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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

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Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis
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Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

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Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations

Irene Papatheodorou1, Matthias Ziehm, Daniela Wieser

  • 1European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. irenep@ebi.ac.uk

Plos One
|December 20, 2012
PubMed
Summary

Systems biology integrates pathway knowledge with experimental data to understand ageing and longevity. This study uses logic-based Answer Set Programming to infer insulin signaling pathway effects on lifespan in Drosophila mutants.

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Last Updated: May 15, 2026

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis
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The Replica Set Method: A High-throughput Approach to Quantitatively Measure Caenorhabditis elegans Lifespan
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The Replica Set Method: A High-throughput Approach to Quantitatively Measure Caenorhabditis elegans Lifespan

Published on: June 29, 2018

Area of Science:

  • Systems Biology
  • Computational Biology
  • Genetics

Background:

  • Ageing research often yields incomplete data, hindering integration of RNA expression, biological processes, and ageing phenotypes like longevity.
  • Systems biology faces challenges in integrating incomplete pathway knowledge with experimental data and linking it to measured phenotypes.

Purpose of the Study:

  • To develop and apply a logic-based method using Answer Set Programming (ASP) to infer signaling effects of genetic perturbations in the insulin signaling pathway.
  • To deduce how the insulin signaling pathway influences lifespan in Drosophila mutants by analyzing RNA expression data.
  • To identify homeostatic mechanisms and feedback loops within the insulin signaling pathway in relation to ageing and lifespan.

Main Methods:

  • Developed a logic-based method employing Answer Set Programming (ASP) to model and infer signaling effects.
  • Applied the method to RNA expression data from Drosophila mutants affecting lifespan in a foxo-dependent manner.
  • Utilized ASP's efficient search capabilities to explore pathways, integrate molecular changes with phenotypes, and infer in vivo signaling effects.

Main Results:

  • Inferred signaling effects of genetic perturbations in the insulin pathway on Drosophila lifespan.
  • Identified consistent homeostatic mechanisms across long- and short-lived mutants, with transcriptional changes often providing negative feedback.
  • Discovered S6K-mediated feedback in long-lived mutants, suggesting pathway crosstalk in insulin pathway mutants.

Conclusions:

  • The logic-based ASP approach effectively integrates incomplete pathway knowledge with experimental data to infer complex biological mechanisms.
  • The study reveals conserved homeostatic mechanisms and feedback loops influencing lifespan in Drosophila.
  • The NetEffects web service provides a tool for applying these methods to study signaling in whole-organism mutants.