Reverse engineering biomolecular systems using -omic data: Challenges, progress and opportunities

Chang F. Quo, Chanchala Kaddi, John H. Phan, Amin Zollanvari, Mingqing Xu, May D. Wang, Gil Alterovitz

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)


Recent advances in high-throughput biotechnologies have led to the rapid growing research interest in reverse engineering of biomolecular systems (REBMS). 'Data-driven' approaches, i.e. data mining, can be used to extract patterns from large volumes of biochemical data at molecular-level resolution while 'design-driven' approaches, i.e. systems modeling, can be used to simulate emergent system properties. Consequently, both data- and design-driven approaches applied to -omic data may lead to novel insights in reverse engineering biological systems that could not be expected before using low-throughput platforms. However, there exist several challenges in this fast growing field of reverse engineering biomolecular systems: (i) to integrate heterogeneous biochemical data for data mining, (ii) to combine top-down and bottom-up approaches for systems modeling and (iii) to validate system models experimentally. In addition to reviewing progress made by the community and opportunities encountered in addressing these challenges, we explore the emerging field of synthetic biology, which is an exciting approach to validate and analyze theoretical system models directly through experimental synthesis, i.e. analysis-by-synthesis. The ultimate goal is to address the present and future challenges in reverse engineering biomolecular systems (REBMS) using integrated workflow of data mining, systems modeling and synthetic biology.

Original languageEnglish
Article numberbbs026
Pages (from-to)430-445
Number of pages16
JournalBriefings in bioinformatics
Issue number4
Publication statusPublished - Jul 2012


  • -omic data
  • Analysis-by-synthesis
  • High-throughput technology
  • Reverse engineering biological systems
  • Synthetic biology

ASJC Scopus subject areas

  • Information Systems
  • Molecular Biology

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