CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
New probabilistic graphical models for genetic regulatory networks studies
Journal of Biomedical Informatics
Inferring time-varying network topologies from gene expression data
EURASIP Journal on Bioinformatics and Systems Biology
International Journal of Data Mining and Bioinformatics
Robust filtering for gene expression time series data with variance constraints
International Journal of Computer Mathematics - Bioinformatics
A Partial Granger Causality Approach to Explore Causal Networks Derived From Multi-parameter Data
CMSB '08 Proceedings of the 6th International Conference on Computational Methods in Systems Biology
Transition dependency: a gene-gene interactionmeasure for times seriesmicroarray data
EURASIP Journal on Bioinformatics and Systems Biology - Special issue on network structure and biological function: Reconstruction, modelling, and statistical approaches
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Reverse engineering of gene regulatory networks: a comparative study
EURASIP Journal on Bioinformatics and Systems Biology - Special issue on network structure and biological function: Reconstruction, modelling, and statistical approaches
IEEE Transactions on Information Technology in Biomedicine
Using a state-space model and location analysis to infer time-delayed regulatory networks
EURASIP Journal on Bioinformatics and Systems Biology
The Journal of Machine Learning Research
Robust state estimation for stochastic genetic regulatory networks
International Journal of Systems Science - Dynamics Analysis of Gene Regulatory Networks
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
ITBAM'10 Proceedings of the First international conference on Information technology in bio- and medical informatics
Gene regulatory networks validation framework based in KEGG
HAIS'11 Proceedings of the 6th international conference on Hybrid artificial intelligent systems - Volume Part II
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Estimating gene networks with cDNA microarray data using state-space models
ICCSA'05 Proceedings of the 2005 international conference on Computational Science and Its Applications - Volume Part III
Reverse engineering of gene regulatory networks from biological data
Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery
Learning bi-clustered vector autoregressive models
ECML PKDD'12 Proceedings of the 2012 European conference on Machine Learning and Knowledge Discovery in Databases - Volume Part II
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Motivation: We have used state-space models to reverse engineer transcriptional networks from highly replicated gene expression profiling time series data obtained from a well-established model of T-cell activation. State space models are a class of dynamic Bayesian networks that assume that the observed measurements depend on some hidden state variables that evolve according to Markovian dynamics. These hidden variables can capture effects that cannot be measured in a gene expression profiling experiment, e.g. genes that have not been included in the microarray, levels of regulatory proteins, the effects of messenger RNA and protein degradation, etc. Results: Bootstrap confidence intervals are developed for parameters representing 'gene--gene' interactions over time. Our models represent the dynamics of T-cell activation and provide a methodology for the development of rational and experimentally testable hypotheses. Availability: Supplementary data and Matlab computer source code will be made available on the web at the URL given below. Supplementary information: http://public.kgi.edu/~wild/LDS/index.htm