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Modelling uncertainty in transcriptome measurements enhances network component analysis of yeast metabolic cycle
2009
2009 IEEE International Conference on Acoustics, Speech and Signal Processing
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We incorporated probe level uncertainties in gene expression measurements into the NCA analysis by the application of probabilistic principal component analysis (PPCA), and applied the method to data from ...
the network component analysis (NCA) approach. ...
We have used probabilistic principal component analysis to propagate probe level uncertainty in microarray measurements through such network analysis. ...
doi:10.1109/icassp.2009.4959947
dblp:conf/icassp/ChangHN09
fatcat:5525rmrtbfcevnd6ynsjhdqc34
A Guide to Integrating Transcriptional Regulatory and Metabolic Networks Using PROM (Probabilistic Regulation of Metabolism)
[chapter]
2013
Msphere
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Here, we present a guide to PROM (probabilistic regulation of metabolism), an automated method for the construction and simulation of integrated metabolic and transcriptional regulatory networks that enables ...
The integration of transcriptional regulatory and metabolic networks is a crucial step in the process of predicting metabolic behaviors that emerge from either genetic or environmental changes. ...
From these data, the transcriptional regulatory network of the organism can be quantified statistically, similar to the probabilistic Boolean networks of Shmulevich et al. (20) . ...
doi:10.1007/978-1-62703-299-5_6
pmid:23417801
fatcat:dajvwggo2ng5xpjgmenkh5filu
Network-based approaches for analysis of complex biological systems
2016
Current Opinion in Biotechnology
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functions (reviewed by Kim et al. [11]). 30 Expression-based network inference has been approached in two ways: by reconstructing regulatory programs for (i) individual genes at a time ("per-gene" methods ...
Towards this end, Arrieta-Ortiz and Hafemeister et. al. [23] first use network component analysis [24] to predict the activity of TFs given a prior network, and then use these TF activities to predict ...
Network component analysis: reconstruction of regulatory signals in biological systems. Proceedings of the National Academy of Sciences 2003;100(26):15522-15527. doi:10.1073/pnas.2136632100. 25. ...
doi:10.1016/j.copbio.2016.04.007
pmid:27115495
fatcat:3ppskhtoifbobayer5bzpqz6qq
Bayesian Integrative Modeling of Genome-Scale Metabolic and Regulatory Networks
2020
Informatics
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Thus, the integration of the transcriptional regulatory information is required to improve the accuracy and predictive ability of metabolic models. ...
In this paper, we propose an integrative predictive model based on techniques combining semantic web, probabilistic modeling, and constraint-based modeling methods. ...
Reconstruction of Regulatory Networks A crucial step in our integrated model is the reconstruction of the transcriptional regulatory network. ...
doi:10.3390/informatics7010001
fatcat:plvr2d64qzdxnp77wbsdia5qtm
Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution
2015
Annual Review of Cell and Developmental Biology
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Here, we review computational methods developed to study transcriptional regulatory networks using comparative genomics, from sequences to functional data. ...
In recent years, advances in genomic and computational tools have led to a wealth of methods for such analysis at the sequence, expression, pathway, module, and entire network level. ...
D.T. is supported by the NIH (R01CA119176-01). A.R. is supported by HHMI, the NIH (R01CA119176-01, P50HG006193), and the Sloan Foundation. ...
doi:10.1146/annurev-cellbio-100913-012908
pmid:26355593
fatcat:sryxj3e2gvapnnnkmnzdhnyzr4
Data-driven integration of genome-scale regulatory and metabolic network models
2015
Frontiers in Microbiology
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Individual models of biological networks (such as metabolism, transcription, and signaling) have played pivotal roles in driving microbial research through the years. ...
Citation: Imam S, Schäuble S, Brooks AN, Baliga NS and Price ND (2015) Data-driven integration of genome-scale regulatory and metabolic network models. Front. Microbiol. 6:409. ...
Acknowledgments This work was funded in part by DOE-ABY (DEEE0006315) (NSB, NDP), DOE ARPA-E program (DE-AR0000426) (NDP), ...
doi:10.3389/fmicb.2015.00409
pmid:25999934
pmcid:PMC4419725
fatcat:vp3skde33rgs3asbda7vhgrqly
Reconstruction of microbial transcriptional regulatory networks
2004
Current Opinion in Biotechnology
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Although metabolic networks can be readily reconstructed through comparative genomics, the reconstruction of regulatory networks has been hindered by the relatively low level of evolutionary conservation ...
This data together with literature-derived knowledge has opened the way for genome-scale reconstruction of transcriptional regulatory networks. ...
