Cargando…

Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways

BACKGROUND: The study of cellular metabolism in the context of high-throughput -omics data has allowed us to decipher novel mechanisms of importance in biotechnology and health. To continue with this progress, it is essential to efficiently integrate experimental data into metabolic modeling. RESULT...

Descripción completa

Detalles Bibliográficos
Autores principales:	Pey, Jon, Valgepea, Kaspar, Rubio, Angel, Beasley, John E, Planes, Francisco J
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2013
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878952/ https://www.ncbi.nlm.nih.gov/pubmed/24314206 http://dx.doi.org/10.1186/1752-0509-7-134

Ejemplares similares

Inferring branching pathways in genome-scale metabolic networks
por: Pitkänen, Esa, et al.
Publicado: (2009)

Path finding methods accounting for stoichiometry in metabolic networks
por: Pey, Jon, et al.
Publicado: (2011)

A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype
por: Pey, Jon, et al.
Publicado: (2013)

In-Silico Prediction of Key Metabolic Differences between Two Non-Small Cell Lung Cancer Subtypes
por: Rezola, Alberto, et al.
Publicado: (2014)

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks
por: Radrich, Karin, et al.
Publicado: (2010)

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
por: Reiss, David J, et al.
Publicado: (2006)

A Novel Multi-Scale Modeling Approach to Infer Whole Genome Divergence
por: Reuveni, Eli, et al.
Publicado: (2012)

A graphical model approach for inferring large-scale networks integrating gene expression and genetic polymorphism
por: Chu, Jen-hwa, et al.
Publicado: (2009)

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks
por: Zhou, Zhichao, et al.
Publicado: (2022)

Dynamic interaction network inference from longitudinal microbiome data
por: Lugo-Martinez, Jose, et al.
Publicado: (2019)

Network-based scoring system for genome-scale metabolic reconstructions
por: Serrano, M Ángeles, et al.
Publicado: (2011)

Boolean networks using the chi-square test for inferring large-scale gene regulatory networks
por: Kim, Haseong, et al.
Publicado: (2007)

Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data
por: Gong, Wuming, et al.
Publicado: (2015)

Dynamic probabilistic threshold networks to infer signaling pathways from time-course perturbation data
por: Kiani, Narsis A, et al.
Publicado: (2014)

An algorithm for the reduction of genome-scale metabolic network models to meaningful core models
por: Erdrich, Philipp, et al.
Publicado: (2015)

A framework for integrating inferred movement behavior into disease risk models
por: Dougherty, Eric R., et al.
Publicado: (2022)

CSN: unsupervised approach for inferring biological networks based on the genome alone
por: Galili, Maya, et al.
Publicado: (2020)

Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast Context-Specific Network Reconstruction Method
por: Tobalina, Luis, et al.
Publicado: (2016)

Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology
por: Santra, Tapesh, et al.
Publicado: (2013)

Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells
por: Barrena, Naroa, et al.
Publicado: (2023)

Algorithm of OMA for large-scale orthology inference
por: Roth, Alexander CJ, et al.
Publicado: (2008)

A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks
por: Röhl, Annika, et al.
Publicado: (2017)

Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization
por: Nair, Govind, et al.
Publicado: (2017)

Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis
por: Park, Sung-Joon, et al.
Publicado: (2013)

Functional networks inference from rule-based machine learning models
por: Lazzarini, Nicola, et al.
Publicado: (2016)

Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data
por: Gundogdu, Pelin, et al.
Publicado: (2022)

Enabling network inference methods to handle missing data and outliers
por: Folch-Fortuny, Abel, et al.
Publicado: (2015)

Consistency of biological networks inferred from microarray and sequencing data
por: Vinciotti, Veronica, et al.
Publicado: (2016)

Data-driven inference for the spatial scan statistic
por: Almeida, Alexandre CL, et al.
Publicado: (2011)

Study of Meta-analysis strategies for network inference using information-theoretic approaches
por: Pham, Ngoc C., et al.
Publicado: (2017)

DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference
por: Jiao, Yan, et al.
Publicado: (2011)

Integrating mutation and gene expression cross-sectional data to infer cancer progression
por: Fleck, Julia L., et al.
Publicado: (2016)

Lean-Proteome Strains – Next Step in Metabolic Engineering
por: Valgepea, Kaspar, et al.
Publicado: (2015)

BiologicalNetworks - tools enabling the integration of multi-scale data for the host-pathogen studies
por: Kozhenkov, Sergey, et al.
Publicado: (2011)

Inferring microRNA and transcription factor regulatory networks in heterogeneous data
por: Le, Thuc D, et al.
Publicado: (2013)

Characterizing Cancer-Specific Networks by Integrating TCGA Data
por: Xu, Yanxun, et al.
Publicado: (2015)

Weighted likelihood inference of genomic autozygosity patterns in dense genotype data
por: Blant, Alexandra, et al.
Publicado: (2017)

Inferring the role of transcription factors in regulatory networks
por: Veber, Philippe, et al.
Publicado: (2008)

Gene annotation and network inference by phylogenetic profiling
por: Wu, Jie, et al.
Publicado: (2006)

Inferring gene regression networks with model trees
por: Nepomuceno-Chamorro , Isabel A, et al.
Publicado: (2010)

Cannot write session to /tmp/vufind_sessions/sess_b71275kiob1lpdpka08g44ehat