Related papers: Cell Cycling Models of Carcinogenesis: A Complex S…
Carcinogenesis is a complex process that involves dynamically inter-connected modular sub-networks that evolve under the influence of micro-environmentally induced perturbations, in non-random, pseudo-Markov chain processes. An appropriate…
The cell cycle is tightly regulated by cyclins and their catalytic moieties, the cyclin-dependent kinases (CDKs). Cyclin D1, in association with CDK4/6, acts as a mitogenic sensor and integrates extracellular mitogenic signals and cell…
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…
Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently…
Deciphering regulatory events that drive malignant transformation represents a major challenge for systems biology. Here we analyzed genome-wide transcription profiling of an in-vitro transformation process. We focused on a cluster of genes…
Cancers remain the lead cause of disease-related, pediatric death in North America. The emerging field of complex systems has redefined cancer networks as a computational system with intractable algorithmic complexity. Herein, a tumor and…
Cancer cells are widely known to be protected from apoptosis, which is a major hurdle to successful anti-cancer therapy. Over-expression of several anti-apoptotic proteins, or mutations in pro-apoptotic factors, has been recognized to…
Signaling pathways are responsible for the regulation of cell processes, such as monitoring the external environment, transmitting information across membranes, and making cell fate decisions. Given the increasing amount of biological data…
Four chapters of the synthesis represent four major areas of my research interests: 1) data analysis in molecular biology, 2) mathematical modeling of biological networks, 3) genome evolution, and 4) cancer systems biology. The first…
There is a widening recognition that cancer cells are products of complex developmental processes. Carcinogenesis and metastasis formation are increasingly described as systems-level, network phenomena. Here we propose that malignant…
Cancer is a complex disease driven by dynamic regulatory shifts that cannot be fully captured by individual molecular profiling. We employ a data-driven approach to construct a coarse-grained dynamic network model based on hallmark…
We consider the decision making by mammalian cells, looking them as dynamic systems with rhythms. We calculate the effective dimension of the cell division model of the healthy mammalian cells consistent with the data: it is described via a…
Mechanics and biochemical signaling are both often deregulated in cancer, leading to cancer cell phenotypes that exhibit increased invasiveness, proliferation, and survival. The dynamics and interactions of cytoskeletal components control…
Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. Understanding the cybernetics of cancer requires…
The spread of metastases is a crucial process in which some questions remain unanswered. In this work, we focus on tumor cells circulating in the bloodstream, the so-called Circulating Tumor Cells (CTCs). Our aim is to characterize their…
Background: Differential expression analysis of (individual) genes is often used to study their roles in diseases. However, diseases such as cancer are a result of the combined effect of multiple genes. Gene products such as proteins seldom…
Predictive modeling of the evolutionary dynamics of cancer is a challenge issue in computational cancer biology. In this paper, we propose a general mathematical model framework for the evolutionary dynamics of cancer with plasticity and…
Networks are versatile representations of the interactions between entities in complex systems. Cycles on such networks represent feedback processes which play a central role in system dynamics. In this work, we introduce a measure of the…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
In this study, we provide a dynamical systems perspective to the modelling of pathological states induced by tumors or infection. A unified disease model is established using the innate immune system as the reference point. We propose a…