{"id":"https://openalex.org/W2950655801","doi":"https://doi.org/10.1093/bioinformatics/bty717","title":"C3D: a tool to predict 3D genomic interactions between cis-regulatory elements","display_name":"C3D: a tool to predict 3D genomic interactions between cis-regulatory elements","publication_year":2018,"publication_date":"2018-08-22","ids":{"openalex":"https://openalex.org/W2950655801","doi":"https://doi.org/10.1093/bioinformatics/bty717","mag":"2950655801","pmid":"https://pubmed.ncbi.nlm.nih.gov/30816925"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty717","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty717","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"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/A5044125964","display_name":"Tahmid Mehdi","orcid":null},"institutions":[{"id":"https://openalex.org/I1325899441","display_name":"University Health Network","ror":"https://ror.org/042xt5161","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441"]},{"id":"https://openalex.org/I151746483","display_name":"University of Waterloo","ror":"https://ror.org/01aff2v68","country_code":"CA","type":"education","lineage":["https://openalex.org/I151746483"]},{"id":"https://openalex.org/I2802654988","display_name":"Princess Margaret Cancer Centre","ror":"https://ror.org/03zayce58","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Tahmid Mehdi","raw_affiliation_strings":["Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada","Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, ON, Canada","institution_ids":["https://openalex.org/I151746483"]},{"raw_affiliation_string":"Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada","institution_ids":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045164116","display_name":"Swneke D. Bailey","orcid":"https://orcid.org/0000-0003-3778-8391"},"institutions":[{"id":"https://openalex.org/I1325899441","display_name":"University Health Network","ror":"https://ror.org/042xt5161","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441"]},{"id":"https://openalex.org/I2802654988","display_name":"Princess Margaret Cancer Centre","ror":"https://ror.org/03zayce58","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Swneke D Bailey","raw_affiliation_strings":["Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada","institution_ids":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035384039","display_name":"Paul Guilhamon","orcid":"https://orcid.org/0000-0001-8276-5987"},"institutions":[{"id":"https://openalex.org/I1325899441","display_name":"University Health Network","ror":"https://ror.org/042xt5161","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441"]},{"id":"https://openalex.org/I2802654988","display_name":"Princess Margaret Cancer Centre","ror":"https://ror.org/03zayce58","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Paul Guilhamon","raw_affiliation_strings":["Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada","institution_ids":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004938979","display_name":"Mathieu Lupien","orcid":"https://orcid.org/0000-0003-0929-9478"},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]},{"id":"https://openalex.org/I1325899441","display_name":"University Health Network","ror":"https://ror.org/042xt5161","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441"]},{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I2802654988","display_name":"Princess Margaret Cancer Centre","ror":"https://ror.org/03zayce58","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Mathieu Lupien","raw_affiliation_strings":["Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada","Ontario Institute for Cancer Research, Toronto, ON, Canada","Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada"],"raw_orcid":"https://orcid.org/0000-0003-0929-9478","affiliations":[{"raw_affiliation_string":"Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Ontario Institute for Cancer Research, Toronto, ON, Canada","institution_ids":["https://openalex.org/I112260969"]},{"raw_affiliation_string":"Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada","institution_ids":["https://openalex.org/I1325899441","https://openalex.org/I2802654988"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5004938979","https://openalex.org/A5044125964"],"corresponding_institution_ids":["https://openalex.org/I112260969","https://openalex.org/I1325899441","https://openalex.org/I151746483","https://openalex.org/I185261750","https://openalex.org/I2802654988"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.6617,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.67961391,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"5","first_page":"877","last_page":"879"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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/T10604","display_name":"RNA Research and Splicing","score":0.9957000017166138,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.993399977684021,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant 