{"id":"https://openalex.org/W2055762617","doi":"https://doi.org/10.1109/tbme.2015.2412533","title":"A Stochastic Algorithm for Generating Realistic Virtual Interstitial Cell of Cajal Networks","display_name":"A Stochastic Algorithm for Generating Realistic Virtual Interstitial Cell of Cajal Networks","publication_year":2015,"publication_date":"2015-03-13","ids":{"openalex":"https://openalex.org/W2055762617","doi":"https://doi.org/10.1109/tbme.2015.2412533","mag":"2055762617","pmid":"https://pubmed.ncbi.nlm.nih.gov/25781477"},"language":"en","primary_location":{"id":"doi:10.1109/tbme.2015.2412533","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tbme.2015.2412533","pdf_url":null,"source":{"id":"https://openalex.org/S5240358","display_name":"IEEE Transactions on Biomedical Engineering","issn_l":"0018-9294","issn":["0018-9294","1558-2531"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["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 Biomedical Engineering","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4628824","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074631753","display_name":"Jerry Gao","orcid":"https://orcid.org/0000-0002-1051-5839"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Jerry Gao","raw_affiliation_strings":["Auckland Bioengineering Institute, University of Auckland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, University of Auckland","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012632598","display_name":"Shameer Sathar","orcid":"https://orcid.org/0000-0002-6566-8947"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Shameer Sathar","raw_affiliation_strings":["Auckland Bioengineering Institute, University of Auckland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, University of Auckland","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000581854","display_name":"Gregory O\u2019Grady","orcid":"https://orcid.org/0000-0002-5998-1080"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Gregory OGrady","raw_affiliation_strings":["Auckland Bioengineering Institute, University of Auckland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, University of Auckland","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035118280","display_name":"Rosalind Archer","orcid":"https://orcid.org/0000-0003-2250-0471"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Rosalind Archer","raw_affiliation_strings":["Department of Engineering Science, University of Auckland","Department of Engineering Science, University of Auckland,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Engineering Science, University of Auckland","institution_ids":["https://openalex.org/I154130895"]},{"raw_affiliation_string":"Department of Engineering Science, University of Auckland,","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036297582","display_name":"Leo K. Cheng","orcid":"https://orcid.org/0000-0003-2426-8987"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]},{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["NZ","US"],"is_corresponding":false,"raw_author_name":"Leo K. Cheng","raw_affiliation_strings":["Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand","Department of Surgery, Vanderbilt University, Nashville, TN, USA","Auckland Bioengineering Institute, University of Auckland Auckland New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]},{"raw_affiliation_string":"Department of Surgery, Vanderbilt University, Nashville, TN, USA","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Auckland Bioengineering Institute, University of Auckland Auckland New Zealand","institution_ids":["https://openalex.org/I154130895"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4642,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.66499739,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"62","issue":"8","first_page":"2070","last_page":"2078"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10365","display_name":"Gastrointestinal motility and disorders","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2715","display_name":"Gastroenterology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10365","display_name":"Gastrointestinal motility and disorders","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2715","display_name":"Gastroenterology"},"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/T12267","display_name":"Diet and metabolism studies","score":0.9620000123977661,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"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/T12192","display_name":"Polysaccharides Composition and Applications","score":0.9327999949455261,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interstitial-cell-of-cajal","display_name":"Interstitial cell of Cajal","score":0.9091148376464844},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6676161289215088},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6110759973526001},{"id":"https://openalex.org/keywords/intestinal-motility","display_name":"Intestinal motility","score":0.46002402901649475},{"id":"https://openalex.org/keywords/motility","display_name":"Motility","score":0.32181021571159363},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18785473704338074}],"concepts":[{"id":"https://openalex.org/C201539569","wikidata":"https://www.wikidata.org/wiki/Q2596185","display_name":"Interstitial cell of Cajal","level":3,"score":0.9091148376464844},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6676161289215088},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6110759973526001},{"id":"https://openalex.org/C2994163159","wikidata":"https://www.wikidata.org/wiki/Q5526845","display_name":"Intestinal motility","level":3,"score":0.46002402901649475},{"id":"https://openalex.org/C58207958","wikidata":"https://www.wikidata.org/wiki/Q33596","display_name":"Motility","level":2,"score":0.32181021571159363},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18785473704338074},{"id":"https://openalex.org/C204232928","wikidata":"https://www.wikidata.org/wiki/Q899285","display_name":"Immunohistochemistry","level":2,"score":0.0},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","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":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018345","descriptor_name":"Mice, Knockout","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018345","descriptor_name":"Mice, Knockout","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018345","descriptor_name":"Mice, Knockout","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018613","descriptor_name":"Microscopy, Confocal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018613","descriptor_name":"Microscopy, Confocal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018613","descriptor_name":"Microscopy, Confocal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056885","descriptor_name":"Interstitial