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The well-known issue of reconstructing regulatory networks from gene expression measurements has been somewhat disrupted by the emergence and rapid development of single-cell data. Indeed, the traditional way of seeing a gene regulatory…
In many organisms the expression levels of each gene are controlled by the activation levels of known "Transcription Factors" (TF). A problem of considerable interest is that of estimating the "Transcription Regulation Networks" (TRN)…
Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…
Profiling of whole transcriptomes has become a cornerstone of molecular biology and an invaluable tool for the characterization of clinical phenotypes and the identification of disease subtypes. Analyses of these data are becoming ever more…
Sequences arise in many real-world scenarios; thus, identifying the mechanisms behind symbol generation is essential to understanding many complex systems. This paper analyzes sequences generated by agents walking on a networked topology.…
Cellular regulatory dynamics is driven by large and intricate networks of interactions at the molecular scale, whose sheer size obfuscates understanding. In light of limited experimental data, many parameters of such dynamics are unknown,…
Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…
Transcriptional interactions in a cell are modulated by a variety of mechanisms that prevent their representation as pure pairwise interactions between a transcription factor and its target(s). These include, among others, transcription…
Multipotent stem or progenitor cells undergo a sequential series of binary fate decisions, which ultimately generate the diversity of differentiated cells. Efforts to understand cell fate control have focused on simple gene regulatory…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
Boolean networks have been successfully used in modelling gene regulatory networks. In this paper we propose a reduction method that reduces the complexity of a Boolean network but keeps dynamical properties and topological features and…
In systems biology, attractor landscape analysis of gene regulatory networks is recognized as a powerful computational tool for studying various cellular states from proliferation and differentiation to senescence and apoptosis. Therefore,…
Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables…
Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. What mechanisms might be responsible for these low in-degrees? Starting with an accepted framework of the…
Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed…
From the perspective of network analysis, the ubiquitous networks are comprised of regular and irregular components, which makes uncovering the complexity of network structures to be a fundamental challenge. Exploring the regular…
We study treatment effect modifiers for causal analysis in a social network, where neighbors' characteristics or network structure may affect the outcome of a unit, and the goal is to identify sub-populations with varying treatment effects…