{"id":"https://openalex.org/W4403211226","doi":"https://doi.org/10.1109/cibcb58642.2024.10702161","title":"Clustering density based gene expression data in the mouse brainstem and comparison to actual neuroanatomy","display_name":"Clustering density based gene expression data in the mouse brainstem and comparison to actual neuroanatomy","publication_year":2024,"publication_date":"2024-08-27","ids":{"openalex":"https://openalex.org/W4403211226","doi":"https://doi.org/10.1109/cibcb58642.2024.10702161"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb58642.2024.10702161","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb58642.2024.10702161","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","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/A5107820601","display_name":"Colin Buenvenida","orcid":null},"institutions":[{"id":"https://openalex.org/I118353179","display_name":"DePaul University","ror":"https://ror.org/04xtx5t16","country_code":"US","type":"education","lineage":["https://openalex.org/I118353179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Colin Buenvenida","raw_affiliation_strings":["DePaul University,School of Computing,Chicago,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DePaul University,School of Computing,Chicago,USA","institution_ids":["https://openalex.org/I118353179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021257189","display_name":"Brandon Kong","orcid":null},"institutions":[{"id":"https://openalex.org/I118353179","display_name":"DePaul University","ror":"https://ror.org/04xtx5t16","country_code":"US","type":"education","lineage":["https://openalex.org/I118353179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brandon Kong","raw_affiliation_strings":["DePaul University,School of Computing,Chicago,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DePaul University,School of Computing,Chicago,USA","institution_ids":["https://openalex.org/I118353179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113422617","display_name":"Shane Jung","orcid":null},"institutions":[{"id":"https://openalex.org/I118353179","display_name":"DePaul University","ror":"https://ror.org/04xtx5t16","country_code":"US","type":"education","lineage":["https://openalex.org/I118353179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shane Jung","raw_affiliation_strings":["DePaul University,School of Computing,Chicago,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DePaul University,School of Computing,Chicago,USA","institution_ids":["https://openalex.org/I118353179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050615931","display_name":"Kaiwen Kam","orcid":"https://orcid.org/0000-0002-8479-0542"},"institutions":[{"id":"https://openalex.org/I189273616","display_name":"Rosalind Franklin University of Medicine and Science","ror":"https://ror.org/04fegvg32","country_code":"US","type":"education","lineage":["https://openalex.org/I189273616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kaiwen Kam","raw_affiliation_strings":["Rosalind Franklin University of Medicine and Science (RFUMS),Cell Biology and Anatomy,North Chicago,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Rosalind Franklin University of Medicine and Science (RFUMS),Cell Biology and Anatomy,North Chicago,USA","institution_ids":["https://openalex.org/I189273616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001027068","display_name":"Jacob Furst","orcid":null},"institutions":[{"id":"https://openalex.org/I118353179","display_name":"DePaul University","ror":"https://ror.org/04xtx5t16","country_code":"US","type":"education","lineage":["https://openalex.org/I118353179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob Furst","raw_affiliation_strings":["DePaul University,School of Computing,Chicago,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DePaul University,School of Computing,Chicago,USA","institution_ids":["https://openalex.org/I118353179"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083833340","display_name":"Thiruvarangan Ramaraj","orcid":"https://orcid.org/0000-0002-7333-1041"},"institutions":[{"id":"https://openalex.org/I118353179","display_name":"DePaul University","ror":"https://ror.org/04xtx5t16","country_code":"US","type":"education","lineage":["https://openalex.org/I118353179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thiruvarangan Ramaraj","raw_affiliation_strings":["DePaul University,School of Computing,Chicago,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"DePaul University,School of Computing,Chicago,USA","institution_ids":["https://openalex.org/I118353179"]}]}],"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":0.15090966,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.7907999753952026,"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/T10885","display_name":"Gene expression and cancer