Publications

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8 Publications matching the given criteria: (Clear all filters)
Project: SysMO DB8
Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models

Abstract (Expand)

Mathematical modelling is increasingly becoming an indispensable tool for the study of cellular processes, allowing their analysis in a systematic and comprehensive manner. In the vast majority of the … cases, models focus on specific subsystems, and in particular describe either metabolism, gene expression or signal transduction. Integrated models that are able to span and interconnect these layers are, by contrast, rare as their construction and analysis face multiple challenges. Such methods, however, would represent extremely useful tools to understand cell behaviour, with application in distinct fields of biological and medical research. In particular, they could be useful tools to study genotype-phenotype mappings, and the way they are affected by specific conditions or perturbations. Here, we review existing computational approaches that integrate signalling, gene regulation and/or metabolism. We describe existing challenges, available methods and point at potentially useful strategies.

Authors: Emanuel Gonçalves, Joachim Bucher, Anke Ryll, Jens Niklas, Klaus Mauch, Steffen Klamt, Miguel Rocha, Julio Saez-Rodriguez

Date Published: 4th Jun 2013

Publication Type: Not specified

The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels

Abstract (Expand)

The African annual fish Nothobranchius furzeri has over recent years been established as a model species for ageing-related studies. This is mainly based on its exceptionally short lifespan and the … presence of typical characteristics of vertebrate ageing. To substantiate its role as an alternative vertebrate ageing model, a transcript catalogue is needed, which can serve e.g. as basis for identifying ageing-related genes.

Authors: Andreas Petzold, Kathrin Reichwald, Marco Groth, Stefan Taudien, Nils Hartmann, Steffen Priebe, Dmitry Shagin, Christoph Englert, Matthias Platzer

Date Published: 16th Mar 2013

Publication Type: Not specified

Biggest challenges in bioinformatics

Abstract (Expand)

The third Heidelberg Unseminars in Bioinformatics (HUB) was held on 18th October 2012, at Heidelberg University, Germany. HUB brought together around 40 bioinformaticians from academia and industry to … discuss the 'Biggest Challenges in Bioinformatics' in a 'World Cafe' style event.

Authors: J. C. Fuller, P. Khoueiry, H. Dinkel, K. Forslund, A. Stamatakis, J. Barry, A. Budd, T. G. Soldatos, K. Linssen, A. M. Rajput

Date Published: 15th Mar 2013

Publication Type: Not specified

Stealthy annotation of experimental biology by spreadsheets

Abstract

Not specified

Authors: Firstname Lastname, Firstname Lastname, Matthew Horridge, Simon Jupp, Firstname Lastname, Firstname Lastname, Firstname Lastname, Wolfgang Mueller, Robert Stevens, Firstname Lastname

Date Published: 1st Feb 2013

Publication Type: Not specified

A Mechanistic, Model-Based Approach to Safety Assessment in Clinical Development

Abstract

Not specified

Editor:

Date Published: 2013

Publication Type: Not specified

Inferring statin-induced gene regulatory relationships in primary human hepatocytes

Abstract (Expand)

MOTIVATION: Statins are the most widely used cholesterol-lowering drugs. The primary target of statins is HMG-CoA reductase, a key enzyme in cholesterol synthesis. However, statins elicit pleitropic … responses including beneficial as well as adverse effects in the liver or other organs. Today, the regulatory mechanisms that cause these pleiotropic effects are not sufficiently understood. RESULTS: In this work, genome-wide RNA expression changes in primary human hepatocytes of six individuals were measured at up to six time points upon atorvastatin treatment. A computational analysis workflow was applied to reconstruct regulatory mechanisms based on these drug-response data and available knowledge about transcription factor (TF) binding specificities and protein-drug interactions. Several previously unknown TFs were predicted to be involved in atorvastatin-responsive gene expression. The novel relationships of nuclear receptors NR2C2 and PPARA on CYP3A4 were successfully validated in wet-lab experiments. AVAILABILITY: Microarray data are available at the Gene Expression Omnibus (GEO) database at www.ncbi.nlm.nih.gov/geo/, under accession number GSE29868. CONTACT: andreas.zell@uni-tuebingen.de; adrian.schroeder@uni-tuebingen.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Authors: A. Schroder, J. Wollnik, C. Wrzodek, A. Drager, M. Bonin, O. Burk, M. Thomas, W. E. Thasler, U. M. Zanger, A. Zell

Date Published: 14th Jul 2011

Publication Type: Not specified

Identification and characterization of the PhhR regulon in Pseudomonas putida

Abstract

Not specified

Authors: M. Carmen Herrera, Estrella Duque, José J. Rodríguez-Herva, Ana M. Fernández-Escamilla, Juan L. Ramos

Date Published: 2010

Publication Type: Not specified

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