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Genomic Science Program

Abstracts and Summaries

Research Summary
2018 Genomic Sciences Program Annual Principal Investigator (PI) Meeting

Abstract Book PDF

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, 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.

2018 Genomic Sciences Program Annual Principal Investigator (PI) Meeting and USDA-DOE Plant Feedstock Genomics for Bioenergy Meeting, February 25 – 28, 2018, Abstract Book PDF provided by Oak Ridge Associated Universities (ORAU).

Agenda PDF

Meeting Introduction
Todd Anderson, Director, Biological Systems Science Division, DOE BER

Individual Abstract PDFs

Principal Investigator Abstract Title
Adams, Paul Characterization of Microorganisms Resistant to Multiple Metals from the Contaminated Environment at the Oak Ridge Reservation
Adams, Paul Coupling of Field- and Lab-based Experiments to resolve controls of Nitrate Respiration Pathway Partitioning at the Oak Ridge Shallow Aquifer
Adams, Paul Ecological Stochasticity in Subsurface Microbial Community Assembly under Stress Gradient: Application of A General Quantitative Framework
Adams, Paul ENIGMA Science Focus Area
Adams, Paul Field-relevant Isolates from the Oak Ridge FRC and their Deep Characterization and Functional Analysis
Adams, Paul In situ demonstration of sustained adaptation of a natural microbial community to transform substrates
Adams, Paul Integration of metagenomics and consortia data to study microbial interactions and community assembly
Adams, Paul Isolates and their Deep Characterization
Adams, Paul Linking Activity to Phylogeny in Groundwater/Soil Ecosystems
Adams, Paul Management and Analysis of ENIGMA Data using KBase
Adams, Paul Microbial Community Assembly and Evolution Analyzed at Single Cell Level
Adams, Paul Management and Analysis of ENIGMA Data using KBase
Adams, Paul Microbial Community Assembly and Evolution Analyzed at Single Cell Level
Adams, Paul Natural Organic Matter Dynamics and ExoMetabolomics for Microbial Cultivation from the Shallow Subsurface at the Oak Ridge FRC
Adams, Paul Strain isolation, genome sequencing, and functional genomics reveals adaptive evolution of a Pseudomonas population at a human impacted field site
Allen, Andrew A Systems Level Study of the Marine Diatom Phaeodactylum Reveals an Unexpected Mitochondrial Fatty Acid Beta Oxidation Pathway
Allen, Andrew Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in P. tricornutum
Allen, Andrew Defining the Cellular Systems in Marine Diatoms That Provide for Their Predominant Acquisition of Dissolved Nitrate in World Oceans
Allen, Andrew Illuminating Diatom Cell Biology with a Genetically Encodable Tag for Electron Microscopy and Subcellular Proteomics
Allen, Andrew Nitrate sensing with a model pennate diatom, Phaeodactylum tricornutum
Allen, Andrew Optimization of Genome Engineering in the Model Pennate Diatom Phaeodactylum tricornutum using CRISPR-CAS9
Allison, Steven Fungal and Bacterial Communities Vary in their Carbon Cycling Response to Climate
Alonso, Ana Paula Development of Resources and Tools to Improve Oil Content and Quality in Pennycress
Altpeter, Fredy Targeted Precision Nucleotide Substitutions in Sugarcane Following CRISPR/Cas9 and Template Mediated Genome Editing Confer 'Gain of Function'
Amador-Noguez, Daniel Exposure to oxygen induces a transient bottleneck in the methylerythritol 4-phosphate pathway in Zymomonas mobilis: the role of iron-sulfur cluster assembly proteins and flavodoxin reductase in recovering pathway activity
Arkin, Adam P. Assembling and Annotating Prokaryotic Genomes in KBase
Arkin, Adam P. Auxotrophy Prediction and Community Metabolic Modeling Reveals Functional Delegation in a Variety of Microbiome Systems
Arkin, Adam P. Connecting JGI and KBAse
Arkin, Adam P. Comparative Phylogenomics in KBase
Arkin, Adam P. Fungal Model Construction in KBase
Arkin, Adam P. KBase: An Integrated Systems Biology Knowledgebase for Predictive Biological and Environmental Research
Arkin, Adam P. KBase's App Catalog
