{"id":"https://openalex.org/W4413741816","doi":"https://doi.org/10.1093/bib/bbaf435","title":"Pore-C Pipeline-Toolbox: a comprehensive pipeline for Pore-C data analysis","display_name":"Pore-C Pipeline-Toolbox: a comprehensive pipeline for Pore-C data analysis","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4413741816","doi":"https://doi.org/10.1093/bib/bbaf435","pmid":"https://pubmed.ncbi.nlm.nih.gov/40862515"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf435","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf435","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf435/64143039/bbaf435.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf435/64143039/bbaf435.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069179010","display_name":"Zhenji Wang","orcid":"https://orcid.org/0009-0006-6975-6078"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I4210157677","display_name":"Hubei Academy of Agricultural Sciences","ror":"https://ror.org/04qg81z57","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210157677"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenji Wang","raw_affiliation_strings":["Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,"],"raw_orcid":"https://orcid.org/0009-0006-6975-6078","affiliations":[{"raw_affiliation_string":"Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248","https://openalex.org/I4210157677"]},{"raw_affiliation_string":"Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067880166","display_name":"Qingqin Fu","orcid":null},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I4210157677","display_name":"Hubei Academy of Agricultural Sciences","ror":"https://ror.org/04qg81z57","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210157677"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiangqiang Fu","raw_affiliation_strings":["Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,"],"raw_orcid":"https://orcid.org/0009-0008-2556-8619","affiliations":[{"raw_affiliation_string":"Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248","https://openalex.org/I4210157677"]},{"raw_affiliation_string":"Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104128156","display_name":"Fuming Lai","orcid":"https://orcid.org/0009-0002-6944-8244"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I4210157677","display_name":"Hubei Academy of Agricultural Sciences","ror":"https://ror.org/04qg81z57","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210157677"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fuming Lai","raw_affiliation_strings":["Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,"],"raw_orcid":"https://orcid.org/0009-0002-6944-8244","affiliations":[{"raw_affiliation_string":"Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248","https://openalex.org/I4210157677"]},{"raw_affiliation_string":"Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008485039","display_name":"Qiangwei Zhou","orcid":"https://orcid.org/0000-0002-7948-177X"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I4210157677","display_name":"Hubei Academy of Agricultural Sciences","ror":"https://ror.org/04qg81z57","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210157677"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiangwei Zhou","raw_affiliation_strings":["Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,"],"raw_orcid":"https://orcid.org/0000-0002-7948-177X","affiliations":[{"raw_affiliation_string":"Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248","https://openalex.org/I4210157677"]},{"raw_affiliation_string":"Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008133107","display_name":"Yaping Fang","orcid":"https://orcid.org/0000-0001-6075-0768"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I4210157677","display_name":"Hubei Academy of Agricultural Sciences","ror":"https://ror.org/04qg81z57","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210157677"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaping Fang","raw_affiliation_strings":["Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,"],"raw_orcid":"https://orcid.org/0000-0001-6075-0768","affiliations":[{"raw_affiliation_string":"Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248","https://openalex.org/I4210157677"]},{"raw_affiliation_string":"Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100404163","display_name":"Guoliang Li","orcid":"https://orcid.org/0000-0003-1601-6640"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]},{"id":"https://openalex.org/I4210157677","display_name":"Hubei Academy of Agricultural Sciences","ror":"https://ror.org/04qg81z57","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210157677"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guoliang Li","raw_affiliation_strings":["Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,"],"raw_orcid":"https://orcid.org/0000-0003-1601-6640","affiliations":[{"raw_affiliation_string":"Agricultural Bioinformatics Key Laboratory of Hubei Province and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248","https://openalex.org/I4210157677"]},{"raw_affiliation_string":"Hubei Hongshan Laboratory, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248"]},{"raw_affiliation_string":"National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University , 66 Nanhu Avenue, Wuhan, Hubei Province, Wuhan 430070 ,","institution_ids":["https://openalex.org/I204823248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.17202501,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9854000210762024,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9854000210762024,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9577000141143799,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10399","display_name":"Hydrocarbon exploration and reservoir analysis","score":0.9435999989509583,"subfield":{"id":"https://openalex.org/subfields/2211","display_name":"Mechanics