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Abstracts and Summaries

Research Summary
Genomic Science Program and USDA-DOE Plant Feedstock Genomics for Bioenergy
February 2015

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.

Genomic Science Contractors– Grantees Meeting XIII and USDA-DOE Plant Feedstock Genomics for Bioenergy Meeting, February 22-25, 2015 Abstract Book PDF provided by Oak Ridge Associated Universities (ORAU).

Individual Abstract PDFs

Principal Investigator Abstract Title
Adams, Paul A novel method to retain viability of obligate anaerobic microorganisms during single cell sorting 
Adams, Paul Altered Biofilm Formation in Desulfovibrio vulgaris Hildenborough by Laboratory-Driven Evolution 
Adams, Paul Groundwater-fed Bioreactors Show Distinct Colonization and Community-wide Response Dynamics to Perturbations
Adams, Paul High-throughput genetic characterization of environmental bacteria 
Adams, Paul Microbial Interactions with Native Natural Organic Matter in Groundwater and Sediment from the Oak Ridge FRC
Adams, Paul Mutations in the Gene Regulatory Network Facilitate Adaptation to Variable Environments
Adams, Paul Novel single-cell sequencing methods link target genes with bacterial hosts
Adams, Paul Screening for Genetic Interactions in Desulfovibrio vulgaris Hildenborough 
Adams, Paul Temporal Variation in Groundwater Geochemistry and Microbial Community Structure at the Oak Ridge Field Site 
Adams, Paul Towards Rapid Characterization of Microbial Communities, Interactions, and Community Assembly 
Adams, Paul Understanding the Role of Pelosinus In Uranium-Contaminated Environments 
Allen, Andrew Gene editing, artificial chromosomes, and highly efficient conjugal gene transfer in diatoms
Allen, Andrew Systems biology of nitrogen assimilation in the diatom Phaeodactylum tricornutum 
Allen, Andrew Towards a Comprehensive Knowledge Base for the Marine Diatom Phaeodactylum tricornutum 
Alm, Eric The Ecology of Algal Polysaccharide Degradation: Characterizing Novel Fucoidan- Degrading Bacteria
Amasino, Richard Genetic and molecular anayses of the regulation of flowering in the temperate grass, Brachypodium distachyon 
Arkin, Adam 'Species Filter' Effects on Sediment Biofilms and Groundwater Source Diversity
Arkin, Adam HT-CRISPRi studies of gene regulation and function in E. Coli 
Arkin, Adam 'Species Filter' Effects on Sediment Biofilms and Groundwater Source Diversity
Arkin, Adam A Platform E. coli Strain for Optimizing Biosynthetic Pathways via High-throughput Genome Engineering and Screening
Arp, Daniel Responses of and interactions between nitrifying bacteria to environmental changes: a systems level approach 
Auer, Manfred Ultrastructure of plant cells by electron microscopy: towards increased biofuel production 
Banfield, Jillian Multi-“Omic” Analyses of the Dynamics, Mechanisms, and Pathways for Carbon Turnover in Grassland Soil .
Beller, Harry Substantial Improvements in Methyl Ketone Production in E. coli from Rational Metabolic Engineering and Random Mutagenesis 
Betenbaugh, Michael Systems Biology of Autotrophic-Heterotrophic Symbionts for Bioenergy
Blake, Robert A Spectroscopic Device to Monitor Respiratory Electron Transfer in Suspensions of Live Organisms
Blumwald, Eduardo Expanding the breeder's toolbox for perennial grasses: The use of the model perennial grass Brachypodium sylvaticum to identify combinations of transgenes conferring tolerance to multiple abiotic stresses.
