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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

Individual Abstract PDFs

Principal Investigator Abstract Title
Adams, PaulCharacterization of Microorganisms Resistant to Multiple Metals from the Contaminated Environment at the Oak Ridge Reservation [48 KB]
Adams, PaulCoupling of Field- and Lab-based Experiments to resolve controls of Nitrate Respiration Pathway Partitioning at the Oak Ridge Shallow Aquifer [119 KB]
Adams, PaulEcological Stochasticity in Subsurface Microbial Community Assembly under Stress Gradient: Application of A General Quantitative Framework [109 KB]
Adams, PaulENIGMA Science Focus Area [97 KB]
Adams, PaulField-relevant Isolates from the Oak Ridge FRC and their Deep Characterization and Functional Analysis [92 KB]
Adams, PaulIn situ demonstration of sustained adaptation of a natural microbial community to transform substrates [91 KB]
Adams, PaulIntegration of metagenomics and consortia data to study microbial interactions and community assembly [49 KB]
Adams, PaulIsolates and their Deep Characterization [93 KB]
Adams, PaulLinking Activity to Phylogeny in Groundwater/Soil Ecosystems [24 KB]
Adams, PaulManagement and Analysis of ENIGMA Data using KBase [99 KB]
Adams, PaulMicrobial Community Assembly and Evolution Analyzed at Single Cell Level [91 KB]
Adams, PaulNatural Organic Matter Dynamics and ExoMetabolomics for Microbial Cultivation from the Shallow Subsurface at the Oak Ridge FRC [99 KB]
Adams, PaulStrain isolation, genome sequencing, and functional genomics reveals adaptive evolution of a Pseudomonas population at a human impacted field site [15 KB]
Allen, AndrewA Systems Level Study of the Marine Diatom Phaeodactylum Reveals an Unexpected Mitochondrial Fatty Acid Beta Oxidation Pathway [106 KB]
Allen, AndrewCross-compartment metabolic coupling enables flexible photoprotective mechanisms in P. tricornutum [14 KB]
Allen, AndrewDefining the Cellular Systems in Marine Diatoms That Provide for Their Predominant Acquisition of Dissolved Nitrate in World Oceans [80 KB]
Allen, AndrewIlluminating Diatom Cell Biology with a Genetically Encodable Tag for Electron Microscopy and Subcellular Proteomics [225 KB]
Allen, AndrewNitrate sensing with a model pennate diatom, Phaeodactylum tricornutum [12 KB]
Allen, AndrewOptimization of Genome Engineering in the Model Pennate Diatom Phaeodactylum tricornutum using CRISPR-CAS9 [169 KB]
Allison, StevenFungal and Bacterial Communities Vary in their Carbon Cycling Response to Climate [183 KB]
Alonso, Ana PaulaDevelopment of Resources and Tools to Improve Oil Content and Quality in Pennycress [48 KB]
Altpeter, FredyTargeted Precision Nucleotide Substitutions in Sugarcane Following CRISPR/Cas9 and Template Mediated Genome Editing Confer "Gain of Function" [15 KB]
Amador-Noguez, DanielExposure 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 [123 KB]
Arkin, Adam P.Assembling and Annotating Prokaryotic Genomes in KBase [136 KB]
Arkin, Adam P.Auxotrophy Prediction and Community Metabolic Modeling Reveals Functional Delegation in a Variety of Microbiome Systems [459 KB]
Arkin, Adam P.Connecting JGI and KBAse [351 KB]
Arkin, Adam P.Comparative Phylogenomics in KBase [239 KB]
Arkin, Adam P.Fungal Model Construction in KBase [258 KB]
Arkin, Adam P.KBase: An Integrated Systems Biology Knowledgebase for Predictive Biological and Environmental Research [365 KB]
Arkin, Adam P.KBase's App Catalog [219 KB]
Arkin, Adam P.KBase's Narrative Interface: A User Interface for Creating Reproducible Systems Biology Workflows [285 KB]