By contrast, the two primary data types useful for the regulatory network reconstruction taskgenome-wide mRNA expression and location analysis data -are widely available. ...
doi:10.1016/j.copbio.2003.11.002
pmid:15102470
fatcat:zzadypbtcbchzdtwz7xyzbgaq4
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis
2010
Proceedings of the National Academy of Sciences of the United States of America
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Metabolic networks are typically reconstructed and analyzed by using detailed chemistry-based methods (1, 2), whereas transcriptional regulatory networks have typically been reconstructed based on high-throughput ...
bridging two important classes of systems biology models that are rarely combined quantitatively. constraint-based modeling | flux balance analysis | metabolic networks | transcriptional regulation | probabilistic ...
This work was supported by a National Institutes of Health/National Cancer Institute Howard Temin Pathway to Independence Award in Cancer Research, a Young Investigator Grant from the Roy J. ...
doi:10.1073/pnas.1005139107
pmid:20876091
pmcid:PMC2955152
fatcat:zh7slr2mgvd4hle2k3vtbk5bwq
Reconstruction of biochemical networks in microorganisms
2008
Nature Reviews Microbiology
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network components. ...
Such studies are enabled by reconstruction, at the genomic scale, of the biochemical reaction networks that underlie cellular processes. ...
A.M.F. and I.T. were supported by National Institutes of Health (NIH) grant R01 GM057089 and M.J.H. was supported by NIH grant R01 GM071808. ...
doi:10.1038/nrmicro1949
pmid:19116616
pmcid:PMC3119670
fatcat:rzxjs54qizdl7gnzjeuisc6lw4
CRITICAL ANALYSIS OF TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL REGULATORY NETWORKS IN MULTIPLE MYELOMA
[chapter]
2009
Biocomputing 2010
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In this study, critical analysis of network components has been applied to inspect the transcriptional and post-transcriptional regulatory networks reconstructed from mRNA and microRNA expression data ...
The application of critical analysis to transcriptional and post-transcriptional regulatory networks allowed inferring novel regulatory relations potentially functional in multiple myeloma. * These authors ...
Here, the analysis of the network critical components was applied on the nodes of transcriptional and posttranscriptional regulatory networks reconstructed from mRNA and miRNA expression data of multiple ...
doi:10.1142/9789814295291_0042
fatcat:ojvh4ruy5bezpnpyai4u35sfpe
Enriching for direct regulatory targets in perturbed gene-expression profiles
2004
Genome Biology
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The updated algorithm can process networks containing feedback loops, incorporate positive and negative regulatory relationships during network reconstruction, and utilize data from double mutants to resolve ...
When applied to experimental data the reconstruction procedure preferentially retains direct transcription factor-target relationships. ...
This work was supported by the W. M. Keck Foundation. ...
doi:10.1186/gb-2004-5-4-r29
pmid:15059262
pmcid:PMC395788
fatcat:jj2by66qpjbkbmwfkx55gtp6hu
A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks
2020
BMC Bioinformatics
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network reconstruction algorithms. ...
Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. ...
Decomposition of a genome-wide Transcriptional Regulatory Network (TRN) allows to operate on the TF-TF Component, characterized by many regulatory loops, e.g. feedback loop (as shown in the magnifying ...
doi:10.1186/s12859-020-3510-1
pmid:32471360
fatcat:3v6orxxiyjaktmui6opbjebrxm
Iterative Reconstruction of Transcriptional Regulatory Networks: an Algorithmic Approach
2005
PLoS Computational Biology
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Principal among these will be transcriptional regulatory networks. ...
This paper presents an algorithm for experimental design to systematically and efficiently reconstruct transcriptional regulatory networks. ...
CLB conceived and designed the experiments, performed the experiments, analyzed the data, and contributed reagents/materials/analysis tools. BOP made the work possible by having a lab. ...
doi:10.1371/journal.pcbi.0020052.eor
fatcat:7iromi42jbbh5kbh5bidixkyea
Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach
2006
PLoS Computational Biology
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Principal among these will be transcriptional regulatory networks. ...
This paper presents an algorithm for experimental design to systematically and efficiently reconstruct transcriptional regulatory networks. ...
CLB conceived and designed the experiments, performed the experiments, analyzed the data, and contributed reagents/materials/analysis tools. BOP made the work possible by having a lab. ...
doi:10.1371/journal.pcbi.0020052
pmid:16710450
pmcid:PMC1463018
fatcat:bbxcn27ibngqlgawcffnjkp2oq
Inferring gene regulatory networks by thermodynamic modeling
2008
BMC Genomics
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To date, the reconstruction of gene regulatory networks from gene expression data has primarily relied on the correlation between the expression of transcription regulators and that of target genes. ...
This network suggests that Oct4, Sox2 and Klf4 indirectly repress lineage specific differentiation genes by activating transcriptional repressors of Ctbp2, Rest and Mtf2. ...
Acknowledgements This work is supported by National Center for Supercomputing Applications (SZ). ...
doi:10.1186/1471-2164-9-s2-s19
pmid:18831784
pmcid:PMC2559883
fatcat:gg7cpggfofbrzmlbnmm3eoor4u
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