Bohn, Paul Correlated Molecular Imaging Applied to Chemically Communicating Microbial Communities of Relevance to the Rhizosphere 
Bohn, Paul Correlated Molecular Imaging Applied to Chemically Communicating Microbial Communities of Relevance to the Rhizosphere 
Brandizzi, Frederica Modulating plant cell wall for biofuel at GLBRC 
Brodie, Eoin The Passalid Beetle (Odontotaenius disjunctus) Microbiome and its Metabolic Potential for Lignocellulose Degradation 
Brunner, Amy Abiotic Stress Networks Converging on FT2 to Control Growth in Populus 
Brutnell, Thomas A versatile phenotyping system and analytics platform reveals diverse temporal responses to water limitation in Setaria
Brutnell, Thomas Geminivirus replicons for targeted modification of cereal genomes 
Brutnell, Thomas Rapid Hemispherical Photographic Phenotyping of Productivity and Canopy Dynamics in a Setaria RIL Population 
Brutnell, Thomas Screening for Water-Use Efficiency with Stable Isotopes in the Model C4 Grass Setaria viridis 
Brutnell, Thomas Sequence-Enabled Gene Discovery in Setaria viridis: A Model Panicoid Grass 
Brutnell, Thomas Zbrowse: An interactive GWAS results browser 
Brutnell, Thomas De novo assembly of a Setaria viridis reference genome
Buell, C. Robin Using Natural Variation in Switchgrass to Identify Genes Relevant for Biomass Production and Improved Breeding Strategies 
Buell, C. Robin Exploiting natural diversity to Identify alleles and Mechanisms of Cold Adaption in Switchgrass
Cavalier, David The Great Lakes Bioenergy Center Material Production Chain: Integrated Production and Characterization of Feedstocks, Pretreated Biomass, and Hydrolysate as Standardized Reagents for Center-Wide Research 
Chapman, Kent Regulation of Neutral Lipid Compartmentalization in Vegetative Plant Tissues 
Chapple, Clint Measurement and modeling of phenylpropanoid metabolic flux in Arabidopsis
Church, George Synthetic Biology-Enabled Biosystems Design and Construction of Radically Recoded Organisms 
Cole, James RDP: Data and Tools for Studying Structure and Function of Microbial Communities
Coleman, Heather Inducible Extreme Expression of Enzymes in Poplar
Collart, Frank Characterizing the Pseudomonas Sulfur Regulome 
Collart, Frank Effect of Nitrogen and Phosphorus Limitation on the Growth and Morphology of Engineered Microbial-Plant Communities
Collart, Frank Methionine Importers in Soil Bacteria: Potential for Transporter-Component Crosstalk 
Comai, Luca A novel poplar biomass germplasm resource for functional genomics and breeding 
Cseke, Leland Nutrient Cycling for Biomass: A multi-omics approach to model ectomycorrhizal regulatory networks 
Cushman, John Engineering Crassulacean Acid Metabolism (CAM) Photosynthetic Machinery into C3 Arabidopsis 
Cushman, John Engineering Crassulacean Acid Metabolism (CAM) to Improve Water-use Efficiency of Bioenergy Feedstocks 
Dangl, Jeff Exploiting Plant Growth-Promoting Root Endophytes to Improve Feedstock Nitrogen Acquisition 
Davison, Brian Hydration Control of Cellulose Surface Structure and Dynamics 
Davison, Brian Investigation of Water Dynamics in a Model Cellulosic System
Davison, Brian Morphological Changes in the Cellulose and Lignin Components of Biomass Occur at Different Stages During Steam Pretreatment
Devos, Katrien Improving Cold Tolerance in Lowland Switchgrass 
Dinneny, Jose New tools for studying water deficit responses in roots 
Donohue, Timothy Structural studies of ß-aryl ether lignin degradation
Dudareva, Natalia Metabolic Engineering of Increased 2-Phenylethanol Production in Plants 
Dueber, John Repurposing the Yeast Peroxisome to Compartmentalize Engineered Metabolic Pathways 
Dunbar, John Interactions between Ascomycete fungi and Actinomycete bacteria during litter decomposition under an N gradient 
Dunlop, Mary Engineering Robust Hosts for Microbial Biofuel Production
Ecker, Joseph Next Generation Protein Interactomes for Plant Systems Biology and Biomass Feedstocks Research 
Firestone, Mary How do plant-microbial interactions regulate litter decomposition? 