Arkin, Adam P.Learning to Use KBase to Accelerate Your Research [374 KB]
Arkin, Adam P.Microbiome Genome Extraction and Matabolic Modeling of Species Interactions in KBase [244 KB]
Arkin, Adam P.RNA-Seq Analysis in KBase [124 KB]
Arkin, Adam P.The KBase Platform [660 KB]
Arkin, Adam P.The KBase Software Development Kit Makes KBase an Extensible Community Resource [177 KB]
Arkin, Adam P.Tools and Data for Metabolic Modeling in KBase [211 KB]
Baidoo, EdwardA Metabolomic Based Approach to Identifying Bottlenecks in Biosynthetic Pathways [119 KB]
Banfield, JillianMicrobial community proteogenomic analyses indicate extensive depth-dependent CO oxidation and C1 metabolism in soil and increased capacity for N2O reduction with increased rainfall [86 KB]
Bart, RebeccaOptimizing Tradeoffs Implicit During Bioenergy Crop Improvement: Understanding the Effect of Altered Cell Wall and Sugar Content on Sorghum-associated Pathogenic Bacteria [90 KB]
Baxter, IvanTrait Components of whole plant water use efficiency are defined by unique environmentally responsive genetic signatures in the model C4 grass Setaria [12 KB]
Beller, HarryDiscovery of Phenylacetate Decarboxylase, a New Glycyl Radical Enzyme Enabling First-Time Biochemical Production of Toluene [143 KB]
Blaby, CrystenProtein Function Discovery and Sequence-Function Understanding of Stress Tolerance in the Green Lineage [58 KB]
Blumwald, Eduardo"SyPro Poplar" Improving Poplar Biomass Production under Abiotic Stress Conditions: An Integrated Omics, Bioinformatics, Synthetic Biology and Genetic Engineering Approach [339 KB]
Bouskill, NickMicrobial environmental feedbacks and the evolution of soil organic matter [39 KB]
Brandizzi, FedericaModulating hemicellulose to improve bioenergy crop [168 KB]
Brodie, Eoin L.A Trait Based Approach to Exploring the Impacts of Species Diversity and Functional Diversity on Algal Community Productivity [98 KB]
Brown, JackDeveloping Non-food Grade Brassica Biofuel Feedstock Cultivars with High Yield, Oil Content, and Oil Quality that are Suitable for Low Input Production Dryland Systems [20 KB]
Bruns, ThomasDetermination of the Roles of Pyrophilous Microbes in the Breakdown and Sequestration of Pyrolyzed Forms of SOM [108 KB]
Brutnell, ThomasLeaf carbon isotope composition in Setaria: genetic contribution and potential for high throughput screening for water use effiency in C4 plants [94 KB]
Brutnell, ThomasPhenomics of stomata and water use efficiency in C4 species [123 KB]
Brutnell, ThomasUsing systems approaches to improve photosynthesis and water use efficiency in sorghum [14 KB]
Brutnell, ThomasUsing systems approaches to improve water use efficiency in sorghum by engineering root architecture [71 KB]
Buckley, Daniel H.Microbial contributions to carbon cycling differ qualitatively and quantitatively in agricultural, forest and meadow soils [88 KB]
Buckley, Daniel H.The Role of Surface-related Microbial Ecology in Organo-Mineral Stabilization of Carbon in Soil [55 KB]
Cannon, WilliamMulti-scale Modeling of Circadian Rhythms: From Metabolism to Regulation and Back [2 MB]
Chain, Patrick S. G.Using Data Mining and High-Throughput Cultivation Methods to Better Understand Bacterial:Fungal Interactions [93 KB]
Chen, JayPlant-Microbe Interfaces: Genetic mapping and genomic resequencing identify a lectinreceptor-like kinase as a regulator of Populus-Laccaria bicolor interaction [101 KB]
Church, GeorgeEncoding new non-standard amino acid designs into proteins can address limitations of fluorescent proteins and facilitate genome editing approaches [113 KB]
Church, GeorgeEngineering a reduced 57-codon genetic code in Escherichia coli [121 KB]
