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https://www.readbyqxmd.com/read/27932399/novel-hybrid-phenotype-revealed-in-small-cell-lung-cancer-by-a-transcription-factor-network-model-that-can-explain-tumor-heterogeneity
#1
Akshata R Udyavar, David J Wooten, Megan D Hoeksema, Mukesh Bansal, Andrea Califano, Lourdes Estrada, Santiago Schnell, Jonathan M Irish, Pierre P Massion, Vito Quaranta
Small cell lung cancer (SCLC) is a devastating disease due to its propensity for early invasion and refractory relapse after initial treatment response. Although these aggressive traits have been associated with phenotypic heterogeneity, our understanding of this association remains incomplete. To fill this knowledge gap, we inferred a set of 33 transcription factors (TF) associated with gene signatures of the known neuroendocrine/epithelial (NE) and non-neuroendocrine/mesenchymal-like (ML) SCLC phenotypes...
December 8, 2016: Cancer Research
https://www.readbyqxmd.com/read/27908005/occurrence-and-stability-of-chimera-states-in-coupled-externally-excited-oscillators
#2
Dawid Dudkowski, Yuri Maistrenko, Tomasz Kapitaniak
We studied the phenomenon of chimera states in networks of non-locally coupled externally excited oscillators. Units of the considered networks are bi-stable, having two co-existing attractors of different types (chaotic and periodic). The occurrence of chimeras is discussed, and the influence of coupling radius and coupling strength on their co-existence is analyzed (including typical bifurcation scenarios). We present a statistical analysis and investigate sensitivity of the probability of observing chimeras to the initial conditions and parameter values...
November 2016: Chaos
https://www.readbyqxmd.com/read/27903783/uncovering-the-mechanisms-of-caenorhabditis-elegans-ageing-from-global-quantification-of-the-underlying-landscape
#3
Lei Zhao, Jin Wang
Recent studies on Caenorhabditis elegans reveal that gene manipulations can extend its lifespan several fold. However, how the genes work together to determine longevity is still an open question. Here we construct a gene regulatory network for worm ageing and quantify its underlying potential and flux landscape. We found ageing and rejuvenation states can emerge as basins of attraction at certain gene expression levels. The system state can switch from one attractor to another driven by the intrinsic or external perturbations through genetics or the environment...
November 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/27870120/continuous-attractor-network-models-of-grid-cell-firing-based-on-excitatory-inhibitory-interactions
#4
Oliver Shipston-Sharman, Lukas Solanka, Matthew F Nolan
Neurons in the medial entorhinal cortex encode location through spatial firing fields that have a grid-like organisation. The challenge of identifying mechanisms for grid firing has been addressed through experimental and theoretical investigations of medial entorhinal circuits. Here, we discuss evidence for continuous attractor network models that account for grid firing by synaptic interactions between excitatory and inhibitory cells. These models assume that grid-like firing patterns are the result of computation of location from velocity inputs, with additional spatial input required to oppose drift in the attractor state...
November 15, 2016: Journal of Physiology
https://www.readbyqxmd.com/read/27866978/stability-and-structural-properties-of-gene-regulation-networks-with-coregulation-rules
#5
Jonathan Warrell, Musa Mhlanga
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated expression of modules (and module groups) of functionally related genes across the genome. Coregulation can also arise through the physical association of multi-gene complexes through chromosomal looping, which are then transcribed together. We present a general formalism for modeling coregulation rules in the framework of Random Boolean Networks (RBN), and develop specific models for transcription factor networks with modular structure (including module groups, and multi-input modules (MIM) with autoregulation) and multi-gene complexes (including hierarchical differentiation between multi-gene complex members)...
November 17, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27861624/an-algorithm-for-finding-the-singleton-attractors-and-pre-images-in-strong-inhibition-boolean-networks
#6
Zhiwei He, Meng Zhan, Shuai Liu, Zebo Fang, Chenggui Yao
The detection of the singleton attractors is of great significance for the systematic study of genetic regulatory network. In this paper, we design an algorithm to compute the singleton attractors and pre-images of the strong-inhibition Boolean networks which is a biophysically plausible gene model. Our algorithm can not only identify accurately the singleton attractors, but also find easily the pre-images of the network. Based on extensive computational experiments, we show that the computational time of the algorithm is proportional to the number of the singleton attractors, which indicates the algorithm has much advantage in finding the singleton attractors for the networks with high average degree and less inhibitory interactions...
2016: PloS One
https://www.readbyqxmd.com/read/27853431/developing-dynamic-field-theory-architectures-for-embodied-cognitive-systems-with-cedar
#7
Oliver Lomp, Mathis Richter, Stephan K U Zibner, Gregor Schöner
Embodied artificial cognitive systems, such as autonomous robots or intelligent observers, connect cognitive processes to sensory and effector systems in real time. Prime candidates for such embodied intelligence are neurally inspired architectures. While components such as forward neural networks are well established, designing pervasively autonomous neural architectures remains a challenge. This includes the problem of tuning the parameters of such architectures so that they deliver specified functionality under variable environmental conditions and retain these functions as the architectures are expanded...
