{"id":"https://openalex.org/W4415491820","doi":"https://doi.org/10.1093/bioinformatics/btaf575","title":"SHICEDO: single-cell Hi-C data enhancement with reduced over-smoothing","display_name":"SHICEDO: single-cell Hi-C data enhancement with reduced over-smoothing","publication_year":2025,"publication_date":"2025-10-14","ids":{"openalex":"https://openalex.org/W4415491820","doi":"https://doi.org/10.1093/bioinformatics/btaf575","pmid":"https://pubmed.ncbi.nlm.nih.gov/41129292"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf575","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf575","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btaf575","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088347666","display_name":"Jingong Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jingong Huang","raw_affiliation_strings":["University of California Riverside Department of Computer Science and Engineering, , CA 92521,","Department of Computer Science and Engineering, University of California, Riverside, CA 92521, United States"],"affiliations":[{"raw_affiliation_string":"University of California Riverside Department of Computer Science and Engineering, , CA 92521,","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, Riverside, CA 92521, United States","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022546634","display_name":"Rui Ma","orcid":"https://orcid.org/0000-0003-0512-8751"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rui Ma","raw_affiliation_strings":["University of California Riverside Department of Statistics, , CA 92521,","Department of Statistics, University of California, Riverside, CA 92521, United States"],"affiliations":[{"raw_affiliation_string":"University of California Riverside Department of Statistics, , CA 92521,","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"Department of Statistics, University of California, Riverside, CA 92521, United States","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110340971","display_name":"Michael Strobel","orcid":"https://orcid.org/0009-0000-3829-0048"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Strobel","raw_affiliation_strings":["University of California Riverside Department of Computer Science and Engineering, , CA 92521,","Department of Computer Science and Engineering, University of California, Riverside, CA 92521, United States"],"affiliations":[{"raw_affiliation_string":"University of California Riverside Department of Computer Science and Engineering, , CA 92521,","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, Riverside, CA 92521, United States","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101075955","display_name":"Yangyang Hu","orcid":null},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yangyang Hu","raw_affiliation_strings":["University of California Riverside Department of Computer Science and Engineering, , CA 92521,","Department of Computer Science and Engineering, University of California, Riverside, CA 92521, United States"],"affiliations":[{"raw_affiliation_string":"University of California Riverside Department of Computer Science and Engineering, , CA 92521,","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, Riverside, CA 92521, United States","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003480019","display_name":"Tiantian Ye","orcid":"https://orcid.org/0009-0000-7262-8970"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tiantian Ye","raw_affiliation_strings":["University of California Riverside Department of Statistics, , CA 92521,","Department of Statistics, University of California, Riverside, CA 92521, United States"],"affiliations":[{"raw_affiliation_string":"University of California Riverside Department of Statistics, , CA 92521,","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"Department of Statistics, University of California, Riverside, CA 92521, United States","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101911266","display_name":"Tao Jiang","orcid":"https://orcid.org/0000-0003-3833-4498"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tao Jiang","raw_affiliation_strings":["University of California Riverside Department of Computer Science and Engineering, , CA 92521,","University of California Riverside Institute of Integrative Genome Biology, , CA 92521,","Department of Computer Science and Engineering, University of California, Riverside, CA 92521, United States"],"affiliations":[{"raw_affiliation_string":"University of California Riverside Department of Computer Science and Engineering, , CA 92521,","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"University of California Riverside Institute of Integrative Genome Biology, , CA 92521,","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, Riverside, CA 92521, United States","institution_ids":["https://openalex.org/I103635307"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064373045","display_name":"Wenxiu Ma","orcid":"https://orcid.org/0000-0003-4097-1621"},"institutions":[{"id":"https://openalex.org/I103635307","display_name":"University of California, Riverside","ror":"https://ror.org/03nawhv43","country_code":"US","type":"education","lineage":["https://openalex.org/I103635307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenxiu Ma","raw_affiliation_strings":["University of California Riverside Department of Statistics, , CA 92521,","University of California Riverside Institute of Integrative Genome Biology, , CA 92521,","Department of Statistics, University of California, Riverside, CA 92521, United States"],"affiliations":[{"raw_affiliation_string":"University of California Riverside Department of Statistics, , CA 92521,","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"University of California Riverside Institute of Integrative Genome Biology, , CA 92521,","institution_ids":["https://openalex.org/I103635307"]},{"raw_affiliation_string":"Department of Statistics, University of California, Riverside, CA 92521, United States","institution_ids":["https://openalex.org/I103635307"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5088347666"],"corresponding_institution_ids":["https://openalex.org/I103635307"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.35317842,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.8568000197410583,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.8568000197410583,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.8065000176429749,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41659998893737793},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.2637999951839447},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.2578999996185303},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.23729999363422394}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5788999795913696},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41659998893737793},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3244999945163727},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3147999942302704},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3046000003814697},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.2637999951839447},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2578999996185303},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.23729999363422394},{"id":"https://openalex.org/C133462117","wikidata":"https://www.wikidata.org/wiki/Q4929239","display_name":"Data collection","level":2,"score":0.23399999737739563},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.20419999957084656}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"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":"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":"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":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf575","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf575","pdf_url":null,"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:41129292","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41129292","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:escholarship.org:ark:/13030/qt6qg0w6sw","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/6qg0w6sw","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 41, iss 12","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf575","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf575","pdf_url":null,"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/G1929891357","display_name":null,"funder_award_id":"MRI-2215705","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3024476056","display_name":null,"funder_award_id":"MRI-1429826","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5956556336","display_name":null,"funder_award_id":"DBI-1751317","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1965863160","https://openalex.org/W1973062929","https://openalex.org/W2070021921","https://openalex.org/W2090037139","https://openalex.org/W2111997778","https://openalex.org/W2145619687","https://openalex.org/W2582946425","https://openalex.org/W2731989040","https://openalex.org/W2803256172","https://openalex.org/W2949773289","https://openalex.org/W2951559295","https://openalex.org/W2952940726","https://openalex.org/W2953462601","https://openalex.org/W2972380686","https://openalex.org/W3007609047","https://openalex.org/W3089191828","https://openalex.org/W3124454906","https://openalex.org/W3128067917","https://openalex.org/W3180346860","https://openalex.org/W3194691506","https://openalex.org/W3207880742","https://openalex.org/W4379792586","https://openalex.org/W4385294448","https://openalex.org/W4409473344"],"related_works":[],"abstract_inverted_index":{"SHICEDO":[0],"is":[1],"publicly":[2],"available":[3],"at":[4],"https://github.com/wmalab/SHICEDO.":[5]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-24T00:00:00"}
