Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites

[1]  R. Pidsley,et al.  Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels , 2020, Clinical Epigenetics.

[2]  R. Pidsley,et al.  Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels , 2020, Clinical Epigenetics.

[3]  M. Nikolic,et al.  New targeted approaches for epigenetic age predictions , 2019, bioRxiv.

[4]  H. Shin,et al.  Global DNA Methylation Pattern of Fibroblasts in Idiopathic Pulmonary Fibrosis. , 2019, DNA and cell biology.

[5]  N. Erez,et al.  The Dark Side of Fibroblasts: Cancer-Associated Fibroblasts as Mediators of Immunosuppression in the Tumor Microenvironment , 2019, Front. Immunol..

[6]  L. Butler,et al.  Cancer-associated fibroblasts—heroes or villains? , 2019, British Journal of Cancer.

[7]  Taiping Chen,et al.  DNA Methylation Reprogramming during Mammalian Development , 2019, Genes.

[8]  S. Holdenrieder,et al.  The emerging role of cell-free DNA as a molecular marker for cancer management , 2019, Biomolecular detection and quantification.

[9]  W. Wagner,et al.  Senescence-Associated Metabolomic Phenotype in Primary and iPSC-Derived Mesenchymal Stromal Cells , 2019, bioRxiv.

[10]  K. Mengersen,et al.  Critical evaluation of linear regression models for cell-subtype specific methylation signal from mixed blood cell DNA , 2018, PloS one.

[11]  Endre Kiss,et al.  Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease , 2018, Nature Communications.

[12]  Shijie C. Zheng,et al.  Identification of differentially methylated cell-types in Epigenome-Wide Association Studies , 2018, Nature Methods.

[13]  M. Schimek,et al.  Human fetoplacental arterial and venous endothelial cells are differentially programmed by gestational diabetes mellitus, resulting in cell-specific barrier function changes , 2018, Diabetologia.

[14]  R. Conroy,et al.  Toward mapping the human body at a cellular resolution , 2018, Molecular biology of the cell.

[15]  P. Laird,et al.  SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions , 2018, Nucleic acids research.

[16]  Nancy R. Zhang,et al.  Bulk tissue cell type deconvolution with multi-subject single-cell expression reference , 2018, Nature Communications.

[17]  Suresh Kannan,et al.  Fibroblasts and mesenchymal stem cells: Two sides of the same coin? , 2018, Journal of cellular physiology.

[18]  Hannes P. Eggertsson,et al.  DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis , 2018, Nature Communications.

[19]  Francisco Avila Cobos,et al.  Computational deconvolution of transcriptomics data from mixed cell populations , 2018, Bioinform..

[20]  T. Salo,et al.  Prognostic value of the immunohistochemical detection of cancer‐associated fibroblasts in oral cancer: A systematic review and meta‐analysis , 2018, Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology.

[21]  Timothy J. Peters,et al.  Enduring epigenetic landmarks define the cancer microenvironment , 2018, Genome research.

[22]  M. Kobor,et al.  Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD , 2018, Clinical Epigenetics.

[23]  J. Panse,et al.  Leukocyte Counts Based on DNA Methylation at Individual Cytosines. , 2018, Clinical chemistry.

[24]  Alexander M. Morin,et al.  DNA methylation as a predictor of fetal alcohol spectrum disorder , 2018, Clinical Epigenetics.

[25]  F. Watt,et al.  Fibroblast heterogeneity: implications for human disease , 2018, The Journal of clinical investigation.

[26]  Parantu K. Shah,et al.  TRIM28 and Interacting KRAB-ZNFs Control Self-Renewal of Human Pluripotent Stem Cells through Epigenetic Repression of Pro-differentiation Genes , 2017, Stem cell reports.

[27]  Andrew P. Stubbs,et al.  Early- and late-onset preeclampsia and the tissue-specific epigenome of the placenta and newborn. , 2017, Placenta.

[28]  Mihaela M. Martis,et al.  Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects , 2017, Scientific Reports.

[29]  L. Servais,et al.  Methylome and transcriptome profiling in Myasthenia Gravis monozygotic twins. , 2017, Journal of autoimmunity.

[30]  B. Christensen,et al.  Cell-type deconvolution from DNA methylation: a review of recent applications , 2017, Human molecular genetics.

[31]  P. Hoffmann,et al.  Human Platelet Lysate versus Fetal Calf Serum: These Supplements Do Not Select for Different Mesenchymal Stromal Cells , 2017, Scientific Reports.