Arkin, Adam P. KBase's Narrative Interface: A User Interface for Creating Reproducible Systems Biology Workflows
Arkin, Adam P. Learning to Use KBase to Accelerate Your Research
Arkin, Adam P. Microbiome Genome Extraction and Matabolic Modeling of Species Interactions in KBase
Arkin, Adam P. RNA-Seq Analysis in KBase
Arkin, Adam P. The KBase Platform
Arkin, Adam P. The KBase Software Development Kit Makes KBase an Extensible Community Resource
Arkin, Adam P. Tools and Data for Metabolic Modeling in KBase
Baidoo, Edward A Metabolomic Based Approach to Identifying Bottlenecks in Biosynthetic Pathways
Balint-Kurti, Peter Physiological And Molecular-Genetic Characterization Of Basal Resistance In Sorghum
Banfield, Jillian Microbial community proteogenomic analyses indicate extensive depth-dependent CO oxidation and C1 metabolism in soil and increased capacity for N2O reduction with increased rainfall
Bart, Rebecca Optimizing Tradeoffs Implicit During Bioenergy Crop Improvement: Understanding the Effect of Altered Cell Wall and Sugar Content on Sorghum-associated Pathogenic Bacteria
Baxter, Ivan Trait Components of whole plant water use efficiency are defined by unique environmentally responsive genetic signatures in the model C4 grass Setaria
Beller, Harry Discovery of Phenylacetate Decarboxylase, a New Glycyl Radical Enzyme Enabling First-Time Biochemical Production of Toluene
Blaby, Crysten Protein Function Discovery and Sequence-Function Understanding of Stress Tolerance in the Green Lineage
Blumwald, Eduardo SyPro Poplar - Improving Poplar Biomass Production under Abiotic Stress Conditions: An Integrated Omics, Bioinformatics, Synthetic Biology and Genetic Engineering Approach
Bouskill, Nick Microbial environmental feedbacks and the evolution of soil organic matter
Brandizzi, Federica Modulating hemicellulose to improve bioenergy crop
Brodie, Eoin L. A Trait Based Approach to Exploring the Impacts of Species Diversity and Functional Diversity on Algal Community Productivity
Brown, Jack Developing Non-food Grade Brassica Biofuel Feedstock Cultivars with High Yield, Oil Content, and Oil Quality that are Suitable for Low Input Production Dryland Systems
Bruns, Thomas Determination of the Roles of Pyrophilous Microbes in the Breakdown and Sequestration of Pyrolyzed Forms of SOM
Brutnell, Thomas Leaf carbon isotope composition in Setaria: genetic contribution and potential for high throughput screening for water use effiency in C4 plants
Brutnell, Thomas Phenomics of stomata and water use efficiency in C4 species
Brutnell, Thomas Using systems approaches to improve photosynthesis and water use efficiency in sorghum
Brutnell, Thomas Using systems approaches to improve water use efficiency in sorghum by engineering root architecture
Buckley, Daniel H. Microbial contributions to carbon cycling differ qualitatively and quantitatively in agricultural, forest and meadow soils
Buckley, Daniel H. The Role of Surface-related Microbial Ecology in Organo-Mineral Stabilization of Carbon in Soil
Cannon, William Multi-scale Modeling of Circadian Rhythms: From Metabolism to Regulation and Back
Chain, Patrick S. G. Using Data Mining and High-Throughput Cultivation Methods to Better Understand Bacterial:Fungal Interactions
Chen, Jay Plant-Microbe Interfaces: Genetic mapping and genomic resequencing identify a lectinreceptor-like kinase as a regulator of Populus-Laccaria bicolor interaction
Church, George Encoding new non-standard amino acid designs into proteins can address limitations of fluorescent proteins and facilitate genome editing approaches
Church, George Engineering a reduced 57-codon genetic code in Escherichia coli
Church, George Exploring the Species Specificity of Lambda Red Recombination
Clubb, Robert Toward Recombinant Cellulolytic Bacteria: Stabilizing Displayed Cellulases on Vegetative Bacillus subtilis Cells
Coleman, Heather D. Post-harvest Induction of Hyperthermophilic Cellulases Reduces Recalcitrance in Poplar
Comai, Luca Discovery and characterization of disease resistance loci in popular
