{"id":"https://openalex.org/W2991184346","doi":"https://doi.org/10.1101/856823","title":"Leopard: fast decoding cell type-specific transcription factor binding landscape at single-nucleotide resolution","display_name":"Leopard: fast decoding cell type-specific transcription factor binding landscape at single-nucleotide resolution","publication_year":2019,"publication_date":"2019-11-27","ids":{"openalex":"https://openalex.org/W2991184346","doi":"https://doi.org/10.1101/856823","mag":"2991184346"},"language":"en","primary_location":{"id":"doi:10.1101/856823","doi":"https://doi.org/10.1101/856823","is_oa":true,"landing_page_url":"https://doi.org/10.1101/856823","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/11/27/856823.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2019/11/27/856823.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100450562","display_name":"Hongyang Li","orcid":"https://orcid.org/0000-0002-7902-4157","observed_orcids":["https://orcid.org/0000-0002-7902-4157"]},"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":"Hongyang Li","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA","Department of Computational Medicine and Bioinformatics, University of Michigan, 00 Washtenaw Avenue, Ann Arbor, MI 4809, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, 00 Washtenaw Avenue, Ann Arbor, MI 4809, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011032655","display_name":"Yuanfang Guan","orcid":"https://orcid.org/0000-0001-8275-2852","observed_orcids":["https://orcid.org/0000-0001-8275-2852","https://orcid.org/0009-0004-2391-9164"]},"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":"Yuanfang Guan","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA","Department of Computational Medicine and Bioinformatics, University of Michigan, 00 Washtenaw Avenue, Ann Arbor, MI 4809, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, 00 Washtenaw Avenue, Ann Arbor, MI 4809, USA","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5011032655"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9487000107765198,"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":0.9487000107765198,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.020899999886751175,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.0020000000949949026,"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/transcription-factor-binding-site-prediction","display_name":"transcription factor binding site prediction","score":0.8679999709129333},{"id":"https://openalex.org/keywords/cell-type-specific-binding","display_name":"cell type-specific binding","score":0.7020000219345093},{"id":"https://openalex.org/keywords/single-nucleotide-resolution","display_name":"single-nucleotide resolution","score":0.9629999995231628},{"id":"https://openalex.org/keywords/deep-learning","display_name":"deep learning","score":0.8610000014305115},{"id":"https://openalex.org/keywords/chromatin-regulatory-elements","display_name":"chromatin regulatory elements","score":0.5120000243186951},{"id":"https://openalex.org/keywords/computational-genomics","display_name":"computational genomics","score":0.527999997138977},{"id":"https://openalex.org/keywords/leopard","display_name":"leopard","score":0.5210000276565552}],"concepts":[{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.6474317312240601},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6075324416160583},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.546965479850769},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5450577735900879},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47631725668907166},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.4490009546279907},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.44807201623916626},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.4142422080039978},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37477123737335205},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33632320165634155},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25036680698394775},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.24029844999313354},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2193293571472168},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09530532360076904},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1101/856823","doi":"https://doi.org/10.1101/856823","is_oa":true,"landing_page_url":"https://doi.org/10.1101/856823","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/11/27/856823.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1101/856823","doi":"https://doi.org/10.1101/856823","is_oa":true,"landing_page_url":"https://doi.org/10.1101/856823","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2019/11/27/856823.