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Genomic Science Program

Abstracts and Summaries

Research Summary
Genomic Science Program
February 2013

The Genomic Science program within DOE’s Office of Biological and Environmental Research supports fundamental research to achieve a predictive, systems-level understanding of plants, microbes, and biological communities through the integration of fundamental science and technology development.

Major research areas include the DOE Systems Biology Knowledgebase, Bioenergy Research Centers, USDA-DOE Plant Feedstocks Genomics for Bioenergy program, microbial and plant Biofuels studies, Biosystems Design projects to enable next-generation biofuels, characterization and genomic-based analyses of Microbes and Microbial Communities, and Biological Systems Research on the Role of Microbial Communities in Carbon Cycling. The Genomic Science program also supports Small Business Innovation Research relevant to DOE energy and environmental missions.

Listed below for each of these areas are ongoing research projects in or associated with the program in 2013.

DOE Systems Biology Knowledgebase (KBase)

  • KBase: An Integrated Knowledgebase for Predictive Biology and Environmental Research
    Adam Arkin, Argonne National Laboratory
  • The DOE Systems Biology Knowledgebase: Microbial Communities Science Domain
    Adam Arkin, Argonne National Laboratory
  • The DOE Systems Biology Knowledgebase: Microbial Science Domain
    Adam Arkin, Lawrence Berkeley National Laboratory
  • The DOE Systems Biology Knowledgebase: Plants Science Domain
    Adam Arkin, Cold Spring Harbor Laboratory
  • The KBase Architecture and Infrastructure Design
    Adam Arkin, Argonne National Laboratory
  • Development of a Regulated Model for Clostridia acetybutilicum
    Costas Maranas, Pennsylvania State University
  • Defining Complex Worlds in COMETS: Multiple Species and Dynamic Environments
    Daniel Segre, Boston University
  • The Ribosomal Database Project: Data and Tools for Microbial Analysis
    James Cole, Michigan State University
  • PhyloFacts FAT-CAT: A New DOE Webserver for Genome Functional Annotation
    Kimmen Sjolander, University of California, Berkeley
  • Comparison of Soil Microbial Communities Under Different Bioenergy Crops Suggests Sustainable Options
    Kirsten Hofmockel, Folker Meyer, Iowa State University
  • Bioenergy-Related Curation of the MetaCyc Database of Metabolic Pathways
    Peter D. Karp, SRI International
  • Computation of Atom Mappings and Novel Synthetic Pathways
    Peter Karp, SRI International
  • The Pathway Tools Software and BioCyc Database Collection
    Peter Karp, SRI International
  • Network Portal: An Integrated Framework for Storing, Analyzing, and Visualizing Biological Networks
    Serdar Turkarslan, Institute for Systems Biology
  • Kinetic Model of Methanogenesis in Methanosarcina acetivorans
    Zaida Luthey-Schulten, University of Illinois, Urbana-Champaign
  • Using MetRxn in Metabolic Model Development and Strain Design
    Costas Maranas, Pennsylvania State University, University Park
  • Extension of the Ensemble Modeling of Metabolic Networks to Genome-Scale Descriptions
    James Liao, Costas Maranas, and Gregory Stephanopoulos; University of California, Los Angeles; Pennsylvania State University; and Massachusetts Institute of Technology
  • RegPrecise 2.1: Toward Systems Biology Knowledgebase on Transcriptional Regulation in Bacteria
    Dmitry Rodionov, Lawrence Berkeley National Laboratory

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Bioenergy Research Centers

BioEnergy Science Center (BESC)

