{"id":"https://openalex.org/W4283800374","doi":"https://doi.org/10.1093/bioinformatics/btac442","title":"HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization","display_name":"HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization","publication_year":2022,"publication_date":"2022-07-04","ids":{"openalex":"https://openalex.org/W4283800374","doi":"https://doi.org/10.1093/bioinformatics/btac442","pmid":"https://pubmed.ncbi.nlm.nih.gov/35781332"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac442","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac442","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/4030/49890075/btac442.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":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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/4030/49890075/btac442.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082104022","display_name":"Matej Lexa","orcid":"https://orcid.org/0000-0002-4213-5259"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210089928","display_name":"Czech Academy of Sciences, Institute of Biophysics","ror":"https://ror.org/00angvn73","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210089928"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Matej Lexa","raw_affiliation_strings":["Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , 61200 Brno, Czech Republic","Faculty of Informatics, Masaryk University , 60200 Brno, Czech Republic"],"raw_orcid":"https://orcid.org/0000-0002-4213-5259","affiliations":[{"raw_affiliation_string":"Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , 61200 Brno, Czech Republic","institution_ids":["https://openalex.org/I4210089928"]},{"raw_affiliation_string":"Faculty of Informatics, Masaryk University , 60200 Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067616652","display_name":"Monika \u010cechov\u00e1","orcid":"https://orcid.org/0000-0002-7420-2663"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Monika Cechova","raw_affiliation_strings":["Faculty of Informatics, Masaryk University , 60200 Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Informatics, Masaryk University , 60200 Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084237237","display_name":"Son Hoang Nguyen","orcid":"https://orcid.org/0000-0003-3802-908X"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Son Hoang Nguyen","raw_affiliation_strings":["Faculty of Informatics, Masaryk University , 60200 Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Informatics, Masaryk University , 60200 Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029393283","display_name":"Pavel Jedli\u010dka","orcid":"https://orcid.org/0000-0001-9324-5151"},"institutions":[{"id":"https://openalex.org/I4210089928","display_name":"Czech Academy of Sciences, Institute of Biophysics","ror":"https://ror.org/00angvn73","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210089928"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Pavel Jedlicka","raw_affiliation_strings":["Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , 61200 Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , 61200 Brno, Czech Republic","institution_ids":["https://openalex.org/I4210089928"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019634109","display_name":"Viktor Tokan","orcid":"https://orcid.org/0000-0003-4478-6853"},"institutions":[{"id":"https://openalex.org/I4210089928","display_name":"Czech Academy of Sciences, Institute of Biophysics","ror":"https://ror.org/00angvn73","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210089928"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Viktor Tokan","raw_affiliation_strings":["Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , 61200 Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , 61200 Brno, Czech Republic","institution_ids":["https://openalex.org/I4210089928"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069132186","display_name":"Zden\u011bk Kub\u00e1t","orcid":"https://orcid.org/0000-0001-8278-9495"},"institutions":[{"id":"https://openalex.org/I4210089928","display_name":"Czech Academy of Sciences, Institute of Biophysics","ror":"https://ror.org/00angvn73","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210089928"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Zdenek Kubat","raw_affiliation_strings":["Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , 61200 Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , 61200 Brno, Czech Republic","institution_ids":["https://openalex.org/I4210089928"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058896041","display_name":"Roman Hobza","orcid":"https://orcid.org/0000-0003-3062-2962"},"institutions":[{"id":"https://openalex.org/I4210089928","display_name":"Czech Academy of Sciences, Institute of Biophysics","ror":"https://ror.org/00angvn73","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210089928"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Roman Hobza","raw_affiliation_strings":["Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , 61200 Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , 61200 Brno, Czech Republic","institution_ids":["https://openalex.org/I4210089928"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056103583","display_name":"Eduard Kejnovsk\u00fd","orcid":"https://orcid.org/0000-0001-5401-6655"},"institutions":[{"id":"https://openalex.org/I4210089928","display_name":"Czech Academy of Sciences, Institute of Biophysics","ror":"https://ror.org/00angvn73","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210089928"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Eduard Kejnovsky","raw_affiliation_strings":["Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , 61200 Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences , 61200 Brno, Czech Republic","institution_ids":["https://openalex.org/I4210089928"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5056103583","https://openalex.org/A5082104022"],"corresponding_institution_ids":["https://openalex.org/I21449261","https://openalex.org/I4210089928"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.3619,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.82132443,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"38","issue":"16","first_page":"4030","last_page":"4032"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9441999793052673,"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"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9441999793052673,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.009200000204145908,"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/T10949","display_name":"Genetic Neurodegenerative Diseases","score":0.008500000461935997,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/retrotransposon","display_name":"Retrotransposon","score":0.7935978174209595},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6920144557952881},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6721480488777161},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.576465368270874},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5336554646492004},{"id":"https://openalex.org/keywords/repressor-lexa","display_name":"Repressor lexA","score":0.4532715380191803},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.4312973916530609},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4026501476764679},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3589751720428467},{"id":"https://openalex.org/keywords/transposable-element","display_name":"Transposable element","score":0.33374345302581787},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.20630690455436707},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13410815596580505}],"concepts":[{"id":"https://openalex.org/C7029365","wikidata":"https://www.wikidata.org/wiki/Q413988","display_name":"Retrotransposon","level":5,"score":0.7935978174209595},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6920144557952881},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6721480488777161},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.576465368270874},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5336554646492004},{"id":"https://openalex.org/C413212","wikidata":"https://www.wikidata.org/wiki/Q7314274","display_name":"Repressor lexA","level":5,"score":0.4532715380191803},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.4312973916530609},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4026501476764679},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3589751720428467},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.33374345302581787},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.20630690455436707},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13410815596580505},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.0},{"id":"https://openalex.org/C158448853","wikidata":"https://www.wikidata.org/wiki/Q425218","display_name":"Repressor","level":4,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","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":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":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":false},{"descriptor_ui":"D018626","descriptor_name":"Retroelements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018626","descriptor_name":"Retroelements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018626","descriptor_name":"Retroelements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac442","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac442","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/4030/49890075/btac442.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35781332","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35781332","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac442","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac442","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/4030/49890075/btac442.