New probabilistic graphical models for genetic regulatory networks studies
Journal of Biomedical Informatics
Reconstructing networks using co-temporal functions
Proceedings of the 44th annual Southeast regional conference
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Knowledge and Information Systems
Learning robust cell signalling models from high throughput proteomic data
International Journal of Bioinformatics Research and Applications
Causality quantification and its applications: structuring and modeling of multivariate time series
Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining
Reverse Engineering of Regulatory Relations in Gene Networks by a Probabilistic Approach
WILF '09 Proceedings of the 8th International Workshop on Fuzzy Logic and Applications
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
Using knowledge driven matrix factorization to reconstruct modular gene regulatory network
AAAI'08 Proceedings of the 23rd national conference on Artificial intelligence - Volume 2
Scalable approach for effective control of gene regulatory networks
Artificial Intelligence in Medicine
Inference of genetic networks using linear programming machines: application of a priori knowledge
IJCNN'09 Proceedings of the 2009 international joint conference on Neural Networks
A new multiple regression approach for the construction of genetic regulatory networks
Artificial Intelligence in Medicine
Robust inference in Bayesian networks with application to gene expression temporal data
MCS'07 Proceedings of the 7th international conference on Multiple classifier systems
DILS'07 Proceedings of the 4th international conference on Data integration in the life sciences
Learning gene regulatory networks via globally regularized risk minimization
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Improving inference of transcriptional regulatory networks based on network evolutionary models
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Meta analysis algorithms for microarray gene expression data using Gene Regulatory Networks
International Journal of Data Mining and Bioinformatics
CIBB'09 Proceedings of the 6th international conference on Computational intelligence methods for bioinformatics and biostatistics
MC4: a tempering algorithm for large-sample network inference
PRIB'10 Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics
Learning Genetic Regulatory Network Connectivity from Time Series Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Genetic Networks and Soft Computing
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A Study on Gene Regulatory Network Reconstruction and Simulation
Proceedings of the 2011 conference on Neural Nets WIRN10: Proceedings of the 20th Italian Workshop on Neural Nets
Finding an optimal DE model for biological network inference
ICS'06 Proceedings of the 10th WSEAS international conference on Systems
Brief paper: Robust dynamical network structure reconstruction
Automatica (Journal of IFAC)
A new evolutionary gene regulatory network reverse engineering tool
EvoBIO'11 Proceedings of the 9th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
Inferring cell cycle feedback regulation from gene expression data
Journal of Biomedical Informatics
Analysis of nasopharyngeal carcinoma risk factors with Bayesian networks
Artificial Intelligence in Medicine
Learning genetic regulatory network connectivity from time series data
IEA/AIE'06 Proceedings of the 19th international conference on Advances in Applied Artificial Intelligence: industrial, Engineering and Other Applications of Applied Intelligent Systems
The evolution of higher-level biochemical reaction models
Genetic Programming and Evolvable Machines
ICONIP'11 Proceedings of the 18th international conference on Neural Information Processing - Volume Part II
Dynamic bayesian network modeling of cyanobacterial biological processes via gene clustering
ICONIP'11 Proceedings of the 18th international conference on Neural Information Processing - Volume Part I
AI'11 Proceedings of the 24th international conference on Advances in Artificial Intelligence
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
EvoBIO'12 Proceedings of the 10th European conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
ADANET: inferring gene regulatory networks using ensemble classifiers
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
FusGP: bayesian co-learning of gene regulatory networks and protein interaction networks
ICONIP'12 Proceedings of the 19th international conference on Neural Information Processing - Volume Part V
Data discretization for dynamic bayesian network based modeling of genetic networks
ICONIP'12 Proceedings of the 19th international conference on Neural Information Processing - Volume Part II
mDBN: motif based learning of gene regulatory networks using dynamic bayesian networks
Proceedings of the 15th annual conference on Genetic and evolutionary computation
Inferring large scale genetic networks with S-system model
Proceedings of the 15th annual conference on Genetic and evolutionary computation
Inference of the Genetic Network Regulating Lateral Root Initiation in Arabidopsis thaliana
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Computational Reconstruction of Transcriptional Relationships from ChIP-Chip Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A practical simulation method for social networks
AWC '13 Proceedings of the First Australasian Web Conference - Volume 144
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Motivation: Network inference algorithms are powerful computational tools for identifying putative causal interactions among variables from observational data. Bayesian network inference algorithms hold particular promise in that they can capture linear, non-linear, combinatorial, stochastic and other types of relationships among variables across multiple levels of biological organization. However, challenges remain when applying these algorithms to limited quantities of experimental data collected from biological systems. Here, we use a simulation approach to make advances in our dynamic Bayesian network (DBN) inference algorithm, especially in the context of limited quantities of biological data. Results: We test a range of scoring metrics and search heuristics to find an effective algorithm configuration for evaluating our methodological advances. We also identify sampling intervals and levels of data discretization that allow the best recovery of the simulated networks. We develop a novel influence score for DBNs that attempts to estimate both the sign (activation or repression) and relative magnitude of interactions among variables. When faced with limited quantities of observational data, combining our influence score with moderate data interpolation reduces a significant portion of false positive interactions in the recovered networks. Together, our advances allow DBN inference algorithms to be more effective in recovering biological networks from experimentally collected data. Availability: Source code and simulated data are available upon request. Supplementary information: http://www.jarvislab.net/Bioinformatics/BNAdvances/