    • Advances in High-Throughput Screening of Biomass Recalcitrance
      Paul Gilna, BioEnergy Science Center
    • An Arabidopsis Cell Wall Proteoglycan Consists of Pectin and Arabinoxylan Covalently Linked to an Arabinogalactan Protein
      Paul Gilna, BioEnergy Science Center
    • Application of Chemical Imaging by TOF-SOMS to Understand Recalcitrance
      Paul Gilna, BioEnergy Science Center
    • Characterization of GXMT1 Reveals a New Family of Co2+-Dependent Enzymes that Catalyze the Methylation of Glucuronoxylan
      Paul Gilna, BioEnergy Science Center
    • Chemical Control in Lignin Bioynthesis: Molecular Orbital Analyses of H and G Lignans
      Paul Gilna, BioEnergy Science Center
    • Clostridium thermocellum Transcriptomic Profiles After Exposure to Ethanol, Furfural, or Heat Stress
      Paul Gilna, BioEnergy Science Center
    • Comparative Glycomics of Plant Cell Walls/Biomass: Insights into Composition, Diversity, Formation and Recalcitrance
      Paul Gilna, BioEnergy Science Center
    • High Solubilization of Grassy Feedstocks Via Consolidated Bioproccessing (CBP) Without Pretreatment
      Paul Gilna, BioEnergy Science Center
    • Implications of the Improved Dedicated Feedstock, Populus
      Paul Gilna, BioEnergy Science Center
    • Improving Clostridium thermocellum and Caldicellulosiruptor bescii to Enhance Cellulose Digestion
      Paul Gilna, BioEnergy Science Center
    • Integration of Metabolomics with Association Genetics for Large-Scale Gene Discovery in Populus trichocarpa
      Paul Gilna, BioEnergy Science Center
    • Metabolic Engineering of Clostridium thermocellum for Biofuel Production from Cellulosic Substrates
      Paul Gilna, BioEnergy Science Center
    • Methylation by Cognate Methyltransferases is Essential for DNA Transformation of Caldicellulosiruptor Species: Extending Genetic Methods to Members of this Genus
      Paul Gilna, BioEnergy Science Center
    • Molecular Breeding of Switchgrass for Enhanced Biomass Yield and Quality
      Paul Gilna, BioEnergy Science Center
    • Population Genomics and Association Mapping in Populus trichocarpa
      Paul Gilna, BioEnergy Science Center
    • Protease-Optimized Spectral Indexing (POSI) Increases Confidence in Label-Free Quantification of Shotgun Proteomics Datasets
      Paul Gilna, BioEnergy Science Center
    • PvMYB4-Overexpression Switchgrass Yields Very High Cellulosic Ethanol Levels Without Pretreatment
      Paul Gilna, BioEnergy Science Center
    • Real-Time Nanoscale Imaging Provides New Insights into Improvement of Biomass Pretreatment and Enzyme Hydrolysis
      Paul Gilna, BioEnergy Science Center
    • Extracellular, Cell-Associated Proteins Play a Role in Plant Biomass Degradation by Extremely Thermophilic Caldicellulosiruptor Species
      Robert M. Kelly, North Carolina State University

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Joint BioEnergy Institute (JBEI)