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1210676548","display_name":null,"funder_award_id":"21\u201300580S","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G152920340","display_name":null,"funder_award_id":"e\u2010INFRA CZ LM2018140","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G2507177754","display_name":null,"funder_award_id":"CZ LM2018140","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G2629758493","display_name":null,"funder_award_id":"LM2018140","funder_id":"https://openalex.org/F4320321006","funder_display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky"},{"id":"https://openalex.org/G485196324","display_name":null,"funder_award_id":"CZ\u2010LM2018140","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G5470076797","display_name":"e-Infrastructure CZ","funder_award_id":"LM2018140","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"}],"funders":[{"id":"https://openalex.org/F4320321005","display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy","ror":"https://ror.org/037n8p820"},{"id":"https://openalex.org/F4320321006","display_name":"Grantov\u00e1 Agentura \u010cesk\u00e9 Republiky","ror":"https://ror.org/01pv73b02"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4283800374.pdf","grobid_xml":"https://content.openalex.org/works/W4283800374.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1968603622","https://openalex.org/W1972296697","https://openalex.org/W1991082245","https://openalex.org/W1997270596","https://openalex.org/W2014704298","https://openalex.org/W2042086471","https://openalex.org/W2102619694","https://openalex.org/W2107940314","https://openalex.org/W2128599926","https://openalex.org/W2155824171","https://openalex.org/W2170551349","https://openalex.org/W2605897695","https://openalex.org/W2748182739","https://openalex.org/W2770852695","https://openalex.org/W2809355118","https://openalex.org/W2914067549","https://openalex.org/W2951194089","https://openalex.org/W2952527196","https://openalex.org/W2958290985","https://openalex.org/W3017119031","https://openalex.org/W3025192267","https://openalex.org/W3043090500","https://openalex.org/W3125962248","https://openalex.org/W3132338293","https://openalex.org/W4220999759","https://openalex.org/W4225265866"],"related_works":["https://openalex.org/W2047580672","https://openalex.org/W2141418144","https://openalex.org/W2073763229","https://openalex.org/W1539891695","https://openalex.org/W2073118794","https://openalex.org/W3003340460","https://openalex.org/W2018485959","https://openalex.org/W2955897131","https://openalex.org/W2089350008","https://openalex.org/W2152447080"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1],"role":[2,188],"of":[3,10,17,22,28,41,88,121,189,196],"repetitive":[4,190],"DNA":[5,140],"in":[6,153,192],"the":[7,11,86,117,143,159,187,193],"3D":[8,23,194],"organization":[9,195],"interphase":[12],"nucleus":[13,24],"is":[14],"a":[15,80,180],"subject":[16],"intensive":[18],"study.":[19],"In":[20],"studies":[21],"organization,":[25],"mutual":[26],"contacts":[27,87],"various":[29],"loci":[30],"can":[31,145,171],"be":[32,146,172],"identified":[33],"by":[34,44,52],"Hi-C":[35,69],"sequencing.":[36],"Typical":[37],"analyses":[38],"use":[39,50],"binning":[40,51],"read":[42],"pairs":[43],"location":[45],"to":[46,56,148,185],"reduce":[47],"noise.":[48],"We":[49],"repeat":[53,61,77,90,106],"families":[54,130],"instead":[55],"make":[57],"similar":[58],"conclusions":[59],"about":[60],"regions.":[62],"RESULTS:":[63],"To":[64],"achieve":[65],"this,":[66],"we":[67,115],"combined":[68],"data,":[70,114],"reference":[71],"genome":[72],"data":[73,205],"and":[74,84,102,126,138,166,182],"tools":[75],"for":[76],"analysis":[78],"into":[79],"Nextflow":[81],"pipeline":[82,96,111,144,178],"identifying":[83],"quantifying":[85],"specific":[89],"families.":[91],"As":[92],"an":[93],"output,":[94],"our":[95,110],"produces":[97],"heatmaps":[98],"showing":[99],"contact":[100,107,135],"frequency":[101],"circular":[103],"diagrams":[104],"visualizing":[105],"localization.":[108],"Using":[109],"with":[112],"tomato":[113],"revealed":[116],"preferential":[118],"homotypic":[119],"interactions":[120],"ribosomal":[122],"DNA,":[123],"centromeric":[124],"satellites":[125],"some":[127],"LTR":[128,167],"retrotransposon":[129],"and,":[131],"as":[132],"expected,":[133],"little":[134],"between":[136],"organellar":[137],"nuclear":[139],"elements.":[141],"While":[142],"applied":[147],"any":[149],"eukaryotic":[150],"genome,":[151],"results":[152],"plants":[154],"provide":[155],"better":[156],"coverage,":[157],"since":[158],"built-in":[160],"TE-greedy-nester":[161],"software":[162],"only":[163],"detects":[164],"tandems":[165],"retrotransposons.":[168],"Other":[169],"repeats":[170],"fed":[173],"via":[174],"GFF3":[175],"files.":[176],"This":[177],"represents":[179],"novel":[181],"reproducible":[183],"way":[184],"analyze":[186],"elements":[191],"genomes.":[197],"AVAILABILITY":[198],"AND":[199],"IMPLEMENTATION:":[200],"https://gitlab.fi.muni.cz/lexa/hic-te/.":[201],"SUPPLEMENTARY":[202],"INFORMATION:":[203],"Supplementary":[204],"are":[206],"available":[207],"at":[208],"Bioinformatics":[209],"online.":[210]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":2}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
