Reference-free deconvolution of DNA methylation data and mediation by cell composition effects

被引:0
|
作者
E. Andres Houseman
Molly L. Kile
David C. Christiani
Tan A. Ince
Karl T. Kelsey
Carmen J. Marsit
机构
[1] Oregon State University,School of Biological and Population Health Sciences, College of Public Health and Human Sciences
[2] Harvard T. H. Chan School of Public Health,Department of Environmental Health
[3] University of Miami,Department of Pathology
[4] Miller School of Medicine,Department of Epidemiology, Department of Pathology and Laboratory Medicine
[5] Brown University,Department of Community and Family Medicine
[6] Dartmouth Medical School,undefined
来源
关键词
Deconvolution; DNA methylation; Epigenetics; Non-negative matrix factorization;
D O I
暂无
中图分类号
学科分类号
摘要
引用
收藏
相关论文
共 50 条
  • [31] Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective
    E Andres Houseman
    Karl T Kelsey
    John K Wiencke
    Carmen J Marsit
    [J]. BMC Bioinformatics, 16
  • [32] Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective
    Houseman, E. Andres
    Kelsey, Karl T.
    Wiencke, John K.
    Marsit, Carmen J.
    [J]. BMC BIOINFORMATICS, 2015, 16
  • [33] Reference-free inference of tumor phylogenies from single-cell sequencing data
    Subramanian, Ayshwarya
    Schwartz, Russell
    [J]. BMC GENOMICS, 2015, 16
  • [34] Reference-free Inference of Tumor Phylogenies from Single-Cell Sequencing Data
    Subramanian, Ayshwarya
    Schwartz, Russell
    [J]. 2014 IEEE 4TH INTERNATIONAL CONFERENCE ON COMPUTATIONAL ADVANCES IN BIO AND MEDICAL SCIENCES (ICCABS), 2014,
  • [35] Reference Materials for the Analysis of Methylation in Circulating Cell-Free DNA
    Ramprakash, J.
    Butler, M.
    Xia, D.
    Konigshofer, Y.
    Garlick, R.
    [J]. JOURNAL OF MOLECULAR DIAGNOSTICS, 2022, 24 (10): : S137 - S137
  • [36] PRISM: methylation pattern-based, reference-free inference of subclonal makeup
    Lee, Dohoon
    Lee, Sangseon
    Kim, Sun
    [J]. BIOINFORMATICS, 2019, 35 (14) : I520 - I529
  • [37] Reference materials for analysis of DNA methylation in cell-free circulating tumor DNA
    Higgs, Alysha
    Ryan, Angelique
    Ramprakash, Jayanthi
    Lowe, Dana Ruminski
    Konigshofer, Yves
    Huang, Catherine
    Anfora, Andrew
    Garlick, Russell
    Anekella, Bharathi
    [J]. CANCER RESEARCH, 2024, 84 (06)
  • [38] Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data
    Gervin, Kristina
    Salas, Lucas A.
    Bakulski, Kelly M.
    van Zelm, Menno C.
    Koestler, Devin C.
    Wiencke, John K.
    Duijts, Liesbeth
    Moll, Henriette A.
    Kelsey, Karl T.
    Kobor, Michael S.
    Lyle, Robert
    Christensen, Brock C.
    Felix, Janine F.
    Jones, Meaghan J.
    [J]. CLINICAL EPIGENETICS, 2019, 11 (01)
  • [39] Systematic evaluation and validation of reference and library selection methods for deconvolution of cord blood DNA methylation data
    Kristina Gervin
    Lucas A. Salas
    Kelly M. Bakulski
    Menno C. van Zelm
    Devin C. Koestler
    John K. Wiencke
    Liesbeth Duijts
    Henriëtte A. Moll
    Karl T. Kelsey
    Michael S. Kobor
    Robert Lyle
    Brock C. Christensen
    Janine F. Felix
    Meaghan J. Jones
    [J]. Clinical Epigenetics, 2019, 11
  • [40] Computational deconvolution of DNA methylation data from mixed DNA samples
    dos Santos, Maisa R. Ferro
    Giuili, Edoardo
    De Koker, Andries
    Everaert, Celine
    De Preter, Katleen
    [J]. BRIEFINGS IN BIOINFORMATICS, 2024, 25 (03)