8 documents found, page 1 of 1
Corrigendum to “Post-translational regulation of metabolism in fumarate hydrata...
Gonçalves, Emanuel; Sciacovelli, Marco; Costa, Ana S. H.; Tran, Maxine Gia Binh; Johnson, Timothy Isaac; Machado, Daniel; Frezza, ChristianThe authors regret to inform the readers that the 2SC staining for the normal kidney of Patient 1 in Fig. 4C was an unintentional duplication of the PDH-E1a-pSer232 staining of the same patient that occurred during the final assembly of the figure. The correct panel is now included in this Corrigendum. We thank the anonymous reader in Pubpeer for pointing this mistake out.
Causal integration of multi-omics data with prior knowledge to generate mechani...
Dugourd, Aurelien; Kuppe, Christoph; Sciacovelli, Marco; Gjerga, Enio; Gabor, Attila; Emdal, Kristina B.; Vieira, Vítor; Bekker-Jensen, Dorte B.Multi-omics datasets can provide molecular insights beyond the sum of individual omics. Various tools have been recently developed to integrate such datasets, but there are limited strategies to systematically extract mechanistic hypotheses from them. Here, we present COSMOS (Causal Oriented Search of Multi-Omics Space), a method that integrates phosphoproteomics, transcriptomics, and metabolomics datasets. COS...
Post-translational regulation of metabolism in fumarate hydratase deficient can...
Gonçalves, Emanuel; Sciacovelli, Marco; Costa, Ana S. H.; Tran, Maxine Gia Binh; Johnson, Timothy Isaac; Machado, Daniel; Frezza, ChristianDeregulated signal transduction and energy metabolism are hallmarks of cancer and both play a fundamental role in tumorigenesis. While it is increasingly recognised that signalling and metabolism are highly interconnected, the underpinning mechanisms of their co-regulation are still largely unknown. Here we designed and acquired proteomics, phosphoproteomics, and metabolomics experiments in fumarate hydratase (...
Data-driven reverse engineering of signaling pathways using ensembles of dynami...
Henriques, David; Villaverde, Alejandro F.; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R.Signaling pathways play a key role in complex diseases such as cancer, for which the development of novel therapies is a difficult, expensive and laborious task. Computational models that can predict the effect of a new combination of drugs without having to test it experimentally can help in accelerating this process. In particular, network-based dynamic models of these pathways hold promise to both understand...
Logical Modeling and Dynamical Analysis of Cellular Networks
Abou-Jaoudé, Wassim; Traynard, Pauline; Monteiro, Pedro T.; Saez-Rodriguez, Julio; Helikar, Tomáš; Thieffry, Denis; Chaouiya, ClaudineThe logical (or logic) formalism is increasingly used to model regulatory and signaling networks. Complementing these applications, several groups contributed various methods and tools to support the definition and analysis of logical models. After an introduction to the logical modeling framework and to several of its variants, we review here a number of recent methodological advances to ease the analysis of l...
Reverse engineering of logic-based differential equation models using a mixed-i...
Henriques, David; Rocha, Miguel; Saez-Rodriguez, Julio; Banga, Julio R.Motivation: Systems biology models can be used to test new hypotheses formulated on the basis of previous knowledge or new experimental data, contradictory with a previously existing model. New hypotheses often come in the shape of a set of possible regulatory mechanisms. This search is usually not limited to finding a single regulation link, but rather a combination of links subject to great uncertainty or no ...
SBML qualitative models: a model representation format and infrastructure to fo...
Chaouiya, Claudine; Bérenguier, Duncan; Keating, Sarah M; Naldi, Aurélien; van Iersel, Martijn P; Rodriguez, Nicolas; Dräger, Andreas; Büchel, FinjaQualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qual...
Path2Models: large-scale generation of computational models from biochemical pa...
Büchel, Finja; Rodriguez, Nicolas; Swainston, Neil; Wrzodek, Clemens; Czauderna, Tobias; Keller, Roland; Mittag, Florian; Schubert, MichaelSystems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data.