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An effective framework for reconstructing gene regulatory networks from genetical genomics data

R. J. Flassig, S. Heise, K. Sundmacher, S. Klamt
2012 Bioinformatics  
Results: We present a framework for reconstructing gene regulatory networks from genetical genomics data where genotype and phenotype correlation measures are used to derive an initial graph which is subsequently  ...  However, although genetical genomics data contain rich information, a clear dissection of causes and effects as required for reconstructing gene regulatory networks is not easily possible.  ...  ACKNOWLEDGEMENTS We thank A. de la Fuente for providing us with the yeast data from Brem and Kruglyak (2005) in preprocessed form.  ... 
doi:10.1093/bioinformatics/bts679 pmid:23175757 fatcat:xpjedbe4obcrxjuiigyihlyfii

Reconstruction of microbial transcriptional regulatory networks

Markus J Herrgård, Markus W Covert, Bernhard Ø Palsson
2004 Current Opinion in Biotechnology  
This data together with literature-derived knowledge has opened the way for genome-scale reconstruction of transcriptional regulatory networks.  ...  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  ...  The authors present a scalable method to identify linear models of regulatory networks from gene expression (quantitative PCR) data and an application to the SOS regulatory network in E. coli.  ... 
doi:10.1016/j.copbio.2003.11.002 pmid:15102470 fatcat:zzadypbtcbchzdtwz7xyzbgaq4

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

Andrea Califano, Atul J Butte, Stephen Friend, Trey Ideker, Eric Schadt
2012 Nature Genetics  
We thus favor an alternative approach requiring the simultaneous reconstruction of context-specific gene regulatory networks 15 as well as of the genetic and epigenetic variability they harbor.  ...  The context-specific networks of molecular interactions that determine cell behavior provide a particularly relevant framework for the integration of data from multiple 'omics' .  ...  Gene networks dissected from DNA variability data can elucidate gene subnetworks driven by common genetic factors in an unbiased, data-driven fashion.  ... 
doi:10.1038/ng.2355 pmid:22836096 pmcid:PMC3593099 fatcat:dya2g4exzzcpfht4du27hfpyiq

Bayesian Integrative Modeling of Genome-Scale Metabolic and Regulatory Networks

Hanen Mhamdi, Jérémie Bourdon, Abdelhalim Larhlimi, Mourad Elloumi
2020 Informatics  
The integration of high-throughput data to build predictive computational models of cellular metabolism is a major challenge of systems biology.  ...  Integrative modeling is of primary importance to guide the search for various applications such as discovering novel potential drug targets to develop efficient therapeutic strategies for various diseases  ...  Results As shown in Figure 1 , the construction of an integrated metabolic-regulatory network using BayRegMet requires (i) a functional reconstructed genome-scale metabolic network formally represented  ... 
doi:10.3390/informatics7010001 fatcat:plvr2d64qzdxnp77wbsdia5qtm

Using gene networks to drug target identification

Zhenran Jiang, Yanhong Zhou
2005 Journal of Integrative Bioinformatics  
the biological regulatory mechanisms in diseases, which are playing an increasingly important role in searching for novel drug targets from the information contained in genomics.  ...  Gene network technique holds the promise of providing a conceptual framework for analysis of the profusion of biological data being generated on potential drug targets and providing insights to understand  ... Tool for reconstruction of genetic networks [60] GenePath Tool for automated construction of genetic networks from mutant data [61  ... 
doi:10.1515/jib-2005-14 fatcat:osugzd6pbvhl7egnsdv7wrfma4

Gene Expression Profiling and the Use of Genome-Scale In Silico Models of Escherichia coli for Analysis: Providing Context for Content

N. E. Lewis, B.-K. Cho, E. M. Knight, B. O. Palsson
2009 Journal of Bacteriology  
Overall, our experience shows that informative results can also be obtained if data are analyzed in the context of a genome-scale network reconstruction and with the use of an in silico model.  ...  (ii) Regulon-and network-level analysis in the modeling framework.  ...  Overall, our experience shows that informative results can also be obtained if data are analyzed in the context of a genome-scale network reconstruction and with the use of an in silico model.  ... 
doi:10.1128/jb.00034-09 pmid:19363119 pmcid:PMC2681886 fatcat:mbky7wcujjfmfamcd5o4fjavn4

Genome-scale modeling for metabolic engineering

Evangelos Simeonidis, Nathan D. Price
2015 Journal of Industrial Microbiology & Biotechnology  
Finally, we emphasize the importance of integrating metabolic networks with regulatory information-an area which we expect will become increasingly important for metabolic engineering-and present recent  ...  In large part owing to the advent of genomics and systems biology, we nowadays have a number of new tools that generate a wealth of data for analysis, contributing to our understanding of metabolism and  ...  Acknowledgments The authors gratefully acknowledge funding from the Luxembourg Centre for Systems Biomedicine (ES), and the DOE ARPA-E program (DE-AR0000426), an NIH Center for Systems Biology (2P50 GM076547  ... 
doi:10.1007/s10295-014-1576-3 pmid:25578304 pmcid:PMC4455951 fatcat:jrn652uygvaojb6tibg2iu5hqa

Integration of Epigenetic Data in Bayesian Network Modeling of Gene Regulatory Network [chapter]

