{"id":"https://openalex.org/W2549664084","doi":"https://doi.org/10.1186/s12859-016-1380-3","title":"ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons","display_name":"ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons","publication_year":2016,"publication_date":"2016-11-25","ids":{"openalex":"https://openalex.org/W2549664084","doi":"https://doi.org/10.1186/s12859-016-1380-3","mag":"2549664084","pmid":"https://pubmed.ncbi.nlm.nih.gov/27884103"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-016-1380-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1380-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1380-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1380-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Giovanni Scala","orcid":"https://orcid.org/0000-0002-9619-9426"},"institutions":[{"id":"https://openalex.org/I160013858","display_name":"Istituto Nazionale di Fisica Nucleare","ror":"https://ror.org/005ta0471","country_code":"IT","type":"government","lineage":["https://openalex.org/I160013858"]},{"id":"https://openalex.org/I4210108560","display_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Napoli","ror":"https://ror.org/015kcdd40","country_code":"IT","type":"facility","lineage":["https://openalex.org/I160013858","https://openalex.org/I4210108560"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Giovanni Scala","raw_affiliation_strings":["Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Naples, Italy. gscala@na.infn.it","Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Naples, Italy"],"raw_orcid":"https://orcid.org/0000-0002-9619-9426","affiliations":[{"raw_affiliation_string":"Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Naples, Italy. gscala@na.infn.it","institution_ids":["https://openalex.org/I4210108560","https://openalex.org/I160013858"]},{"raw_affiliation_string":"Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Naples, Italy","institution_ids":["https://openalex.org/I4210108560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075839797","display_name":"Ornella Affinito","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139435","display_name":"Institute for Experimental Endocrinology and Oncology","ror":"https://ror.org/04sn06036","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210139435","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Ornella Affinito","raw_affiliation_strings":["Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli \"Federico II\", Naples, Italy","Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) \"Gaetano Salvatore\", Consiglio Nazionale delle Ricerche CNR, Naples, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli \"Federico II\", Naples, Italy","institution_ids":["https://openalex.org/I71267560"]},{"raw_affiliation_string":"Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) \"Gaetano Salvatore\", Consiglio Nazionale delle Ricerche CNR, Naples, Italy","institution_ids":["https://openalex.org/I4210139435"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018679325","display_name":"Domenico Palumbo","orcid":"https://orcid.org/0000-0001-5878-9428"},"institutions":[{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Domenico Palumbo","raw_affiliation_strings":["Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli \"Federico II\", Naples, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli \"Federico II\", Naples, Italy","institution_ids":["https://openalex.org/I71267560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026901199","display_name":"Ermanno Florio","orcid":"https://orcid.org/0000-0001-6961-0059"},"institutions":[{"id":"https://openalex.org/I4210139435","display_name":"Institute for Experimental Endocrinology and Oncology","ror":"https://ror.org/04sn06036","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210139435","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Ermanno Florio","raw_affiliation_strings":["Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli \"Federico II\", Naples, Italy","Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) \"Gaetano Salvatore\", Consiglio Nazionale delle Ricerche CNR, Naples, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli \"Federico II\", Naples, Italy","institution_ids":["https://openalex.org/I71267560"]},{"raw_affiliation_string":"Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) \"Gaetano Salvatore\", Consiglio Nazionale delle Ricerche CNR, Naples, Italy","institution_ids":["https://openalex.org/I4210139435"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088832095","display_name":"Antonella Monticelli","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139435","display_name":"Institute for Experimental Endocrinology and Oncology","ror":"https://ror.org/04sn06036","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210139435","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Antonella Monticelli","raw_affiliation_strings":["Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) \"Gaetano Salvatore\", Consiglio Nazionale delle Ricerche CNR, Naples, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) \"Gaetano Salvatore\", Consiglio Nazionale delle Ricerche CNR, Naples, Italy","institution_ids":["https://openalex.org/I4210139435"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043315785","display_name":"Gennaro Miele","orcid":"https://orcid.org/0000-0002-2028-0578"},"institutions":[{"id":"https://openalex.org/I4210108560","display_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Napoli","ror":"https://ror.org/015kcdd40","country_code":"IT","type":"facility","lineage":["https://openalex.org/I160013858","https://openalex.org/I4210108560"]},{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gennaro