Church, GeorgeExploring the Species Specificity of Lambda Red Recombination [103 KB]
Clubb, RobertToward Recombinant Cellulolytic Bacteria: Stabilizing Displayed Cellulases on Vegetative Bacillus subtilis Cells [36 KB]
Coleman, Heather D.Post-harvest Induction of Hyperthermophilic Cellulases Reduces Recalcitrance in Poplar [17 KB]
Comai, LucaDiscovery and characterization of disease resistance loci in popular [419 KB]
Coruzzi, GloriaEvoNet: A Phylogenomic and Systems Biology approach to identify genes underlying plant survival in marginal, low-Nitrogen soils [175 KB]
Cuevas, HugoGenomic dissection of anthracnose resistant response in sorghum [Sorghum bicolor(L.) Moench] [24 KB]
Dantas, GautamMulti-omics analysis of Rhodococcus opacus strains evolved for optimized lignocellulose bioconversion [97 KB]
Davison, Brian H.Impact of Hydration and Temperature History on the Structure and Dynamics of Lignin [222 KB]
Davison, Brian H.Insights into Hemicellulose-Cellulose Interactions from Thermochemical Pretreatment of Model Composite Materials [115 KB]
Davison, Brian H.Molecular Interactions Enhanced by Co-Solvent Use for Effective Biomass Pretreatment [928 KB]
DeAngelis, Kristen M.The "Who" and "How" of Microbial Control over Soil Carbon Dynamics: a Multi –omics, Stable Isotope Probing, and Modeling Approach [117 KB]
DeLucia, Evan H.Center for Advanced Bioenergy and Bioproducts Innovation - CABBI [283 KB]
D'haeseleer, PatrikCombining multiple functional annotation tools increases completeness of metabolic annotation [98 KB]
Ding, Shi-YouImaging Native Structure of Plant Cell Wall Cellulose Microfibril [383 KB]
Donohue, TimothyFrom Field to Fuel: How Do Feedstock Variability and Plant-Experienced Stresses Affect Microbial Conversion? [99 KB]
Donohue, TimothyMicrobial Valorization of Lignin: Using Bacteria and Their Enzymes to Develop Biological Systems for Deplymerizing Lignin [43 KB]
Dumesic, James A.Fractionation of Lignocellulosic Biomass using biomass derived γ-valerolactone as solvent [220 KB]
Dunbar, JohnLinking Genes to Ecosystem Processes: Microbial Nitrogen and Carbon Cycling [91 KB]
Dunbar, JohnMicrobial Communities As Carbon Conductors: Elucidating Universal Traits Across Litter Types [87 KB]
Dunbar, JohnTime-Dependent Tradeoff In Microbe-Plant Interactions Under Drought: Short-TermStress Dampening Versus Long-Term Accelerated Mortality [89 KB]
Dyer, JohnGenomics and Phenomics to Identify Yield and Drought Tolerance Alleles for Improvement of Camelina as a Biofuel Crop [96 KB]
Edmé, SergeGenetics and Genomics of Pathogen Resistance in Switchgrass [58 KB]
Eisenstein, EdwardElucidating Mechanisms of Rust Pathogenesis for Engineering Resistance in Poplar [92 KB]
Eng, ThomasAdaptive Laboratory Evolution Provides a Route to Improve Biofuel Production Under Ionic Liquid Stress [63 KB]
Evans, SarahPlant and Biogeochemical Controls on the Switchgrass Microbiome: Perspectives from a fine-scale time series [112 KB]
Evans, SarahSoil- and Root-associated Microbiomes Across Tweleve Switchgrass Cultivars [123 KB]
Firestone, MaryCharacterizing the Multitrophic Interactions that Mediate Carbon Flow in Soil [107 KB]
Firestone, MaryDeeply rooted: impacts of depth and soil type on root biomass, carbon turnover and microbial communities under switchgrass cultivation [106 KB]
Firestone, MaryExometabolomics of Switchgrass-Microbe Interactions in natural and fabricated ecosystems [97 KB]
Firestone, MaryIdentifying microbial traits driving microbial successsion and C transformation in the rhizosphere of Avena sp. [103 KB]
