},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5221750736236572},{"id":"https://openalex.org/C47432892","wikidata":"https://www.wikidata.org/wiki/Q831390","display_name":"Wavelet","level":2,"score":0.5157973766326904},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5104590654373169},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3361471891403198},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.31548652052879333},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2788771986961365},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25993475317955017},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.14464262127876282},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07898768782615662}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3638569.3638574","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3638569.3638574","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3638569.3638574","source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2023 7th International Conference on Computational Biology and Bioinformatics","raw_type":"proceedings-article"},{"id":"pmh:oai:dspace.mit.edu:1721.1/154065","is_oa":true,"landing_page_url":"https://hdl.handle.net/1721.1/154065","pdf_url":"https://dspace.mit.edu/bitstream/1721.1/154065/1/3638569.3638574.pdf","source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM","raw_type":"http://purl.org/eprint/type/ConferencePaper"}],"best_oa_location":{"id":"doi:10.1145/3638569.3638574","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3638569.3638574","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3638569.3638574","source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2023 7th International Conference on Computational Biology and Bioinformatics","raw_type":"proceedings-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392568117.pdf","grobid_xml":"https://content.openalex.org/works/W4392568117.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W229097380","https://openalex.org/W1533942137","https://openalex.org/W2044740110","https://openalex.org/W2082704080","https://openalex.org/W2539630895","https://openalex.org/W2947189704","https://openalex.org/W3129233083","https://openalex.org/W4254687493","https://openalex.org/W4255272544","https://openalex.org/W4384816694","https://openalex.org/W4385063412","https://openalex.org/W6925203558","https://openalex.org/W6959643953"],"related_works":["https://openalex.org/W177137871","https://openalex.org/W2382174632","https://openalex.org/W2129959498","https://openalex.org/W4292302930","https://openalex.org/W4386960635","https://openalex.org/W3195112886","https://openalex.org/W4389089607","https://openalex.org/W3195480349","https://openalex.org/W2892201447","https://openalex.org/W2590543013"],"abstract_inverted_index":{"The":[0],"interplay":[1,137,242],"between":[2,139],"microbiome":[3,25,35,44,54,116,140,162,244],"metabolites":[4,141,163,245],"and":[5,10,16,27,36,46,81,100,108,142,150,155,169,205,220,231,246,252],"human":[6,14,250],"cells":[7,204,248],"is":[8,22],"crucial":[9],"mechanistically":[11],"linked":[12,23,166],"to":[13,24,119,130,167,182],"health":[15,251],"disease.":[17,253],"Inflammatory":[18],"bowel":[19],"disease":[20],"(IBD)":[21],"metabolite":[26,55],"host":[28,37,47,120,143,247],"gene":[29,185],"expression.":[30],"However,":[31],"details":[32],"of":[33,51,98,113,135,148,161,173,228,243],"the":[34,62,78,96,115,124,136,170,176,183,189,240],"interplays":[38],"remain":[39],"elusive.":[40],"We":[41,102],"carry":[42],"out":[43,105],"metabolome-wide":[45],"transcriptome-wide":[48],"association":[49],"studies":[50],"IBD":[52,65,149,168],"with":[53,153,214],"targeted":[56,107,177,198],"cell":[57,89,199],"types":[58],"discovery":[59],"via":[60],"leveraging":[61],"publicly":[63],"available":[64],"data":[66,80,117],"sets":[67],"from":[68],"Human":[69],"Microbiome":[70],"Project":[71],"2":[72],"(HMP2).":[73],"By":[74],"performing":[75],"deconvolution":[76],"on":[77,239],"transcriptomic":[79,121,171],"applying":[82],"discrete":[83],"wavelet":[84],"transform":[85],"(DWT),":[86],"we":[87,93,157,179,208],"obtained":[88],"type-metabolite":[90],"correlations,":[91],"which":[92],"visualize":[94],"in":[95,128,223,249],"form":[97],"heatmaps":[99],"networks.":[101],"also":[103,180],"carried":[104],"both":[106],"untargeted":[109],"approaches":[110,236],"by":[111],"mean":[112],"correlating":[114],"matrix":[118],"data.":[122],"Given":[123],"limited":[125],"sample":[126],"size,":[127],"addition":[129],"visualizing":[131],"a":[132,159,193,224],"global":[133],"picture":[134],"landscape":[138],"genes":[144],"alongside":[145],"distinct":[146],"clusters":[147],"healthy":[151],"controls":[152],"UMAP":[154],"t-SNE,":[156],"found":[158],"set":[160],"most":[164],"likely":[165],"signature":[172,186],"IBD.":[174,232],"For":[175],"approach,":[178],"refer":[181],"single-cell":[184],"dataset,":[187],"i.e.,":[188],"MSigDB":[190],"C8,":[191],"uncovering":[192],"bile":[194],"acid,":[195],"namely,":[196],"lithocholate,":[197],"types,":[200],"including":[201],"intestine":[202],"lymphoid":[203],"enterocytes.":[206],"Moreover,":[207],"utilized":[209],"Mendelian":[210],"Randomization":[211],"causality":[212,226],"tests":[213],"ursodeoxycholic":[215],"acid":[216],"(UDCA),":[217],"RUNX1":[218],"gene,":[219],"IBD,":[221],"resulting":[222],"putative":[225],"network":[227],"RUNX1,":[229],"UDCA,":[230],"Taken":[233],"together,":[234],"our":[235],"shed":[237],"light":[238],"mechanistic":[241]},"counts_by_year":[],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}