{"id":"https://openalex.org/W4412454092","doi":"https://doi.org/10.1093/bioinformatics/btaf231","title":"Soffritto: a deep learning model for predicting high-resolution replication timing","display_name":"Soffritto: a deep learning model for predicting high-resolution replication timing","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412454092","doi":"https://doi.org/10.1093/bioinformatics/btaf231","pmid":"https://pubmed.ncbi.nlm.nih.gov/40662815"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf231","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf231","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i580/63745552/btaf231.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i580/63745552/btaf231.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087100409","display_name":"Dante Bolzan","orcid":"https://orcid.org/0000-0002-1004-4213"},"institutions":[{"id":"https://openalex.org/I1311191458","display_name":"La Jolla Institute for Immunology","ror":"https://ror.org/05vkpd318","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311191458"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dante Bolzan","raw_affiliation_strings":["Bioinformatics and Systems Biology PhD Program, University of California, San Diego , La Jolla, CA 92093,","Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology , La Jolla, CA 92037,"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology PhD Program, University of California, San Diego , La Jolla, CA 92093,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology , La Jolla, CA 92037,","institution_ids":["https://openalex.org/I1311191458"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036380790","display_name":"Ferhat Ay","orcid":"https://orcid.org/0000-0002-0708-6914"},"institutions":[{"id":"https://openalex.org/I1311191458","display_name":"La Jolla Institute for Immunology","ror":"https://ror.org/05vkpd318","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1311191458"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ferhat Ay","raw_affiliation_strings":["Bioinformatics and Systems Biology PhD Program, University of California, San Diego , La Jolla, CA 92093,","Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology , La Jolla, CA 92037,","Department of Pediatrics, University of California, San Diego , La Jolla, CA 92093,"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology PhD Program, University of California, San Diego , La Jolla, CA 92093,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology , La Jolla, CA 92037,","institution_ids":["https://openalex.org/I1311191458"]},{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego , La Jolla, CA 92093,","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5087100409"],"corresponding_institution_ids":["https://openalex.org/I1311191458","https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7625,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.73197651,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"41","issue":"Supplement_1","first_page":"i580","last_page":"i589"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9997000098228455,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9979000091552734,"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/computer-science","display_name":"Computer science","score":0.6249111294746399},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5175525546073914},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5091816782951355},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.45569127798080444},{"id":"https://openalex.org/keywords/fraction","display_name":"Fraction (chemistry)","score":0.42938685417175293},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40650486946105957},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.36239364743232727},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35558366775512695},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3290128707885742},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3221297860145569},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2582123577594757}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6249111294746399},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5175525546073914},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5091816782951355},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.45569127798080444},{"id":"https://openalex.org/C149629883","wikidata":"https://www.wikidata.org/wiki/Q660926","display_name":"Fraction (chemistry)","level":2,"score":0.42938685417175293},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40650486946105957},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.36239364743232727},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35558366775512695},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3290128707885742},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3221297860145569},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2582123577594757},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"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":"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":"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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D042522","descriptor_name":"DNA Replication Timing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D042522","descriptor_name":"DNA Replication Timing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D042522","descriptor_name":"DNA Replication Timing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D042522","descriptor_name":"DNA Replication Timing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D042522","descriptor_name":"DNA Replication Timing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf231","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf231","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i580/63745552/btaf231.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40662815","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40662815","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:pubmedcentral.nih.gov:12261407","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12261407","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf231","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf231","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i580/63745552/btaf231.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3358760164","display_name":null,"funder_award_id":"GM128938","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6240949075","display_name":null,"funder_award_id":"R35-GM128938","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412454092.pdf","grobid_xml":"https://content.openalex.org/works/W4412454092.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W2032938251","https://openalex.org/W2064675550","https://openalex.org/W2071698610","https://openalex.org/W2072288967","https://openalex.org/W2103626064","https://openalex.org/W2144141448","https://openalex.org/W2153087859","https://openalex.org/W2765567136","https://openalex.org/W2794609805","https://openalex.org/W2898598946","https://openalex.org/W2953622121","https://openalex.org/W2971932838","https://openalex.org/W2988126442","https://openalex.org/W3013964298","https://openalex.org/W3134683881","https://openalex.org/W3155818854","https://openalex.org/W4225279860","https://openalex.org/W4255375128","https://openalex.org/W4295312788"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W4375867731","https://openalex.org/W178140751","https://openalex.org/W1191014223","https://openalex.org/W1137063513","https://openalex.org/W2611989081","https://openalex.org/W2731899572","https://openalex.org/W4230611425","https://openalex.org/W4387682966","https://openalex.org/W4294635752"],"abstract_inverted_index":{"Soffritto":[0],"is":[1],"available":[2],"at":[3],"https://github.com/ay-lab/Soffritto.":[4]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}