DiSH simulator: Capturing dynamics of cellular signaling with heterogeneous knowledge
In this paper, we present DiSH, a simulator for large discrete models of biological signal
transduction pathways, capable of simulating networks with multi-valued elements in both …
transduction pathways, capable of simulating networks with multi-valued elements in both …
Exploring the dynamics of large-scale gene regulatory networks using hardware acceleration on a heterogeneous cpu-fpga platform
Systems Biology pose computational challenges that surpass the capabilities of current
computing platforms. A particular challenge in this regard is simulating the dynamics of …
computing platforms. A particular challenge in this regard is simulating the dynamics of …
Tractable learning and inference for large-scale probabilistic Boolean networks
Probabilistic Boolean networks (PBNs) have previously been proposed so as to gain
insights into complex dynamical systems. However, identification of large networks and their …
insights into complex dynamical systems. However, identification of large networks and their …
Fpga accelerated analysis of boolean gene regulatory networks
Boolean models are a powerful abstraction for qualitative modeling of gene regulatory
networks. With the recent availability of advanced high-throughput technologies, Boolean …
networks. With the recent availability of advanced high-throughput technologies, Boolean …
THiMED: Time in hierarchical model extraction and design
We describe our approach to modeling timing of cell signaling systems in which existing
information about the system spans from detailed mechanistic knowledge to much coarser …
information about the system spans from detailed mechanistic knowledge to much coarser …
Accelerated analysis of Boolean gene regulatory networks
In Systems Biology, Boolean models are gaining popularity in modeling and analysis of
qualitative dynamics of gene regulatory mechanisms. With the development of advanced …
qualitative dynamics of gene regulatory mechanisms. With the development of advanced …
Dynamic behavior of cell signaling networks: model design and analysis automation
Recent work has presented logical models and showed the benefits of applying logical
approaches to studying the dynamics of biological networks. In this work, we develop a …
approaches to studying the dynamics of biological networks. In this work, we develop a …
Gene regulatory accelerators on cloud FPGA
Gene regulatory networks (GRN) are dynamic models in time and space. These models are
used to predict diseases and in drugs research. GRN models are discrete, and Boolean …
used to predict diseases and in drugs research. GRN models are discrete, and Boolean …
Disorder of localized inflammation in wound healing: a systems perspective
Wound healing is a well-coordinated concerted event in response to injury and its
microenvironment, which aims at reinstating normal tissue homeostasis. Being a well …
microenvironment, which aims at reinstating normal tissue homeostasis. Being a well …
Automation of biological model learning, design and analysis
Although there have been several recent attempts to automate steps of the process of model
development and analysis in cell signaling networks, closing the overall cycle between …
development and analysis in cell signaling networks, closing the overall cycle between …