Coruzzi, Gloria EvoNet: A Phylogenomic and Systems Biology approach to identify genes underlying plant survival in marginal, low-Nitrogen soils
Cuevas, Hugo Genomic dissection of anthracnose resistant response in sorghum [Sorghum bicolor(L.) Moench]
Dantas, Gautam Multi-omics analysis of Rhodococcus opacus strains evolved for optimized lignocellulose bioconversion
Davison, Brian H. Impact of Hydration and Temperature History on the Structure and Dynamics of Lignin
Davison, Brian H. Insights into Hemicellulose-Cellulose Interactions from Thermochemical Pretreatment of Model Composite Materials
Davison, Brian H. Molecular Interactions Enhanced by Co-Solvent Use for Effective Biomass Pretreatment
DeAngelis, Kristen M. The 'Who' and 'How' of Microbial Control over Soil Carbon Dynamics: a Multi 'omics, Stable Isotope Probing, and Modeling Approach
DeLucia, Evan H. Center for Advanced Bioenergy and Bioproducts Innovation - CABBI
D'haeseleer, Patrik Combining multiple functional annotation tools increases completeness of metabolic annotation
Ding, Shi-You Imaging Native Structure of Plant Cell Wall Cellulose Microfibril
Donohue, Timothy From Field to Fuel: How Do Feedstock Variability and Plant-Experienced Stresses Affect Microbial Conversion?
Donohue, Timothy Microbial Valorization of Lignin: Using Bacteria and Their Enzymes to Develop Biological Systems for Deplymerizing Lignin
Dumesic, James A. Fractionation of Lignocellulosic Biomass using biomass derived γ-valerolactone as solvent
Dunbar, John Linking Genes to Ecosystem Processes: Microbial Nitrogen and Carbon Cycling
Dunbar, John Microbial Communities As Carbon Conductors: Elucidating Universal Traits Across Litter Types
Dunbar, John Time-Dependent Tradeoff In Microbe-Plant Interactions Under Drought: Short-TermStress Dampening Versus Long-Term Accelerated Mortality
Dyer, John Genomics and Phenomics to Identify Yield and Drought Tolerance Alleles for Improvement of Camelina as a Biofuel Crop
Edmé, Serge Genetics and Genomics of Pathogen Resistance in Switchgrass
Eisenstein, Edward Elucidating Mechanisms of Rust Pathogenesis for Engineering Resistance in Poplar
Eng, Thomas Adaptive Laboratory Evolution Provides a Route to Improve Biofuel Production Under Ionic Liquid Stress
Evans, Sarah Plant and Biogeochemical Controls on the Switchgrass Microbiome: Perspectives from a fine-scale time series
Evans, Sarah Soil- and Root-associated Microbiomes Across Tweleve Switchgrass Cultivars
Firestone, Mary Characterizing the Multitrophic Interactions that Mediate Carbon Flow in Soil
Firestone, Mary Deeply rooted: impacts of depth and soil type on root biomass, carbon turnover and microbial communities under switchgrass cultivation
Firestone, Mary Exometabolomics of Switchgrass-Microbe Interactions in natural and fabricated ecosystems
Firestone, Mary Identifying microbial traits driving microbial successsion and C transformation in the rhizosphere of Avena sp.
Firestone, Mary Plant-microbe and microbe-microbe interactions mediate switchgrass sustainability: following rhizosphere microbial communities during switchgrass establishment
Firestone, Mary Stable isotope-enabled metagenomics reveal phages active in rhizosphere soil
Firestone, Mary Unravelling Rhizosphere-microbial Interactions in the Rhizosphere of Alamo Switchgrass (Panicum virgatum) under Abiotic Stresses
Firestone, Mary Using iDIRECT (Inference of Direct and Indirect Relationship with Efficient Copula-based Transitivity) to improve network modelling of rhizosphere microbial assemblages
Fleming, Ronan ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Soft-ware
Fleming, Ronan Creation and Analysis of Biochemical Constraint-based Models: the COBRA Toolbox v3.0
Fleming, Ronan Mathematical Properties Of Stoichiometric Matrices
Fleming, Ronan Numerical Properties of Stoichiometric Matrices
Funnell-Harris, Deanna Resistance to Stalk Pathogens for Bioenergy Sorghum
Garcia Martin, Hector Quantitative metabolic modeling at the Joint BioEnergy Institute
Gardner, Jeffrey G. Comprehensive Functional Characterization of the Glycoside Hydrolase Family 3 Enzymes from Cellvibrio japonicus Reveals Unique Metabolic Roles in Biomass Saccharification