  • Impact of Mixed Feedstocks and Feedstock Densification on Ionic Liquid Pretreatment Efficiency
    Blake A. Simmons, Joint BioEnergy Institute
  • Design and Optimization of Novel Ionic Liquids for Biomass Pretreatment
    Blake Simmons, Joint BioEnergy Institute
  • Recent Developments in Fatty Acid-Derived Fuels at JBEI
    Harry Beller, Joint BioEnergy Institute and Lawrence Berkeley National Laboratory
  • Identification of Glycosyltransferases Involved in Galactan Biosynthesis
    Henrik V. Scheller, Joint Bioenergy Institute
  • Quantitative Metabolic Modeling in JBEI's Fuel Synthesis Division
    Jay Keasling, Lawrence Berkeley National Laboratory
  • Isolation of Golgi Proteomes from Grasses
    Joshua Heazlewood, Lawrence Berkeley National Laboratory
  • Engineering Bacterial Tolerance to an Ionic Liquid Used in Advanced Biofuel Production
    Michael Thelen, Joint Bioenergy Institute
  • PR-PR Programming a Robot — Laboratory Automation Platform
    Nathan J. Hillson, Joint BioEnergy Institute and Lawrence Berkeley National Laboratory
  • Inactivation of Xylosyl Arabinosyl Substitution of Xylan 1 (XAX1) in Rice Leads to Decreased Ferulic Acid and Increased Saccharification
    Pamela Ronald, Lawrence Berkeley National Laboratory
  • Structure-Based Engineering of Sulfolobus acidocaldarius Geranylgeranyl Reductase
    Paul Adams, Joint BioEnergy Institute
  • A Multiplexed, High-Throughput Screening Pipeline for Lignocellulosic Enzyme Discovery and Evolution
    Richard Heins, Joint BioEnergy Institute
  • Thermoascus aurantiacus is a Promising Thermophilic Fungal Platform for Enzymatic Biomass Deconstruction
    Steven Singer, Joint BioEnergy Institute and Lawrence Berkeley National Laboratory
  • High-Titer Production of Isopentenol Through Rational Pathway Engineering
    Taek Soon Lee, Joint BioEnergy Institute and Lawrence Berkeley National Laboratory
  • Large-Scale Characterization of Glycoside Hydrolase Enzymes for Biofuel Development
    Trent R. Northen, Joint BioEnergy Institute and Lawrence Berkeley National Laboratory
  • Studies of Biomass Enzymatic Hydrolysis by Tagged Glycans
    Trent R. Northen, Joint BioEnergy Institute

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Great Lakes Bioenergy Research Center (GLBRC)

  • A Phylogenetic-Based, Systems-Analysis of Biomass Deconstruction in the Genus Streptomyces
    Cameron Currie, University of Wisconsin, Madison
  • Mixed-Linkage Glucan Stored in Stem Parenchyma Tissue as a Path to Better Plants for Biofuel Feedstocks
    Curtis G. Wilkerson, Great Lakes Bioenergy Research Center
  • Transcriptome and Genome Diversity in Switchgrass
    Kevin Childs, Great Lake Bioenergy Research Center and Michigan State University
  • Productivity of Biomass Cropping Systems in the Upper Midwest
    Kurt Thelen, Michigan State University
  • Phenolic Inhibitors Derived from Ammonia-Pretreated Lignocellulose Activate Specific Regulatory Circuits and Inhibit Bacterial Conversion of Xylose to Ethanol
    Robert Landick, Great Lakes Bioenergy Research Center and University of Wisconsin, Madison
  • Catalysis with Cu(bpy) Improves AHP Pretreatment of Woody Biomass
    Timothy Donohue, Great Lakes Bioenergy Research Center
  • Characterization of Xylose Fermentation from AFEX™-Pretreated Corn Stover Hydrolysate by Evolved, Stress-Tolerant Yeast Strains
    Trey K. Sato, Great Lakes Bioenergy Research Center and University of Wisconsin, Madison
  • Production of a "Drop-in" Diesel Fuel in Crops
    John Ohlrogge, Michigan State University
  • Phenotypic and Genetic Dissection of Maize Internode Length
    Natalia De Leon, Great Lakes Bioenergy Research Center and Michigan State University

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USDA-DOE Plant Feedstock Genomics for Bioenergy

