Functional genomics, proteomics, metabolomics and bioinformatics for systems biology

Stéphane Ballereau*, Enrico Glaab, Alexei Kolodkin, Amphun Chaiboonchoe, Maria Biryukov, Nikos Vlassis, Hassan Ahmed, Johann Pellet, Nitin Baliga, Leroy Hood, Reinhard Schneider, Rudi Balling, Charles Auffray

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

4 Citations (Scopus)


This chapter introduces Systems Biology, its context, aims, concepts and strategies, then describes approaches used in genomics, epigenomics, transcriptomics, proteomics, metabolomics and lipidomics, and how recent technological advances in these fields have moved the bottleneck from data production to data analysis. Methods for clustering, feature selection, prediction analysis, text mining and pathway analysis used to analyse and integrate the data produced are then presented.

Original languageEnglish
Title of host publicationSystems Biology
Subtitle of host publicationIntegrative Biology and Simulation Tools
PublisherSpringer Netherlands
Number of pages39
ISBN (Electronic)9789400768031
ISBN (Print)9789400768024
Publication statusPublished - 1 Jan 2013
Externally publishedYes


  • Bioinformatics
  • Bottom-up
  • Clustering
  • Curse of dimensionality
  • Data integration
  • Emergence
  • Epigenomics
  • Feature selection
  • Functional genomics
  • High-dimensionality
  • High-throughput
  • Holistic
  • Interactions
  • Knowledge management
  • Mass spectrometry
  • Mathematical model
  • Metabolomics
  • Middle-out
  • Network
  • Next generation sequencing
  • Ontology
  • Pathway
  • Prediction analysis
  • Proteomics
  • Text-mining
  • Top-down
  • Transcriptomics


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