Gasch, Audrey P. Rerouted PKA Signaling Coordinates Sugar And Hypoxia Responses For Anaerobic Xylose Fermentation In Yeast
Ghirardi, Maria The Algal Ferredoxin Interactome
Gill, Ryan Design and engineering of native regulatory networks
Glass, Louise m-CAFÉs Development of novel CRISPR-Cas technologies for precise manipulation of microbial networks
Glass, Louise m-CAFÉs: Microbial Community Analysis and Functional Evaluation in Soils
Glass, Louise m-CAFÉs -EcoFABs: Model Ecosystems to Advance Microbiome Science I
Glass, Louise m-CAFÉs -EcoFABs: Model Ecosystems to Advance Microbiome Science II
Groover, Andrew Discovery and characterization of disease resistance loci in poplar
Hegg, Eric Progress Towards N2O Source Apportionment in Biofuel Soils: Understanding Sources of Variation in Isotopic Discrimination During Denitrification
Hettich, Robert Plant-Microbe Interfaces: Developments in integrated omics to link microbial metabolism to community structure/function in plant/microbial systems
Hillson, Nathan J. DIVA Services: PCR, Full DNA Construction, and MiSeq Validation
Hittinger, Chris Evolutionary Dynamics of a Secondary Metabolite Gene Cluster in Budding Yeasts
Hofmockel, Kirsten Molecular interactions of the plant-soil-microbe continuum of bioenergy ecosystems
Hungate, Bruce Are the activities of microbial taxa consistent across ecosystems?
Hungate, Bruce Exploring Biome-scale Variation in Microbial Taxon-Specific Growth and Mortality at different temperatures through quantitative Stable Isotope Probing with H218O.
Hungate, Bruce Field Measurements of Taxon-Specific Microbial Growth in Soil at Two Elevation Gradient Sites Using Quantitative Stable Isotope Probing (qSIP)
Hungate, Bruce Understanding Soil Metabolism from Carbon Release And Carbon Incorporation from Position-Specific 13C-Labeled Substrates
Jacobson, Daniel Plant-Microbe Interfaces: AI-GWAPA, explainable AI-based approaches to genome wide phytobiome association
Jacobson, Daniel Plant-Microbe Interfaces: Phytobiome and transcriptional adapation of Populus deltoides to acute progressive drought and cyclic drought
Jansson, Janet K. Elucidation of Chemical Dark Matter in Soil Using 'Standards-free' Small Molecule Identification
Jansson, Janet K. Modeling of Context-dependent Microbial Interactions in Biopolymer Degradation Networks
Jansson, Janet K. Phenotypic Response of the Soil Microbiome to Environmental Perturbations
Jansson, Janet K. Visualizing Spatial Metabolic Interactions Within a Soil Microbiome
Jewett, Michael C. Building a Bridge between Cell-Free Experimentation and Cellular Metabolic Engineering
Jin, Yong-Su Microbial metabolic engineering to produce alcohols from cellulosic hydrolysates
Juenger, Thomas Climate adaptation and sustainability in switchgrass: exploring plant-microbe-soil interactions across continental scale environmental gradients
Kalluri, Udaya C Plant-Microbe Interfaces: Altered root metabolome composition impacts microbiome composition in Populus PdKOR1 RNAi plants
Khanna, Madhu Center for Advanced Bioenergy and Bioproducts Innovation: Sustainability Theme
Kirst, Matias Phylogenomic Discovery and Engineering of Nitrogen Fixation into the Bioenergy Woody Crop Poplar
Labbé, Jessy Plant-Microbe Interfaces: The key fungal lineage of the Russulaceae, a new resource for untangling and linking beneficial plant-fungal associations and ecosystem functions
LeBoldus, Jared Towards durable resistance to Septoria stem canker and leaf spot: a molecular understanding of resistance.
Lemaux, Peggy From Leaves to Roots to Microbes: How Sorghum Responds to Drought
Lidstrom, Mary E. Role of Lanthanides in the Complex Interplay of Alternative Enzyme Systems Involved in Methanotrophy
Lipton, Mary Bridging the Soil Metagenome and Metaphenome Through Integrated Omics Analyses
Long, Stephen Building on success in systems design of high yielding low-input energycanes for marginal lands OR Renewable Oil Generated with Ultra-productive Energycanes (ROGUE)