Firestone, MaryPlant-microbe and microbe-microbe interactions mediate switchgrass sustainability: following rhizosphere microbial communities during switchgrass establishment [115 KB]
Firestone, MaryStable isotope-enabled metagenomics reveal phages active in rhizosphere soil [98 KB]
Firestone, MaryUnravelling Rhizosphere-microbial Interactions in the Rhizosphere of Alamo Switchgrass (Panicum virgatum) under Abiotic Stresses [114 KB]
Firestone, MaryUsing iDIRECT (Inference of Direct and Indirect Relationship with Efficient Copula-based Transitivity) to improve network modelling of rhizosphere microbial assemblages [96 KB]
Fleming, RonanARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Soft-ware [102 KB]
Fleming, RonanCreation and Analysis of Biochemical Constraint-based Models: the COBRA Toolbox v3.0 [120 KB]
Fleming, RonanMathematical Properties Of Stoichiometric Matrices [90 KB]
Fleming, RonanNumerical Properties of Stoichiometric Matrices [100 KB]
Funnell-Harris, DeannaResistance to Stalk Pathogens for Bioenergy Sorghum [240 KB]
Garcia Martin, HectorQuantitative metabolic modeling at the Joint BioEnergy Institute [90 KB]
Gardner, Jeffrey G.Comprehensive Functional Characterization of the Glycoside Hydrolase Family 3 Enzymes from Cellvibrio japonicus Reveals Unique Metabolic Roles in Biomass Saccharification [111 KB]
Gasch, Audrey P.Rerouted PKA Signaling Coordinates Sugar And Hypoxia Responses For Anaerobic Xylose Fermentation In Yeast [83 KB]
Ghirardi, MariaThe Algal Ferredoxin Interactome [177 KB]
Gill, RyanDesign and engineering of native regulatory networks [106 KB]
Glass, Louisem-CAFÉs Development of novel CRISPR-Cas technologies for precise manipulation of microbial networks [80 KB]
Glass, Louisem-CAFÉs: Microbial Community Analysis and Functional Evaluation in Soils [87 KB]
Glass, Louisem-CAFÉs -EcoFABs: Model Ecosystems to Advance Microbiome Science I [82 KB]
Glass, Louisem-CAFÉs -EcoFABs: Model Ecosystems to Advance Microbiome Science II [103 KB]
Groover, AndrewDiscovery and characterization of disease resistance loci in poplar [419 KB]
Hegg, EricProgress Towards N2O Source Apportionment in Biofuel Soils: Understanding Sources of Variation in Isotopic Discrimination During Denitrification [516 KB]
Hettich, RobertPlant-Microbe Interfaces: Developments in integrated omics to link microbial metabolism to community structure/function in plant/microbial systems [100 KB]
Hillson, Nathan J. DIVA Services: PCR, Full DNA Construction, and MiSeq Validation [75 KB]
Hittinger, ChrisEvolutionary Dynamics of a Secondary Metabolite Gene Cluster in Budding Yeasts [16 KB]
Hofmockel, KirstenMolecular interactions of the plant-soil-microbe continuum of bioenergy ecosystems [91 KB]
Hungate, BruceAre the activities of microbial taxa consistent across ecosystems? [81 KB]
Hungate, BruceExploring Biome-scale Variation in Microbial Taxon-Specific Growth and Mortality at different temperatures through quantitative Stable Isotope Probing with H218O. [101 KB]
Hungate, BruceField Measurements of Taxon-Specific Microbial Growth in Soil at Two Elevation Gradient Sites Using Quantitative Stable Isotope Probing (qSIP) [119 KB]
Hungate, BruceUnderstanding Soil Metabolism from Carbon Release And Carbon Incorporation from Position-Specific 13C-Labeled Substrates [31 KB]
Jacobson, DanielPlant-Microbe Interfaces: AI-GWAPA, explainable AI-based approaches to genome wide phytobiome association [94 KB]
Jacobson, DanielPlant-Microbe Interfaces: Phytobiome and transcriptional adapation of Populus deltoides to acute progressive drought and cyclic drought [97 KB]
Jansson, Janet K.Elucidation of Chemical Dark Matter in Soil Using 'Standards-free' Small Molecule Identification [26 KB]
