Getting Closer to the Whole Picture

  title={Getting Closer to the Whole Picture},
  author={Uwe H. Sauer and Matthias Heinemann and Nicola Zamboni},
  pages={550 - 551}
A quantitative data set of RNA, proteins, and metabolites provides an unprecedented starting point to understand, at a systems level, the effects of perturbations on a cell. 
Grid and High-Performance Computing for Applied Bioinformatics
The beginning of the twenty-first century has been characterized by an explosion of biological information. The avalanche of data grows daily and arises as a consequence of advances in the fields o
Genomic data integration for ecological and evolutionary traits in non-model organisms
System biology initiatives such as ENCODE on non-model organisms and their effects on model organisms are studied in detail to help develop system biology initiatives.
Grand Challenges in Plant Systems Biology: Closing the Circle(s)
  • A. Fernie
  • Computer Science
    Front. Plant Sci.
  • 2012
The reductionist approach has successfully identified most of the components and many of the interactions but, unfortunately, offers no convincing concepts or methods to understand how system
Omics Techniques in Crop Research: An Overview
While phase one of omics technologies aims at nontargeted identification of transcripts, proteins, and metabolites (essentially gene products) in a given biological sample, phase two deals with a very challenging analysis of data eventually leading to the dissection of the qualitative and quantitative dynamics of biological systems.
Model Checking of Metabolic Networks: Application to Metabolic Diseases
The prominent Model Checking technology is used to build executable models of Metabolic Networks and is tested on a genome-scale metabolic network model of the human hepatocyte to investigate on a mendelian disease called Primary Hyperoxaluria type I.
PMID and text of abstracts axo_combined gene_a gene_b status Interaction data from proteomics and literature.
Parasites, proteomes and systems: has Descartes’ clock run out of time?
How well positioned is proteomics to deliver the data necessary to support meaningful systems modelling in parasite biology and why a new generation of quantitative proteomics data is now needed to underpin effective systems modelling is discussed.
Comparative Analysis of Biological Networks: Hidden Markov model and Markov chain-based approach
This study reviewed the application of Markov models to various comparative network analysis problems which provides a powerful means of gaining novel system-level understanding of diverse biological
Network Systems Biology for Drug Discovery
Systems biology provides a platform for integrating multiple components and interactions underlying cell, organ, and organism processes in health and disease, and bioinformatic network analysis of high‐throughput data sets offers an opportunity for integrated biological complexity and multilevel connectivity.
Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism
The responses of a bacterium to changing nutritional conditions are explored and an initial understanding of why certain regulatory strategies may be favored during evolution of dynamic control systems is offered.


The model organism as a system: integrating 'omics' data sets
Researchers are rising to the challenge by using omics data integration to address fundamental biological questions that would increase the understanding of systems as a whole.
Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations
E. coli seems to use complementary strategies that result in a metabolic network robust against perturbations, and actively regulated enzyme levels to maintain a stable metabolic state in response to changes in growth rate.
Integration of metabolome data with metabolic networks reveals reporter reactions
The algorithm thus enables identification of reporter reactions, which are reactions where there are significant coordinated changes in the level of surrounding metabolites following environmental/genetic perturbations, and shows that it is possible to infer whether the reactions are hierarchically or metabolically regulated.
Computational systems biology
The reviews in this Insight cover many different aspects of this energetic field, although all, in one way or another, illuminate the functioning of modular circuits, including their robustness, design and manipulation.
Metabolic networks in motion: 13C-based flux analysis
  • U. Sauer
  • Biology
    Molecular systems biology
  • 2006
It is argued here that intracellular reaction rates are the functional end points of these interactions in metabolic networks, hence are highly relevant for systems biology.
Regulation of yeast oscillatory dynamics
The regulation of the respiratory oscillation revolves around coupled subgraphs containing large numbers of proteins and metabolites, with a potential to oscillate, and no definable hierarchy, i.e., heterarchical control.
Continuous culture--making a comeback?
This review is intended to remind microbiologists of the value of continuous cultivation in a wide range of biological investigations, and describes some advantages and recent advances in applications of continuous culture in post-genomic studies.