Miele","raw_affiliation_strings":["Dipartimento di Fisica, Universit\u00e0 degli Studi di Napoli \"Federico II\", Naples, Italy","Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Naples, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Fisica, Universit\u00e0 degli Studi di Napoli \"Federico II\", Naples, Italy","institution_ids":["https://openalex.org/I71267560"]},{"raw_affiliation_string":"Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Naples, Italy","institution_ids":["https://openalex.org/I4210108560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089906264","display_name":"Lorenzo Chiariotti","orcid":"https://orcid.org/0000-0001-6097-4171"},"institutions":[{"id":"https://openalex.org/I4210139435","display_name":"Institute for Experimental Endocrinology and Oncology","ror":"https://ror.org/04sn06036","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210139435","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Lorenzo Chiariotti","raw_affiliation_strings":["Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli \"Federico II\", Naples, Italy","Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) \"Gaetano Salvatore\", Consiglio Nazionale delle Ricerche CNR, Naples, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli \"Federico II\", Naples, Italy","institution_ids":["https://openalex.org/I71267560"]},{"raw_affiliation_string":"Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) \"Gaetano Salvatore\", Consiglio Nazionale delle Ricerche CNR, Naples, Italy","institution_ids":["https://openalex.org/I4210139435"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074861019","display_name":"Sergio Cocozza","orcid":"https://orcid.org/0000-0002-5009-8558"},"institutions":[{"id":"https://openalex.org/I4210139435","display_name":"Institute for Experimental Endocrinology and Oncology","ror":"https://ror.org/04sn06036","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210139435","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I71267560","display_name":"University of Naples Federico II","ror":"https://ror.org/05290cv24","country_code":"IT","type":"education","lineage":["https://openalex.org/I71267560"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Sergio Cocozza","raw_affiliation_strings":["Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli \"Federico II\", Naples, Italy","Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) \"Gaetano Salvatore\", Consiglio Nazionale delle Ricerche CNR, Naples, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Universit\u00e0 degli Studi di Napoli \"Federico II\", Naples, Italy","institution_ids":["https://openalex.org/I71267560"]},{"raw_affiliation_string":"Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) \"Gaetano Salvatore\", Consiglio Nazionale delle Ricerche CNR, Naples, Italy","institution_ids":["https://openalex.org/I4210139435"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I160013858","https://openalex.org/I4210108560"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.0447,"has_fulltext":true,"cited_by_count":29,"citation_normalized_percentile":{"value":0.79214258,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"17","issue":"1","first_page":"484","last_page":"484"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9526000022888184,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9526000022888184,"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":0.021400000900030136,"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/T13157","display_name":"Cancer-related gene regulation","score":0.011699999682605267,"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/bisulfite","display_name":"Bisulfite","score":0.6788527965545654},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6783148646354675},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.6696851253509521},{"id":"https://openalex.org/keywords/amplicon","display_name":"Amplicon","score":0.6628578305244446},{"id":"https://openalex.org/keywords/bisulfite-sequencing","display_name":"Bisulfite sequencing","score":0.6529788970947266},{"id":"https://openalex.org/keywords/cpg-site","display_name":"CpG site","score":0.5269200205802917},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5129920840263367},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.4919440448284149},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.48900043964385986},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46956634521484375},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.3544771671295166},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3159179091453552},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17243868112564087},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16651055216789246},{"id":"https://openalex.org/keywords/polymerase-chain-reaction","display_name":"Polymerase chain reaction","score":0.11122658848762512}],"concepts":[{"id":"https://openalex.org/C2775959680","wikidata":"https://www.wikidata.org/wiki/Q2718222","display_name":"Bisulfite","level":5,"score":0.6788527965545654},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6783148646354675},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.6696851253509521},{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.6628578305244446},{"id":"https://openalex.org/C189235521","wikidata":"https://www.wikidata.org/wiki/Q4087270","display_name":"Bisulfite sequencing","level":5,"score":0.6529788970947266},{"id":"https://openalex.org/C140173407","wikidata":"https://www.wikidata.org/wiki/Q1138358","display_name":"CpG