Description
Participants present posters of their previous work, getting to know the other presenters and participants in the process.
The aim of my PhD project is to develop a widely applicable framework tailored for the molecular characterization of single cells. Thank to single-cell techniques it is possible to analyze transcriptome, genome and the protein level at single-cell resolution. While these technical achievements are now used for characterizing cellular heterogeneity, a systematic approach interpreting and using...
Induced Pluripotent Stem Cell (iPS) lines can be derived by de-differentiating adult fibroblasts previously isolated from patients suffering from Parkinson’s Disease (PD). Following specific protocols, these cells, which are carrying PD-associated mutations, can then be re-differentiated into dopaminergic (DA) neurons, as these correspond to the neuronal subtype most affected by this...
Atomistic simulations of biomolecular systems have been used for decades to complement experiments. However, even with the rapid increase in the available computational power, atomistic simulations are still strictly limited to the nanoscale regime. Contemporary classical atomistic MD simulations typically feature ~10,000 - 1,000,000 atoms, studied over time scales of ~10 - 1,000 ns. These...
Isaac Newton, one of the founders of the theory of differential equations, was also one of the first scholars to realize its great significance for the study of natural laws. Indeed, since a couple of centuries ago one cannot imagine physics, biology, economics and many other fields without differential equations which are the universal language for the scientists. Despite this, the theory of...
EM or the Expectation Maximization algorithm is a procedure for estimating parameters of statistical models with latent variables. Recently, it has been shown that reaction networks can be used as computational machines to perform the EM algorithm[1] [2]. Further, DNA strand displacement can be used to implement CRNs with desired kinetics[3] [4]. We explore how to design a DNA strand...
Most cancer treatment induces DNA damage to eliminate highly proliferative cells. This process, however, also affects healthy cells creating numerous side effects ranging from infertility to heart problems. Cells respond differently to DNA damage depending on where they are in their cell cycle at the time of the treatment. Intriguingly, circadian rhythms provide temporal information to the...
Immune reactions are governed by highly complex molecular mechanisms. Because of the
high complexity of the biological data, it is often difficult to unravel these molecular
mechanisms. A systems biology approach consisting of a combination of mathematical
modeling and quantitative biological experimentation promises deeper insights into the
processes of living system.
In this study, we focus...
Spreading of antibiotic resistance Escherichia Coli represents a real concern worldwide. Furthermore, Escherichia coli remains one of the most frequent causes of several common bacterial infections in humans and animals. Studies assessing the role in the resistance of genes to particular drugs classify antibiotic resistance due to mutated/altered genes or presence of particular genes. Some...
developing a "Drug Simulation Model for Pharmacodynamic –Pharmacokinetic Interaction". This interaction is defined as a Pharmacometrics Systems Biology Model simulation. This project is running at children's cancer Hospital Egypt CCHE 57357.The simulation Model is built using MATLAB Sim-Biology® software application and R programming language built-in R studios® software. The project is aiming...
In the last few decades due to the new high-throughput techniques and the Mass spectrometry we gained a big amount of data about Protein-Protein Interactions (PPI) and Domain-Domain Interactions (DDI). This opened the opportunity for computational methods to predicts protein complexes. Clustering algorithms can predict qualitative information about protein complexes, but it is important in the...
Random walks are a well studied concept, that has been extensively used in many areas of science with notorious success. Meanwhile, quantum science has made an enormous step forward, from the initial Feynman papers to the first quantum computers. We try to give a small but self-consistent and pedagogical insight into the question of how quantum analogies to random walks are being developed in...
Theory predicts that populations should evolve towards a higher fitness. The process of a population’s continual fitness improvement is often represented by a fitness landscape. Rarely, however, has there been opportunity to experimentally simulate a fitness landscape, and test the repeatability of evolution towards a local optimum. We have taken advantage of knowledge of the adaptive...