  • Burkholderia phytofirmans Strain PsJN Enhances the Growth of Switchgrass
    Chuansheng Mei, Institute for Advanced Learning and Research and Virginia Polytechnic Institute and State University
  • Effect of the Endophytic Bacterium Burkholderia phytofirmans Strain PsJN on Drought-Stessed Switchgrass
    Chuansheng Mei, Virginia Polytechnic Institute and State University and the Institute for Advanced Learning and Research
  • Genetic Responses of Switchgrass to the Endophytic Bacterium Burkholderia phytofirmans Strain PsJN
    Chuansheng Mei, Institute for Advanced Learning and Research
  • Tubulins as New Targets for Bioenergy Trait Improvement
    CJ Tsai, University of Georgia
  • Functional Genomics of Sugar Content in Sweet Sorghum Stems
    David Braun, University of Missouri
  • The Ability of XylemM NAC Domain 1 to Block Xylem Differentiation Depends on its Retinoblastoma Related Interaction Domain
    Eric Beers, Virginia Polytechnic Institute and State University
  • The Interactions of Poplar and Arabidopsis ROP GTPases with CSN5A: Negative Regulation of CSN5A by ROP11
    Eric Beers, Virginia Polytechnic Institute and State University
  • The Interactome Network of a Novel Endomembrane Protein in Populus trichocarpa
    Eric Beers, Virginia Polytechnic Institute and State University
  • The Poplar RWI Protein Binds to Myb Domain and Homeodomain Proteins Through Its Distinct Myb-Like N-Terminal and DUF3755 C-Terminal Domains
    Eric Beers, Virginia Polytechnic Institute and State University
  • Genetic Structure of Miscanthus sinensis from Asia and the United States
    Erik Sacks, University of Illinois
  • An Integrated Approach to Improving Plant Biomass Production
    Jan Leach, Colorado State University
  • Exploring Genetic Diversity in the World Collection of Sugarcane and Related Grasses
    Jianping Wang, University of Florida
  • Insertional Mutagenesis of Brachypodium distachyon
    John Vogel, U.S. Department of Agriculture, Agricultural Research Service
  • Phenomic Analysis of Natural and Induced Variation in Brachypodium distachyon
    John Vogel, U.S. Department of Agriculture, Agricultural Research Service
  • Identifying Differences in Abiotic Stress Gene Networks Between Lowland and Upland Ecotypes of Switchgrass
    Kevin L. Childs, Michigan State University and Virginia Polytechnic Institute and State University
  • Development of Genomic Resources and Novel Species Hybrids for the Genetic Improvement of Shrub Willow Feedstock Crops
    Larry Smart, Cornell University
  • Association Genetics and Functional Genomics of Switchgrass Cell Wall Quality Regulation
    Laura Bartley, University of Oklahoma
  • Identification of Putative Secondary Cell Wall Regulators Through a Comparative Analysis of the R2R3 MYB Family Across Arabidopsis, Poplar, Rice, Maize, and Switchgrass
    Laura E. Bartley, University of Oklahoma
  • Expression of Putative Arabinoxylan Feruloyl Transferase Genes in Brachypodium distachyon
    Marcia M. De Oliveira Buanafina, Pennsylvania State University
  • Maize Candy-Leaf (Cal) Mutants as Feedstocks with Improved Biorefinery Characteristics
    Markus Pauly, University of California, Berkeley
  • Co-Ordinate Regulation of Growth and Development Genes by MiRNA in Perennial Miscanthus
    Matthew Hudson, University of Illinois
  • Genome-Wide Analysis of MiRNA Targets in Brachypodium and Biomass Energy Crops
    Pamela Green, University of Delaware
  • Altered Salicin Partitioning in SUT4-RNAi Poplars
    Scott Harding, University of Georgia
  • Genomic and Breeding Foundations for Bioenergy Sorghum Hybrids
    Stephen Kresovich, University of South Carolina
  • Associating Genetic Variation in the Shoot Maturation Pathway with Bioenergy Traits in Sorghum
    Stephen Moose, University of Illinois
  • The Genetics of Biofuel Traits in Panicum Grasses: Developing a Model System with Panicum haliii
    Thomas Juenger, University of Texas, Austin
  • Regulation of Root Development in Populus in Response to Nitrogen Deficiency
    Victor Busov, Michigan Technological University
  • Construction of a Gene Interaction Network for Poplar
    Pankaj Jaiswal, Oregon State University

