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Fast Bayesian inference for gene regulatory networks using ScanBMA

William Young, Adrian E Raftery, Ka Yeung
2014 BMC Systems Biology  
Genome-wide time-series data provide a rich set of information for discovering gene regulatory relationships.  ...  for the integration of multiple data sources, and yield robust, accurate and compact gene-to-gene relationships.  ...  Roger Bumgarner and Chris Fraley for helpful discussion. http://www.biomedcentral.com/1752-0509/8/47  ... 
doi:10.1186/1752-0509-8-47 pmid:24742092 pmcid:PMC4006459 fatcat:czkofbafefanjk3zrl4ajovrbi

Single-cell gene regulatory network inference at scale: The Inferelator 3.0 [article]

Claudia Skok Gibbs, Christopher A Jackson, Giuseppe-Antonio Saldi, Aashna Shah, Andreas Tj&aumlrnberg, Aaron Watters, Nicholas De Veaux, Konstantine Tchourine, Ren Yi, Tymor Hamamsy, Dayanne M Castro, Nicholas Carriero (+3 others)
2021 bioRxiv   pre-print
Gene regulatory networks define regulatory relationships between transcription factors and target genes within a biological system, and reconstructing them is essential for understanding cellular growth  ...  We demonstrate its capabilities by learning networks for multiple distinct neuronal and glial cell types in the developing Mus musculus brain at E18 from a large (1.3 million) single-cell gene expression  ...  Acknowledgements We thank past and present members of the Gresham, Miraldi, and Bonneau labs for discussions and valuable feedback on this manuscript.  ... 
doi:10.1101/2021.05.03.442499 fatcat:opfezyn6xjebzkd2toyup5zpgy

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

Zhi-Ping Liu, Canglin Wu, Hongyu Miao, Hulin Wu
2015 Database: The Journal of Biological Databases and Curation  
for potential extensions to include gene regulatory networks for other organisms in the future.  ...  Therefore, in this work, we build a knowledge-based database, named 'RegNetwork', of gene regulatory networks for human and mouse by collecting and integrating the documented regulatory interactions among  ...  Prior knowledge on gene regulatory relationships from multiple sources (e.g. genomic context, conserved gene coexpression, knockout or high-throughput experiment) spreads out in various databases and literature  ... 
doi:10.1093/database/bav095 pmid:26424082 pmcid:PMC4589691 fatcat:iax5idoulfad7iz4z5iqmn4swu

Sparse and Stable Reconstruction of Genetic Regulatory Networks Using Time Series Gene Expression Data

Roozbeh Manshaei, Matthew Kyan
2007 Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics - BCB'13  
Gene regulatory networks represent the regulatory and physical interactions between genes of an organism.  ...  To this end, we formulate an algorithm for reconstructing a genetic regulatory network to explain time series data obtained from genetic experiments.  ...  CONCLUSIONS In this paper, we described a novel algorithm based on convex optimization for gene regulatory network reconstruction.  ... 
doi:10.1145/2506583.2512380 dblp:conf/bcb/ManshaeiK13 fatcat:h27zefvgezc5rjwfin5f47bhxa

Data-based Reconstruction of Gene Regulatory Networks of Fungal Pathogens

Reinhard Guthke, Silvia Gerber, Theresia Conrad, Sebastian Vlaic, Saliha Durmuş, Tunahan Çakır, F. E. Sevilgen, Ekaterina Shelest, Jörg Linde
2016 Frontiers in Microbiology  
The crucial point of genome-wide GRN modeling is the experimental evidence, both used for inferring the networks (omics 'first-hand' data as well as literature data used as prior knowledge) and for validation  ...  In the emerging field of systems biology of fungal infection, one of the central roles belongs to the modeling of gene regulatory networks (GRNs).  ...  GRN reconstruction is mainly based on transcriptome data supported by prior knowledge interactions derived from literature.  ... 
doi:10.3389/fmicb.2016.00570 pmid:27148247 pmcid:PMC4840211 fatcat:hxo64y5c7zf2dlu3kt7zwcfdby

Inferring Transcriptional Regulatory Relationships Among Genes in Breast Cancer: An Application of Bayes' Theorem

Emmanuel S. Adabor, George K. Acquaah-Mensah, Francis T. Oduro
2014 International Journal of Statistics and Probability  
Gene networks may be inferred from such microarray data.  ...  The identified causal networks are potentially useful for understanding complex drug actions and dysfunctional signaling in breast cancer.  ...  The nodes denote the genes in a gene network. Figure 1 is an example of a BN describing a gene regulatory network.  ... 
doi:10.5539/ijsp.v3n2p52 fatcat:5nqktk4i45ggvawo5d3kvfwwq4

AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks

S. K. Palaniswamy, S. James, H. Sun, R. S. Lamb, R. V. Davuluri, E. Grotewold
2006 Plant Physiology  
The growing identification of direct target genes for key transcription factors (TFs) through traditional and high-throughput experimental approaches has facilitated the elucidation of regulatory networks  ...  AGRIS can be accessed at Curators for AGRIS Currently, there are curators for some families; based on our request and their expertise, the curators help us validate data through cross-verification approach  ...  ACKNOWLEDGMENTS We thank Sarat Subramanian for his help in AtTFDB, and Twyla Pohar for her comments and header design for the Web site.  ... 
doi:10.1104/pp.105.072280 pmid:16524982 pmcid:PMC1400579 fatcat:nozjjocitnbm5ilyfdfsjasyei

mirConnX: condition-specific mRNA-microRNA network integrator

G. T. Huang, C. Athanassiou, P. V. Benos
2011 Nucleic Acids Research  
The prior network is supplemented with known interactions from the literature.  ...  mirConnX is a user-friendly web interface for inferring, displaying and parsing mRNA and microRNA (miRNA) gene regulatory networks. mirConnX combines sequence information with gene expression data analysis  ...  ACKNOWLEDGEMENTS The authors would like to thank Dr Naftali Kaminski and his group for beta-testing the web site and for helpful suggestions.  ... 
doi:10.1093/nar/gkr276 pmid:21558324 pmcid:PMC3125733 fatcat:4xj7lu76bnbk5cx6is6jtr2s4q