Firestone, Mary Mapping soil carbon from cradle to grave: Identifying metabolic processes underlying patterns of rhizosphere microbial succession and organic matter priming 
Firestone, Mary Tracing the Influence of Mineralogy, Microbiology, and Exudate Chemistry on the Stabilization of Root- Derived Carbon
Fleming, Ronan Conditions For Duality Between Fluxes and Concentrations in Biochemical Networks
Fleming, Ronan Consistent Estimation of Gibbs Energy Using Component Contributions
Fleming, Ronan Constraint-based reconstruction and analysis toolbox extensions for parallel network reconstruction and CellDesigner interoperability 
Fleming, Ronan Globally Convergent Algorithms to Solve Systems of Non-linear Biochemical Reaction Equations
Fleming, Ronan Identification of Conserved Metabolic Moieties by Graph Theoretical Analysis of Atom Transition Networks 
Frederickson, Jim Assessing In Situ Metabolic Carbon Dynamics in a Phototrophic Microbial Mat
Frederickson, Jim Metagenomic Sequencing of Parallel Consortia Enables Genome Reconstruction of Rare and Closely Related Organisms
Frederickson, Jim Omics and Chemical Probe Strategies for Assessing Interactions Among Microbial Community Members.
Frederickson, Jim Using Genome-Resolved Metagenomics to Uncover Trophic Structure in Microbial Communities: Its Influence on Community Dynamics
Garcia Martin, Hector Quantitative Metabolic Modeling at Fuel Synthesis Division (JBEI)
Garrity, George Semantic Index of Phenotypic and Genotypic Data 
Ghirardi, Maria Design Principles Controlling Hydrogen Metabolism in Phototrophic Organisms 
Ghirardi, Maria Design Principles Controlling Hydrogen Metabolism in Phototrophic Organisms 
Gill, Ryan A Strategy for Genome-scale Design, Redesign, and Optimization for Ethylene Production in E. coli
Gill, Ryan Flux balance analysis constraint modification to locate metabolic engineering targets for ethylene production in Escherichia coli 
Gill, Ryan The LASER Database: a comprehensive resource for metabolic engineering designs 
Gilna, Paul BESC Switchgrass and Populus TOP Lines: Identifying and Analyzing the Best Candidate Lines for Enhanced Biofuel Production
Gilna, Paul Biological Lignocellulose Solubilization: Comparative Evaluation of Feedstock-Biocatalyst Combinations and Enhancement via Co-Treatment by Intermediate Milling
Gilna, Paul Biomass Deconstruction by Members of the Genus Caldicellulosiruptor
Gilna, Paul Building the Cell Wall: Insights Into Xylan Synthesis Using Recombinant Enzymes
Gilna, Paul Characterizing Cell Wall Crosslinking and/or Entanglement in Reduced Recalcitrance Feedstocks 
Gilna, Paul Consolidated Bioprocessing of Cellulose to Isobutanol in Clostridium thermocellum 
Gilna, Paul Development of a LC-MS/MS-Based Cell Density Assay for Assessing Microbial Growth on Complex Solid Biomass Substrates
Gilna, Paul Engineering a New Alcohol Production Pathway Into the Cellulolytic Thermophile Caldicellulosiruptor Bescii.
