{"id":"https://openalex.org/W2111607063","doi":"https://doi.org/10.1093/bioinformatics/bts719","title":"NucleoFinder: a statistical approach for the detection of nucleosome positions","display_name":"NucleoFinder: a statistical approach for the detection of nucleosome positions","publication_year":2013,"publication_date":"2013-01-06","ids":{"openalex":"https://openalex.org/W2111607063","doi":"https://doi.org/10.1093/bioinformatics/bts719","mag":"2111607063","pmid":"https://pubmed.ncbi.nlm.nih.gov/23297036"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts719","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts719","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/711/48898316/bioinformatics_29_6_711.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/711/48898316/bioinformatics_29_6_711.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037020142","display_name":"J\u00e9r\u00e9mie Becker","orcid":"https://orcid.org/0000-0001-8747-3748"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210086857","display_name":"Mary Lyon Centre at MRC Harwell","ror":"https://ror.org/0001h1y25","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210086857","https://openalex.org/I4210087105","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jeremie Becker","raw_affiliation_strings":["1 Department of Statistics, University of Oxford, Oxford OX1 3TG, 2MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD and 3Department of Physiology, Development and Neuroscience, Cambridge CB2 3EG, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, University of Oxford, Oxford OX1 3TG, 2MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD and 3Department of Physiology, Development and Neuroscience, Cambridge CB2 3EG, UK","institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210086857"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084571119","display_name":"Christopher Yau","orcid":"https://orcid.org/0000-0001-7615-8523"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210086857","display_name":"Mary Lyon Centre at MRC Harwell","ror":"https://ror.org/0001h1y25","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210086857","https://openalex.org/I4210087105","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christopher Yau","raw_affiliation_strings":["1 Department of Statistics, University of Oxford, Oxford OX1 3TG, 2MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD and 3Department of Physiology, Development and Neuroscience, Cambridge CB2 3EG, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, University of Oxford, Oxford OX1 3TG, 2MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD and 3Department of Physiology, Development and Neuroscience, Cambridge CB2 3EG, UK","institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210086857"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030731998","display_name":"John M. Hancock","orcid":"https://orcid.org/0000-0003-2991-2217"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210086857","display_name":"Mary Lyon Centre at MRC Harwell","ror":"https://ror.org/0001h1y25","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210086857","https://openalex.org/I4210087105","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"John M. Hancock","raw_affiliation_strings":["1 Department of Statistics, University of Oxford, Oxford OX1 3TG, 2MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD and 3Department of Physiology, Development and Neuroscience, Cambridge CB2 3EG, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, University of Oxford, Oxford OX1 3TG, 2MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD and 3Department of Physiology, Development and Neuroscience, Cambridge CB2 3EG, UK","institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210086857"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100649922","display_name":"Chris Holmes","orcid":"https://orcid.org/0000-0002-6667-4943"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210086857","display_name":"Mary Lyon Centre at MRC Harwell","ror":"https://ror.org/0001h1y25","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210086857","https://openalex.org/I4210087105","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Christopher C. Holmes","raw_affiliation_strings":["1 Department of Statistics, University of Oxford, Oxford OX1 3TG, 2MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD and 3Department of Physiology, Development and Neuroscience, Cambridge CB2 3EG, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, University of Oxford, Oxford OX1 3TG, 2MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD and 3Department of Physiology, Development and Neuroscience, Cambridge CB2 3EG, UK","institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210086857"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100649922"],"corresponding_institution_ids":["https://openalex.org/I40120149","https://openalex.org/I4210086857"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":1.9449,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.86189463,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"29","issue":"6","first_page":"711","last_page":"716"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9613000154495239,"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":0.9613000154495239,"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":0.026499999687075615,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.0034000000450760126,"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/nucleosome","display_name":"Nucleosome","score":0.9528980255126953},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.6584447026252747},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6036130785942078},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5096912384033203},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.48936909437179565},{"id":"https://openalex.org/keywords/outlier","display_name":"Outlier","score":0.48661741614341736},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.447286993265152},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4102882742881775},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3666800856590271},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.3630722165107727},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3520934581756592},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.33414286375045776},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3315292298793793},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.27971261739730835},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2049523890018463},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20414552092552185},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.10664314031600952}],"concepts":[{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.9528980255126953},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6584447026252747},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6036130785942078},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5096912384033203},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.48936909437179565},{"id":"https://openalex.org/C79337645","wikidata":"https://www.wikidata.org/wiki/Q779824","display_name":"Outlier","level":2,"score":0.48661741614341736},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.447286993265152},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4102882742881775},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3666800856590271},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3630722165107727},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3520934581756592},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33414286375045776},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3315292298793793},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.27971261739730835},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2049523890018463},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20414552092552185},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.10664314031600952},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","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":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1093/bioinformatics/bts719","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts719","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/711/48898316/bioinformatics_29_6_711.