[32]  W. Seeger,et al.  Epigenetic silencing of downstream genes mediated by tandem orientation in lung cancer , 2017, Scientific Reports.

[33]  V. Jin,et al.  Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns , 2017, Scientific Reports.

[34]  D. Absher,et al.  Epigenome-wide association study of rheumatoid arthritis identifies differentially methylated loci in B cells , 2017, Human molecular genetics.

[35]  S. Horvath,et al.  DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epigenetic Age , 2017, Genes.

[36]  Fabian J Theis,et al.  The Human Cell Atlas , 2017, bioRxiv.

[37]  S. Rose-John,et al.  Modelling IRF8 Deficient Human Hematopoiesis and Dendritic Cell Development with Engineered iPS Cells , 2017, Stem cells.

[38]  Andrew E. Teschendorff,et al.  A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies , 2017, BMC Bioinformatics.

[39]  F. Sato,et al.  Circulating cell-free DNA-based epigenetic assay can detect early breast cancer , 2016, Breast Cancer Research.

[40]  Yoav Gilad,et al.  DNA methylation in lung cells is associated with asthma endotypes and genetic risk. , 2016, JCI insight.

[41]  V. Beneš,et al.  Senescence‐associated DNA methylation is stochastically acquired in subpopulations of mesenchymal stem cells , 2016, Aging cell.

[42]  Timothy J. Peters,et al.  Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling , 2016, Genome Biology.

[43]  Zhi-Qiang Zhu,et al.  Stromal Myofibroblasts Are Associated with Poor Prognosis in Solid Cancers: A Meta-Analysis of Published Studies , 2016, PloS one.

[44]  Jean-Philippe Fortin,et al.  Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi , 2016, bioRxiv.

[45]  Kimberly Walter,et al.  Quantitative comparison of DNA methylation assays for biomarker development and clinical applications , 2016, Nature Biotechnology.

[46]  B. Tycko,et al.  Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation. , 2016, American journal of human genetics.

[47]  M. Ringnér,et al.  An integrated genomics analysis of epigenetic subtypes in human breast tumors links DNA methylation patterns to chromatin states in normal mammary cells , 2016, Breast Cancer Research.

[48]  M. Zenke,et al.  Epigenetic Classification of Human Mesenchymal Stromal Cells , 2016, Stem cell reports.

[49]  A. Metspalu,et al.  Epigenetic profiling in CD4+ and CD8+ T cells from Graves' disease patients reveals changes in genes associated with T cell receptor signaling. , 2016, Journal of autoimmunity.

[50]  S. Beck,et al.  Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells , 2016, Nature Communications.

[51]  J. Pritchard,et al.  Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs , 2016, PLoS genetics.

[52]  Gianluca Bontempi,et al.  TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data , 2015, Nucleic acids research.

[53]  Takaya Nagasaki,et al.  Cancer-Associated Fibroblasts: Their Characteristics and Their Roles in Tumor Growth , 2015, Cancers.

[54]  J. Wegiel,et al.  Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models , 2015, Genome Biology.

[55]  A. Bigot,et al.  Age-Associated Methylation Suppresses SPRY1, Leading to a Failure of Re-quiescence and Loss of the Reserve Stem Cell Pool in Elderly Muscle. , 2015, Cell reports.

[56]  A. Consiglio,et al.  Aberrant epigenome in iPSC‐derived dopaminergic neurons from Parkinson's disease patients , 2015, EMBO molecular medicine.

[57]  Andrew P. Feinberg,et al.  An LSC epigenetic signature is largely mutation independent and implicates the HOXA cluster in AML pathogenesis , 2015, Nature Communications.

[58]  J. Alcaraz,et al.  Aberrant DNA methylation in non-small cell lung cancer-associated fibroblasts , 2015, Carcinogenesis.

[59]  A. Moser,et al.  Induced pluripotent stem cell models of Zellweger spectrum disorder show impaired peroxisome assembly and cell type-specific lipid abnormalities , 2015, Stem Cell Research & Therapy.

[60]  J. Kleinman,et al.  Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age , 2015, bioRxiv.

[61]  Ariel Miller,et al.  Integrative analysis of methylome and transcriptome in human blood identifies extensive sex- and immune cell-specific differentially methylated regions , 2015, Epigenetics.

[62]  Andres Metspalu,et al.  Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes , 2015, Scientific Reports.

[63]  M. Wielscher,et al.  Diagnostic Performance of Plasma DNA Methylation Profiles in Lung Cancer, Pulmonary Fibrosis and COPD , 2015, EBioMedicine.