of Materials"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.8723068237304688},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.7947944402694702},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4989297389984131},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.358642578125},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10926780104637146}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8723068237304688},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.7947944402694702},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4989297389984131},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.358642578125},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10926780104637146}],"mesh":[{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":"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":"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":"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":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf435","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf435","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf435/64143039/bbaf435.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40862515","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40862515","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11190251","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12381758","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf435","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf435","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf435/64143039/bbaf435.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1203807175","display_name":null,"funder_award_id":"2021YFC2701201","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G3213437852","display_name":null,"funder_award_id":"2021YFC2701201","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5830289686","display_name":null,"funder_award_id":"32250710678","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7991575319","display_name":null,"funder_award_id":"32370630","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413741816.pdf","grobid_xml":"https://content.openalex.org/works/W4413741816.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1973062929","https://openalex.org/W1985621639","https://openalex.org/W2011463791","https://openalex.org/W2020912279","https://openalex.org/W2081870862","https://openalex.org/W2090037139","https://openalex.org/W2149943693","https://openalex.org/W2185693210","https://openalex.org/W2481029670","https://openalex.org/W2765567136","https://openalex.org/W2789843538","https://openalex.org/W2911835695","https://openalex.org/W2950121474","https://openalex.org/W2960979937","https://openalex.org/W2999719567","https://openalex.org/W3046950215","https://openalex.org/W3112752014","https://openalex.org/W3193986928","https://openalex.org/W4225836315","https://openalex.org/W4281976431","https://openalex.org/W4283318743","https://openalex.org/W4296774313","https://openalex.org/W4306353463","https://openalex.org/W4307804779","https://openalex.org/W4310665498","https://openalex.org/W4323316351","https://openalex.org/W4366811281","https://openalex.org/W4386215932","https://openalex.org/W4387965480","https://openalex.org/W4393004084","https://openalex.org/W4406471462","https://openalex.org/W4408156909"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4205140848","https://openalex.org/W2068663075","https://openalex.org/W2978678743","https://openalex.org/W2797837731","https://openalex.org/W4393677513","https://openalex.org/W4390832911","https://openalex.org/W829257147"],"abstract_inverted_index":{"Three-dimensional":[0],"(3D)":[1],"genomic":[2],"architecture":[3],"is":[4,28,148,172],"crucial":[5],"for":[6,86,112,118],"the":[7,14,51,55,62,134,169],"regulation":[8],"of":[9,16,57,64,90,101,145],"different":[10],"biological":[11],"processes,":[12],"and":[13,59,121,129,154,164],"study":[15],"multi-way":[17,47,91,107,113,119,160],"chromatin":[18,48,92],"structures":[19],"represents":[20],"a":[21,83,87,99,141,152],"cutting-edge":[22],"area":[23],"in":[24,159,168],"this":[25,75],"field.":[26,170],"Pore-C":[27,65,79,95],"an":[29],"advanced":[30,115],"experimental":[31],"technique":[32],"integrating":[33],"chromosome":[34],"conformation":[35],"capture":[36,45],"(3C)":[37],"with":[38],"Nanopore":[39],"long-read":[40],"sequencing,":[41],"which":[42],"can":[43],"effectively":[44],"complex":[46],"contacts":[49],"across":[50],"genome.":[52],"Due":[53],"to":[54,150],"absence":[56],"comprehensive":[58,88,143],"dedicated":[60],"tools,":[61],"analysis":[63,89],"data":[66],"remains":[67],"challenging,":[68],"restricting":[69],"its":[70],"broader":[71],"application.":[72],"To":[73],"address":[74],"limitation,":[76],"we":[77],"developed":[78],"Pipeline":[80],"Toolbox":[81],"(PPL-Toolbox),":[82],"specialized":[84],"software":[85],"interactions":[93],"from":[94],"data.":[96],"PPL-Toolbox":[97,135,147,171],"incorporates":[98],"suite":[100],"optimized":[102],"modules,":[103],"including":[104],"quality":[105],"control,":[106],"interaction":[108],"extraction,":[109],"noise":[110],"reduction":[111],"contacts,":[114,120],"visualization":[116],"tools":[117],"haplotype":[122],"map":[123],"generation.":[124],"Evaluation":[125],"on":[126,175],"both":[127],"simulated":[128],"real":[130],"datasets":[131],"demonstrates":[132],"that":[133],"outperforms":[136],"existing":[137],"methods":[138],"by":[139],"providing":[140],"more":[142],"set":[144],"results.":[146],"expected":[149],"become":[151],"powerful":[153],"versatile":[155],"tool,":[156],"driving":[157],"advance":[158],"3D":[161],"genomics":[162],"research,":[163],"enabling":[165],"new":[166],"discoveries":[167],"publicly":[173],"available":[174],"GitHub":[176],"(https://github.com/versarchey/PPL-Toolbox).":[177]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
