{"id":"https://openalex.org/W2135667448","doi":"https://doi.org/10.1093/bioinformatics/btn096","title":"An analytical pipeline for genomic representations used for cytosine methylation studies","display_name":"An analytical pipeline for genomic representations used for cytosine methylation studies","publication_year":2008,"publication_date":"2008-03-18","ids":{"openalex":"https://openalex.org/W2135667448","doi":"https://doi.org/10.1093/bioinformatics/btn096","mag":"2135667448","pmid":"https://pubmed.ncbi.nlm.nih.gov/18353789"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn096","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn096","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/9/1161/49046847/bioinformatics_24_9_1161.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/9/1161/49046847/bioinformatics_24_9_1161.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088872826","display_name":"Reid F. Thompson","orcid":"https://orcid.org/0000-0003-3661-5296"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]},{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Reid F. Thompson","raw_affiliation_strings":["1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","institution_ids":["https://openalex.org/I129975664","https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112343439","display_name":"Mark Reimers","orcid":null},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]},{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Reimers","raw_affiliation_strings":["1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","institution_ids":["https://openalex.org/I129975664","https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042645070","display_name":"Batbayar Khulan","orcid":"https://orcid.org/0009-0008-0146-2334"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]},{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Batbayar Khulan","raw_affiliation_strings":["1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","institution_ids":["https://openalex.org/I129975664","https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002603079","display_name":"Mathieu Gissot","orcid":"https://orcid.org/0000-0003-0047-8189"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]},{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mathieu Gissot","raw_affiliation_strings":["1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","institution_ids":["https://openalex.org/I129975664","https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071945201","display_name":"Todd Richmond","orcid":"https://orcid.org/0000-0003-1508-6540"},"institutions":[{"id":"https://openalex.org/I118019719","display_name":"Roche (Switzerland)","ror":"https://ror.org/00by1q217","country_code":"CH","type":"company","lineage":["https://openalex.org/I118019719"]},{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]},{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["CH","US"],"is_corresponding":false,"raw_author_name":"Todd A. Richmond","raw_affiliation_strings":["1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","F.Hoffmann-La Roche AG"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","institution_ids":["https://openalex.org/I129975664","https://openalex.org/I184840846"]},{"raw_affiliation_string":"F.Hoffmann-La Roche AG","institution_ids":["https://openalex.org/I118019719"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044371076","display_name":"Quan Chen","orcid":"https://orcid.org/0000-0002-2098-3644"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]},{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Quan Chen","raw_affiliation_strings":["1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","institution_ids":["https://openalex.org/I129975664","https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103262005","display_name":"Xin Zheng","orcid":"https://orcid.org/0000-0002-6603-6511"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]},{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xin Zheng","raw_affiliation_strings":["1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","institution_ids":["https://openalex.org/I129975664","https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042341113","display_name":"Kami Kim","orcid":"https://orcid.org/0000-0003-3384-152X"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]},{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kami Kim","raw_affiliation_strings":["1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","institution_ids":["https://openalex.org/I129975664","https://openalex.org/I184840846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048839844","display_name":"John M. Greally","orcid":"https://orcid.org/0000-0001-6069-7960"},"institutions":[{"id":"https://openalex.org/I129975664","display_name":"Albert Einstein College of Medicine","ror":"https://ror.org/05cf8a891","country_code":"US","type":"education","lineage":["https://openalex.org/I129975664","https://openalex.org/I4210112371"]},{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John M. Greally","raw_affiliation_strings":["1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 2Department of Biostatistics, Virginia Commonwealth University, 730 East Broad Street, Richmond, VA 23298, 3Department of Medicine (Infectious Diseases), 4Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, 5Roche NimbleGen, 1 Science Court, Madison, WI 53711, 6Department of Pathology, 7Bioinformatics Shared Resource and 8Department of Medicine (Hematology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA","institution_ids":["https://openalex.org/I129975664","https://openalex.org/I184840846"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5048839844"],"corresponding_institution_ids":["https://openalex.org/I129975664","https://openalex.org/I184840846"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.6505,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.93577379,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"24","issue":"9","first_page":"1161","last_page":"1167"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9994000196456909,"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":0.9994000196456909,"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/T11482","display_name":"RNA modifications and cancer","score":0.9965000152587891,"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":0.9937999844551086,"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/pipeline","display_name":"Pipeline (software)","score":0.7690919637680054},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.5781795382499695},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5633535385131836},{"id":"https://openalex.org/keywords/cytosine","display_name":"Cytosine","score":0.5612545013427734},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5459470152854919},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.4210672974586487},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.33372920751571655},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2904823422431946},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19840902090072632},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.1934528350830078},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12761130928993225}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7690919637680054},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.5781795382499695},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5633535385131836},{"id":"https://openalex.org/C2776023528","wikidata":"https://www.wikidata.org/wiki/Q178425","display_name":"Cytosine","level":3,"score":0.5612545013427734},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5459470152854919},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.4210672974586487},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.33372920751571655},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2904823422431946},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19840902090072632},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.1934528350830078},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12761130928993225},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003596","descriptor_name":"Cytosine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003596","descriptor_name":"Cytosine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003596","descriptor_name":"Cytosine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012680","descriptor_name":"Sensitivity