Jansson, Janet K.Modeling of Context-dependent Microbial Interactions in Biopolymer Degradation Networks [93 KB]
Jansson, Janet K.Phenotypic Response of the Soil Microbiome to Environmental Perturbations [71 KB]
Jansson, Janet K.Visualizing Spatial Metabolic Interactions Within a Soil Microbiome [52 KB]
Jewett, Michael C. Building a Bridge between Cell-Free Experimentation and Cellular Metabolic Engineering [3.17 MB]
Jin, Yong-SuMicrobial metabolic engineering to produce alcohols from cellulosic hydrolysates [96 KB]
Juenger, ThomasClimate adaptation and sustainability in switchgrass: exploring plant-microbe-soil interactions across continental scale environmental gradients [25 KB]
Kalluri, Udaya C Plant-Microbe Interfaces: Altered root metabolome composition impacts microbiome composition in Populus PdKOR1 RNAi plants [108 KB]
Khanna, MadhuCenter for Advanced Bioenergy and Bioproducts Innovation: Sustainability Theme [66 KB]
Kirst, MatiasPhylogenomic Discovery and Engineering of Nitrogen Fixation into the Bioenergy Woody Crop Poplar [73 KB]
Labbé, JessyPlant-Microbe Interfaces: The key fungal lineage of the Russulaceae, a new resource for untangling and linking beneficial plant-fungal associations and ecosystem functions [94 KB]
LeBoldus, JaredTowards durable resistance to Septoria stem canker and leaf spot: a molecular understanding of resistance. [60 KB]
Lemaux, PeggyFrom Leaves to Roots to Microbes: How Sorghum Responds to Drought [108 KB]
Lidstrom, Mary E. Role of Lanthanides in the Complex Interplay of Alternative Enzyme Systems Involved in Methanotrophy [104 KB]
Lipton, MaryBridging the Soil Metagenome and Metaphenome Through Integrated Omics Analyses [416 KB]
Long, StephenBuilding on success in systems design of high yielding low-input energycanes for marginal lands OR Renewable Oil Generated with Ultra-productive Energycanes (ROGUE) [195 KB]
Loqué, DominiqueSbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum [73 KB]
Lowry, David B.Identification of Adaptive Fungal Pathogen Resistance Loci in Switchgrass [102 KB]
Lu, ChaofuSystems Biology to Improve Camelina Seed and Oil Quality Traits [172 KB]
Lu, YiExpanding the Scope of Biofuels and Chemicals Produced by Microorganisms through Design of Artificial Enzymes Containing Unnatural Amino Acids and Non-native Cofactors [48 KB]
Maranas, CostasDevelopment of an accelerated prodedure for parameterizing kinetic metabolic models for C. thermocellum [100 KB]
Maranas, CostasnovoStoic: Pathway design using de novo steps through uncharted biochemical spaces [319 KB]
Maranas, CostasSteadyCom: Predicting Microbial Abundances whille Ensuring Community Stability [610 KB]
Maravelias, ChristosA Framework for the Identification of Economically Promising Bio-Based Chemicals [447 KB]
Martienssen, RobertBiological Design of Lemnaceae Aquatic Plants for Biodiesel Production [118 KB]
Mayali, XavierNanoscale Stable Isotope Tracing and Compound-Specific Radioisotope Analysis to Investigate Metabolic Interactions between Bacteria and Biofuel-producing Algae [193 KB]
McKinlay, James B. Competition for a cross-fed nutrient between bacterial mutualists [103 KB]
Meile, ChristofMicrobial Interactions in The Anaerobic Oxidation of Methane: Model Simulations Constrained by Process Rates and Activity Patterns [128 KB]
Merchant, SabeehaA Day in the Life of Chlamydomonas [150 KB]
Merchant, SabeehaTrace Metal Storage in Metal-Specific, Lysosome-Related Vacuolar Compartments [112 KB]
Moon, Tae Seok Development of a Genetic Toolkit in Rhodococcus opacus PD630 for Lignin Valorization [91 KB]