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Biofuels Research

Microbes, Archaea, and Fungi

  • Engineering Biofuel Tolerance in Microbes*
    Mary Dunlop, University of Vermont
  • Construction of Metabolic Models for a Family of Cyanobacteria
    Himadri Pakrasi, Washington University
  • Pathways and Regulatory Network of Hydrogen Production from Cellulose by Clostridium thermocellum
    JH David Wu, University of Rochester
  • Metabolomics of Sugar Catabolism in C. cellulolyticum
    Josh D. Rabinowitz, Princeton University
  • Functional and Evolutionary Genomics of Nanoarchaeota Systems
    Mircea Podar, University of Tennessee
  • 13C Metabolic Flux Analysis of Clostridial Cell Growth
    Eleftherios T. Papoutsakis, University of Delaware
  • Mimicking Fungal Biomass Decomposition, Assuming a Biphasic Mechanism
    Jonathan P. Schilling, University of Minnesota
  • Analysis of the Butanol Stress Response Regulatory Network in Clostridium acetobutylicum
    Eleftherios T. Papoutsakis, University of Delaware
  • Systems Analysis of the Clostridium Metabolite Stress Response for Bioenergy Applications
    Eleftherios T. Papoutsakis, University of Delaware
  • The Small RNome of Clostridium acetobutylicum with and Without Metabolite Stress
    Eleftherios T. Papoutsakis, University of Delaware
  • Sensitive Staining Method for Detection and Localization of Acid Groups Formed on Lignocellulose During Deconstruction
    Kenneth Hammel, University of Wisconsin, Madison

National Renewable Energy Laboratory Science Focus Area

    • Design Principles Controlling Hydrogen Metabolism in Phototrophic Organisms
      Maria Ghirardi, National Renewable Energy Laboratory

Oak Ridge National Laboratory Science Focus Area

    • Insights Into Cel7A Structure During Cellulose Digestion
      Brian H. Davison, Oak Ridge National Laboratory
    • The Physical Processes Driving Biomass Pretreatment for Bioproducts
      Brian H. Davison, Oak Ridge National Laboratory

Plants

  • Next-Generation Protein Interactomes for Plant Systems Biology and Biomass Feedstock
    Joseph Ecker, Howard Hughes Medical Institute and Salk Institute
  • Temperature Cycles Primarily Drive Diurnal Growth Rhythms in the Model Grass, Brachypodium distachyon
    Steve Kay, University of Southern California
  • Uncovering Genetic Mechanisms for Biological Conversion Efficiency in Brachypodium distachyon*
    Samuel Hazen, University of Massachusetts
  • Whole-Genome Association Analysis of the Molecular Regulation of Biomass Growth and Composition in Populus deltoides*
    Matias Kirst, University of Florida
  • Regulation of Neutral Lipid Accumulation in Plant Leaves
    Kent Chapman, University of North Texas
  • A Splice Variant of the SND1 Transcription Factor is a Dominant Negative of the SND1 Family Members and the SND1-Regulated Network in Populus trichocarpa
    Vincent L. Chiang, Forest Biotechnology Group, North Carolina State University
  • Defining Determinants and Dynamics of Cellulose Microfibril Biosynthesis, Assembly, and Degradation
    Jocelyn Rose, Cornell University
  • Development of Quantum Dot Probes for Studies of Synergy Between the Components of Wood-Degrading Fungal Enzymes
    Haw Yang, Princeton University
  • Study of Plant Cell Wall Polymers Affected by Metal Accumulation Using Stimulated Raman Scattering Microscopy
    Sunney Xie, Harvard University

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Biosystems Design

Microbes

    • Stoichiometric and Dynamic Models of Oleaginous Yeasts
      Gregory Stephanopoulos, Massachusetts Institute of Technology
    • A Platform for Genome-Scale Design, Redesign, and Optimization of Bacterial Systems
      Ryan Gill, University of Colorado, Boulder
    • Comparing the Transcriptomes of Fibrobacter succinogenes S85 Associated with Growth on Cellulose or Glucose*
      Garret Suen, University of Wisconsin, Madison
    • Repurposing the Saccharomyces cerevisiae Peroxisome for Compartmentalizing Multi-Enzyme Pathways*
      John Dueber, University of California, Berkeley