Loqué, Dominique SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum
Lowry, David B. Identification of Adaptive Fungal Pathogen Resistance Loci in Switchgrass
Lu, Chaofu Systems Biology to Improve Camelina Seed and Oil Quality Traits
Lu, Yi Expanding the Scope of Biofuels and Chemicals Produced by Microorganisms through Design of Artificial Enzymes Containing Unnatural Amino Acids and Non-native Cofactors
Maranas, Costas Development of an accelerated prodedure for parameterizing kinetic metabolic models for C. thermocellum
Maranas, Costas novoStoic: Pathway design using de novo steps through uncharted biochemical spaces
Maranas, Costas SteadyCom: Predicting Microbial Abundances whille Ensuring Community Stability
Maravelias, Christos A Framework for the Identification of Economically Promising Bio-Based Chemicals
Martienssen, Robert Biological Design of Lemnaceae Aquatic Plants for Biodiesel Production
Mayali, Xavier Nanoscale Stable Isotope Tracing and Compound-Specific Radioisotope Analysis to Investigate Metabolic Interactions between Bacteria and Biofuel-producing Algae
McKinlay, James B. Competition for a cross-fed nutrient between bacterial mutualists
Meile, Christof Microbial Interactions in The Anaerobic Oxidation of Methane: Model Simulations Constrained by Process Rates and Activity Patterns
Merchant, Sabeeha A Day in the Life of Chlamydomonas
Merchant, Sabeeha Trace Metal Storage in Metal-Specific, Lysosome-Related Vacuolar Compartments
Moon, Tae Seok Development of a Genetic Toolkit in Rhodococcus opacus PD630 for Lignin Valorization
Moran, James Spatially Resolved Rhizosphere Function for Elucidating Key Controls on Below-ground Nutrient Interactions
Morrell-Falvey, Jennifer Plant-Microbe Interfaces: Characterization of IAA biosynthesis pathways in Populus-associated microbes
Mortimer, Jenny Plant Sphingolipid Glycosylation And Its Role In Immunity And Cell Wall Organization
Muchero, Wellington Genomic divergence in pattern recognition receptors and its implications on endophytic microbial associations in the genus Salix
Navid, Ali In silico system-level analysis of interactions in algal-bacterial co-cultures
Newcombe, George Characterizing the Defense Hierarchy of Populus trichocarpa and its Hybrids
Niyogi, Krishna Systems Analysis and Engineering of Biofuel Production in Chromochloris zofingiensis, an Emerging Model Green Alga
Noirot, Philippe A Mycorrhizal Helper Bacteria Increases Mycorrhization in Aspen Seedlings by Modulating Expression of Defense Response Genes in Roots
Noirot, Philippe CRISPRi-Mediated Analysis of Biofilm Formation in Plant Growth Promoting Pseudomonas fluorescens
Northen, Trent Synthetic Chemical Probes for Studying Lignin Deconstruction and Analysis of Biofuel Molecules Using nanostructure-initiator Mass Spectrometry (NIMS)
Northen, Trent The importance of biocrust organics revealed by metabolite sorption studies and in situ imagery
O'Malley, Michelle A. Engineering Anaerobic Gut Fungi for Lignocellulose Breakdown
Orphan, Victoria Comparative Genomics, Transcriptomic Analysis, and Ecophysiology of Individual Environmental Methane-oxidizing Syntrophic Consortia
Pakrasi, Himadri MinGenome: An in silico top-down approach for the synthesis of minimized genomes
Papa, Gabriella Development and screening of one-pot IL conversion technologies
Peay, Kabir Climate Predicts the Dominant Form of Plant-Microbe Symbiosis in Forests at a Global Scale
Peay, Kabir How Does Precipitation Impact the Taxonomic and Functional Diversity of the Populus trichocarpa Soil Microbiome?
Pelletier, Dale A. Plant-Microbe Interfaces: Characterization of natural products from the Populus microbiome
Pett-Ridge, Jennifer How Plant-Microbial Interactions Shape Resource Allocation in Perennial Bioenergy Grasses
Pett-Ridge, Jennifer Redox Fluctuations Control Coupled Iron-Carbon Cycling and Microbial Community Structure in Tropical Soils
Pett-Ridge, Jennifer Sequential Growth of Bacteria Following the Rewetting of a Seasonally Dried Grassland Soil
Pett-Ridge, Jennifer Understanding Microbial Stress Responses in Soil Using Metagenome and Metatranscriptome Analysis