Moran, JamesSpatially Resolved Rhizosphere Function for Elucidating Key Controls on Below-ground Nutrient Interactions [148 KB]
Morrell-Falvey, JenniferPlant-Microbe Interfaces: Characterization of IAA biosynthesis pathways in Populus-associated microbes [99 KB]
Mortimer, JennyPlant Sphingolipid Glycosylation And Its Role In Immunity And Cell Wall Organization [59 KB]
Muchero, WellingtonGenomic divergence in pattern recognition receptors and its implications on endophytic microbial associations in the genus Salix [97 KB]
Navid, AliIn silico system-level analysis of interactions in algal-bacterial co-cultures [104 KB]
Newcombe, GeorgeCharacterizing the Defense Hierarchy of Populus trichocarpa and its Hybrids [390 KB]
Niyogi, KrishnaSystems Analysis and Engineering of Biofuel Production in Chromochloris zofingiensis, an Emerging Model Green Alga [95 KB]
Noirot, PhilippeA Mycorrhizal Helper Bacteria Increases Mycorrhization in Aspen Seedlings by Modulating Expression of Defense Response Genes in Roots [258 KB]
Noirot, PhilippeCRISPRi-Mediated Analysis of Biofilm Formation in Plant Growth Promoting Pseudomonas fluorescens [101 KB]
Northen, TrentSynthetic Chemical Probes for Studying Lignin Deconstruction and Analysis of Biofuel Molecules Using nanostructure-initiator Mass Spectrometry (NIMS) [117 KB]
Northen, TrentThe importance of biocrust organics revealed by metabolite sorption studies and in situ imagery [116 KB]
O'Malley, Michelle A. Engineering Anaerobic Gut Fungi for Lignocellulose Breakdown [78 KB]
Orphan, VictoriaComparative Genomics, Transcriptomic Analysis, and Ecophysiology of Individual Environmental Methane-oxidizing Syntrophic Consortia [99 KB]
Pakrasi, HimadriMinGenome: An in silico top-down approach for the synthesis of minimized genomes [151 KB]
Papa, GabriellaDevelopment and screening of one-pot IL conversion technologies [57 KB]
Peay, KabirClimate Predicts the Dominant Form of Plant-Microbe Symbiosis in Forests at a Global Scale [98 KB]
Peay, KabirHow Does Precipitation Impact the Taxonomic and Functional Diversity of the Populus trichocarpa Soil Microbiome? [240 KB]
Pelletier, Dale A. Plant-Microbe Interfaces: Characterization of natural products from the Populus microbiome [96 KB]
Pett-Ridge, JenniferHow Plant-Microbial Interactions Shape Resource Allocation in Perennial Bioenergy Grasses [98 KB]
Pett-Ridge, JenniferRedox Fluctuations Control Coupled Iron-Carbon Cycling and Microbial Community Structure in Tropical Soils [90 KB]
Pett-Ridge, JenniferSequential Growth of Bacteria Following the Rewetting of a Seasonally Dried Grassland Soil [138 KB]
Pett-Ridge, JenniferUnderstanding Microbial Stress Responses in Soil Using Metagenome and Metatranscriptome Analysis [197 KB]
Pfleger, Brian F. A Better Understanding of Bacterial RNA Turnover Developed Through RNA Sequencing [295 KB]
Ralph, John"Ideal lignin" facilitates full biomass utilization [113 KB]
Rao, ChristopherEngineering the oleaginous yeast Rhodosporidium toruloides for the production of lipids and lipid-based chemicals [102 KB]
Rao, ChristopherQuantification of Multiple Post-Translational Modifications by 'One-Pot' Affinity Enrichment - Applications in E. coli [150 KB]
Rao, ChristopherRegulation of acetate metabolism by pH in Escherichia coli [96 KB]
Reed, JenniferMachine learning techniques help accelerate enzyme engineering: a case study with glycoside hydrolases [246 KB]
Retterer, Scott T. Plant Microbe Interfaces: Emerging analytical techniques for controlling and monitoring architectural changes in developing multi-kingdom systems [93 KB]