Gilna, Paul Field Experiments of Seven Switchgrass TOP Lines
Gilna, Paul Improving Cellulolytic Activity of the C. thermocellum Secretome by Engineering the CipA Scaffoldin 
Gilna, Paul Integrating Conventional and Novel Pretreatments with C. thermocellum CBP to Overcome Biomass Recalcitrance 
Gilna, Paul Integration of Multi-Omic Data for Advanced Consolidated Bioprocesses 
Gilna, Paul Metabolic Engineering of Clostridium Thermocellum for High-Yield Ethanol Production 
Gilna, Paul Populus Natural Variation Study, from Single Nucleotide Polymorphisms to Reduced Recalcitrance Biomass and Elucidation of New Function for an EPSP Gene 
Gilna, Paul Progress towards Molecular Breeding of Switchgrass for Feedstock Yield and Quality
Gilna, Paul Selection of Superior Transgenic Switchgrass Through Microbial Bioconversion for Enhanced Ethanol Production 
Gilna, Paul Solid Residuals from Populus trichocarpa Demonstrate that Recalcitrance Persists During Consolidated Bioprocessing 
Gilna, Paul Understanding Why Knockdown Expression of Populus GAUT12.1 Results in Decreased Recalcitrance and Increased Growth in This Woody Feedstock 
Gross, Katherin Diversity and Stability in Experimental Fields of Perennial Bioenery Crops 
Harrison, Maria Genetic dissection of AM symbiosis to improve the sustainability of feedstock production 
Hazen, Samuel Linking genotype and phenotype in a model grass: Building tools for genome-wide- association studies in Brachypodium 
Hillson, Nathan DIVA: More Science, Less DNA Construction 
Hofmockel, Kirsten Key microbial decomposition pathways in soils from bioenergy agroecosystems 
Hurst, Gregory Plant Microbe Interfaces: Proteome Characterization of Plant-Bacterial and Fungal- Bacterial Interactions 
Jacobson, Dan Plant-Microbe Interfaces: Correlotypes: Discovering complex, heterogenous genotypes in the Populus pan genome responsible for phenotypes and microbiomic associations.
Jaiswal, Pankaj Abiotic stress induced Poplar transcriptome analyses 
Jiang, Yiwei Genetic Control of Flowering in Switchgrass 
Juenger, Thomas The Genetics of Divergence Between Upland and Lowland Ecotypes of Panicum virgatum 
Kaeppler, Shawn Candidate Gene Discovery and Validation by Analysis of Natural Variation for Cell Wall Compositional Traits in Maize 
Keasling, Jay Expanding the chemical diversity of E.coli derived products
Kirst, Matias A Systems Biology, Whole-Genome Association Analysis of The Molecular Regulation of Biomass Growth and Composition in Populus deltoides 
Kirst, Matias Accelerated Development of Optimal Feedstock for Bioenergy Using Genome-Wide Selection 
Kuske, Cheryl Metatranscriptomes to explore the effects of nitrogen enrichment on forest soil microbial communities .
Kuske, Cheryl Microhabitat-dependent responses of bacterial and fungal communities to experimental nitrogen additions in arid ecosystems
Landick, Robert Chemical genomic analysis reveals feedstock specific differences in the microbial response to lignocellulosic hydrolysates 
Langan, Paul New Capabilities at the Center for Structural Molecular Biology at ORNL
Lee, Taek Soon Advanced pathways for microbial production of branched C5 alcohols 
Liao, James Ensemble modeling for increasing lipid production in Yarrowia lipolytica
Lidstrom, Mary New Insights into the Factors Defining the Composition of Methane-oxidizing Communities and the Role of Oxygen 
Löffler, Frank Denitrification in the Absence of Bacterial Nitrite Reductases
Löffler, Frank Detecting and quantifying genes in soil short-read metagenomes: implications for the Nitrogen cycle.
Loque, Dominique Tackling biomass recalcitrance with novel biological approaches 
LoQue, Dominique Universal expression tools to improve nutrient acquisition of energy crops 
Magnunson, Jon Genetic Parts Screening and Artificial N-glycosylation Motif Engineering for Heterologous Protein Production in Aspergillus niger
Magnunson, Jon Heterologous Expression of Ionic Liquid Tolerant Cellulases in Aspergillus niger
Maranas, Costas Development of A Regulated Model for Clostridium acetobutylicum 
Maranas, Costas Ensemble cell-wide kinetic modeling of anaerobic organisms to support fuels and chemicals production .
