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With the introduction of cyber-physical genome sequencing and editing technologies, such as CRISPR, researchers can more easily access tools to investigate and create remedies for a variety of topics in genetics and health science (e.g.…
Gene Regulatory Networks are networks of interactions in biological organisms responsible for determining the production levels of proteins and peptides. Proteins are workers of a cell factory, and their production defines the goal of a…
The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton's laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
The discovery of CRISPR-mediated gene activation (CRISPRa) has transformed the way in which we perform genetic screening, bioproduction and therapeutics through its ability to scale and multiplex. However, the emergence of loads on the key…
Genetic and environmental perturbation experiments have been used to study microbes in a bid to gain insight into transcriptional regulation, adaptive evolution, and other cellular dynamics. These studies have potential in enabling rational…
CRISPR-Cas13 is a system that utilizes single stranded RNAs for RNA editing. Prediction of on-target and off-target effects for the CRISPR-Cas13d dependency enables us to design specific single guide RNAs (sgRNAs) that help locate the…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
The maintainance of a stable periodicity during the yeast metabolic cycle involving approximately half of the genome requires a very strict and efficient control of gene expression. For this reason, the metabolic cycle is a very good…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
Gene regulation is an important fundamental biological process. The regulation of gene expression is managed through a variety of methods including epigenetic processes (e.g., DNA methylation). Understanding the role of epigenetic changes…
In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…
We investigate the ability of algorithms developed for reverse engineering of transcriptional regulatory networks to reconstruct metabolic networks from high-throughput metabolite profiling data. For this, we generate synthetic metabolic…
For the application of MPC design in on-line regulation or tracking control problems, several studies have attempted to develop an accurate model, and realize adequate uncertainty description of linear or non-linear plants of the processes.…
Recent developments in synthetic biology, next-generation sequencing, and machine learning provide an unprecedented opportunity to rationally design new disease treatments based on measured responses to gene perturbations and drugs to…
Dynamic metabolic control allows key metabolic fluxes to be modulated in real time, enhancing bioprocess flexibility and expanding available optimization degrees of freedom. This is achieved, e.g., via targeted modulation of metabolic…
Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…
Designing regulatory DNA sequences that achieve precise cell-type-specific gene expression is crucial for advancements in synthetic biology, gene therapy and precision medicine. Although transformer-based language models (LMs) can…
The design and implementation of regulation motifs ensuring robust perfect adaptation are challenging problems in synthetic biology. Indeed, the design of high-yield robust metabolic pathways producing, for instance, drug precursors and…
The rapidly expanding market for regenerative medicines and cell therapies highlights the need to advance the understanding of cellular metabolisms and improve the prediction of cultivation production process for human induced pluripotent…