Related papers: Inferring disease causing genes and their pathways…
Cardiac development is complex, multiscale process encompassing cell fate adoption, differentiation and morphogenesis. To elucidate pathways underlying this process, a recently developed algorithm to reverse engineer gene regulatory…
Causal effect estimation in networked systems is central to data-driven decision making. In such settings, interventions on one unit can spill over to others, and in complex physical or social systems, the interaction pathways driving these…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…
The term "interference" has been used to describe any setting in which one subject's exposure may affect another subject's outcome. We use causal diagrams to distinguish among three causal mechanisms that give rise to interference. The…
In this paper, we conduct theoretical analyses on inferring the structure of gene regulatory networks. Depending on the experimental method and data type, the inference problem is classified into 20 different scenarios. For each scenario,…
The vast amount of sequencing data presently available allow the scientific community to explore a range of genetic variables that may drive and progress cancer. A myriad of predictive tools has been proposed, allowing researchers and…
Infectious disease remains, despite centuries of work to control and mitigate its effects, a major problem facing humanity. This paper reviews the mathematical modelling of infectious disease epidemics on networks, starting from the…
One of the important techniques of Data mining is Classification. Many real world problems in various fields such as business, science, industry and medicine can be solved by using classification approach. Neural Networks have emerged as an…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
We consider a causal inference model in which individuals interact in a social network and they may not comply with the assigned treatments. In particular, we suppose that the form of network interference is unknown to researchers. To…
Modern causal decision-making increasingly demands individualized treatment-effect estimation in networks where interventions are high-dimensional, combinatorial vectors. While network interference, effect heterogeneity, and…
By linking conceptual theories with observed data, generative models can support reasoning in complex situations. They have come to play a central role both within and beyond statistics, providing the basis for power analysis in molecular…
Network science is already making an impact on the study of complex systems and offers a promising variety of tools to understand their formation and evolution (1-4) in many disparate fields from large communication networks (5,6),…
Plant diseases are considered one of the main factors influencing food production and minimize losses in production, and it is essential that crop diseases have fast detection and recognition. The recent expansion of deep learning methods…
Fueled by breakthrough technology developments, the biological, biomedical, and behavioral sciences are now collecting more data than ever before. There is a critical need for time- and cost-efficient strategies to analyze and interpret…
Effective therapy of complex diseases requires control of highly non-linear complex networks that remain incompletely characterized. In particular, drug intervention can be seen as control of signaling in cellular networks. Identification…
Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the…
One of the important issues in oncology is finding the genes that perturbation the cell functionality, and result in cancer propagation. The genes, namely driver genes, when they mutate in expression, result in cancer through activation of…
The biological processes of cellular decision making and differentiation involve a plethora of signalling pathways and gene regulatory circuits. These networks, in their turn, exhibit a multitude of motifs playing crucial parts in…