Maranas, Costas Improving computational strain design strategies by incorporation of kinetic information 
Maranas, Costas Metabolic modeling of multi-tissue and multi-organism systems 
Maranas, Costas MetRxn2.0: Integrating atom mapping information for pathway comparisons and metabolic flux elucidation through MFA
Marcu, Oana Protection from Oxidative Stress in Algal-Bacterial Co-Cultures
Marks, Michael Demonstrating Agrobacterium-mediated transformation of Pennycress (Thlaspi arvense) by expressing EaDAcT to alter seed oil composition 
Marks, Michael Using mutation-based breeding approaches to domesticate pennycress into a new oilseed crop
McKay, John Biofuels in the (arid) West: germplasm development for sustainable production of Camelina oilseed 
McKinlay, James Characterization of an Obligately Syntrophic H2-producing Bacterial Coculture
Methe, Barbara Genome-scale Metabolic Modeling of Microbial Communities at Sites Undergoing Natural and Stimulated Attenuation of Uranium 
Methe, Barbara The use of ‘Metaomic’ and Modeling Approaches at Subsurface Sites to Study Carbon, Nutrient and Metal Cycling in Microbial Communities 
Ming, Ray Pyramiding genes and alleles for improving energy cane biomass yield 
Morgan, John Metabolite Profiling of the Monolignol Biosynthesis Pathway Using Reversed Phase Liquid Chromatography Coupled with Tandem Mass Spectrometry 
Morrell-Falvey, Jennifer Plant-Microbe Interfaces: Probing the Molecular Mechanisms of Plant-Bacterial Interactions 
Mortimer, Jenny GONST1 and 2 are GIPC Specific GDP-Mannose Transporters 
Mullet, John Genomics of Energy Sorghum's Water Use Efficiency/Drought Resilience
Nielsen, Jens Analysis of Lipid Metabolism in Saccharomyces cerevisiae: Elucidating Regulation of Triacylglyceride Synthesis
Nielsen, Jens Regulatory Changes During Lipid Accumulation in Yarrowia lipolytica 
Northen, Trent Soil Metabolomics to Decipher the Metabolic Foodwebs in Biological Soil Crusts 
Northen, Trent Understanding microbial carbon cycling in soils using novel metabolomics approaches
Northen, Trent ENIGMA Sediment Metabolomics 
Northen, Trent Development of a High Throughput Platform for Screening GH Enzymes and Methyl Ketones based on Oxime-NIMS (Nanostructure-Initiator Mass Spectrometry) 
O'Malley, Michelle Engineering Anaerobic Gut Fungi for Lignocellulose Breakdown 
O'Malley, Michelle Engineering Synthetic Anaerobic Consortia for Sustainable Chemical Production from Biomass 
Orphan, Victoria Isotopic and click chemistry-based approaches for tracking activity in single cells and newly synthesized proteins in uncultured microorganisms catalyzing anaerobic methane oxidation
Pakrasi, Himadri Systems Level Study of a Novel Fast-Growing Cyanobacterial Strain for Next-Generation Biofuel Production 
Paterson, Andrew Genomics of Bioenergy Grass Architecture
Payne, Samuel The PNNL Biodiversity Library 
Pelletier, Dale Plant-Microbe Interfaces: Carbon Utilization Reflects Nutritional Environment of Pseudomonas Isolates .
Pett-Ridge, Jennifer Diel Metagenomics and Metatranscriptomics of Elkhorn Slough Hypersaline Microbial Mat 
Pett-Ridge, Jennifer Identifying Microbial Resource Use with Chip-SIP
Pett-Ridge, Jennifer Intracellular Iron Distribution in Chlamydomonas in Response to Fe Nutrition Status 
Pett-ridge, Jennifer Elucidating Cyanobacterial Recycling of Microbial Mat Extracellular Matrix
Petzold, Christopher Applications of a high-throughput targeted proteomics assay for analysis of engineered Escherichia coli.