Plants

    • Modeling and Manipulating Phenylpropanoid Pathway Flux for Bioenergy
      Clint Chapple, Purdue University
    • Expanding the Breeder's Toolbox for Perennial Grasses
      Eduardo Blumwald, University of California, Davis
    • Engineering CAM Photosynthetic Machinery into Bioenergy Crops for Biofuels Production in Marginal Environments
      John C. Cushman, University of Nevada
    • Getting to the Root of Drought Stress in the Model C4 Grass Setaria viridis
      Jose R. Dinneny, Carnegie Institution for Science
    • A Systems-Level Analysis of Drought and Density Response in the Model C4 Grass Setaria viridis
      Thomas P. Brutnell, Donald Danforth Plant Science Center

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Microbes and Microbial Communities

  • Systems Biology of Marine Green Algae: Insights from the Dual Micromonas Model
    Alexandra Worden, Monterey Bay Aquarium Research Institute
  • Heterogeneity in Protein Expression Induces Metabolic Variability in a Modeled E. coli Population
    Zaida Luthey-Schulten, University of Utah
  • Methanobactin and MmoD Work in Concert to Act as the “Copper-Switch” in Methanotrophs
    Jeremy Semrau, Iowa State University

Microbial Communities

    • Tracking Dynamics of Alleles, Genotypes, or Species in Synthetic Microbial Consortia
      Christopher Marx, Harvard University
    • Toward Validation of a Genome-Scale Model of Nitrosomonas europaea and N. winogradskyi Using Absolute Gene Expression
      Daniel J. Arp, Oregon State University
    • Discovery of Geobacter sulfurreducens Proteins Essential for Electron Transfer and Biofilm Conductivity Via Massively Parallel Mutant Analysis
      Daniel R. Bond, University of Minnesota
    • Phylogenetic Diversity and Abundance Patterns of Thaumarchaeal and Bacterial AmoA Genes in Soils Influenced by Cultivars of Potential Biofuels Crops
      David Stahl, University of Washington
    • Detecting Nitrous Oxide Reductase (nosZ) Genes in Metagenomes: Method Development and Application to Midwestern Soils
      Frank Löeffler, Georgia Institute of Technology
    • PUNCS: Towards Predictive Understanding of Nitrogen Cycling in Soils —> the Role of Ammonia-Forming Nitrite Reductase (NrfA)
      Frank Löffler, University of Illinois, Urbana-Champaign
    • In Situ Correlated Molecular Imaging of Chemically Communicating Microbial Communities
      Paul W. Bohn, University of Notre Dame
    • In Situ Spectroscopy on Intact Leptospirillum ferriphilum Reveals That Cytochrome 579 Behaves Differently in Situ Than It Does in Vitro
      Robert Blake II, Xavier University of Louisiana
    • Improved Understanding of Microbial Iron and Sulfate Reduction Through a Combination of Bottom-Up and Top-Down Functional Proteomics Assays
      Ruth E. Richardson, Cornell University
    • Metagenomic Approaches to the Study of Microbial Communities at Subsurface Sites Undergoing Natural Attenuation of Uranium
      Barbara Methe, J. Craig Venter Institute
    • Pan-Genome-Scale Reconstruction of the Geobacteraceae Metabolic Network Based on Metagenome from Subsurface Samples
      Barbara Methe and Radhakrishnan Mahadevan, University of Toronto
    • Advances in Proteomic and Biochemical Analysis During Poplar – Laccaria Mycorrhizal Interactions
      Leland Cseke, University of Alabama, Huntsville