site","level":5,"score":0.5269200205802917},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5129920840263367},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.4919440448284149},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.48900043964385986},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46956634521484375},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3544771671295166},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3159179091453552},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17243868112564087},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16651055216789246},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.11122658848762512},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D013447","descriptor_name":"Sulfites","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013447","descriptor_name":"Sulfites","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013447","descriptor_name":"Sulfites","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D041981","descriptor_name":"Gastrointestinal Tract","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D050804","descriptor_name":"D-Aspartate Oxidase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050804","descriptor_name":"D-Aspartate Oxidase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050804","descriptor_name":"D-Aspartate Oxidase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"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:10.1186/s12859-016-1380-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1380-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1380-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27884103","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27884103","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5123276","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5123276","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-016-1380-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-016-1380-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1380-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2549664084.pdf","grobid_xml":"https://content.openalex.org/works/W2549664084.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1496933752","https://openalex.org/W1972944037","https://openalex.org/W1992917107","https://openalex.org/W2026844663","https://openalex.org/W2046646392","https://openalex.org/W2072970694","https://openalex.org/W2093144236","https://openalex.org/W2117038014","https://openalex.org/W2121180999","https://openalex.org/W2128711701","https://openalex.org/W2130731460","https://openalex.org/W2142678478","https://openalex.org/W2167200938","https://openalex.org/W2279206987"],"related_works":["https://openalex.org/W2805216920","https://openalex.org/W2619376220","https://openalex.org/W2064302386","https://openalex.org/W2134949149","https://openalex.org/W2035236309","https://openalex.org/W2895945844","https://openalex.org/W2033196363","https://openalex.org/W1964177829","https://openalex.org/W2075918583","https://openalex.org/W2615278652"],"abstract_inverted_index":{"BACKGROUND:":[0],"CpG":[1,106],"sites":[2],"in":[3,9,176],"an":[4,34,153],"individual":[5,18],"molecule":[6,76,112],"may":[7],"exist":[8],"a":[10,22,28,128,181],"binary":[11],"state":[12],"(methylated":[13],"or":[14],"unmethylated)":[15],"and":[16,90,114,134,155,161,179,186,196,205],"each":[17],"DNA":[19,42,147],"molecule,":[20],"containing":[21],"certain":[23],"number":[24],"of":[25,30,52,67,138,145,166,184],"CpGs,":[26],"is":[27,174,202],"combination":[29],"these":[31],"states":[32],"defining":[33],"epihaplotype.":[35],"Classic":[36],"quantification":[37],"based":[38,58],"approaches":[39],"to":[40,47,70,159],"study":[41],"methylation":[43,55,65,98,107],"are":[44],"intrinsically":[45],"unable":[46],"fully":[48],"represent":[49],"the":[50,53,61,74,110,132,163],"complexity":[51],"underlying":[54],"substrate.":[56],"Epihaplotype":[57],"approaches,":[59],"on":[60,194],"other":[62],"hand,":[63],"allow":[64],"profiles":[66,108],"cell":[68],"populations":[69],"be":[71,85,192],"studied":[72],"at":[73,109,208],"single":[75,111],"level.":[77],"For":[78],"such":[79],"investigations,":[80],"next-generation":[81],"sequencing":[82,144,171],"techniques":[83],"can":[84,191],"used,":[86],"both":[87],"for":[88,91,97,120,131],"quantitative":[89],"epihaplotype":[92,136,164],"analysis.":[93],"Currently":[94],"available":[95,207],"tools":[96,119],"analysis":[99,137],"lack":[100],"output":[101],"formats":[102],"that":[103,115],"explicitly":[104],"report":[105],"level":[113],"have":[116],"suited":[117],"statistical":[118,135],"their":[121],"interpretation.":[122],"RESULTS:":[123],"Here":[124],"we":[125],"present":[126],"ampliMethProfiler,":[127],"python-based":[129],"pipeline":[130],"extraction":[133],"amplicons":[139],"from":[140,168],"targeted":[141,169],"deep":[142],"bisulfite":[143,170],"multiple":[146],"regions.":[148],"CONCLUSIONS:":[149],"ampliMethProfiler":[150,173],"tool":[151],"provides":[152],"easy":[154],"user":[156],"friendly":[157],"way":[158],"extract":[160],"analyze":[162],"composition":[165],"reads":[167],"experiments.":[172],"written":[175],"python":[177],"language":[178],"requires":[180],"local":[182],"installation":[183],"BLAST":[185],"(optionally)":[187],"QIIME":[188],"tools.":[189],"It":[190],"run":[193],"Linux":[195],"OS":[197],"X":[198],"platforms.":[199],"The":[200],"software":[201],"open":[203],"source":[204],"freely":[206],"http://amplimethprofiler.sourceforge.net":[209],".":[210]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
