{"id":"https://openalex.org/W4387439788","doi":"https://doi.org/10.1093/bioinformatics/btad616","title":"DeepPeptide predicts cleaved peptides in proteins using conditional random fields","display_name":"DeepPeptide predicts cleaved peptides in proteins using conditional random fields","publication_year":2023,"publication_date":"2023-10-01","ids":{"openalex":"https://openalex.org/W4387439788","doi":"https://doi.org/10.1093/bioinformatics/btad616","pmid":"https://pubmed.ncbi.nlm.nih.gov/37812217"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad616","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad616","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad616/51960023/btad616.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/advance-article-pdf/doi/10.1093/bioinformatics/btad616/51960023/btad616.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025098840","display_name":"Felix Teufel","orcid":"https://orcid.org/0000-0003-1275-8065"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I189090001","display_name":"Novo Nordisk (Denmark)","ror":"https://ror.org/0435rc536","country_code":"DK","type":"company","lineage":["https://openalex.org/I189090001","https://openalex.org/I2801134892","https://openalex.org/I4210159963"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Felix Teufel","raw_affiliation_strings":["Department of Biology, University of Copenhagen , Ole Maal\u00f8es Vej 5 , Copenhagen 2200, Denmark","Digital Science & Innovation, Novo Nordisk A/S , Novo Nordisk Park , M\u00e5l\u00f8v 2760, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Copenhagen , Ole Maal\u00f8es Vej 5 , Copenhagen 2200, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Digital Science & Innovation, Novo Nordisk A/S , Novo Nordisk Park , M\u00e5l\u00f8v 2760, Denmark","institution_ids":["https://openalex.org/I189090001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080778199","display_name":"Jan C. Refsgaard","orcid":"https://orcid.org/0000-0002-2781-0367"},"institutions":[{"id":"https://openalex.org/I189090001","display_name":"Novo Nordisk (Denmark)","ror":"https://ror.org/0435rc536","country_code":"DK","type":"company","lineage":["https://openalex.org/I189090001","https://openalex.org/I2801134892","https://openalex.org/I4210159963"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Jan Christian Refsgaard","raw_affiliation_strings":["Digital Science & Innovation, Novo Nordisk A/S , Novo Nordisk Park , M\u00e5l\u00f8v 2760, Denmark"],"affiliations":[{"raw_affiliation_string":"Digital Science & Innovation, Novo Nordisk A/S , Novo Nordisk Park , M\u00e5l\u00f8v 2760, Denmark","institution_ids":["https://openalex.org/I189090001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044859624","display_name":"Christian T. Madsen","orcid":"https://orcid.org/0000-0003-3268-5350"},"institutions":[{"id":"https://openalex.org/I189090001","display_name":"Novo Nordisk (Denmark)","ror":"https://ror.org/0435rc536","country_code":"DK","type":"company","lineage":["https://openalex.org/I189090001","https://openalex.org/I2801134892","https://openalex.org/I4210159963"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Christian Toft Madsen","raw_affiliation_strings":["Global Translation, Novo Nordisk A/S , Novo Nordisk Park , M\u00e5l\u00f8v 2760, Denmark"],"affiliations":[{"raw_affiliation_string":"Global Translation, Novo Nordisk A/S , Novo Nordisk Park , M\u00e5l\u00f8v 2760, Denmark","institution_ids":["https://openalex.org/I189090001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051534470","display_name":"Carsten Stahlhut","orcid":"https://orcid.org/0000-0002-6445-6010"},"institutions":[{"id":"https://openalex.org/I189090001","display_name":"Novo Nordisk (Denmark)","ror":"https://ror.org/0435rc536","country_code":"DK","type":"company","lineage":["https://openalex.org/I189090001","https://openalex.org/I2801134892","https://openalex.org/I4210159963"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Carsten Stahlhut","raw_affiliation_strings":["Digital Science & Innovation, Novo Nordisk A/S , Novo Nordisk Park , M\u00e5l\u00f8v 2760, Denmark"],"affiliations":[{"raw_affiliation_string":"Digital Science & Innovation, Novo Nordisk A/S , Novo Nordisk Park , M\u00e5l\u00f8v 2760, Denmark","institution_ids":["https://openalex.org/I189090001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014181394","display_name":"Mads Gr\u00f8nborg","orcid":"https://orcid.org/0000-0003-4011-6406"},"institutions":[{"id":"https://openalex.org/I189090001","display_name":"Novo Nordisk (Denmark)","ror":"https://ror.org/0435rc536","country_code":"DK","type":"company","lineage":["https://openalex.org/I189090001","https://openalex.org/I2801134892","https://openalex.org/I4210159963"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Mads Gr\u00f8nborg","raw_affiliation_strings":["Global Translation, Novo Nordisk A/S , Novo Nordisk Park , M\u00e5l\u00f8v 2760, Denmark"],"affiliations":[{"raw_affiliation_string":"Global Translation, Novo Nordisk A/S , Novo Nordisk Park , M\u00e5l\u00f8v 2760, Denmark","institution_ids":["https://openalex.org/I189090001"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082357240","display_name":"Ole Winther","orcid":"https://orcid.org/0000-0002-1966-3205"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Ole Winther","raw_affiliation_strings":["Department of Applied Mathematics and Computer Science, Technical University of Denmark , Lyngby 2800, Denmark","Department of Biology, University of Copenhagen , Ole Maal\u00f8es Vej 5 , Copenhagen 2200, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Computer Science, Technical University of Denmark , Lyngby 2800, Denmark","institution_ids":["https://openalex.org/I96673099"]},{"raw_affiliation_string":"Department of Biology, University of Copenhagen , Ole Maal\u00f8es Vej 5 , Copenhagen 