Zobrazeno 1 - 10
of 24
pro vyhledávání: '"Sean K. Maden"'
Autor:
Sean K. Maden, Sang Ho Kwon, Louise A. Huuki-Myers, Leonardo Collado-Torres, Stephanie C. Hicks, Kristen R. Maynard
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-26 (2023)
Abstract Deconvolution of cell mixtures in “bulk” transcriptomic samples from homogenate human tissue is important for understanding disease pathologies. However, several experimental and computational challenges impede transcriptomics-based deco
Externí odkaz:
https://doaj.org/article/934d17d7f4b148708efb8c0435e4ba59
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-22 (2022)
Abstract Background There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is comp
Externí odkaz:
https://doaj.org/article/ea62db3678a941dabe74f0c088a5f2e6
Autor:
William M. Grady, John M. Inadomi, Yanxin Luo, Andrew M. Kaz, Maria Westerhoff, Polly A. Newcomb, Cornelia M. Ulrich, Christopher I. Li, Paul D. Lampe, Wynn Burke, Kelly T. Carter, Ming Yu, Sean K. Maden, Kit Curtius, William D. Hazelton, Georg E. Luebeck
This file provides a list of drift-related CGI-gene pairs for which methylation is significantly correlated with gene expression (q-value ) in left colon (including rectum) and right colon.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3f5289f92cf5546594bcfb2716dc9f86
https://doi.org/10.1158/0008-5472.22422023.v1
https://doi.org/10.1158/0008-5472.22422023.v1
Autor:
William M. Grady, John M. Inadomi, Yanxin Luo, Andrew M. Kaz, Maria Westerhoff, Polly A. Newcomb, Cornelia M. Ulrich, Christopher I. Li, Paul D. Lampe, Wynn Burke, Kelly T. Carter, Ming Yu, Sean K. Maden, Kit Curtius, William D. Hazelton, Georg E. Luebeck
Many normal tissues undergo age-related drift in DNA methylation, providing a quantitative measure of tissue age. Here, we identify and validate 781 CpG islands (CGI) that undergo significant methylomic drift in 232 normal colorectal tissues and show
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::dfe81d072d3b4d98214b6bb6be3dc85d
https://doi.org/10.1158/0008-5472.c.6511112.v1
https://doi.org/10.1158/0008-5472.c.6511112.v1
Autor:
William M. Grady, John M. Inadomi, Yanxin Luo, Andrew M. Kaz, Maria Westerhoff, Polly A. Newcomb, Cornelia M. Ulrich, Christopher I. Li, Paul D. Lampe, Wynn Burke, Kelly T. Carter, Ming Yu, Sean K. Maden, Kit Curtius, William D. Hazelton, Georg E. Luebeck
Derivation of adenoma to carcinoma sojourn times, with table S1 showing estimated methylation drift rate parameters and table S2 showing estimated sojourn times for three tissue age models.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::387086829e2f16edc62f32ab39e210d5
https://doi.org/10.1158/0008-5472.22422017.v1
https://doi.org/10.1158/0008-5472.22422017.v1
Publikováno v:
Bioinformatics Advances. 3
SummaryThousands of DNA methylation (DNAm) array samples from human blood are publicly available on the Gene Expression Omnibus (GEO), but they remain underutilized for experiment planning, replication and cross-study and cross-platform analyses. To
Autor:
Sean K. Maden, Brian Walsh, Kyle Ellrott, Kasper D. Hansen, Reid F. Thompson, Abhinav Nellore
Thousands of DNA methylation (DNAm) array samples from human blood are publicly available on the Gene Expression Omnibus (GEO), but they remain underutilized for experiment planning, replication, and cross-study and cross-platform analyses. To facili
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::6c62601118a05388b63e74f2d5d68dc8
https://doi.org/10.1101/2022.05.19.492680
https://doi.org/10.1101/2022.05.19.492680
Publikováno v:
NAR Genomics and Bioinformatics
While DNA methylation (DNAm) is the most-studied epigenetic mark, few recent studies probe the breadth of publicly available DNAm array samples. We collectively analyzed 35 360 Illumina Infinium HumanMethylation450K DNAm array samples published on th
Autor:
Reid F. Thompson, Abhinav Nellore, Mary A. Wood, Benjamin R. Weeder, Julianne K. David, Austin Nguyen, Sean K. Maden
Genetic variability across the three major histocompatibility complex (MHC) class I genes (human leukocyte antigen [HLA] A, B, and C) may affect susceptibility to and severity of severe acute respiratory syndrome 2 (SARS-CoV-2), the virus responsible
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fec3538a20034a622a7b67b47dc1a42d
Publikováno v:
NAR Cancer
This study probes the distribution of putatively cancer-specific junctions across a broad set of publicly available non-cancer human RNA sequencing (RNA-seq) datasets. We compared cancer and non-cancer RNA-seq data from The Cancer Genome Atlas (TCGA)