Rich, VirginiaModeling the Pathways to Carbon Liberation: Microbiologically-Informed C-Cycle Modeling in a Thawing Permafrost Landscape, for Scaling from Molecules to the Earth System [205 KB]
Rich, VirginiaSubarctic Lake Sediment Microbial Community Contributions to Methane Emission Patterns [88 KB]
Sacks, ErikIntrogression of Novel Disease Resistance Genes from Miscanthus into Energycane [51 KB]
Sale, KennethCo-Optimization of Multicomponent Enzyme Mixtures and Saccharification Conditions [113 KB]
Sattely, ElizabethIdentifying a Minimal Set of Genes Required for Valorization of Lignin Biomass [63 KB]
Schachtman, DanielDefining the Functional Genome Associated with Enhanced Water and Nitrogen Use Efficiency in Bioenergy Sorghum [78 KB]
Schachtman, DanielIdentifying 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 [289 KB]
Schachtman, DanielLeaf Carbon and Nitrogen Isotope Composition in Diverse Sorghum Lines Under Differential Water and Nitrogen Treatments [68 KB]
Schachtman, DanielUsing Metabolomics to Uncover Metabolic Pathways Utilized in Nitrogen Stress and Plant-Microbe Interactions in Energy Sorghum [110 KB]
Schadt, Christopher W. Plant-Microbe Interfaces: The contribution of host chemotype as a driver of rhizosphere microbial community structure [109 KB]
Scheller, Henrik V. A Dominant Approach to Reduce Xylan in Bioenergy Crops [84 KB]
Schilling, JonathanSpatial Connectomics to Identify Agents Relevant to Lignocellulose Deconstruction in Fungi [129 KB]
Schnell, Danny J. Engineering mitochondrial metabolic networks to increase yield and water use efficiency in Camelina sativa [88 KB]
Scown, CorinneSimulating Near-Term Scale-Up of Cellulosic Biofuel Production Using Crop Residues and Biomass Sorghum [67 KB]
Sedbrook, JohnAdvancing Field Pennycress as a New Oilseed Biofuels Feedstock that does not Require New Land Commitments [106 KB]
Shade, AshleyMicrobiome diversity and assembly in the phyllosphere of perennial bioenergy crops [403 KB]
Simmons, BlakeEngineering CRISPR/Cas9 platform to industrialize lignin modifying enzymes (LMEs) using Aspergillus niger [94 KB]
Singer, Steven W. Bioconversion of Sugars and Aromatics from Engineered Plants to Methyl Ketones [99 KB]
Singh, AnupAn Automated Microfluidic System for Gene Editing Processes [116 KB]
Smart, Lawrence B. Dissecting Genetic Resistance to Willow Leaf Rust (Melampsora spp.) in Shrub Willow (Salix spp.) [74 KB]
Stuart, Rhona K. Multi-Component Characterizations of Algal Pond Ecosystems Reveal Algal Influence on Heterotroph Dynamics [99 KB]
Sullivan, Matthew B. Host-Linked Soil Viral Ecology along a Permafrost Thaw Gradient [93 KB]
Sweedler, JonathanA general, high-throughput platform for molecular prototyping of microbial cell factories via optically guided mass spectrometry [154 KB]
Tas, NeslihanUnderstanding the microbial controls on biogeochemical cycles in permafrost ecosystems [73 KB]
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 [82 KB]
Tringe, SusannahDiverse sorghum microbiome discovery and characterization in nitrogen- and waterlimited soils for improved biomass production [100 KB]
Tuskan, GeraldA Comparison of Lignocellulose Solubilization by Cellulolytic Monocultures and a Mixed [27 KB]
Tuskan, GeraldAdvances in Lignin Valorization via Biological and Catalytic Transformations [21 KB]
Tuskan, GeraldAgile Technoeconomic and Life Cycle Assessments at the CBI [21 KB]
Tuskan, GeraldCELF/CBP for Enhanced Utilization of Polysaccharides and Lignin [19 KB]
Tuskan, GeraldHighly Resolved Genome-Wide Association Mapping (GWAS) Reveals Novel Variants for Engineering Increased Biomass Yield in Populus trichocarpa [19 KB]
