{"id":"https://openalex.org/W4404426560","doi":"https://doi.org/10.3389/fbinf.2024.1462923","title":"Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads","display_name":"Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads","publication_year":2024,"publication_date":"2024-11-15","ids":{"openalex":"https://openalex.org/W4404426560","doi":"https://doi.org/10.3389/fbinf.2024.1462923","pmid":"https://pubmed.ncbi.nlm.nih.gov/39619774"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2024.1462923","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1462923","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3389/fbinf.2024.1462923","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032064578","display_name":"Lia Obinu","orcid":"https://orcid.org/0000-0002-3208-323X"},"institutions":[{"id":"https://openalex.org/I4210137845","display_name":"Edinburgh Genomics","ror":"https://ror.org/02z3r7t23","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210137845"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]},{"id":"https://openalex.org/I159650629","display_name":"University of Sassari","ror":"https://ror.org/01bnjbv91","country_code":"IT","type":"education","lineage":["https://openalex.org/I159650629"]}],"countries":["GB","IT"],"is_corresponding":true,"raw_author_name":"Lia Obinu","raw_affiliation_strings":["Department of Agricultural Sciences, University of Sassari, Sassari, Sardinia, Italy","Edinburgh Genomics, The University of Edinburgh, Edinburgh, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Agricultural Sciences, University of Sassari, Sassari, Sardinia, Italy","institution_ids":["https://openalex.org/I159650629"]},{"raw_affiliation_string":"Edinburgh Genomics, The University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I4210137845","https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086687948","display_name":"Urmi Trivedi","orcid":"https://orcid.org/0000-0002-2056-4511"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]},{"id":"https://openalex.org/I4210137845","display_name":"Edinburgh Genomics","ror":"https://ror.org/02z3r7t23","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210137845"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Urmi Trivedi","raw_affiliation_strings":["Edinburgh Genomics, The University of Edinburgh, Edinburgh, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Edinburgh Genomics, The University of Edinburgh, Edinburgh, United Kingdom","institution_ids":["https://openalex.org/I4210137845","https://openalex.org/I98677209"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037881364","display_name":"Andrea Porceddu","orcid":"https://orcid.org/0000-0001-7126-9048"},"institutions":[{"id":"https://openalex.org/I159650629","display_name":"University of Sassari","ror":"https://ror.org/01bnjbv91","country_code":"IT","type":"education","lineage":["https://openalex.org/I159650629"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Porceddu","raw_affiliation_strings":["Department of Agricultural Sciences, University of Sassari, Sassari, Sardinia, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Agricultural Sciences, University of Sassari, Sassari, Sardinia, Italy","institution_ids":["https://openalex.org/I159650629"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5032064578"],"corresponding_institution_ids":["https://openalex.org/I159650629","https://openalex.org/I4210137845","https://openalex.org/I98677209"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.8855,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.74433273,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"4","issue":null,"first_page":"1462923","last_page":"1462923"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9973999857902527,"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/T11470","display_name":"Legume Nitrogen Fixing Symbiosis","score":0.992900013923645,"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/genome","display_name":"Genome","score":0.7572615146636963},{"id":"https://openalex.org/keywords/sequence-assembly","display_name":"Sequence assembly","score":0.6196708679199219},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5363242626190186},{"id":"https://openalex.org/keywords/arabidopsis-thaliana","display_name":"Arabidopsis thaliana","score":0.5161019563674927},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.4782611131668091},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4512816369533539},{"id":"https://openalex.org/keywords/correctness","display_name":"Correctness","score":0.43190380930900574},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3978004455566406},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26103705167770386},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14381280541419983},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11071974039077759}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7572615146636963},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.6196708679199219},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5363242626190186},{"id":"https://openalex.org/C2775988993","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Arabidopsis thaliana","level":4,"score":0.5161019563674927},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.4782611131668091},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4512816369533539},{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.43190380930900574},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3978004455566406},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26103705167770386},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14381280541419983},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11071974039077759},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.0},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.3389/fbinf.2024.1462923","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1462923","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39619774","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39619774","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11604747","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11604747","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:5b6e0caaa16447d2bcd45db834f6f475","is_oa":true,"landing_page_url":"https://doaj.org/article/5b6e0caaa16447d2bcd45db834f6f475","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 4 (2024)","raw_type":"article"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/fe837de4-f36b-457a-bb2f-35575a2bf2d7","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/fe837de4-f36b-457a-bb2f-35575a2bf2d7","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"Obinu, L, Trivedi, U & Porceddu, A 2024, 'Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads', Frontiers in Bioinformatics, vol. 4, 1462923. https://doi.org/10.3389/fbinf.2024.1462923","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pure.ed.ac.uk:publications/fe837de4-f36b-457a-bb2f-35575a2bf2d7","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/files/485958880/fbinf-2-1462923.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"Obinu, L, Trivedi, U & Porceddu, A 2024, 'Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads', Frontiers in Bioinformatics, vol. 4, 1462923. https://doi.org/10.3389/fbinf.2024.1462923","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2024.1462923","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2024.1462923","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1492565411","https://openalex.org/W1494075612","https://openalex.org/W2090037139","https://openalex.org/W2094270919","https://openalex.org/W2097927039","https://openalex.org/W2118970626","https://openalex.org/W2396077153","https://openalex.org/W2481029670","https://openalex.org/W2575750030","https://openalex.org/W2784788330","https://openalex.org/W2788228074","https://openalex.org/W2789843538","https://openalex.org/W2789849365","https://openalex.org/W2808352813","https://openalex.org/W2948487375","https://openalex.org/W2949711305","https://openalex.org/W2950354111","https://openalex.org/W2950698362","https://openalex.org/W2951278111","https://openalex.org/W2952020649","https://openalex.org/W2965879979","https://openalex.org/W2969330652","https://openalex.org/W3002362821","https://openalex.org/W3002583775","https://openalex.org/W3007075333","https://openalex.org/W3047598142","https://openalex.org/W3085758516","https://openalex.org/W3113162057","https://openalex.org/W3128198169","https://openalex.org/W3129402903","https://openalex.org/W3150113646","https://openalex.org/W3164036323","https://openalex.org/W3186309583","https://openalex.org/W3198332687","https://openalex.org/W3202547677","https://openalex.org/W3216110456","https://openalex.org/W4205846574","https://openalex.org/W4280618935","https://openalex.org/W4311663808","https://openalex.org/W4389058735"],"related_works":["https://openalex.org/W2962743744","https://openalex.org/W3009176350","https://openalex.org/W3021840362","https://openalex.org/W3090794301","https://openalex.org/W2951397007","https://openalex.org/W3022783334","https://openalex.org/W2580258113","https://openalex.org/W2763726643","https://openalex.org/W2952788979","https://openalex.org/W2607669908"],"abstract_inverted_index":{".":[0]},"counts_by_year":[{"year":2025,"cited_by_count":4}],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2025-10-10T00:00:00"}