Pfleger, Brian F. A Better Understanding of Bacterial RNA Turnover Developed Through RNA Sequencing
Ralph, John 'Ideal lignin' facilitates full biomass utilization
Rao, Christopher Engineering the oleaginous yeast Rhodosporidium toruloides for the production of lipids and lipid-based chemicals
Rao, Christopher Quantification of Multiple Post-Translational Modifications by 'One-Pot' Affinity Enrichment - Applications in E. coli
Rao, Christopher Regulation of acetate metabolism by pH in Escherichia coli
Reed, Jennifer Machine learning techniques help accelerate enzyme engineering: a case study with glycoside hydrolases
Retterer, Scott T. Plant Microbe Interfaces: Emerging analytical techniques for controlling and monitoring architectural changes in developing multi-kingdom systems
Rich, Virginia Modeling the Pathways to Carbon Liberation: Microbiologically-Informed C-Cycle Modeling in a Thawing Permafrost Landscape, for Scaling from Molecules to the Earth System
Rich, Virginia Subarctic Lake Sediment Microbial Community Contributions to Methane Emission Patterns
Sacks, Erik Introgression of Novel Disease Resistance Genes from Miscanthus into Energycane
Sale, Kenneth Co-Optimization of Multicomponent Enzyme Mixtures and Saccharification Conditions
Sattely, Elizabeth Identifying a Minimal Set of Genes Required for Valorization of Lignin Biomass
Schachtman, Daniel Defining the Functional Genome Associated with Enhanced Water and Nitrogen Use Efficiency in Bioenergy Sorghum
Schachtman, Daniel Identifying productive energy sorghum germplasm for water-limited and nitrogen-limited environments using classical and advanced phenotyping methods - one piece of the puzzle for creating sustainable biomass production systems
Schachtman, Daniel Leaf Carbon and Nitrogen Isotope Composition in Diverse Sorghum Lines Under Differential Water and Nitrogen Treatments
Schachtman, Daniel Using Metabolomics to Uncover Metabolic Pathways Utilized in Nitrogen Stress and Plant-Microbe Interactions in Energy Sorghum
Schadt, Christopher W. Plant-Microbe Interfaces: The contribution of host chemotype as a driver of rhizosphere microbial community structure
Scheller, Henrik V. A Dominant Approach to Reduce Xylan in Bioenergy Crops
Schilling, Jonathan Spatial Connectomics to Identify Agents Relevant to Lignocellulose Deconstruction in Fungi
Schnell, Danny J. Engineering mitochondrial metabolic networks to increase yield and water use efficiency in Camelina sativa
Scown, Corinne Simulating Near-Term Scale-Up of Cellulosic Biofuel Production Using Crop Residues and Biomass Sorghum
Sedbrook, John Advancing Field Pennycress as a New Oilseed Biofuels Feedstock that does not Require New Land Commitments
Shade, Ashley Microbiome diversity and assembly in the phyllosphere of perennial bioenergy crops
Simmons, Blake Engineering CRISPR/Cas9 platform to industrialize lignin modifying enzymes (LMEs) using Aspergillus niger
Singer, Steven W. Bioconversion of Sugars and Aromatics from Engineered Plants to Methyl Ketones
Singh, Anup An Automated Microfluidic System for Gene Editing Processes
Smart, Lawrence B. Dissecting Genetic Resistance to Willow Leaf Rust (Melampsora spp.) in Shrub Willow (Salix spp.)
Stuart, Rhona K. Multi-Component Characterizations of Algal Pond Ecosystems Reveal Algal Influence on Heterotroph Dynamics
Sullivan, Matthew B. Host-Linked Soil Viral Ecology along a Permafrost Thaw Gradient
Sweedler, Jonathan A general, high-throughput platform for molecular prototyping of microbial cell factories via optically guided mass spectrometry
Tas, Neslihan Understanding the microbial controls on biogeochemical cycles in permafrost ecosystems
Thompson, Janelle R. Systems biology towards a continuous platform for biofuels production: Engineering an environmentally-isolated Bacillus strain for biofuel production and recovery under supercritical CO2
Tringe, Susannah Diverse sorghum microbiome discovery and characterization in nitrogen- and waterlimited soils for improved biomass production