[64]  C. Ling,et al.  The fat cell epigenetic signature in post-obese women is characterized by global hypomethylation and differential DNA methylation of adipogenesis genes , 2015, International Journal of Obesity.

[65]  I. Weissman,et al.  Epigenetic and in vivo comparison of diverse MSC sources reveals an endochondral signature for human hematopoietic niche formation. , 2015, Blood.

[66]  Gustavo F. Bayón,et al.  H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells , 2015, Genome research.

[67]  Rochelle L. Tiedemann,et al.  Epigenetic signatures of alcohol abuse and hepatitis infection during human hepatocarcinogenesis , 2014, Oncotarget.

[68]  M. Weirauch,et al.  DNA methylation dynamics during ex vivo differentiation and maturation of human dendritic cells , 2014, Epigenetics & Chromatin.

[69]  Mathieu Blanchette,et al.  The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts , 2014, Genome Biology.

[70]  E. Andres Houseman,et al.  Reference-free cell mixture adjustments in analysis of DNA methylation data , 2014, Bioinform..

[71]  Michael A. Langston,et al.  DNA Methylation Changes Separate Allergic Patients from Healthy Controls and May Reflect Altered CD4+ T-Cell Population Structure , 2014, PLoS genetics.

[72]  Aarno Palotie,et al.  Genome-wide methylation analyses of primary human leukocyte subsets identifies functionally important cell-type-specific hypomethylated regions. , 2013, Blood.

[73]  J. Nielsen,et al.  Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics* , 2013, Molecular & Cellular Proteomics.

[74]  Tom C Freeman,et al.  An expression atlas of human primary cells: inference of gene function from coexpression networks , 2013, BMC Genomics.

[75]  D. Absher,et al.  Genome-Wide DNA Methylation Analysis of Systemic Lupus Erythematosus Reveals Persistent Hypomethylation of Interferon Genes and Compositional Changes to CD4+ T-cell Populations , 2013, PLoS genetics.

[76]  Margaret R Karagas,et al.  Blood-based profiles of DNA methylation predict the underlying distribution of cell types , 2013, Epigenetics.

[77]  Timothy E. Reddy,et al.  Dynamic DNA methylation across diverse human cell lines and tissues , 2013, Genome research.

[78]  Martin J. Aryee,et al.  A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression , 2013, Epigenetics.

[79]  Zachary D. Smith,et al.  DNA methylation: roles in mammalian development , 2013, Nature Reviews Genetics.

[80]  A. Singleton,et al.  Cell population-specific expression analysis of human cerebellum , 2012, BMC Genomics.

[81]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[82]  Devin C. Koestler,et al.  DNA methylation arrays as surrogate measures of cell mixture distribution , 2012, BMC Bioinformatics.

[83]  T. Bosch,et al.  DNA methylation regulates lineage-specifying genes in primary lymphatic and blood endothelial cells , 2012, Angiogenesis.

[84]  C. Suschek,et al.  Specific Age-Associated DNA Methylation Changes in Human Dermal Fibroblasts , 2011, PloS one.

[85]  J. Rinn,et al.  DNA methylation and epigenetic control of cellular differentiation , 2010, Cell cycle.

[86]  Margaret R. Karagas,et al.  Copy number variation has little impact on bead-array-based measures of DNA methylation , 2009, Bioinform..

[87]  Mark Goadrich,et al.  The relationship between Precision-Recall and ROC curves , 2006, ICML.

[88]  J. Shabanowitz,et al.  The HA-2 Minor Histocompatibility Antigen Is Derived from a Diallelic Gene Encoding a Novel Human Class I Myosin Protein , 2001, The Journal of Immunology.

[89]  J. Henzen.  Publisher's note , 1979, Brain Research.

[90]  Ash A. Alizadeh,et al.  SUPPLEMENTARY NOTE , 1879, Botanical Gazette.

[91]  Michael P. Schroeder,et al.  Molecular alterations in bone marrow mesenchymal stromal cells derived from acute myeloid leukemia patients , 2017, Leukemia.

[92]  M. Toyoda,et al.  DNA hypermethylation enhanced telomerase reverse transcriptase expression in human-induced pluripotent stem cells , 2017, Human Cell.

[93]  S. Garg,et al.  Analysis of DNA Methylation by Pyrosequencing. , 2015, Methods in molecular biology.

[94]  H. Sebastian Seung,et al.  Algorithms for Non-negative Matrix Factorization , 2000, NIPS.

[95]  Terry M. Therneau,et al.  Extending the Cox Model , 1997 .