2016: Frontiers in Neurorobotics
https://www.readbyqxmd.com/read/27797783/pyboolnet-a-python-package-for-the-generation-analysis-and-visualisation-of-boolean-networks
#8
Hannes Klarner, Adam Streck, Heike Siebert
MOTIVATION: The goal of this project is to provide a simple interface to working with Boolean networks. Emphasis is put on easy access to a large number of common tasks including the generation and manipulation of networks, attractor and basin computation, model checking and trap space computation, execution of established graph algorithms as well as graph drawing and layouts. RESULTS: PyBoolNet is a Python package for working with Boolean networks that supports simple access to model checking via NuSMV, standard graph algorithms via NetworkX and visualisation via dot...
October 26, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27797768/visibool-visualization-and-simulation-of-boolean-networks-with-temporal-constraints
#9
Julian Schwab, Andre Burkovski, Lea Siegle, Christoph Müssel, Hans A Kestler
: Mathematical models and their simulation are increasingly used to gain insights into cellular pathways and regulatory networks. Dynamics of regulatory factors can be modeled using Boolean networks (BN), among others. Text-based representations of models are precise descriptions, but hard to understand and interpret. ViSiBooL aims at providing a graphical way of modeling and simulating networks. By providing visualizations of static and dynamic network properties simultaneously, it is possible to directly observe the effects of changes in the network structure on the behavior...
October 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27796298/spontaneous-emergence-of-fast-attractor-dynamics-in-a-model-of-developing-primary-visual-cortex
#10
Thomas Miconi, Jeffrey L McKinstry, Gerald M Edelman
Recent evidence suggests that neurons in primary sensory cortex arrange into competitive groups, representing stimuli by their joint activity rather than as independent feature analysers. A possible explanation for these results is that sensory cortex implements attractor dynamics, although this proposal remains controversial. Here we report that fast attractor dynamics emerge naturally in a computational model of a patch of primary visual cortex endowed with realistic plasticity (at both feedforward and lateral synapses) and mutual inhibition...
October 31, 2016: Nature Communications
https://www.readbyqxmd.com/read/27781453/patterns-of-patterns-of-synchronization-noise-induced-attractor-switching-in-rings-of-coupled-nonlinear-oscillators
#11
Jeffrey Emenheiser, Airlie Chapman, Márton Pósfai, James P Crutchfield, Mehran Mesbahi, Raissa M D'Souza
Following the long-lived qualitative-dynamics tradition of explaining behavior in complex systems via the architecture of their attractors and basins, we investigate the patterns of switching between distinct trajectories in a network of synchronized oscillators. Our system, consisting of nonlinear amplitude-phase oscillators arranged in a ring topology with reactive nearest-neighbor coupling, is simple and connects directly to experimental realizations. We seek to understand how the multiple stable synchronized states connect to each other in state space by applying Gaussian white noise to each of the oscillators' phases...
September 2016: Chaos
https://www.readbyqxmd.com/read/27781448/super-transient-scaling-in-time-delay-autonomous-boolean-network-motifs
#12
Otti D'Huys, Johannes Lohmann, Nicholas D Haynes, Daniel J Gauthier
Autonomous Boolean networks are commonly used to model the dynamics of gene regulatory networks and allow for the prediction of stable dynamical attractors. However, most models do not account for time delays along the network links and noise, which are crucial features of real biological systems. Concentrating on two paradigmatic motifs, the toggle switch and the repressilator, we develop an experimental testbed that explicitly includes both inter-node time delays and noise using digital logic elements on field-programmable gate arrays...
September 2016: Chaos
https://www.readbyqxmd.com/read/27781441/chaos-in-generically-coupled-phase-oscillator-networks-with-nonpairwise-interactions
#13
Christian Bick, Peter Ashwin, Ana Rodrigues
The Kuramoto-Sakaguchi system of coupled phase oscillators, where interaction between oscillators is determined by a single harmonic of phase differences of pairs of oscillators, has very simple emergent dynamics in the case of identical oscillators that are globally coupled: there is a variational structure that means the only attractors are full synchrony (in-phase) or splay phase (rotating wave/full asynchrony) oscillations and the bifurcation between these states is highly degenerate. Here we show that nonpairwise coupling-including three and four-way interactions of the oscillator phases-that appears generically at the next order in normal-form based calculations can give rise to complex emergent dynamics in symmetric phase oscillator networks...