Pfelger, Brian Towards Engineering mRNA Stability: Global Analysis of mRNA Turnover in Cyanobacteria and E. coli 
Qian, Wei-Jun Quantitative Redox Proteomics and Ultrasensitive Targeted Proteomics for Functional Proteome Analysis
Rabinowitz, Joshua An integrated 'omics approach to large-scale quantitative analysis of cellular metabolic regulation 
Rabinowitz, Joshua Conservation of absolute cellular metabolite concentrations 
Ralph, John Introducing readily cleavable bonds into the lignin backbone: The Zip-Lignin™ Strategy 
Ralph, John Laccases Direct Lignification in the Discrete Secondary Cell Wall Domains of Protoxylem 
Rao, Christopher Characterization of the Alginate Lyases from Vibrio sp 
Rao, Christopher Characterization of the Laminarinases from Vibrio breoganii 1C10 
Rao, Christopher The Systems Biology of Protein Acetylation in Fuel-Producing Microorganisms
Reddy, Anireddy Global Analysis of Alternative Splicing and Epigenetic Regulation of Gene Expression in Response to Drought Stress in Sorghum 
Reed, Jennifer Estimating Intracellular Fluxes Using Relative Expression and Phenotype Datasets (REPPS) 
Robertson, G. Phillip Changes in biophysical climate regulation services from converting native grassland to bioenergy production in the US Midwest 
Robertson, G. Phillip Nitrous oxide emissions from Midwest row-crops: Comparing presence and absence of winter cover crops 
Robertson, G. Phillip Switchgrass Augments Its Nitrogen Supply with Fixed Nitrogen 
Ronald, Pamela Genomic Resources for the Study of Cell Wall Biosynthesis in Grasses
Rose, Jocelyn Defining Determinants and Dynamics of Cellulose Microfibril Biosynthesis, Assembly and Degradation 
Saha, Malay Deciphering Natural Allelic Variation in Switchgrass for Biomass Yield and Quality Using a Nested Association Mapping Population 
Sale, Kenneth Optimization of Recombinant Cellulase Mixtures for Degradation of [C2C1Im][OAc] Pretreated Biomass.
Schadt, Christopher Plant-Microbe Interfaces: Understanding the factors shaping microbiome structure and function within Populus species.
Scheller, Henrik Stacking of Biomass Traits
Schilling, Jonathan Spatial connectomics to identify agents relevant to lignocellulose deconstruction in fungi 
Schilling, Jonathan Spatially co-localizing the incompatible oxidative and enzymatic steps during fungal brown rot wood degradation - Early Career Program 
Schnable, Patrick Genetic Architecture Of Sorghum Biomass Yield Component Traits Identified Using High-Throughput, Field- Based Phenotyping Technologies 
Segre, Daniel Mapping Inter-species Interactions and Metabolic Synergy for Next-generation Biofuel Production
Silver, Pamela Illumination of Photosynthetic Trans-Kingdom Consortia 
Singer, Steven MaxBin: An Automated Metagenomic Binning and Reassembly Algorithm 
Singer, Steven The Unexpected Importance of Actinobacterial GH12 in Hydrolysis of Crystalline Cellulose 
Singh, Anup Droplet Microfluidics for Synthetic Biology
Singh, Seema Ionic Liquid Pretreatment: State of Technology and Future Perspective 
Skerker, Jeffrey Development of the Oleaginous Yeast Rhodosporidium toruloides as a New Model Organism for Systems- Level Analysis of Lipid Productivity
Smart, Lawrence Transcriptome Analysis of Diploid and Triploid Species Hybrids of Shrub Willow
Smith, Richard Pan-omics Biological Applications in the Genome Sciences Program 
Smith, Richard Pan-omics: Development of a Universal Next Generation Pan-omics Measurement Pipeline 
Smith, Richard Pan-omics: Bioinformatics Developments 
Smith,Richard Pan-Omics: Activity-Based Proteomics 
Stahl, David Agricultural land-usage completely reshapes nitrifier diversity 
Stephanopoulos, Gregory Developing a robust genetic and omic tool suite for the oleaginous yeast, Yarrowia lipolytica 
Stephanopoulos, Gregory Determination of lipase gene products relevant to lipid mobilization in Yarrowia lipolytica and characterization of their respective knockout strains
Stephanopoulos, Gregory Improving de novo lipids production through engineering the availability of cytosolic NADPH in Yarrowia lipolytica
