Search Results - "Teschendorff, Andrew E"

Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome by Teschendorff, Andrew E., Enver, Tariq

“…The ability to quantify differentiation potential of single cells is a task of critical importance. Here we demonstrate, using over 7,000 single-cell RNA-Seq…”
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A comparison of epigenetic mitotic-like clocks for cancer risk prediction by Teschendorff, Andrew E

“…DNA methylation changes that accrue in the stem cell pool of an adult tissue in line with the cumulative number of cell divisions may contribute to the…”
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A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies by Teschendorff, Andrew E, Breeze, Charles E, Zheng, Shijie C, Beck, Stephan

“…Intra-sample cellular heterogeneity presents numerous challenges to the identification of biomarkers in large Epigenome-Wide Association Studies (EWAS). While…”
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ChAMP: updated methylation analysis pipeline for Illumina BeadChips by Tian, Yuan, Morris, Tiffany J, Webster, Amy P, Yang, Zhen, Beck, Stephan, Feber, Andrew, Teschendorff, Andrew E

“…The Illumina Infinium HumanMethylationEPIC BeadChip is the new platform for high-throughput DNA methylation analysis, effectively doubling the coverage…”
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Identification of differentially methylated cell types in epigenome-wide association studies by Zheng, Shijie C., Breeze, Charles E., Beck, Stephan, Teschendorff, Andrew E.

“…An outstanding challenge of epigenome-wide association studies (EWASs) performed in complex tissues is the identification of the specific cell type(s)…”
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EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data by Teschendorff, Andrew E, Zhu, Tianyu, Breeze, Charles E, Beck, Stephan

“…Cell type heterogeneity presents a challenge to the interpretation of epigenome data, compounded by the difficulty in generating reliable single-cell DNA…”
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DNA methylation aging clocks: challenges and recommendations by Bell, Christopher G, Lowe, Robert, Adams, Peter D, Baccarelli, Andrea A, Beck, Stephan, Bell, Jordana T, Christensen, Brock C, Gladyshev, Vadim N, Heijmans, Bastiaan T, Horvath, Steve, Ideker, Trey, Issa, Jean-Pierre J, Kelsey, Karl T, Marioni, Riccardo E, Reik, Wolf, Relton, Caroline L, Schalkwyk, Leonard C, Teschendorff, Andrew E, Wagner, Wolfgang, Zhang, Kang, Rakyan, Vardhman K

“…Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular…”
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A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data by Teschendorff, Andrew E, Marabita, Francesco, Lechner, Matthias, Bartlett, Thomas, Tegner, Jesper, Gomez-Cabrero, David, Beck, Stephan

“…The Illumina Infinium 450 k DNA Methylation Beadchip is a prime candidate technology for Epigenome-Wide Association Studies (EWAS). However, a difficulty…”
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Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies by TESCHENDORFF, Andrew E, ZHUANG, Joanna, WIDSCHWENDTER, Martin

“…A common difficulty in large-scale microarray studies is the presence of confounding factors, which may significantly skew estimates of statistical…”
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ChAMP: 450k Chip Analysis Methylation Pipeline by Morris, Tiffany J, Butcher, Lee M, Feber, Andrew, Teschendorff, Andrew E, Chakravarthy, Ankur R, Wojdacz, Tomasz K, Beck, Stephan

“…The Illumina Infinium HumanMethylation450 BeadChip is a new platform for high-throughput DNA methylation analysis. Several methods for normalization and…”
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Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions by Teschendorff, Andrew E, Widschwendter, Martin

“…MOTIVATION: The standard paradigm in omic disciplines has been to identify biologically relevant biomarkers using statistics that reflect differences in mean…”
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Cell-attribute aware community detection improves differential abundance testing from single-cell RNA-Seq data by Maity, Alok K., Teschendorff, Andrew E.

“…Variations of cell-type proportions within tissues could be informative of biological aging and disease risk. Single-cell RNA-sequencing offers the opportunity…”
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Variational Bayesian Matrix Factorization for Bounded Support Data by Zhanyu Ma, Teschendorff, Andrew E., Leijon, Arne, Yuanyuan Qiao, Honggang Zhang, Jun Guo

“…A novel Bayesian matrix factorization method for bounded support data is presented. Each entry in the observation matrix is assumed to be beta distributed. As…”
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DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer by Teschendorff, Andrew E, Gao, Yang, Jones, Allison, Ruebner, Matthias, Beckmann, Matthias W., Wachter, David L., Fasching, Peter A., Widschwendter, Martin

“…Identifying molecular alterations in normal tissue adjacent to cancer is important for understanding cancer aetiology and designing preventive measures. Here…”
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Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development by Chen, Yuting, Widschwendter, Martin, Teschendorff, Andrew E

“…Diverse molecular alterations associated with smoking in normal and precursor lung cancer cells have been reported, yet their role in lung cancer etiology…”
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Menopause accelerates biological aging by Levine, Morgan E., Lu, Ake T., Chen, Brian H., Hernandez, Dena G., Singleton, Andrew B., Ferrucci, Luigi, Bandinelli, Stefania, Salfati, Elias, Manson, JoAnn E., Quach, Austin, Kusters, Cynthia D. J., Kuh, Diana, Wong, Andrew, Teschendorff, Andrew E., Widschwendter, Martin, Ritz, Beate R., Absher, Devin, Assimes, Themistocles L., Horvath, Steve

“…Although epigenetic processes have been linked to aging and disease in other systems, it is not yet known whether they relate to reproductive aging. Recently,…”
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An improved epigenetic counter to track mitotic age in normal and precancerous tissues by Zhu, Tianyu, Tong, Huige, Du, Zhaozhen, Beck, Stephan, Teschendorff, Andrew E.

“…The cumulative number of stem cell divisions in a tissue, known as mitotic age, is thought to be a major determinant of cancer-risk. Somatic mutational and DNA…”
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Differential network entropy reveals cancer system hallmarks by West, James, Bianconi, Ginestra, Severini, Simone, Teschendorff, Andrew E.

“…The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy…”
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dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms by Xu, Feng, Wang, Yifan, Ling, Yunchao, Zhou, Chenfen, Wang, Haizhou, Teschendorff, Andrew E., Zhao, Yi, Zhao, Haitao, He, Yungang, Zhang, Guoqing, Yang, Zhen

“…MicroRNAs (miRNAs) are important regulators in gene expression. The dysregulation of miRNA expression is widely reported in the transformation from…”
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Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus by Bell, Christopher G, Teschendorff, Andrew E, Rakyan, Vardhman K, Maxwell, Alexander P, Beck, Stephan, Savage, David A

“…Diabetic nephropathy is a serious complication of diabetes mellitus and is associated with considerable morbidity and high mortality. There is increasing…”
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