Tuskan, GeraldIdentification and Optimization of CRISPR Systems for Genome Editing in Pseudomonas putida and Clostridium thermocellum [50 KB]
Tuskan, GeraldImproving Nitrogen-Use Efficiency of Switchgrass Production: Past, Present, Future [19 KB]
Tuskan, GeraldMetabolic Reconstruction, Analysis and Design of Metabolic Pathways [42 KB]
Tuskan, GeraldPleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery [44 KB]
Tuskan, GeraldPoplar GWAS and eQTL Analyses Reveal a Key Transferase Gene, HCT2, as a Missing Link in Plant Growth-Defense Tradeoffs [20 KB]
Tuskan, GeraldRapid Domestication of Non-Model Microbial Hosts for Biofuels Production [21 KB]
Tuskan, GeraldSwitchgrass Field Experiments to Enable Rapid Domestication, Increased Sustainability, and a Genome-wide Association Study [72 KB]
Tuskan, GeraldTechnoeconomic Analysis of Biofuel Feedstock Supplies to Inform Plant Development R&D [22 KB]
Tuskan, GeraldTowards Understanding Plant Cell Wall Structure and Properties During Microbial Deconstruction - From Chemical Bonds to Wall Architecture [22 KB]
Tuskan, GeraldUsing Multi-Omic Data to Understand the Response of Clostridium thermocellum to Deletions of Genes for Lactate and Acetate Production [24 KB]
VanLoocke, AndrewEconomic and Environmental Modeling of Bioenergy Production – Policy Impacts on Water Quality [61 KB]
Vilgalys, RytasPlant-Microbe Interfaces: Dissecting the compatibility and diversity of the mycobiome of Populus trichocarpa [99 KB]
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 [94 KB]
Weston, David J. Plant-Microbe Interfaces: Developing a synthetic community system to test preferential allocation to nitrogen-fixing bacteria [93 KB]
Wilkerson, Curtis Gene Increasing biomass in grasses by identifying genes involved in mixed-linkage glucan biosynthesis [113 KB]
Wrighton, KellyMethanogenesis in Oxygenated Soils is a Substantial Fraction of Wetland Methane Emissions [98 KB]
Wühr, MartinAccurate, Sensitive, and Precise Multiplexed Proteomics using the Complement Reporter Ion Cluster [164 KB]
Yang, WendyCarbon Cycling in Biomass-Based Cropping Systems: Improving the Mechanistic Foundations of Plant, Microbial, and Soil Interactions [120 KB]
Yeates, ToddDesigning Self-Assembling Protein Materials for Imaging and Energy Applications [257 KB]
Young, JameyMetabolic phenotyping of cyanobacteria with increased biofuel productivity [264 KB]
Zhang, FuzhongEngineering Bacteria to Produce Branched-chain Fatty Acid Derived Advanced Biofuels [541 KB]
Zhao, HuiminCombinatorial Metabolic Engineering Using an Orthogonal Tri-functional CRISPR System [196 KB]
Zhao, HuiminConstruction of a Kinetic Model for Yeast Lipid Metabolism [257 KB]
Zhao, HuiminConstruction of genome-scale metabolic models for non-model yeast organisms for biofuel and bioproduct engineering [70 KB]
Zhao, HuiminGenome-scale Engineering of Saccharomyces cerevisiae with Single Nucleotide Precision [647 KB]
Zhou, JizhongSuccessional Dynamics of Grassland Microbial Communities in Response to Warming, Precipitation Alternation, and Clipping [143 KB]
Zhou, JizhongTime-series metagenomics of experimentally warmed Alaskan tundra and Oklahoma temperate soils enables fine-resolution assessment of belowground C cycling feedbacks to climate change [186 KB]



2018 Research Summaries [02/18]

GSP Overview Brochure [01/18]

Plant Feedstock Genomics for Bioenergy [01/18]

Biosystems Design to Enable Next-Generation Biofuels (Summary of Funded Projects) [12/17]

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]

ASCR BER Exascale Requirements Review [9/17]




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