Stephanopoulos, Gregory Reprogramming acetyl-CoA metabolism for efficient production of lipid biofuels in Yarrowia lipolytica
Strand, Stuart Nitrous oxide emissions in fields of bioenergy crops are correlated with the form of nitrogen addition and ammonia-oxidizing microbial populations
Strauss, Steven Structural Polymorphisms as Causes of Heterosis in Populus 
Suen, Garret The Novel Cellulolytic Strategy of Cellulomonas gilvus 
Sweedler, Jonathan Advances in mass spectrometry imaging instrumentation and sample treatment protocols for in situ chemical characterization of biological samples
Sweedler, Jonathan Multimodal chemical and architectural characterization of Pseudomonas aeruginosa microbial communities 
Tobias, Christian Expanding the Breeders Toolbox: The Development of Biotechnological Tools for Switchgrass Improvement and Transgene Containment 
Tringe, Susannah Nutrient Stoichiometry Drives Carbon Turnover and Microbial Community Composition in Mineral and Organic Soils Under Rice Cultivation 
Tringe, Susannah The Complex Role of Restoration in Wetland Greenhouse Gas Production 
Tsai, Chung Jui Dual Effect of Tubulin Manipulation on Populus Wood Formation and Stomatal Behavior
Tuskan, Gerald Plant-Microbe Interfaces: Constructed plant and bacterial communities for understanding and predicting community function 
Tuskan, Gerald Plant-Microbe Interfaces: Fungal-bacterial interactions within Populus rhizosphere 
Tuskan, Gerald Plant-Microbe Interfaces: Genome re-sequencing reveals a species-specific whole-gene deletion associated with Populus-Laccaria mycorrhizal symbiosis 
Tyson, Gene The Thaw: Investigating Microbial Contribution to Permafrost Carbon Liberation through Functional Meta- omics 
Tyson, Gene Using GraftM to generate phylogenetically informed gene profiles in thawing permafrost metagenomes.
Ussery, David Plant-Microbe Interfaces: Comparative Genomics of Populus endosphere microbiomes 
Weber, Peter NanoSIMS Isotope Imaging to Investigate Algal-Bacterial Interactions in Biofuel- Producing Communities
Wolfe, Amy Risk and Escape Policies, Perspectives, and Practices: Issues and Implications for Biosystems Design R&D on Microbes, Algae, and Plants
Xie, Sunney Studying lipid accumulation mechanism in oleaginous yeast using hyperspectral SRS microscopy 
Yang, Xiaohan An Innovative Cloning Platform for Pathway Engineering 
Yongqin, Jiao Identification of genomic elements required for uranium resistance by Caulobacter crescentus 
Yongqin, Jiao Uranium exposure elicits a multifaceted stress response in Caulobacter crescentus 
Young, Jamey Isotopically nonstationary 13C flux analysis of isobutyraldehyde production in Synechococcus elongatus 
Zengler, Karsten Predicting Clostridium ljungdahlii Cellular Phenotypes Through a Metabolic and Gene-Expression Model
Zhang, Yaoping Comparative Fermentation of Saccharomyces cerevisiae and Zymomonas mobilis in Lignocellulosic Hydrolysates Produced from Corn Stover and Switchgrass to Investigate the Effect of Interannual Climate Variability on Hydrolysate and Microbial Performance
Zhao, Huimin Engineering a Bacillus subtilis Strain Capable of Utilizing Marine Macroalgae for Biofuels Production 
Zhou, Jizhong Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils
Zhou, Jizhong Expanding the Toolkit for Metagenomics, Implementing in KBase, and Applying It to the Study of the Effects of Experimental Warming in Midwestern and Alaskan Soils 
Zhou, Jizhong Functional and taxonomic characterization of Alaskan permafrost and Oklahoma prairie soils using comparative metagenomics: implications for responses to climate change
Zhou, Jizhong Metagenomics-Enabled Predictive Understanding of Microbial Communities to Climate Warming: Results from Long Term Soil Incubations 
Zhou, Jizhong Methods for estimating temperature sensitivity of soil organic matter based on incubation data: A comparative evaluation 
Zhou, Jizhong Successional Dynamics of Grassland Microbial Communities in Response to Warming, Precipitation Alternation, and Clipping



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