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/chromatin","display_name":"Chromatin","score":0.8266333341598511},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.7160179615020752},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.650285542011261},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6316739320755005},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.5940124988555908},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5227030515670776},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5160071849822998},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.49277547001838684},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.45303428173065186},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4272674322128296},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.36243683099746704},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33850622177124023},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3268175721168518},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2218688726425171},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20076802372932434},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1438940465450287},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.13438904285430908}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.8266333341598511},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.7160179615020752},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.650285542011261},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6316739320755005},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.5940124988555908},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5227030515670776},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5160071849822998},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49277547001838684},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.45303428173065186},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4272674322128296},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36243683099746704},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33850622177124023},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3268175721168518},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2218688726425171},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20076802372932434},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1438940465450287},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13438904285430908}],"mesh":[{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty717","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty717","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30816925","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30816925","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4099999964237213,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1964963969","https://openalex.org/W2010789111","https://openalex.org/W2052684082","https://openalex.org/W2076154138","https://openalex.org/W2117792884","https://openalex.org/W2120865735","https://openalex.org/W2126243836","https://openalex.org/W2156247618","https://openalex.org/W2169389191","https://openalex.org/W2333286569","https://openalex.org/W2535173298","https://openalex.org/W2584394140"],"related_works":["https://openalex.org/W2036021480","https://openalex.org/W2546377002","https://openalex.org/W4285209474","https://openalex.org/W22571951","https://openalex.org/W2046541848","https://openalex.org/W4384009753","https://openalex.org/W4292228088","https://openalex.org/W4309247532","https://openalex.org/W2791776396","https://openalex.org/W2137111266"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"3D":[2],"genome":[3],"architecture":[4],"influences":[5],"the":[6,99,125],"regulation":[7],"of":[8,62],"genes":[9],"by":[10,65],"facilitating":[11],"chromatin":[12,37,47],"interactions":[13,38],"between":[14,68],"distal":[15,71],"cis-regulatory":[16],"elements":[17],"and":[18,60,70,81,92,108,120,133],"gene":[19],"promoters.":[20],"We":[21],"implement":[22],"Cross":[23],"Cell-type":[24],"Correlation":[25],"based":[26],"on":[27,95,112],"DNA":[28],"accessibility":[29],"(C3D),":[30],"a":[31],"customizable":[32],"computational":[33],"tool":[34],"that":[35,43,73],"predicts":[36,57],"using":[39],"an":[40],"unsupervised":[41],"algorithm":[42],"utilizes":[44],"correlations":[45],"in":[46,78,106],"measurements,":[48],"such":[49],"as":[50],"DNaseI":[51,75],"hypersensitivity":[52],"signals.":[53],"RESULTS:":[54],"C3D":[55,103],"accurately":[56],"32.7%,":[58],"18.3%":[59],"24.1%":[61],"interactions,":[63],"validated":[64],"ChIA-PET":[66],"assays,":[67],"promoters":[69],"regions":[72],"overlie":[74],"hypersensitive":[76],"sites":[77],"K562,":[79],"MCF-7":[80],"GM12878":[82],"cells,":[83],"respectively.":[84],"AVAILABILITY":[85],"AND":[86],"IMPLEMENTATION:":[87],"Source":[88],"code":[89],"is":[90,104],"open-source":[91],"freely":[93],"available":[94,140],"GitHub":[96],"(https://github.com/LupienLabOrganization/C3D)":[97],"under":[98],"GNU":[100],"GPLv3":[101],"license.":[102],"implemented":[105],"Bash":[107,116],"R;":[109],"it":[110],"runs":[111],"any":[113],"platform":[114],"with":[115],"(\u22654.0),":[117],"R":[118,127],"(\u22653.1.1)":[119],"BEDTools":[121],"(\u22652.19.0).":[122],"It":[123],"requires":[124],"following":[126],"packages:":[128],"GenomicRanges,":[129],"Sushi,":[130],"data.table,":[131],"preprocessCore":[132],"dynamicTreeCut.":[134],"SUPPLEMENTARY":[135],"INFORMATION:":[136],"Supplementary":[137],"data":[138],"are":[139],"at":[141],"Bioinformatics":[142],"online.":[143]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}