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Our goal is gene network inference in genetical genomics or systems genetics experiments. For species where sequence information is available, we first perform expression quantitative trait locus (eQTL) mapping by jointly utilizing cis-, cis-trans-, and trans-regulation. After using local structural models to identify regulator-target pairs for each eQTL,… (More)

Systems of ordinary differential equations (ODEs) are often used to model the dynamics of complex biological pathways. We construct a discrete state model as a probabilistic approximation of the ODE dynamics by discretizing the value space and the time domain. We then sample a representative set of trajectories and exploit the discretization and the… (More)

- Bing Liu, Jing Zhang, Pei Yi Tan, David Hsu, Anna M. Blom, Benjamin Leong +4 others
- PLoS Computational Biology
- 2011

The complement system is key to innate immunity and its activation is necessary for the clearance of bacteria and apoptotic cells. However, insufficient or excessive complement activation will lead to immune-related diseases. It is so far unknown how the complement activity is up- or down- regulated and what the associated pathophysiological mechanisms are.… (More)

We present a statistical model checking (SMC) based framework for studying ordinary differential equation (ODE) models of bio-pathways. We address cell-to-cell variability explicitly by using probability distributions to model initial concentrations and kinetic rate values. The core component of our framework is an SMC procedure for verifying the dynamical… (More)

Biochemical networks are often modeled as systems of ordinary differential equations (ODEs). Such systems will not admit closed form solutions and hence numerical simulations will have to be used to perform analyses. However, the number of simulations required to carry out tasks such as parameter estimation can become very large. To get around this, we… (More)

MOTIVATION
Biopathways are often modeled as systems of ordinary differential equations (ODEs). Such systems will usually have many unknown parameters and hence will be difficult to calibrate. Since the data available for calibration will have limited precision, an approximate representation of the ODEs dynamics should suffice. One must, however, be able to… (More)

Cellular processes are governed and coordinated by a multitude of biopathways. A pathway can be viewed as a complex network of biochemical reactions. The dynamics of this network largely determines the functioning of the pathway. Hence the modeling and analysis of biochemical networks dynamics is an important problem and is an active area of research. Here… (More)

Hybrid systems whose mode dynamics are governed by non-linear ordinary differential equations (ODEs) are often a natural model for biological processes. However such models are difficult to analyze. To address this, we develop a probabilistic analysis method by approximating the mode transitions as stochastic events. We assume that the probability of making… (More)

- Bing Liu
- 2015

abStract In this chapter, we review the current state of Gene Regulatory Network inference based on 'Genetical Genomics' experiments (Schadt et al., 2003) as a special case of causal network inference in 'Systems Genetics' (Threadgill, 2006). In a Genetical Genomics experiment, a segregating or genetically random-ized population is DNA marker genotyped and… (More)

Dynamic Bayesian Networks (DBNs) can serve as succinct probabilistic dynamic models of biochemical networks [CHECK END OF SENTENCE]. To analyze these models, one must compute the probability distribution over system states at a given time point. Doing this exactly is infeasible for large models; hence one must use approximate algorithms. The Factored… (More)