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About the DOE Genomic Science Program

Advancing Scientific Discovery through Genomics and Systems Biology

The Department of Energy (DOE) Genomic Science program supports systems biology research aimed at identifying the foundational principles driving biological systems of plants, microbes, and multispecies communities relevant to DOE missions in energy and the environment. Building on the foundation of sequenced genomes and metagenomes, the program focuses on a tightly coupled approach that combines experimental physiology, omics-driven analytical techniques, and computational modeling of functional biological networks.

Program Goal

Achieve a predictive, systems-level understanding of plants, microbes, and biological communities to enable biobased solutions to DOE mission challenges in energy and environment.

Objectives

The program's ultimate objectives are to:

  • Determine the molecular mechanisms, regulatory elements, and integrated networks needed to understand genome-scale functional properties of biological systems.
  • Develop omics experimental capabilities and enabling technologies needed to achieve dynamic, systems-level understanding of organism and community function.
  • Flexibly scale understanding of biological processes from defined subsystems to individual organisms, consortial assemblies of multiple organisms, or complex communities operating at ecosystem scales.
  • Understand the foundational rules and “design principles” governing living systems and develop tools for more sophisticated biosystems design, enabling the targeted modification of functional properties at the genome scale.
  • Develop the knowledgebase, computational infrastructure, and modeling capabilities to advance predictive understanding and manipulation of biological systems.

Advancing fundamental knowledge of these systems bridges critical knowledge gaps that must be addressed to enable biological solutions to crucial DOE missions. Development of innovative approaches for sustainable bioenergy production will be accelerated by systems biology–based understanding of nonfood plants that can serve as dedicated bioenergy feedstocks and microbes capable of deconstructing biomass into their sugar subunits and synthesizing next-generation biofuels (either from cellulosic biomass or through direct photosynthetic capture of carbon dioxide). Genomic Science program research also employs the omics-driven tools of modern systems biology to analyze interactions between organisms that form biological communities and their surrounding environments. Understanding the relationships between molecular-scale functional biology and ecosystem-scale environmental processes illuminates the basic mechanisms that drive biogeochemical cycling of metals and nutrients, carbon biosequestration, and greenhouse gas emissions in both terrestrial ecosystems impacted by climate change and in agricultural systems producing bioenergy feedstocks. As new understanding emerges, strategic emphasis will be placed on overcoming knowledge gaps and fostering transformational breakthroughs that most effectively address DOE mission-critical research objectives.

Multi-Scale Explorations

For biological systems central to DOE missions in energy and the environment, Genomic Science program research analyzes properties and processes on three fundamental levels.

  • Molecular: Focusing on genes, proteins, macromolecular complexes, and other biomolecules that provide structure and perform a cellular function. Such an approach aids in understanding how the genome determines dynamic biological structure and function at all scales, from genes to ecosystems, and how proteins and protein complexes function individually or in interactions with other cellular components.
  • Cellular: Investigating dynamic molecular processes, networks, and subsystems controlled and coordinated to enable complex cellular processes such as growth and metabolism.
  • Multicellular and Multiorganismal Systems: Exploring diverse cellular systems that interact to carry out coordinated complex processes that both respond to and alter their environments to determine how cells work in the context of multicellular tissues of plants and multiorganism communities of microbes and plants.

The myriad biological structures and processes that exist within these three system levels are interconnected and coordinated by an intricate set of regulatory controls and continuous interactions with the surrounding environment. To investigate biology at multiple scales, the Genomic Science program is building new multidisciplinary research communities and advancing development of next-generation, automated technologies that increase sample throughput and analytical reliability while reducing analysis time. Key research technology and methodology development areas for the Genomic Science program include genomics, analytical omics, molecular imaging and structural analysis, modeling and simulation, and genome-scale engineering tools that span all three levels of organization.

From Genome Sequences to Understanding

As a leader in systems biology research, the Genomic Science program builds on a foundation of genome sequences, genetic regulatory networks, densely arrayed metabolic pathways, and higher-scale organismal interactions to identify the common fundamental principles that drive living systems. Knowledge of these common principles revealed by studying organisms relevant to any one DOE mission facilitates breakthroughs in basic biology important to other DOE and national needs. By leveraging the increasing availability of sequences from whole organism genomes and environmental samples (metagenomes), Genomic Science program researchers are developing advanced methods to facilitate the translation of genome sequence into predictive understanding of function. These methods cut across DOE missions in energy and the environment.

Genomic Science program systems biology research extends traditional scientific methodology by addressing complex problems through coordinated research among interdisciplinary teams with complementary expertise in the biological, physical, and computational sciences. A nested array of experimental techniques and analytical technologies must be created, refined, and deployed to investigate and understand biological systems, linking different levels of biological discovery to gain a predictive understanding of whole systems—from cells to ecosystems. To accomplish the desired in-depth understanding of biological systems, an unprecedented integration of experimental biology, analytical technologies, data and computation, theory, modeling, simulation, and experimentation must occur. For many program research priorities, a team-oriented approach emphasizing collaboration, communication, and research integration is often critical to the success of the overall program, and this approach is reflected in the diversity of mechanisms used to support Genomic Science program research. These mechanisms range from small collaborative teams of researchers to large-scale, multidisciplinary research centers involving dozens of scientists.

DOE has a successful history of conducting this scale of scientific research and developing the tools and concepts needed to address high-risk, complex problems underlying achievement of DOE mission goals. In this tradition, the Genomic Science program research enterprise (initiated in 2002; formerly called the Genomes to Life program and subsequently Genomics:GTL) is pursuing solutions to biological grand challenges critical to addressing DOE mission goals.

Featuring

Genomic Science Program 2014 Strategic Plan [10/14]


Systems Biology-Enabled Research for Microbial Production of Advanced Biofuels (Summary of Funded Projects) [9/14]


Plant Feedstock Genomics for Bioenergy Abstracts [07/14]


Sustainable Bioenergy [05/14]


Bioenergy Research Centers [02/14]


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