Jie Zheng, Iti Chaturvedi, Jagath C. Rajapakse
2011 Lecture Notes in Computer Science  
The reverse engineering of gene regulatory network (GRN) is an important problem in systems biology.  ...  In this paper, we investigate how epigenetic data are incorporated into reconstruction of GRN. We encode the histone modification data as prior for Bayesian network inference of GRN.  ...  Analogous to genetic code for gene translation, it is hypothesized that there is an "epigenetic code" for controlling gene expression.  ... 
doi:10.1007/978-3-642-24855-9_8 fatcat:i5z6qz5q25dsdikrzkzfjqmzlu

Toward a systems biology approach to investigate cellular networks in normal and malignant B cells

K Basso
2009 Leukemia  
I thank Riccardo Dalla-Favera and Andrea Califano for leading me into an interdisciplinary path where biological and computational sciences walk together.  ...  Acknowledgements I am grateful to Ulf Klein, Pavel Sumazin and Roy L Maute for critical reading of the manuscript and to Govind Bhagat for providing photographic material used in Figure 2 .  ...  Reverse engineering of regulatory networks in mature B cells was performed applying the ARACNe (Algorithm for the Reconstruction of Accurate Cellular Networks) algorithm on a GEP data set, including normal  ... 
doi:10.1038/leu.2009.4 pmid:19194469 fatcat:reeppp7cofc6rp74utuhelmeza

Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data

Zhi-Ping Liu
2015 Current Genomics  
In this review, we summarize and categorize the main frameworks and methods currently available for inferring transcriptional regulatory networks from microarray gene expression profiling data.  ...  Reverse engineering of genome-wide regulatory networks from high-throughput transcriptomic data provides a promising way to characterize the global scenario of regulatory relationships between regulators  ...  However, these methods are not effective for reverse engineering genome-wide regulatory networks. We and Lu et al.  ... 
doi:10.2174/1389202915666141110210634 pmid:25937810 pmcid:PMC4412962 fatcat:tjn25agedzbezek47tdgbw4chu

Network-based approaches for analysis of complex biological systems

Deborah Chasman, Alireza Fotuhi Siahpirani, Sushmita Roy
2016 Current Opinion in Biotechnology  
The goal of network reconstruction (also referred to as network inference) methods is to infer such connections from genome-scale measurements of genes, proteins and metabolites from multiple conditions  ...  Although the idea of inferring networks from expression alone is attractive, genome-scale inference of such networks using current methods is an open challenge.  ...  Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior knowledge. Stat Appl Genet Mol Biol 2007;6:Article15.  ... 
doi:10.1016/j.copbio.2016.04.007 pmid:27115495 fatcat:3ppskhtoifbobayer5bzpqz6qq

Knocking sense into regulatory pathways

Guri Giaever, Corey Nislow
2009 Nature Biotechnology  
Next, they applied an integrative network algorithm that incorporates genetic and phosphoproteomics data to construct a JNK phosphorylation network, allowing them to propose a model of the architecture  ...  A probabilistic computational framework is then applied to reconstruct the phosphorylation signaling network (right panel).  ...  Next, they applied an integrative network algorithm that incorporates genetic and phosphoproteomics data to construct a JNK phosphorylation network, allowing them to propose a model of the architecture  ... 
doi:10.1038/nbt0209-149 pmid:19204694 fatcat:5wkn573rq5gdbgagitqds3vlim

Enriching for direct regulatory targets in perturbed gene-expression profiles

Susannah G Tringe, Andreas Wagner, Stephanie W Ruby
2004 Genome Biology  
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  ...  Here we build on a previously proposed algorithm to infer direct regulatory relationships using gene-expression profiles from cells in which individual genes are deleted or overexpressed.  ...  Bedrick for assistance with statistical analysis, J. Blanchard, M. Fuller and M. Gilchrist for critical reading of the manuscript, and P.  ... 
doi:10.1186/gb-2004-5-4-r29 pmid:15059262 pmcid:PMC395788 fatcat:jj2by66qpjbkbmwfkx55gtp6hu


Kyunga Kim, Marilyn A. L. West, Richard W. Michelmore, Dina A. St. Clair, R. W. Doerge
2004 Conference on Applied Statistics in Agriculture  
This approach allows comprehensive dissection of regulatory networks for complex traits at a systems biology level.  ...  Examples include quantitative trait locus (QTL) analysis and mutant analysis in genetics, genome sequencing and gene expression analysis in genomics.  ...  Network reconstruction Gene regulatory networks Although there is great diversity in biological models of regulatory pathways, three simple models are illustrated for a single structural gene with one  ... 
doi:10.4148/2475-7772.1153 fatcat:ogpwygcrszh3rnylwcbydrnsqe

Reconstructing regulatory network transitions

Jalean J. Petricka, Philip N. Benfey
2011 Trends in Cell Biology  
A transition from a stem cell to differentiated cell state, for example, may occur in response to gene expression changes induced by a transcription factor, or signaling cascades triggered by a hormone  ...  In this review, we highlight approaches to the reconstruction of regulatory networks underlying cellular transitions, with special attention to transcriptional regulatory networks.  ...  Box 3 Considerations for reconstruction of functional regulatory networks The goal of reconstructing functional regulatory networks is to connect phenotypic effects to genes or proteins that are relevant  ... 
doi:10.1016/j.tcb.2011.05.001 pmid:21632251 pmcid:PMC3149721 fatcat:7bi7tdqt2rhtzdzo2r7jlyt6cm
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