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Pacific Northwest National Laboratory Plant-Microbe Science Focus Area

    • Live Cell Characterization of Dynamic Cyclical Redox Regulation by Chemical Profiling in the Photoautotroph Synechococcus
      Alexander Beliaev, Pacific Northwest National Laboratory
    • Maintenance of Fast Growth Under High Irradiances in Synechococcus sp. PCC 7002
      Alexander Beliaev, Pacific Northwest National Laboratory

Oak Ridge National Laboratory Plant-Microbe Science Focus Area

    • Plant-Microbe Interfaces: Factors Associated with Microbial Community Association Patterns in the Populus Rhizosphere
      Mitchel Doktycz, Oak Ridge National Laboratory
    • Plant-Microbe Interfaces: Organizing and Mining Diverse Information
      Mitchel Doktycz, Oak Ridge National Laboratory
    • Plant-Microbe Interfaces
      Mitchel Doktycz, Oak Ridge National Laboratory
    • Plant-Microbe Interfaces: Comparative Genomics of Pseudomonas Isolates from the Populus Microbiome
      Mitchel Doktycz, Oak Ridge National Laboratory
    • Plant-Microbe Interfaces: Dissecting Populus-Fungal-Bacterial Systems
      Mitchel Doktycz, Oak Ridge National Laboratory
    • Plant-Microbe Interfaces: Intra- and Inter-Specific Variations in INDEL Polymorphisms Co-Segregating with QTLs for Populus-Laccaria Interaction
      Mitchel Doktycz, Oak Ridge National Laboratory
    • Plant-Microbe Interfaces: Proteomes of Bacteria, Fungi, and Plants
      Mitchel Doktycz, Oak Ridge National Laboratory
    • Plant-Microbe Interfaces: The Role of Constructed Microbial Communities on the Extended Plant Phenotype
      Mitchel Doktycz, Oak Ridge National Laboratory

Argonne National Laboratory Plant-Microbe Science Focus Area

    • Molecular Mechanisms that Mediate Environment Sensing and Response
      Frank Collart, Argonne National Laboratory

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Biological Systems Research on the Role of Microbial Communities in Carbon Cycling

