U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights

A Genomic-Scale Reconstruction of Mycoplasma genitalium
Published: March 02, 2009
Posted: March 27, 2009

Reconstructing an organism's metabolic pathways is an important step in being able to understand and use those biological capabilities to solve DOE energy and environmental challenges. This rapidly evolving field requires development of sophisticated computational tools to model metabolic networks, tools to bridge gaps in the models, and experiments to resolve inconsistencies. Dr. Costas Maranas of Penn State University describes the systematic reconstruction of pathways involving 40% of the genes in Mycoplasma genitalium, one of the smallest known self-replicating organisms. Their computational model of M. genitalium iPS189 includes 262 biochemical reactions and 274 metabolites and is 87% accurate in capturing genes essential for M. genitalium function. This work provides a roadmap for the automated construction of computer-based metabolic models for other organisms important for DOE mission needs. Details can be found in the journal PLoS Computational Biology, February 2009, Vol. 5 , Issue (2).  This work is jointly sponsored by DOE's Office of Biological and Environmental Science and the Office of Advanced Scientific Computing Research.

Contact: Susan Gregurick, SC-21.1, (301) 903-7672, Christine Chalk, SC-21.1 (301) 903-5152
Topic Areas:

  • Research Area: Microbes and Communities
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: Biosystems Design
  • Research Area: Computational Biology, Bioinformatics, Modeling

Division: SC-23 BER
      (formerly SC-23 OBER)


BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

May 10, 2019
Quantifying Decision Uncertainty in Water Management via a Coupled Agent-Based Model
Considering risk perception can improve the representation of human decision-making processes in age [more...]

May 09, 2019
Projecting Global Urban Area Growth Through 2100 Based on Historical Time Series Data and Future Scenarios
Study provides country-specific urban area growth models and the first dataset on country-level urba [more...]

May 05, 2019
Calibrating Building Energy Demand Models to Refine Long-Term Energy Planning
A new, flexible calibration approach improved model accuracy in capturing year-to-year changes in bu [more...]

May 03, 2019
Calibration and Uncertainty Analysis of Demeter for Better Downscaling of Global Land Use and Land Cover Projections
Researchers improved the Demeter model’s performance by calibrating key parameters and establi [more...]

Apr 22, 2019
Representation of U.S. Warm Temperature Extremes in Global Climate Model Ensembles
Representation of warm temperature events varies considerably among global climate models, which has [more...]

List all highlights (possible long download time)