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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:23297036","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23297036","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:2596307","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3597142","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.798.7306","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.798.7306","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/68/fa/bts719.PMC3597142.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.960.2867","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.960.2867","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2013/01/05/bioinformatics.bts719.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.975.136","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.975.136","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/29/6/711.full.pdf","raw_type":"text"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:174f41f6-dd10-4ce9-aa43-fc2ddaf063d8","is_oa":false,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:174f41f6-dd10-4ce9-aa43-fc2ddaf063d8","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PubMed (http://www.ncbi.nlm.nih.gov/pubmed/)","raw_type":"Journal article"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:ea7f1d02-4aab-4787-aa85-abe4c48cc254","is_oa":true,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:ea7f1d02-4aab-4787-aa85-abe4c48cc254","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"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":"","raw_type":"Journal article"},{"id":"pmh:uuid:ea7f1d02-4aab-4787-aa85-abe4c48cc254","is_oa":true,"landing_page_url":"http://bioinformatics.oxfordjournals.org","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"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":"","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts719","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts719","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/6/711/48898316/bioinformatics_29_6_711.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":[],"funders":[{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2111607063.pdf","grobid_xml":"https://content.openalex.org/works/W2111607063.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1507265336","https://openalex.org/W1969691479","https://openalex.org/W1997519837","https://openalex.org/W2008748285","https://openalex.org/W2014002637","https://openalex.org/W2014119967","https://openalex.org/W2029873987","https://openalex.org/W2045656233","https://openalex.org/W2049855310","https://openalex.org/W2054439707","https://openalex.org/W2060012727","https://openalex.org/W2061111901","https://openalex.org/W2069545688","https://openalex.org/W2072152932","https://openalex.org/W2073374533","https://openalex.org/W2080719230","https://openalex.org/W2081969394","https://openalex.org/W2093071349","https://openalex.org/W2095325933","https://openalex.org/W2106448802","https://openalex.org/W2112582023","https://openalex.org/W2114752404","https://openalex.org/W2114803986","https://openalex.org/W2115219137","https://openalex.org/W2117372146","https://openalex.org/W2131192238","https://openalex.org/W2134314200","https://openalex.org/W2136144150","https://openalex.org/W2144792857","https://openalex.org/W2147734340","https://openalex.org/W2154109129","https://openalex.org/W2154431984","https://openalex.org/W2167764944","https://openalex.org/W2171432823","https://openalex.org/W2171440644","https://openalex.org/W2171808845","https://openalex.org/W2290630051","https://openalex.org/W2503964180","https://openalex.org/W4232383088"],"related_works":["https://openalex.org/W1557094818","https://openalex.org/W2113512405","https://openalex.org/W3124098632","https://openalex.org/W1525192260","https://openalex.org/W3034809213","https://openalex.org/W2082123987","https://openalex.org/W1994506687","https://openalex.org/W2151373518","https://openalex.org/W2123553257","https://openalex.org/W2348141163"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"The":[2,175],"identification":[3,45],"of":[4,18,46,115,140,148,154,160,178],"nucleosomes":[5,48,95],"along":[6],"the":[7,16,43,57,85,113,141,152,158,170],"chromatin":[8],"is":[9],"key":[10],"to":[11,67,108],"understanding":[12],"their":[13],"role":[14],"in":[15,98,161],"regulation":[17],"gene":[19],"expression":[20],"and":[21,38,90,102,134,151,183],"other":[22,130,171],"DNA-related":[23],"processes.":[24],"However,":[25],"current":[26],"experimental":[27,91],"methods":[28,133],"(MNase-ChIP,":[29],"MNase-Seq)":[30],"sample":[31],"nucleosome":[32,69,131,142,145],"positions":[33],"from":[34,189],"a":[35,77,99,104,109],"cell":[36,100],"population":[37,101],"contain":[39],"biases,":[40],"making":[41],"thus":[42],"precise":[44],"individual":[47],"not":[49],"straightforward.":[50],"Recent":[51],"works":[52],"have":[53,64],"only":[54],"focused":[55],"on":[56],"first":[58],"point,":[59],"where":[60],"noise":[61],"reduction":[62],"approaches":[63],"been":[65],"developed":[66],"identify":[68],"positions.":[70],"Results:":[71],"In":[72],"this":[73],"article,":[74],"we":[75,118],"propose":[76],"new":[78],"approach,":[79],"termed":[80],"NucleoFinder,":[81,179],"that":[82,120],"addresses":[83],"both":[84],"positional":[86],"heterogeneity":[87],"across":[88],"cells":[89],"biases":[92],"by":[93],"seeking":[94],"consistently":[96],"positioned":[97],"showing":[103],"significant":[105],"enrichment":[106],"relative":[107],"control":[110],"sample.":[111],"Despite":[112],"absence":[114],"validated":[116],"dataset,":[117],"show":[119],"our":[121],"approach":[122],"(i)":[123],"detects":[124],"fewer":[125],"false":[126],"positives":[127],"than":[128,169],"two":[129,137,172],"calling":[132],"(ii)":[135],"identifies":[136],"important":[138],"features":[139],"organization":[143],"(the":[144],"spacing":[146],"downstream":[147],"active":[149],"promoters":[150],"enrichment/depletion":[153],"GC/AT":[155],"dinucleotides":[156],"at":[157,199],"centre":[159],"vitro":[162],"nucleosomes)":[163],"with":[164],"equal":[165],"or":[166],"greater":[167],"ability":[168],"methods.":[173],"Availability:":[174],"R":[176],"code":[177],"an":[180],"example":[181],"datafile":[182],"instructions":[184],"are":[185,197],"available":[186,198],"for":[187],"download":[188],"https://sites.google.com/site/beckerjeremie/":[190],"Contact:":[191],"cholmes@stats.ox.ac.uk":[192],"Supplementary":[193,195],"information:":[194],"data":[196],"Bioinformatics":[200],"online.":[201]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