2200, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006559916","display_name":"Dennis Madsen","orcid":"https://orcid.org/0000-0003-2099-6880"},"institutions":[{"id":"https://openalex.org/I189090001","display_name":"Novo Nordisk (Denmark)","ror":"https://ror.org/0435rc536","country_code":"DK","type":"company","lineage":["https://openalex.org/I189090001","https://openalex.org/I2801134892","https://openalex.org/I4210159963"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Dennis Madsen","raw_affiliation_strings":["Digital Science & Innovation, Novo Nordisk A/S , Novo Nordisk Park , M\u00e5l\u00f8v 2760, Denmark"],"affiliations":[{"raw_affiliation_string":"Digital Science & Innovation, Novo Nordisk A/S , Novo Nordisk Park , M\u00e5l\u00f8v 2760, Denmark","institution_ids":["https://openalex.org/I189090001"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5025098840"],"corresponding_institution_ids":["https://openalex.org/I124055696","https://openalex.org/I189090001"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.684,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.84396263,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"39","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998999834060669,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976999759674072,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4987630844116211},{"id":"https://openalex.org/keywords/conditional-random-field","display_name":"Conditional random field","score":0.49656087160110474},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4933251440525055},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.335005521774292},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2624180018901825},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.221525639295578}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4987630844116211},{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.49656087160110474},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4933251440525055},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.335005521774292},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2624180018901825},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.221525639295578}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010447","descriptor_name":"Peptide Hydrolases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btad616","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad616","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad616/51960023/btad616.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:37812217","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37812217","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:10585352","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10585352","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10585352/pdf/btad616.pdf","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"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/5902f1c3-efb5-47eb-9c55-1f562a8f2b27","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/5902f1c3-efb5-47eb-9c55-1f562a8f2b27","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"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":"Teufel , F , Refsgaard , J C , Madsen , C T , Stahlhut , C , Gr\u00f8nborg , M , Winther , O & Madsen , D 2023 , ' DeepPeptide predicts cleaved peptides in proteins using conditional random fields ' , Bioinformatics (Oxford, England) , vol. 39 , no. 10 , btad616 . https://doi.org/10.1093/bioinformatics/btad616","raw_type":"article"},{"id":"pmh:oai:pure.atira.dk:publications/ef6eb415-6921-4208-a2e1-b77112a2cdf4","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/ef6eb415-6921-4208-a2e1-b77112a2cdf4","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"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":"Teufel , F , Refsgaard , J C , Madsen , C T , Stahlhut , C , Gr\u00f8nborg , M , Winther , O &amp; Madsen , D 2023 , ' DeepPeptide predicts cleaved peptides in proteins using conditional random fields ' , Bioinformatics , vol. 39 , no. 10 , btad616 . https://doi.org/10.1093/bioinformatics/btad616","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad616","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad616","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad616/51960023/btad616.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/G1154953777","display_name":null,"funder_award_id":"0062606","funder_id":"https://openalex.org/F4320322436","funder_display_name":"Novo Nordisk"},{"id":"https://openalex.org/G8363685846","display_name":null,"funder_award_id":"NNF20OC0062606","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"}],"funders":[{"id":"https://openalex.org/F4320320943","display_name":"Danmarks Grundforskningsfond","ror":"https://ror.org/00znyv691"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387439788.pdf"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1512370882","https://openalex.org/W1991133427","https://openalex.org/W2107158607","https://openalex.org/W2121962408","https://openalex.org/W2154325494","https://openalex.org/W2316262244","https://openalex.org/W2344689512","https://openalex.org/W2779381970","https://openalex.org/W2912990441","https://openalex.org/W2986170540","https://openalex.org/W3112376646","https://openalex.org/W3146944767","https://openalex.org/W3217490919","https://openalex.org/W4205192056","https://openalex.org/W4206950245","https://openalex.org/W4210299062","https://openalex.org/W4212959738","https://openalex.org/W4214943162","https://openalex.org/W4232683318","https://openalex.org/W4306888840","https://openalex.org/W4327550249","https://openalex.org/W4387687322","https://openalex.org/W6762363781"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"DeepPeptide":[0],"is":[1],"available":[2],"online":[3],"at":[4],"ku.biolib.com/DeepPeptide.":[5]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