September 2016: Chaos
https://www.readbyqxmd.com/read/27765600/fixed-points-in-random-boolean-networks-the-impact-of-parallelism-in-the-barab%C3%A3-si-albert-scale-free-topology-case
#14
P Moisset de Espanés, A Osses, I Rapaport
Fixed points are fundamental states in any dynamical system. In the case of gene regulatory networks (GRNs) they correspond to stable genes profiles associated to the various cell types. We use Kauffman's approach to model GRNs with random Boolean networks (RBNs). In this paper we explore how the topology affects the distribution of the number of fixed points in randomly generated networks. We also study the size of the basins of attraction of these fixed points if we assume the α-asynchronous dynamics (where every node is updated independently with probability 0≤α≤1)...
October 17, 2016: Bio Systems
https://www.readbyqxmd.com/read/27765040/attractor-landscape-analysis-of-colorectal-tumorigenesis-and-its-reversion
#15
Sung-Hwan Cho, Sang-Min Park, Ho-Sung Lee, Hwang-Yeol Lee, Kwang-Hyun Cho
BACKGROUND: Colorectal cancer arises from the accumulation of genetic mutations that induce dysfunction of intracellular signaling. However, the underlying mechanism of colorectal tumorigenesis driven by genetic mutations remains yet to be elucidated. RESULTS: To investigate colorectal tumorigenesis at a system-level, we have reconstructed a large-scale Boolean network model of the human signaling network by integrating previous experimental results on canonical signaling pathways related to proliferation, metastasis, and apoptosis...
October 20, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27746583/pathway-analysis-based-on-attractor-and-cross-talk-in-colon-cancer
#16
Yanxia Liu, Lin Wang, Bingping Wang, Meng Yue, Yufeng Cheng
Colon cancer is the third and second most common cancer form in men and women worldwide. It is generally accepted that colon cancer mainly results from diet. The aim of this study was to identify core pathways which elucidated the molecular mechanisms in colon cancer. The microarray data of E-GEOD-44861 was downloaded from ArrayExpress database. All human pathways were obtained from Kyoto Encyclopedia of Genes and Genomes database. In total, 135 differential expressed genes (DEG) were identified using Linear Models for Microarray Data package...
2016: Disease Markers
https://www.readbyqxmd.com/read/27725468/theoretical-approaches-for-the-dynamics-of-complex-biological-systems-from-information-of-networks
#17
Atsushi Mochizuki
Modern biology has provided many examples of large networks describing the interactions between multiple species of bio-molecules. It is believed that the dynamics of molecular activities based on such networks are the origin of biological functions. On the other hand, we have a limited understanding for dynamics of molecular activity based on networks. To overcome this problem, we have developed two structural theories, by which the important aspects of the dynamical properties of the system are determined only from information on the network structure, without assuming other quantitative details...
2016: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/27721205/emergence-of-low-noise-frustrated-states-in-e-i-balanced-neural-networks
#18
I Recio, J J Torres
We study emerging phenomena in binary neural networks where, with a probability c synaptic intensities are chosen according with a Hebbian prescription, and with probability (1-c) there is an extra random contribution to synaptic weights. This new term, randomly taken from a Gaussian bimodal distribution, balances the synaptic population in the network so that one has 80%-20% relation in E/I population ratio, mimicking the balance observed in mammals cortex. For some regions of the relevant parameters, our system depicts standard memory (at low temperature) and non-memory attractors (at high temperature)...
September 8, 2016: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/27717349/an-efficient-algorithm-for-identifying-primary-phenotype-attractors-of-a-large-scale-boolean-network
#19
Sang-Mok Choo, Kwang-Hyun Cho
BACKGROUND: Boolean network modeling has been widely used to model large-scale biomolecular regulatory networks as it can describe the essential dynamical characteristics of complicated networks in a relatively simple way. When we analyze such Boolean network models, we often need to find out attractor states to investigate the converging state features that represent particular cell phenotypes. This is, however, very difficult (often impossible) for a large network due to computational complexity...
October 7, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27716031/boolean-regulatory-network-reconstruction-using-literature-based-knowledge-with-a-genetic-algorithm-optimization-method
#20
Julien Dorier, Isaac Crespo, Anne Niknejad, Robin Liechti, Martin Ebeling, Ioannis Xenarios
BACKGROUND: Prior knowledge networks (PKNs) provide a framework for the development of computational biological models, including Boolean models of regulatory networks which are the focus of this work. PKNs are created by a painstaking process of literature curation, and generally describe all relevant regulatory interactions identified using a variety of experimental conditions and systems, such as specific cell types or tissues. Certain of these regulatory interactions may not occur in all biological contexts of interest, and their presence may dramatically change the dynamical behaviour of the resulting computational model, hindering the elucidation of the underlying mechanisms and reducing the usefulness of model predictions...
October 6, 2016: BMC Bioinformatics
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