{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:22Z","timestamp":1772138062143,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2023,7,4]],"date-time":"2023-07-04T00:00:00Z","timestamp":1688428800000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Cancer Genetics and Epigenetics"},{"name":"Cancer Research Institute Irvington Postdoctoral Fellowship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) has emerged as a promising liquid biopsy technology to detect cancers and monitor treatments. While several bioinformatics tools for DNA methylation analysis have been adapted for cfMeDIP-seq data, an end-to-end pipeline and quality control framework specifically for this data type is still lacking. Here, we present the MEDIPIPE, which provides a one-stop solution for cfMeDIP-seq data quality control, methylation quantification, and sample aggregation. The major advantages of MEDIPIPE are: (i) ease of implementation and reproducibility with Snakemake containerized execution environments that will be automatically deployed via Conda; (ii) flexibility to handle different experimental settings with a single configuration file; and (iii) computationally efficiency for large-scale cfMeDIP-seq profiling data analysis and aggregation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>This pipeline is an open-source software under the MIT license and it is freely available at https:\/\/github.com\/pughlab\/MEDIPIPE.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad423","type":"journal-article","created":{"date-parts":[[2023,7,3]],"date-time":"2023-07-03T17:12:26Z","timestamp":1688404346000},"source":"Crossref","is-referenced-by-count":5,"title":["MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5719-1272","authenticated-orcid":false,"given":"Yong","family":"Zeng","sequence":"first","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network , Toronto, Ontario, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenbin","family":"Ye","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network , Toronto, Ontario, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric Y","family":"Stutheit-Zhao","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network , Toronto, Ontario, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming","family":"Han","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network , Toronto, Ontario, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Scott V","family":"Bratman","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network , Toronto, Ontario, Canada"},{"name":"Department of Medical Biophysics, University of Toronto , Toronto, Ontario, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8073-5888","authenticated-orcid":false,"given":"Trevor J","family":"Pugh","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer Centre, University Health Network , Toronto, Ontario, Canada"},{"name":"Department of Medical Biophysics, University of Toronto , Toronto, Ontario, Canada"},{"name":"Ontario Institute for Cancer Research , Toronto, Ontario, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Housheng Hansen","family":"He","sequence":"additional","affiliation":[{"name":"Princess Margaret Cancer 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