Related papers: Gene targeting in disease networks
Gene regulatory networks are powerful abstractions of biological systems. Since the advent of high-throughput measurement technologies in biology in the late 90s, reconstructing the structure of such networks has been a central…
Gene Regulatory Network (GRN) plays an important role in knowing insight of cellular life cycle. It gives information about at which different environmental conditions genes of particular interest get over expressed or under expressed.…
Raman spectroscopy can provide insight into the molecular composition of cells and tissue. Consequently, it can be used as a powerful diagnostic tool, e.g. to help identify changes in molecular contents with the onset of disease. But robust…
Despite considerable progress in genome- and proteome-based high-throughput screening methods and in rational drug design, the increase in approved drugs in the past decade did not match the increase of drug development costs. Network…
Retrieving gene functional networks from knowledge databases presents a challenge due to the mismatch between disease networks and subtype-specific variations. Current solutions, including statistical and deep learning methods, often fail…
Genome-wide experiments to map the DNA-binding locations of transcription-associated factors (TFs) have shown that the number of genes bound by a TF far exceeds the number of possible direct target genes. Distinguishing functional from…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
The use of networks to integrate different genetic, proteomic, and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases. Here we introduce a new phenotypic database summarizing…
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…
The majority of common diseases are influenced by multiple genetic and environmental factors such as Cancer. Even though uncovering the main causes of disease is deemed difficult due to the complexity of gene-gene and gene-environment…
Phenotype transition takes place in many biological processes such as differentiation, and understanding how a cell reprograms its global gene expression profile is a problem of rate theories. A cell phenotype transition accompanies with…
Drug target identification is of significant commercial interest to pharmaceutical companies, and there is a vast amount of research done related to the topic of therapeutic target identification. Interdisciplinary research in this area…
Identifying key driver genes governing biological processes such as development and disease progression remains a challenge. While existing methods can reconstruct cellular trajectories or infer static gene regulatory networks (GRNs), they…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
Signed networks, i.e., networks with positive and negative edges, commonly arise in various domains from social media to epidemiology. Modeling signed networks has many practical applications, including the creation of synthetic data sets…
Genetic variation affecting gene regulation is a central driver of phenotypic differences between individuals and can be used to uncover how biological processes are organized in a cell. Although detecting cis-eQTLs is now routine,…
The vast amount of biological knowledge accumulated over the years has allowed researchers to identify various biochemical interactions and define different families of pathways. There is an increased interest in identifying pathways and…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of…
Gene regulation involves a hierarchy of events that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. The effects of DNA sequence on these processes have typically been studied based…