{"id":"https://openalex.org/W4416888677","doi":"https://doi.org/10.1093/bioinformatics/btaf645","title":"Chrom-Sig: de-noising 1D genomic profiles by signal processing methods","display_name":"Chrom-Sig: de-noising 1D genomic profiles by signal processing methods","publication_year":2025,"publication_date":"2025-11-27","ids":{"openalex":"https://openalex.org/W4416888677","doi":"https://doi.org/10.1093/bioinformatics/btaf645","pmid":"https://pubmed.ncbi.nlm.nih.gov/41325270"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf645","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf645","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/12/btaf645/65667504/btaf645.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/41/12/btaf645/65667504/btaf645.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047600946","display_name":"N. Gupta","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nandita J Gupta","raw_affiliation_strings":["University of Michigan Department of Electrical and Computer Engineering, , Ann Arbor, MI 48109,","University of Michigan Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, , Ann Arbor, MI 48109,","Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, MI United States"],"affiliations":[{"raw_affiliation_string":"University of Michigan Department of Electrical and Computer Engineering, , Ann Arbor, MI 48109,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"University of Michigan Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, , Ann Arbor, MI 48109,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, MI United States","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119345588","display_name":"Zachary Apell","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zachary Apell","raw_affiliation_strings":["University of Michigan Department of Biostatistics, , Ann Arbor, MI 48109,","University of Michigan Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, , Ann Arbor, MI 48109,","Department of Biostatistics, University of Michigan, Ann Arbor, MI United States"],"affiliations":[{"raw_affiliation_string":"University of Michigan Department of Biostatistics, , Ann Arbor, MI 48109,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"University of Michigan Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, , Ann Arbor, MI 48109,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Biostatistics, University of Michigan, Ann Arbor, MI United States","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100317754","display_name":"Minji Kim","orcid":"https://orcid.org/0000-0002-7282-8224"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Minji Kim","raw_affiliation_strings":["University of Michigan Department of Electrical and Computer Engineering, , Ann Arbor, MI 48109,","University of Michigan Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, , Ann Arbor, MI 48109,","Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI United States"],"affiliations":[{"raw_affiliation_string":"University of Michigan Department of Electrical and Computer Engineering, , Ann Arbor, MI 48109,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"University of Michigan Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, , Ann Arbor, MI 48109,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI United States","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5047600946"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.39941956,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.41449999809265137,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.41449999809265137,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.10750000178813934,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.0851999968290329,"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/signal-processing","display_name":"Signal processing","score":0.6107000112533569},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4632999897003174},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.42910000681877136},{"id":"https://openalex.org/keywords/signal","display_name":"SIGNAL (programming language)","score":0.4081000089645386},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.28839999437332153}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6775000095367432},{"id":"https://openalex.org/C104267543","wikidata":"https://www.wikidata.org/wiki/Q208163","display_name":"Signal processing","level":3,"score":0.6107000112533569},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46939998865127563},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4632999897003174},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.42910000681877136},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.4081000089645386},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3995000123977661},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32510000467300415},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.28839999437332153},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.272599995136261},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.2669999897480011},{"id":"https://openalex.org/C138827492","wikidata":"https://www.wikidata.org/wiki/Q6661985","display_name":"Data processing","level":2,"score":0.266400009393692},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2623000144958496}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012815","descriptor_name":"Signal Processing, Computer-Assisted","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":"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},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf645","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf645","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/12/btaf645/65667504/btaf645.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:41325270","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41325270","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:12715305","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12715305/","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/btaf645","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf645","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/12/btaf645/65667504/btaf645.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/G1409632374","display_name":null,"funder_award_id":"R00-HG011542","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":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4416888677.pdf"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1531821806","https://openalex.org/W1985621639","https://openalex.org/W2059699217","https://openalex.org/W2090037139","https://openalex.org/W2154431984","https://openalex.org/W2157952888","https://openalex.org/W2231865019","https://openalex.org/W2259938310","https://openalex.org/W2341539131","https://openalex.org/W2562443513","https://openalex.org/W2584394140","https://openalex.org/W2790768464","https://openalex.org/W2920191405","https://openalex.org/W2951572348","https://openalex.org/W3005996730","https://openalex.org/W3135168232","https://openalex.org/W4225279860","https://openalex.org/W4379792586"],"related_works":[],"abstract_inverted_index":{"Chrom-Sig":[0],"is":[1],"publicly":[2],"available":[3],"on":[4],"GitHub":[5],"(https://github.com/minjikimlab/chromsig)":[6],"and":[7],"Zenodo":[8],"(doi:":[9],"10.5281/zenodo.17488772)":[10],"under":[11],"the":[12],"MIT":[13],"licence.":[14]},"counts_by_year":[],"updated_date":"2026-03-22T08:09:32.410652","created_date":"2025-12-01T00:00:00"}