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1017449502","display_name":null,"funder_award_id":"19AMTG34850176","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1446823662","display_name":"CAREER: On-line Service for Predicting Protein Phosphorylation Dynamics Under Unseen Perturbations","funder_award_id":"1452656","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2415660164","display_name":"Predicting cardiovascular risk from sleep patterns using deep learning","funder_award_id":"19AMTG34850176","funder_id":"https://openalex.org/F4320306230","funder_display_name":"American Heart Association"},{"id":"https://openalex.org/G4762659463","display_name":null,"funder_award_id":"19AMTG34850176","funder_id":"https://openalex.org/F4320310598","funder_display_name":"Amazon Web Services"},{"id":"https://openalex.org/G578324449","display_name":null,"funder_award_id":"19AMTG34850176","funder_id":"https://openalex.org/F4320309480","funder_display_name":"Nvidia"},{"id":"https://openalex.org/G6189258757","display_name":null,"funder_award_id":"NSF-US14-PAF07599","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","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"},{"id":"https://openalex.org/F4320306230","display_name":"American Heart Association","ror":"https://ror.org/013kjyp64"},{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320310598","display_name":"Amazon Web Services","ror":"https://ror.org/04mv4n011"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2991184346.pdf","grobid_xml":"https://content.openalex.org/works/W2991184346.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1901129140","https://openalex.org/W1964963969","https://openalex.org/W1989419347","https://openalex.org/W1993616000","https://openalex.org/W2008051478","https://openalex.org/W2026690931","https://openalex.org/W2042392223","https://openalex.org/W2063815548","https://openalex.org/W2068379897","https://openalex.org/W2078236750","https://openalex.org/W2081942683","https://openalex.org/W2092988184","https://openalex.org/W2098412979","https://openalex.org/W2102904139","https://openalex.org/W2103441770","https://openalex.org/W2129795133","https://openalex.org/W2140952049","https://openalex.org/W2171808845","https://openalex.org/W2198606573","https://openalex.org/W2336509392","https://openalex.org/W2767749844","https://openalex.org/W2770178180","https://openalex.org/W2785792383","https://openalex.org/W2795735651","https://openalex.org/W2883248903","https://openalex.org/W2883945062","https://openalex.org/W2885530730","https://openalex.org/W2898215009","https://openalex.org/W2901218091","https://openalex.org/W2904110212","https://openalex.org/W2912321349","https://openalex.org/W2935703330","https://openalex.org/W2941548848","https://openalex.org/W2946936654","https://openalex.org/W2951410692","https://openalex.org/W2952186574","https://openalex.org/W2981985696","https://openalex.org/W3104066961","https://openalex.org/W3118262189"],"related_works":["https://openalex.org/W3137533336","https://openalex.org/W7161606531","https://openalex.org/W2951410692","https://openalex.org/W3112390879","https://openalex.org/W4292723135","https://openalex.org/W6964343254","https://openalex.org/W4313527216","https://openalex.org/W2904110212","https://openalex.org/W2973006410","https://openalex.org/W4205751895"],"abstract_inverted_index":{"Abstract":[0],"Decoding":[1],"the":[2,17,35,56,89,110],"cell":[3,63],"type-specific":[4],"transcription":[5],"factor":[6],"(TF)":[7],"binding":[8,41,59],"landscape":[9],"at":[10,85,119],"single-nucleotide":[11,86],"resolution":[12],"is":[13],"crucial":[14],"for":[15,81],"understanding":[16],"regulatory":[18],"mechanisms":[19],"underlying":[20],"many":[21],"fundamental":[22],"biological":[23],"processes":[24],"and":[25,32,107,114],"human":[26],"diseases.":[27],"However,":[28],"limits":[29],"on":[30],"time":[31],"resources":[33],"restrict":[34],"high-resolution":[36],"experimental":[37],"measurements":[38],"of":[39,43,98],"TF":[40,58],"profiles":[42,60],"all":[44],"possible":[45],"TF-cell":[46],"type":[47],"combinations.":[48],"Previous":[49],"computational":[50],"approaches":[51],"either":[52],"can":[53],"not":[54],"distinguish":[55],"cell-context-dependent":[57],"across":[61],"diverse":[62],"types,":[64],"or":[65],"only":[66],"provide":[67],"a":[68,75,120,126],"relatively":[69],"low-resolution":[70],"prediction.":[71],"Here":[72],"we":[73],"present":[74],"novel":[76],"deep":[77],"learning":[78,142],"approach,":[79],"Leopard,":[80],"predicting":[82],"TF-binding":[83],"sites":[84],"resolution,":[87],"achieving":[88],"median":[90],"area":[91],"under":[92],"receiver":[93],"operating":[94],"characteristic":[95],"curve":[96],"(AUROC)":[97],"0.994.":[99],"Our":[100],"method":[101],"substantially":[102],"outperformed":[103],"state-of-the-art":[104],"methods":[105],"Anchor":[106],"FactorNet,":[108],"improving":[109],"performance":[111],"by":[112,124],"19%":[113],"27%":[115],"respectively":[116],"despite":[117],"evaluated":[118],"lower":[121],"resolution.":[122],"Meanwhile,":[123],"leveraging":[125],"many-to-many":[127],"neural":[128],"network":[129],"architecture,":[130],"Leopard":[131],"features":[132],"hundred-fold":[133],"to":[134,138],"thousand-fold":[135],"speedup":[136],"compared":[137],"current":[139],"many-to-one":[140],"machine":[141],"methods.":[143]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":2}],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2019-12-05T00:00:00"}