Cells of Cajal","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D056885","descriptor_name":"Interstitial Cells of Cajal","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D056885","descriptor_name":"Interstitial Cells of Cajal","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D056885","descriptor_name":"Interstitial Cells of Cajal","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D056885","descriptor_name":"Interstitial Cells of Cajal","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D056885","descriptor_name":"Interstitial Cells of Cajal","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tbme.2015.2412533","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tbme.2015.2412533","pdf_url":null,"source":{"id":"https://openalex.org/S5240358","display_name":"IEEE Transactions on Biomedical Engineering","issn_l":"0018-9294","issn":["0018-9294","1558-2531"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["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 Biomedical Engineering","raw_type":"journal-article"},{"id":"pmid:25781477","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25781477","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on bio-medical engineering","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4628824","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4628824","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Biomed Eng","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4628824","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4628824","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Biomed Eng","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G108104565","display_name":null,"funder_award_id":"R01 DK064775","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G1949051517","display_name":null,"funder_award_id":"R01 DK64775","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6395752793","display_name":null,"funder_award_id":"R01 DK64775","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"}],"funders":[{"id":"https://openalex.org/F4320320801","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07"},{"id":"https://openalex.org/F4320330278","display_name":"Riddet Institute","ror":"https://ror.org/053336823"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334749","display_name":"Health Research Council of New Zealand","ror":"https://ror.org/00zbf3d93"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W189203688","https://openalex.org/W1496078382","https://openalex.org/W1537810918","https://openalex.org/W1579142916","https://openalex.org/W1762607089","https://openalex.org/W1970202449","https://openalex.org/W1978362426","https://openalex.org/W1979264182","https://openalex.org/W1982313237","https://openalex.org/W1982684695","https://openalex.org/W1988530903","https://openalex.org/W1991175004","https://openalex.org/W2003893456","https://openalex.org/W2010682403","https://openalex.org/W2025590033","https://openalex.org/W2030297634","https://openalex.org/W2034866712","https://openalex.org/W2049314578","https://openalex.org/W2051669049","https://openalex.org/W2064227044","https://openalex.org/W2068007035","https://openalex.org/W2070564499","https://openalex.org/W2080925139","https://openalex.org/W2098073452","https://openalex.org/W2113316793","https://openalex.org/W2127557160","https://openalex.org/W2141927860","https://openalex.org/W2164872793","https://openalex.org/W2166167540","https://openalex.org/W2169511354","https://openalex.org/W2204896661","https://openalex.org/W2272546316","https://openalex.org/W2279676782","https://openalex.org/W2288830152","https://openalex.org/W2399380607","https://openalex.org/W2435491771","https://openalex.org/W2468210114","https://openalex.org/W6712479083"],"related_works":["https://openalex.org/W2010220644","https://openalex.org/W1963557346","https://openalex.org/W1600619492","https://openalex.org/W2406418095","https://openalex.org/W4232215996","https://openalex.org/W2357657788","https://openalex.org/W4290145760","https://openalex.org/W1922330195","https://openalex.org/W2322490458","https://openalex.org/W2366977316"],"abstract_inverted_index":{"Interstitial":[0],"cells":[1],"of":[2,16,48,57,65,72,81,153,172,178,193,220,234],"Cajal":[3],"(ICC)":[4],"play":[5],"a":[6,46,55,176,183,191,218],"central":[7],"role":[8],"in":[9,86],"coordinating":[10],"normal":[11,91],"gastrointestinal":[12],"(GI)":[13],"motility.":[14],"Depletion":[15],"ICC":[17,33,50,84,96,126,173,213,235],"numbers":[18],"and":[19,38,75,104,118,130,157,181,195,200],"network":[20,51,97,127,214],"integrity":[21],"contributes":[22],"to":[23,35,60,114,140,168,228],"major":[24],"functional":[25,160,196],"GI":[26,36],"motility":[27],"disorders.":[28],"However,":[29],"the":[30,79,89,116,119,135,141,170,211,231],"mechanisms":[31],"relating":[32],"structure":[34],"function":[37],"dysfunction":[39],"remains":[40,69],"unclear,":[41],"partly":[42],"because":[43,71],"there":[44,144],"is":[45],"lack":[47],"large-scale":[49,67,212],"imaging":[52,64,98,215],"data":[53,99,216],"across":[54,175,217],"spectrum":[56,177,219],"depletion":[58,179,221],"levels":[59],"guide":[61],"models.":[62],"Experimental":[63],"these":[66],"networks":[68,85,121,137,174,186],"challenging":[70],"technical":[73],"constraints,":[74],"hence,":[76],"we":[77],"propose":[78],"generation":[80,171],"realistic":[82],"virtual":[83,120,136,185],"silico":[87],"using":[88,125],"single":[90],"equation":[92],"simulation":[93],"(SNESIM)":[94],"algorithm.":[95],"obtained":[100],"from":[101],"wild-type":[102],"(normal)":[103],"5-HT2B":[105],"serotonin":[106],"receptor":[107],"knockout":[108],"(depleted":[109],"ICC)":[110],"mice":[111],"were":[112,123,138,187],"used":[113],"inform":[115,230],"algorithm,":[117],"generated":[122,189],"assessed":[124],"structural":[128,155,194],"metrics":[129,156],"biophysically-based":[131],"computational":[132],"modeling.":[133],"When":[134],"compared":[139],"original":[142],"networks,":[143],"was":[145,165],"less":[146],"than":[147],"10%":[148],"error":[149],"for":[150,209],"four":[151,159],"out":[152],"five":[154],"all":[158],"measures.":[161],"The":[162,198],"SNESIM":[163,199,202],"algorithm":[164],"then":[166],"modified":[167,201],"enable":[169],"levels,":[180],"as":[182],"proof-of-concept,":[184],"successfully":[188],"with":[190],"range":[192],"properties.":[197],"algorithms,":[203],"therefore,":[204],"offer":[205],"an":[206],"alternative":[207],"strategy":[208],"obtaining":[210],"levels.":[222],"These":[223],"models":[224],"can":[225],"be":[226],"applied":[227],"accurately":[229],"physiological":[232],"consequences":[233],"depletion.":[236]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