Tuskan, Gerald A Comparison of Lignocellulose Solubilization by Cellulolytic Monocultures and a Mixed
Tuskan, Gerald Advances in Lignin Valorization via Biological and Catalytic Transformations
Tuskan, Gerald Agile Technoeconomic and Life Cycle Assessments at the CBI
Tuskan, Gerald CELF/CBP for Enhanced Utilization of Polysaccharides and Lignin
Tuskan, Gerald Highly Resolved Genome-Wide Association Mapping (GWAS) Reveals Novel Variants for Engineering Increased Biomass Yield in Populus trichocarpa
Tuskan, Gerald Identification and Optimization of CRISPR Systems for Genome Editing in Pseudomonas putida and Clostridium thermocellum
Tuskan, Gerald Improving Nitrogen-Use Efficiency of Switchgrass Production: Past, Present, Future
Tuskan, Gerald Metabolic Reconstruction, Analysis and Design of Metabolic Pathways
Tuskan, Gerald Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery
Tuskan, Gerald Poplar GWAS and eQTL Analyses Reveal a Key Transferase Gene, HCT2, as a Missing Link in Plant Growth-Defense Tradeoffs
Tuskan, Gerald Rapid Domestication of Non-Model Microbial Hosts for Biofuels Production
Tuskan, Gerald Switchgrass Field Experiments to Enable Rapid Domestication, Increased Sustainability, and a Genome-wide Association Study
Tuskan, Gerald Technoeconomic Analysis of Biofuel Feedstock Supplies to Inform Plant Development R&D
Tuskan, Gerald Towards Understanding Plant Cell Wall Structure and Properties During Microbial Deconstruction - From Chemical Bonds to Wall Architecture
Tuskan, Gerald Using Multi-Omic Data to Understand the Response of Clostridium thermocellum to Deletions of Genes for Lactate and Acetate Production
VanLoocke, Andrew Economic and Environmental Modeling of Bioenergy Production – Policy Impacts on Water Quality
Vilgalys, Rytas Plant-Microbe Interfaces: Dissecting the compatibility and diversity of the mycobiome of Populus trichocarpa
Weston, David J. Determining the genetic and environmental factors underlying mutualism within a plantmicrobiome system: insights from genome sequencing, mass spectrometry imaging and exometabolite characterization
Weston, David J. Plant-Microbe Interfaces: Developing a synthetic community system to test preferential allocation to nitrogen-fixing bacteria
Wilkerson, Curtis Gene Increasing biomass in grasses by identifying genes involved in mixed-linkage glucan biosynthesis
Wrighton, Kelly Methanogenesis in Oxygenated Soils is a Substantial Fraction of Wetland Methane Emissions
Wühr, Martin Accurate, Sensitive, and Precise Multiplexed Proteomics using the Complement Reporter Ion Cluster
Yang, Wendy Carbon Cycling in Biomass-Based Cropping Systems: Improving the Mechanistic Foundations of Plant, Microbial, and Soil Interactions
Yeates, Todd Designing Self-Assembling Protein Materials for Imaging and Energy Applications
Young, Jamey Metabolic phenotyping of cyanobacteria with increased biofuel productivity
Zhang, Fuzhong Engineering Bacteria to Produce Branched-chain Fatty Acid Derived Advanced Biofuels
Zhao, Huimin Combinatorial Metabolic Engineering Using an Orthogonal Tri-functional CRISPR System
Zhao, Huimin Construction of a Kinetic Model for Yeast Lipid Metabolism
Zhao, Huimin Construction of genome-scale metabolic models for non-model yeast organisms for biofuel and bioproduct engineering
Zhao, Huimin Genome-scale Engineering of Saccharomyces cerevisiae with Single Nucleotide Precision
Zhou, Jizhong Successional Dynamics of Grassland Microbial Communities in Response to Warming, Precipitation Alternation, and Clipping
Zhou, Jizhong Time-series metagenomics of experimentally warmed Alaskan tundra and Oklahoma temperate soils enables fine-resolution assessment of belowground C cycling feedbacks to climate change



Interagency Strategic Plan for Microbiome Research, FY 2018-2022 [04/18]

2018 Research Summaries [02/18]

GSP Overview Brochure [01/18]

Grand Challenges for Biological and Environmental Research: Progress and Future Vision [11/17]

Technologies for Characterizing Molecular and Cellular Systems Relevant to Bioenergy and Environment [9/17]



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