Charalampos Kyriakopoulos

Charalampos Kyriakopoulos
Bristol-Myers Squibb | B-MS · Department of Bioanalytical Sciences

Doctor of Engineering

About

23
Publications
1,884
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
201
Citations
Additional affiliations
January 2014 - December 2017
Universität des Saarlandes
Position
  • PhD Student

Publications

Publications (23)
Article
Full-text available
A precise understanding of DNA methylation dynamics is of great importance for a variety of biological processes including cellular reprogramming and differentiation. To date, complex integration of multiple and distinct genome-wide datasets is required to realize this task. We present GwEEP (genome-wide epigenetic efficiency profiling) a versatile...
Chapter
Full-text available
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA methylation can however be subject to specific and fast changes over a short time scale even in non-dividing (i.e. not-r...
Preprint
Full-text available
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA methylation can however be subject to specific and fast changes over a short time scale even in non-dividing (i.e. not-r...
Article
Full-text available
The controlled and stepwise oxidation of 5mC to 5hmC, 5fC and 5caC by Tet enzymes is influencing the chemical and biological properties of cytosine. Besides direct effects on gene regulation, oxidised forms influence the dynamics of demethylation and re-methylation processes. So far, no combined methods exist which allow to precisely determine the...
Article
Full-text available
Complex networks play an important role in human society and in nature. Stochastic multistate processes provide a powerful framework to model a variety of emerging phenomena such as the dynamics of an epidemic or the spreading of information on complex networks. In recent years, mean-field type approximations gained widespread attention as a tool t...
Article
Full-text available
Contact processes form a large and highly interesting class of dynamic processes on networks, including epidemic and information spreading. While devising stochastic models of such processes is relatively easy, analyzing them is very challenging from a computational point of view, particularly for large networks appearing in real applications. One...
Article
Full-text available
Mouse embryonic stem cells are dynamic and heterogeneous. For example, rare cells cycle through a state characterized by decondensed chromatin and expression of transcripts, including the Zscan4 cluster and MERVL endogenous retrovirus, which are usually restricted to preimplantation embryos. Here, we further characterize the dynamics and consequenc...
Article
Full-text available
Motivation: Methylation and hydroxylation of cytosines to form 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) belong to the most important epigenetic modifications and their vital role in the regulation of gene expression has been widely recognized. Recent experimental techniques allow to infer methylation and hydroxylation levels at Cp...
Article
Full-text available
DNA methylation and demethylation are opposing processes that when in balance create stable patterns of epigenetic memory. The control of DNA methylation pattern formation by replication dependent and independent demethylation processes has been suggested to be influenced by Tet mediated oxidation of 5mC. Several alternative mechanisms have been pr...
Data
Details on the theoretical model, the parameter estimation, the statistical analysis of the results and the experimental procedure. (PDF)
Data
Comparison of model prediction and data for IAP, L1mdA, MuERVL, Ttc25 and Snrpn. Plotted according to Fig 5. (PDF)
Data
(Hydroxy-)methylation levels for each single CpG dyad of repetitive elements IAP, L1mdA, L1mdT, mSat, MuERVL and single copy genes Afp, Ttc25, Zim3 and Snrpn over time. The colormap is the same as in Fig 6. (PDF)
Data
Estimated coefficients of the functions μd(t), μm(t) and η(t) and their approximate standard deviations. The p-values have been taken conducting a hypothesis test H0: β1 = 0 using the Wald statistic. (PDF)
Data
BS and oxBS data, Conversion Errors (repetitive elements). (PDF)
Data
Results for loci IAP, L1mdA, MuERVL, Ttc25 and Snrpn. Left: Probabilities of the hidden states. Plotted according to Fig 6. Right: Estimated efficiencies and standard deviations over time. Plotted according to Fig 7 (PDF)
Data
Estimated efficiencies and standard deviations for each single CpG dyad of repetitive elements IAP, L1mdA, L1mdT, mSat, MuERVL and single copy genes Afp, Ttc25, Zim3 and Snrpn over time. In the case of IAP we cover six CpG positions. However, during evolution CpG one and five underwent a transition resulting in a loss of the CpG positions in this p...
Data
BS and oxBS data, Conversion Errors (single copy genes). (PDF)
Data
Test error: Linear vs Constant Assumption. Computed Kullback-Leibler divergence and Bhattacharya distance values given by LOOCV data to compare the test error for assuming linear vs constant efficiencies. (PDF)
Data
Bs and oxBS data for single CpGs. The dataset contains the BS and oxBS data of each single CpG and loci after processing of the sequencing data; error rates are included as separate files. Raw sequencing data are available on request. (ZIP)
Data
Estimated coefficients of the function λ(t) and their approximate standard deviations. The p-values have been taken conducting a hypothesis test H0:β1λ=0∧β2λ=0 using the Wald statistic. (PDF)
Conference Paper
Full-text available
Wet-lab experiments, in which the dynamics within living cells are observed, are usually costly and time consuming. This is particularly true if single-cell measurements are obtained using experimental techniques such as flow-cytometry or fluorescence microscopy. It is therefore important to optimize experiments with respect to the information they...

Network

Cited By