Related papers: Evolution and Controllability of Cancer Networks: …
For years, we have been building models of gene regulatory networks, where recent advances in molecular biology shed some light on new structural and dynamical properties of such highly complex systems. In this work, we propose a novel…
We discuss a cancer hallmark network framework for modelling genome-sequencing data to predict cancer clonal evolution and associated clinical phenotypes. Strategies of using this framework in conjunction with genome sequencing data in an…
Unstable dynamics characterizes the evolution of most solid tumors. Because of an increased failure of maintaining genome integrity, a cumulative increase in the levels of gene mutation and loss is observed. Previous work suggests that…
Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into…
Individual cancer cells carry a bewildering number of distinct genomic alterations i.e., copy number variations and mutations, making it a challenge to uncover genomic-driven mechanisms governing tumorigenesis. Here we performed…
Boolean networks may be viewed as idealizations of biological genetic networks, where each node is represented by an on-off switch which is a function of the binary output from some other nodes. We evolve connectivity in a single Boolean…
Cancer is a systemic heterogeneous disease involving complex molecular networks. Tumor formation involves epithelial-mesenchymal transition (EMT), which promotes both metastasis and plasticity of cancer cells. Recent experiments proposed…
Known as one of the hallmarks of cancer [30], cancer cell invasion of human body tissue is a complicated spatio-temporal multiscale process which enables a localised solid tumour to transform into a systemic, metastatic and fatal disease.…
Integrative network modeling of data arising from multiple genomic platforms provides insight into the holistic picture of the interactive system, as well as the flow of information across many disease domains including cancer. The basic…
Interactive visualization tools are highly desirable to biologist and cancer researchers to explore the complex structures, detect patterns and find out the relationships among bio-molecules responsible for a cancer type. A pathway contains…
The focus of pancreatic cancer research has been shifted from pancreatic cancer cells towards their microenvironment, involving pancreatic stellate cells that interact with cancer cells and influence tumor progression. To quantitatively…
Cancer stem cells are controlled by developmental networks that are often topologically indistinguishable from normal, healthy stem cells. The question is why cancer stem cells can be both phenotypically distinct and have morphological…
Computational modeling of cancer can help unveil dynamics and interactions that are hard to replicate experimentally. Thanks to the advancement in cancer databases and data analysis technologies, these models have become more robust than…
In this paper, we present a probabilistic analysis of a dynamical particle model for the self-adaptive immune response to cancer, as proposed by the first author in a previous work. The model is motivated by the interplay between immune…
In recent years, cancer genome sequencing and other high-throughput studies of cancer genomes have generated many notable discoveries. In this review, Novel genomic alteration mechanisms, such as chromothripsis (chromosomal crisis) and…
A Boolean network is a finite state discrete time dynamical system. At each step, each variable takes a value from a binary set. The value update rule for each variable is a local function which depends only on a selected subset of…
Theoretical reasoning suggests that human cancer may result from knocking down the genetic constraints evolved for maintenance of the metazoan multicellularity, which, however, requires a critical test. Using xenograft-based experimental…
The dynamic stability of the Boolean networks representing a model for the gene transcriptional regulation (Kauffman model) is studied by calculating analytically and numerically the Hamming distance between two evolving configurations.…
While we once thought of cancer as single monolithic diseases affecting a specific organ site, we now understand that there are many subtypes of cancer defined by unique patterns of gene mutations. These gene mutational data, which can be…
This article presents an algorithm that allows modeling of biological networks in a qualitative framework with continuous time. Mathematical modeling is used as a systems biology tool to answer biological questions, and more precisely, to…