  • Metagenomics of Microbial Communities from the Leaf Litter — Insights Into the Plant-Polymers Degradation
    Adam C. Martiny, University of California, Irvine
  • iTEP: An Integrated Toolkit for the Exploration of Pan-Genomes
    Bill Metcalf, University of Illinois
  • Relating Microbial Physiological Performance to Genome Content
    Chris Blackwood, Kent State University
  • Understanding Gene Expression and Physiology in Response to Switching Carbon Substrate
    Chris Blackwood, Kent State University
  • Detection of Latent Biotic Covariation Embedded in Environmental Gradient Responses
    Chris Blackwood and Gail Rosen, Drexel University
  • Navigating the Soil Microbial Food Web: Using 13C-Stable Isotope Probing to Track Carbon Cycling in Complex Microbial Communities
    Daniel H. Buckley, Cornell University
  • A Custom Database for Functional Annotation of Soil Omics Datasets Using Hidden Markov Models
    David Myrold, Oregon State University
  • Multi-Omics Assessment of Active Microbial Communities and their C Cycling Function in Native Prairie Soil
    David Myrold, Oregon State University
  • Multi-Omics of RaMPs Field Study Reveals Impacts of Altered Rainfall Patterns on Carbon Cycling in Native Prairie Soils
    David Myrold, Oregon State University
  • Meta-Omics Analysis of the Mechanisms for Direct Interspecies Electron Transfer (DIET) in Natural Methanogenic Communities and Defined Co-Cultures
    Derek Lovley, University of Massachusetts
  • Microbial Mechanisms Mediating Increased Soil C Storage Under Elevated N Deposition
    Donald R. Zak, University of Michigan
  • Suppression of N Cycle Functional Genes in Response to Chronic Atmospheric N Deposition
    Donald R. Zak, University of Michigan
  • Temperature Sensitivity of Soil Organic Matter Decomposition from Alaskan Tundra
    Edward A.G. Schuur, University of California
  • Functional Fizzy: a Feature Selection Tool Over Varying Sample Phenotypes
    Gail Rosen, Drexel University
  • Approaches to Characterize Community Structure, Nutrient Flow, and Response to Perturbation in a Model Microbial Community Using "Omics" and Stable Isotope Probing
    Jill Banfield, University of California, Berkeley
  • Assessment of Soil Fungal Diversity in Permafrost and Tallgrass Prairie Artificial Warming Soils by 28S LSU Pyrosequencing
    Jizhong Zhou, University of Oklahoma
  • Integrating Functional Groups of Genes into Carbon Decomposition Model
    Jizhong Zhou, University of Oklahoma
  • Microbial Communities and Networks Along a Long-Term Permafrost Thaw Gradient in Alaska
    Jizhong Zhou, University of Oklahoma
  • Microbial Community Responses to Warming in Temperate and Permafrost Soils as Revealed by Comparative Metagenomics
    Jizhong Zhou, Georgia Institute of Technology
  • Soil Microbial Community Determines Vulnerability of Soil Carbon Exposed to Warming in Northern Permafrost
    Jizhong Zhou, University of Oklahoma
  • A Metagenomic Insight into Freshwater Methane-Utilizing Communities and Evidence for Cooperation Between the Methylococcaceae and the Methylophilaceae
    Ludmila Chistoserdova, University of Washington
  • Challenging the Plate Count Anomaly in Grassland Rhizosphere
    Mary Firestone, University of California, Berkeley
  • Microbial Compositional and Functional Succession in the Rhizosphere Soil — Under Elevated and Ambient CO2
    Mary Firestone, University of California, Berkeley
  • Multi-Domain Stable Isotope Probing of Carbon Cycling in the Rhizosphere
    Mary Firestone, University of California, Berkeley
  • Examining the Controls on CH4 Dynamics Along a Permafrost Thaw Gradient: C Isotopes and Organic Matter Structure
    Scott Saleska, University of Arizona
  • Season Drives Precipitation and N Deposition Impacts on Soil Nitrous Oxide, Methane and Carbon Dioxide Emissions, and Microbial Composition in a CA Grassland
    Steve Allison, University of California, Irvine
  • Coupled High-Throughput Functional Metagenomics and Next Generation Sequencing for Reconciling Phylogeny and Function During Plant Litter Decomposition
    Steven Allison, Lawrence Berkeley National Laboratory
  • Resolving Cellular Metabolisms of Diverse Anaerobic Methane Oxidizing Consortia at the Single-Cell Level
    Victoria Orphan, California Institute of Technology
  • Examining the Controls on CH4 Dynamics Along a Permafrost Thaw Gradient: Microbial Community Composition and Expression
    Virginia Rich, University of Arizona
  • A Systems Biology View of the Methanosarcinales
    William W. Metcalf, University of Illinois
  • Carbon Cycling by Microbial Communities in High Arctic Active Layer and Permafrost: A Combined Geochemical, Genomic, and Proteomic Approach
    Tullis Onstott, Princeton University
  • Patterns in Wetland Microbial Community Composition and Functional Gene Repertoire Associated with Biogeochemical Gradients and Methane Emissions*
    Susannah Tringe, DOE Joint Genome Institute

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Small Business Innovation Research (SBIR)

  • Development of a Descriptive Phenotypic Ontology and Associated Online Resources
    George Garrity, NamesforLife, LLC and Michigan State University

 

*Early Career Program

Funding Announcement DE-FOA-0001865:
Systems Biology of Bioenergy-Relevant Microbes to Enable Production of Next-Generation Biofuels and Bioproducts.
Pre-App required 01/08/2018, 5 PM Eastern [12/17]

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