Characterization of the proneural gene regulatory network during mouse telencephalon development

Julia M Gohlke, Olivier Armant, Frederick M Parham, Marjolein V Smith, Celine Zimmer, Diogo S Castro, Laurent Nguyen, Joel S Parker, Gerard Gradwohl, Christopher J Portier, François Guillemot
2008 BMC Biology  
Finally, a gene regulatory network was delineated using a novel Bayesian-based algorithm that can incorporate information from diverse datasets.  ...  binding sites for Ngn2 and Mash1.  ...  Algorithm-based gene regulatory network structure for dorsal and ventral telencephalon development Figure 5 Algorithm-based gene regulatory network structure for dorsal and ventral telencephalon development  ... 
doi:10.1186/1741-7007-6-15 pmid:18377642 pmcid:PMC2330019 fatcat:uiesypadszhglphqoshpzqqkbq

Large-scale modeling of condition-specific gene regulatory networks by information integration and inference

Daniel Christian Ellwanger, Jörn Florian Leonhardt, Hans-Werner Mewes
2014 Nucleic Acids Research  
We developed COGERE (http://mips.helmholtz-muenchen. de/cogere), a method for the inference of conditionspecific gene regulatory networks in human and mouse.  ...  The integration of prior biological knowledge into the modeling process of systems-wide gene regulation enables the large-scale interpretation of gene expression signals in the context of known regulatory  ...  ACKNOWLEDGMENTS We thank Gregor Sturm (Technische Universität München) for his technical support.  ... 
doi:10.1093/nar/gku916 pmid:25294834 pmcid:PMC4245971 fatcat:yubbb5buhraj3gk2z6wtw5xl74

Towards precise reconstruction of gene regulatory networks by data integration

Zhi-Ping Liu
2018 Quantitative Biology  
So far, numerous methods have been developed for reconstructing gene regulatory networks.  ...  We highlight the importance of multi-omics data integration with prior knowledge in gene regulatory network inferences.  ...  For instance, we proposed a network-based screening method for evaluating the prior regulatory networks in response to the gene expression profiling by graphical models [55, 56] .  ... 
doi:10.1007/s40484-018-0139-4 fatcat:c7rzunvk7ngxbbeem3bz226xhm

A Framework for Elucidating Regulatory Networks Based on Prior Information and Expression Data

O. GEVAERT, S. VAN VOOREN, B. DE MOOR
2007 Annals of the New York Academy of Sciences  
In such a way Bayesian networks provide a powerful framework for data integration and regulatory network modeling.  ...  These priors, either separately or combined, have the potential of reducing the complexity of reverseengineering regulatory networks while creating more robust and reliable models.  ...  Text-Based Prior Next, we propose the use of text-based gene-by-gene-similarity matrices as priors.  ... 
doi:10.1196/annals.1407.002 pmid:17925352 fatcat:tyhfdjrt35agjkckpogjw4jnqa

Dynamic modelling of microRNA regulation during mesenchymal stem cell differentiation

Michael Weber, Ana M Sotoca, Peter Kupfer, Reinhard Guthke, Everardus J van Zoelen
2013 BMC Systems Biology  
Network inference was performed using NetGenerator to reconstruct a dynamical regulatory model based on the measured data and prior knowledge.  ...  Network inference from gene expression data is a typical approach to reconstruct gene regulatory networks.  ...  Joris Pothof (ErasmusMC, Rotterdam) for his contribution to the microarray analysis of the miRNAs.  ... 
doi:10.1186/1752-0509-7-124 pmid:24219887 pmcid:PMC4225824 fatcat:ovq72vjl7ndhloqcggkk4zzthi

Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis

Panagiotis Chouvardas, George Kollias, Christoforos Nikolaou
2016 BMC Bioinformatics  
regulatory networks (GRN).  ...  The combination of prior information and novel concept of a hierarchical reconstruction of regulatory interactions makes RNEA a very useful tool for a first-level interpretation of gene expression profiles  ...  The authors would like to thank three anonymous reviewers for their fruitful comments and recommendations for additional resources to be used in the formation of the reference networks.  ... 
doi:10.1186/s12859-016-1040-7 pmid:27295045 pmcid:PMC4905609 fatcat:nkxwyx5ttbgw5dyzegzkd4qktq

The Local Edge Machine: inference of dynamic models of gene regulation

Kevin A. McGoff, Xin Guo, Anastasia Deckard, Christina M. Kelliher, Adam R. Leman, Lauren J. Francey, John B. Hogenesch, Steven B. Haase, John L. Harer
2016 Genome Biology  
We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data.  ...  Finally, we use an atlas of transcription data in a mammalian circadian system to illustrate how the method can be used for discovery in the context of large complex networks.  ...  Thus, given a TF of interest in a gene regulatory network, LEM is a useful tool for scoring probable targets of that TF based on time-series gene expression data.  ... 
doi:10.1186/s13059-016-1076-z pmid:27760556 pmcid:PMC5072315 fatcat:g5mkc3ntzrbdpi4txg4h2nh7qm
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