classification","score":0.7907999753952026,"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/brainstem","display_name":"Brainstem","score":0.7904560565948486},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.7527785301208496},{"id":"https://openalex.org/keywords/neuroanatomy","display_name":"Neuroanatomy","score":0.734700083732605},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.601654589176178},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4833254814147949},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4104982614517212},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.39794620871543884},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3269420266151428},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32486405968666077},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.2934262454509735},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.27318036556243896}],"concepts":[{"id":"https://openalex.org/C551621295","wikidata":"https://www.wikidata.org/wiki/Q182228","display_name":"Brainstem","level":2,"score":0.7904560565948486},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7527785301208496},{"id":"https://openalex.org/C103378370","wikidata":"https://www.wikidata.org/wiki/Q948647","display_name":"Neuroanatomy","level":2,"score":0.734700083732605},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.601654589176178},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4833254814147949},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4104982614517212},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.39794620871543884},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3269420266151428},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32486405968666077},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.2934262454509735},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27318036556243896},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb58642.2024.10702161","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb58642.2024.10702161","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310248","display_name":"DePaul University","ror":"https://ror.org/04xtx5t16"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W988166840","https://openalex.org/W1543425321","https://openalex.org/W1573719564","https://openalex.org/W1978075346","https://openalex.org/W1993436046","https://openalex.org/W1995579155","https://openalex.org/W2018008165","https://openalex.org/W2037688283","https://openalex.org/W2042076636","https://openalex.org/W2054936551","https://openalex.org/W2067401415","https://openalex.org/W2142940228","https://openalex.org/W2160197181","https://openalex.org/W2294662980","https://openalex.org/W2586403510","https://openalex.org/W2989747508","https://openalex.org/W3048538154","https://openalex.org/W3093670216","https://openalex.org/W3139627295","https://openalex.org/W4205816095","https://openalex.org/W4293312694","https://openalex.org/W4310638450","https://openalex.org/W4323295166"],"related_works":["https://openalex.org/W4238641032","https://openalex.org/W4235631914","https://openalex.org/W97694169","https://openalex.org/W3144897284","https://openalex.org/W4391469839","https://openalex.org/W117101081","https://openalex.org/W642119519","https://openalex.org/W2115888107","https://openalex.org/W2072740770","https://openalex.org/W3128097038"],"abstract_inverted_index":{"The":[0],"medullary":[1],"reticular":[2,82,105,131,157,195],"formation":[3,83,106,132],"is":[4,16],"a":[5],"network":[6],"of":[7,18,88,103,129,142,181,193,201],"brainstem":[8,172,203],"nuclei":[9,173],"and":[10,33,40,55,64,91,107,122,213],"neurons":[11,68],"in":[12,44,61,119,146],"the":[13,22,25,67,81,86,101,104,130,143,147,156,179,191,194,199],"brain":[14,23,93,151],"that":[15,117,133,152,174],"composed":[17],"circuit":[19],"pathways":[20],"from":[21,222],"to":[24,59,85,99,155,178,216],"spinal":[26],"cord.":[27],"It":[28],"carries":[29],"out":[30],"vital":[31],"roles":[32],"orofacial":[34,71,110,135,182],"behaviors":[35,112],"such":[36],"as":[37],"vocalization,":[38],"swallowing,":[39,63],"breathing.":[41],"A":[42],"disruption":[43],"these":[45,202],"neuronal":[46],"circuits":[47],"can":[48,125,206],"be":[49],"threatening":[50],"for":[51,189,219],"persons":[52,220],"with":[53,70,166],"neurodevelopmental":[54],"neurodegenerative":[56,210],"disorders,":[57],"leading":[58],"deficits":[60],"breathing,":[62],"communication.":[65],"However,":[66],"associated":[69],"motor":[72,111,136],"controls":[73],"are":[74,113,153,175],"not":[75],"clearly":[76],"defined":[77],"or":[78],"localized":[79],"within":[80],"due":[84],"lack":[87],"molecular":[89],"markers":[90],"distinct":[92],"tissue":[94],"cells.":[95],"This":[96,184],"project":[97],"serves":[98],"understand":[100,208],"organization":[102,192,200],"define":[108],"where":[109],"localized.":[114],"We":[115],"hypothesize":[116],"differences":[118],"gene":[120,139],"expression":[121],"three-dimensional":[123],"proximities":[124],"identify":[126],"functional":[127],"subpopulations":[128],"control":[134,180],"behaviors.":[137,183],"Using":[138],"density":[140],"measures":[141],"coronal":[144],"plane":[145],"adult":[148],"male":[149],"mouse":[150],"attributed":[154],"formation,":[158],"we":[159],"computed":[160],"13":[161],"clusters":[162],"using":[163],"K-Means":[164],"clustering":[165,185],"Euclidean":[167],"distance":[168],"measure":[169],"based":[170],"on":[171],"biologically":[176],"significant":[177],"pattern":[186],"has":[187],"implications":[188],"understanding":[190,198],"formation.":[196],"By":[197],"nuclei,":[204],"neuroscientists":[205],"better":[207],"how":[209],"disorders":[211],"work":[212],"potentially":[214],"lead":[215],"effective":[217],"treatments":[218],"suffering":[221],"them.":[223]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}