{"id":"https://openalex.org/W2949153281","doi":"https://doi.org/10.1093/bioinformatics/btx623","title":"diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data","display_name":"diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data","publication_year":2017,"publication_date":"2017-09-27","ids":{"openalex":"https://openalex.org/W2949153281","doi":"https://doi.org/10.1093/bioinformatics/btx623","mag":"2949153281","pmid":"https://pubmed.ncbi.nlm.nih.gov/29028898"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx623","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx623","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/4/672/25117267/btx623.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/4/672/25117267/btx623.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054483679","display_name":"Caleb A. Lareau","orcid":"https://orcid.org/0000-0003-4179-4807"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Caleb A Lareau","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA, USA","Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA","Department of Pathology, Harvard Medical School, Boston, MA, USA"],"raw_orcid":"https://orcid.org/0000-0003-4179-4807","affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Pathology, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050285238","display_name":"Martin J. Aryee","orcid":"https://orcid.org/0000-0002-6848-1344"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Martin J Aryee","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA, USA","Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA","Department of Pathology, Harvard Medical School, Boston, MA, USA","Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Pathology, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA","institution_ids":["https://openalex.org/I4210087915"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5050285238"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I136199984","https://openalex.org/I4210087915"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.1285,"has_fulltext":false,"cited_by_count":88,"citation_normalized_percentile":{"value":0.8825994,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"34","issue":"4","first_page":"672","last_page":"674"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.515500009059906,"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":0.515500009059906,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.1120000034570694,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.09160000085830688,"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/bioconductor","display_name":"Bioconductor","score":0.9958916902542114},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6229995489120483},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.6144688129425049},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5507902503013611},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.542540431022644},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5365697145462036},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.43001434206962585},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4281325340270996},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.42197397351264954},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.4213560223579407},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39726343750953674},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38675689697265625},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3831464648246765},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.37318626046180725},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31408339738845825},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.2828297019004822}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9958916902542114},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6229995489120483},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.6144688129425049},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5507902503013611},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.542540431022644},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5365697145462036},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.43001434206962585},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4281325340270996},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.42197397351264954},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.4213560223579407},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39726343750953674},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38675689697265625},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3831464648246765},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37318626046180725},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31408339738845825},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2828297019004822},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020014","descriptor_name":"K562 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020014","descriptor_name":"K562 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020014","descriptor_name":"K562 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D061986","descriptor_name":"MCF-7 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D061986","descriptor_name":"MCF-7 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D061986","descriptor_name":"MCF-7 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx623","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx623","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/4/672/25117267/btx623.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29028898","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29028898","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":null},{"id":"pmh:oai:dash.harvard.edu:1/35982229","is_oa":true,"landing_page_url":"http://nrs.harvard.edu/urn-3:HUL.InstRepos:35982229","pdf_url":null,"source":{"id":"https://openalex.org/S4306401540","display_name":"Digital Access to Scholarship at Harvard (DASH) (Harvard University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I136199984","host_organization_name":"Harvard University","host_organization_lineage":["https://openalex.org/I136199984"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5860605","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860605","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx623","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx623","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/4/672/25117267/btx623.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G984541896","display_name":null,"funder_award_id":"DGE1144152","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2949153281.pdf"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1605145036","https://openalex.org/W1862913282","https://openalex.org/W1973062929","https://openalex.org/W2073026107","https://openalex.org/W2114104545","https://openalex.org/W2123227077","https://openalex.org/W2195190137","https://openalex.org/W2222531233","https://openalex.org/W2259938310","https://openalex.org/W2303393194","https://openalex.org/W2523285811","https://openalex.org/W2950020758"],"related_works":["https://openalex.org/W43224192","https://openalex.org/W2158272128","https://openalex.org/W2160379721","https://openalex.org/W90653389","https://openalex.org/W2009935171","https://openalex.org/W2144311691","https://openalex.org/W2146734921","https://openalex.org/W2057568687","https://openalex.org/W3111061871","https://openalex.org/W2151651283"],"abstract_inverted_index":{"Summary:":[0],"The":[1],"3D":[2],"architecture":[3,47],"of":[4,13,60,71],"DNA":[5,27,45,72],"within":[6],"the":[7,63],"nucleus":[8],"is":[9,97],"a":[10,23,58],"key":[11],"determinant":[12],"interactions":[14],"between":[15,48,81],"genes,":[16],"regulatory":[17],"elements,":[18],"and":[19,37,69,85,94],"transcriptional":[20],"machinery.":[21],"As":[22],"result,":[24],"differences":[25,80],"in":[26,34,44,90],"looping":[28,46,87],"structure":[29],"are":[30,112],"associated":[31],"with":[32],"variation":[33],"gene":[35],"expression":[36],"cell":[38],"state.":[39,92],"To":[40],"systematically":[41],"assess":[42],"changes":[43],"samples,":[49],"we":[50],"introduce":[51],"diffloop,":[52],"an":[53,100],"R/Bioconductor":[54,101],"package":[55,102],"that":[56],"provides":[57],"suite":[59],"functions":[61],"for":[62],"quality":[64],"control,":[65],"statistical":[66],"testing,":[67],"annotation,":[68],"visualization":[70],"loops.":[73],"We":[74],"demonstrate":[75],"this":[76],"functionality":[77],"by":[78],"detecting":[79],"ENCODE":[82],"ChIA-PET":[83],"samples":[84],"relate":[86],"to":[88],"variability":[89],"epigenetic":[91],"Availability":[93],"implementation:":[95],"Diffloop":[96],"implemented":[98],"as":[99],"available":[103,113],"at":[104,114],"https://bioconductor.org/packages/release/bioc/html/diffloop.html.":[105],"Contact:":[106],"aryee.martin@mgh.harvard.edu.":[107],"Supplementary":[108,110],"information:":[109],"data":[111],"Bioinformatics":[115],"online.":[116]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":3}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}