and Specificity","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016133","descriptor_name":"Polymerase Chain Reaction","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016477","descriptor_name":"Artifacts","qualifier_ui":null,"qualifier_name":null,"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":"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":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btn096","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn096","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/9/1161/49046847/bioinformatics_24_9_1161.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18353789","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18353789","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:europepmc.org:4015637","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5061929","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn096","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn096","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/9/1161/49046847/bioinformatics_24_9_1161.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1457338957","display_name":null,"funder_award_id":"GM007288","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1627718391","display_name":null,"funder_award_id":"GM007288","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2159425879","display_name":null,"funder_award_id":"T32 GM007288","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2203194010","display_name":null,"funder_award_id":"R01 HD044078","funder_id":"https://openalex.org/F4320337611","funder_display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development"},{"id":"https://openalex.org/G4070743384","display_name":null,"funder_award_id":"P30 AI051519","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5480814337","display_name":null,"funder_award_id":"HSN26620-0400054C","funder_id":"https://openalex.org/F4320332505","funder_display_name":"U.S. Public Health Service"},{"id":"https://openalex.org/G5797121030","display_name":null,"funder_award_id":"5 P30 AI051519","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5812665451","display_name":null,"funder_award_id":"R01 AI060496","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6922303065","display_name":null,"funder_award_id":"P30 AI051519","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G7034112821","display_name":null,"funder_award_id":"AI051519","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7757698000","display_name":null,"funder_award_id":"AI051519","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320309687","display_name":"Albert Einstein Cancer Center","ror":"https://ror.org/045x93337"},{"id":"https://openalex.org/F4320314924","display_name":"Philippe Foundation","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332505","display_name":"U.S. Public Health Service","ror":"https://ror.org/05xf94514"},{"id":"https://openalex.org/F4320332522","display_name":"Albert Einstein College of Medicine, Yeshiva University","ror":"https://ror.org/045x93337"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337611","display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135667448.pdf","grobid_xml":"https://content.openalex.org/works/W2135667448.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1521702495","https://openalex.org/W1669374546","https://openalex.org/W1970761420","https://openalex.org/W1975812358","https://openalex.org/W1978146096","https://openalex.org/W2001278481","https://openalex.org/W2003672519","https://openalex.org/W2005453259","https://openalex.org/W2007886820","https://openalex.org/W2018888124","https://openalex.org/W2020844796","https://openalex.org/W2033157818","https://openalex.org/W2054074282","https://openalex.org/W2071709406","https://openalex.org/W2084118479","https://openalex.org/W2097199830","https://openalex.org/W2098362718","https://openalex.org/W2100668965","https://openalex.org/W2101833157","https://openalex.org/W2112448007","https://openalex.org/W2113054367","https://openalex.org/W2115521447","https://openalex.org/W2125882871","https://openalex.org/W2128016314","https://openalex.org/W2128514316","https://openalex.org/W2135995702","https://openalex.org/W2141410747","https://openalex.org/W2151595196","https://openalex.org/W2155789812","https://openalex.org/W2156465688","https://openalex.org/W2162578061","https://openalex.org/W2170989872","https://openalex.org/W2582743722"],"related_works":["https://openalex.org/W3169949620","https://openalex.org/W2902329290","https://openalex.org/W2052355316","https://openalex.org/W2046964473","https://openalex.org/W2107880877","https://openalex.org/W2151182744","https://openalex.org/W2024490794","https://openalex.org/W2221018455","https://openalex.org/W2054863651","https://openalex.org/W1998349112"],"abstract_inverted_index":{"MOTIVATION:":[0],"Representations":[1],"of":[2,11,14,28,61,90,104,117,127,130],"the":[3,9,23,32,88,91,98,102,105,115,128,131],"genome":[4],"can":[5,134],"be":[6,136],"generated":[7],"by":[8,49,55],"selection":[10],"a":[12,26,56,109],"subpopulation":[13],"restriction":[15,106],"fragments":[16],"using":[17],"ligation-mediated":[18],"PCR.":[19],"Such":[20],"representations":[21],"form":[22],"basis":[24],"for":[25],"number":[27],"high-throughput":[29],"assays,":[30],"including":[31],"HELP":[33,42],"assay":[34],"to":[35,138],"study":[36],"cytosine":[37,62],"methylation.":[38,63],"We":[39],"find":[40],"that":[41,76,113],"data":[43,81,139],"analysis":[44],"is":[45,101],"complicated":[46],"not":[47],"only":[48],"PCR":[50,99],"amplification":[51,100],"heterogeneity":[52],"but":[53],"also":[54,135],"complex":[57],"and":[58,72,82],"variable":[59],"distribution":[60],"To":[64],"address":[65],"this,":[66],"we":[67,124],"created":[68],"an":[69],"analytical":[70,92],"pipeline":[71],"novel":[73],"normalization":[74,111],"approach":[75,112],"improves":[77],"concordance":[78],"between":[79],"microarray-derived":[80],"single":[83],"locus":[84],"validation":[85],"results,":[86],"demonstrating":[87],"value":[89],"approach.":[93],"A":[94],"major":[95],"influence":[96,116],"on":[97,120,145],"size":[103],"fragment,":[107],"requiring":[108],"quantile":[110],"reduces":[114],"fragment":[118],"length":[119],"signal":[121],"intensity.":[122],"Here":[123],"describe":[125],"all":[126],"components":[129],"pipeline,":[132],"which":[133],"applied":[137],"derived":[140],"from":[141],"other":[142],"assays":[143],"based":[144],"genomic":[146],"representations.":[147]},"counts_by_year":[{"year":2023,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":7}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}