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Genomic Science Program

Abstracts and Summaries

Research Summary
Genomic Science Program
February 2014

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.

2014 cover2014 Genomic Science Contractor-Grantee Meeting XII Abstract Book PDF provided by Oak Ridge Associated Universities (ORAU).

Individual Abstract PDFs

A | B | C | D | E | F | G | H | J | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z
A
Principal Investigator Abstract Title
Adams, PaulBiochemical and Structural Studies of Enzymes Involved in Fatty Acid Biosynthesis
Adams, PaulDiscovery of a Novel Colony Invading Phenotype of Pseudomonas stutzeri RCH2
Adams, PaulNatural and Synthetic Ecology in ENIGMA: Determining the links between Microbial Community Structure and Function
Adams, PaulMetal Metabolism in ENIGMA: The Environmental Role of and Regulation by Molybdenum under Denitrifying Conditions
Adams, PaulComputation Component of ENIGMA: from data to predictive models
Adams, PaulSingle Cell Genomics Applications in ENIGMA
Adams, PaulMicrobial Community Structure Predicts Groundwater Geochemistry
Adams, PaulEvolution of alternative adaptive strategies sustaining two-member syntrophic communities
Adams, PaulHigh Throughput Isolation and Environmental Isolate Characterization in ENIGMA
Adams, PaulMicrobial Characterization in ENIGMA: Flexible Tools for Annotating Genes and Pathways in Environmental Bacteria
Allen, AndrewRegulation of Cellular Nitrogen Metabolism in the Model Marine Diatom Phaeodactylum tricornutum
Allen, AndrewInactivation of Phaeodactylum tricornutum urease gene using TALEN-based targeted mutagenesis
Allen, AndrewAssembly of entire Phaeodactylum tricornutum chromosomes in yeast
Allen, AndrewTowards a Comprehensive Knowledge Base for the Marine Diatom Phaeodactylum  tricornutum
Alm, EricAdaptive Radiation after Gene Transfer Leads to Population Specialization and Enhanced Glycan Cycling
Alm, EricThe Ecology of Algal Polysaccharide Degradation: Characterizing Novel Fucoidan- Degrading Bacteria
Alm, EricCharacterization of Algal Polysaccharide Degrading Enzymatic Machinery and its Refactoring via DNA Assembler for Biofuels Production
Aranas, CostasDevelopment of a core Escherichia coli inetic metabolic model using the E formalism
Aranas, CostasIntegrating atom mapping information within MetRxn: Application to metabolic flux elucidation through MFA
Aranas, CostasOpt   orce: train design using inetic models and synthetic biology tools
Aranas, CostasMetabolic modeling of multi tissue and multi organism systems
Aranas, Costassing MetRxn for metabolic model reconstruction, flux elucidation and redesign
Aranas, CostasA   Regulated odel   for   Clostridium   acetobutylicum ased   on   Response   to utanol   and   utyrate tress
Arkin, AdamHigh--throughput genomic studies using CRISPRi
Arkin, AdamKBase Overview
Arkin, AdamThe DOE Systems Biology Knowledgebase: Plant Science Domain
Arkin, AdamAnalysis capabilities for microbial communities in KBase
Arkin, AdamAnalysis of Microbes
Arkin, AdamKBase Outreach and Partnership
Arkin, AdamThe KBase Narrative User Interface
Arkin, AdamCollaborative Workspaces in the DOE Systems Biology Knowledgebase
Arkin, AdamThe KBase User Experience
Arkin, AdamDesign of KBase Infrastructure
Arkin, AdamDeveloping for KBase
Arkin, AdamCommand Line Environment in the DOE Systems Biology Knowledgebase
Arkin, Adam The DOE Systems Biology Knowledgebase (KBase): Progress towards a system for collaborative and reproducible inference and modeling of biological function
Arkin, AdamDoes Scale Impact Structure and Function of Microbial Biofilms?
Arp, DanielTranscriptome profiling of Nitrosomonas europaea grown singly and in co-culture with Nitrobacter winogradskyi

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B
Principal Investigator Abstract Title
Baker, ScottIdentifying biological pathway targets for lipid production in Yarrowia lipolytica
Baliga, NitinThe Network Portal and Gaggle Workspace: New Generation of Tools for Network Biology
Banfield, JillianRapid Binning and Metabolic Profiling of Subsurface Microbial Community Metagenomic Data via an Interactive Online Knowledgebase
Banfield, JillianDeveloping mass spectrometry approaches enabling multi-‘omic’ analyses of the dynamics, mechanisms, and pathways for carbon turnover in grassland soil under two climate regimes
Beliaev, AlexanderAnalysis of the Transcriptional Response of Synechococcus sp. PCC 7002 to Specific Growth Conditions from a Compendium of RNA-seq Data
Beliaev, AlexanderCharacterization of Redox Signaling Pathways in Cyanobacteria during Nutrient Limitation
Beliaev, AlexanderDevelopment of Genome-Scale Dynamic Modeling Framework for Simulating Photoautotrophic Growth of Cyanobacteria
Beller, HenryDeveloping New Fatty Acid-Derived Biofuels at JBEI: Methyl Ketones and Ladderanes
Bianchetti, ChristopherContribution of multifunctional enzymes to biomass hydrolysis
Blackwood, ChristopherOpportunities for Cheating? Transcriptomic Analysis of Model Organisms Exposed to Shifting Communities and Substrates
Blackwood, ChristopherEffects of Competitors or Cheaters and Temperature on Physiological Performance and Gene Transcription of Model Fungi
Blake, RobertThe Multi-Center Iron Respiratory Chain of Acidithiobacillus ferrooxidans Functions as an Ensemble With a Single Macroscopic Redox Potential
Blaschek, HansUnderstanding Fundamental Aspects of Butanol Production by Clostridium beijerinckii
Blumwald, EduardoExpanding the breeder’s toolbox for perennial grasses: Engineered doubled-haploid and gene containment systems
Blumwald, EduardoExpanding 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, PaulIn Situ Correlated Imaging of Chemically Communicating Microbial Communities
Bohn, PaulMultidimensional Chemical Analysis of Microbial Communities by Integrating Fluorescence, Vibrational and Mass Spectrometric Microspectroscopic Imaging
Bond, DanielThe molecular basis for electron flow within metal-reducing biofilms: new insights from genome-scale genetics
Brutnell, ThomasA Systems-Level Analysis of Drought and Density Response in the Model C4 Grass Setaria viridis
Buckley, DanielMicrobial Food Web Mapping: Linking carbon cycling and community structure in soils through next generation sequencing enabled stable isotope probing
Buckley, DanielCross-system analysis of carbon assimilation dynamics in soil microbial communities: Documenting the function of non-cultivated microorganisms in terrestrial ecosystems

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C
Principal Investigator Abstract Title
Chapman, KentRegulation of Neutral Lipid Compartmentalization in Vegetative Plant Tissues
Chapple, ClintMeasurement and manipulation of phenylpropanoid metabolic flux in Arabidopsis
Chapple, ClintStoichiometric and kinetic modeling of phenylpropanoid metabolism in Arabidopsis
Chiang, VincentSND1 Transcription Factor ‚¬ €œDirected Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa
Clubb, RobertRecombinant Bacillus subtilis that grows on untreated plant biomass
Cole, JamesRDP: Data and Tools for Studying Structure and Function of Microbial Communities
Coleman, HeatherInducible Extreme Expression of Cellulases in Poplar
Collart, FrankExperimental Systems to Model Nutrient and Carbon Exchange in Plant-Microbe Symbiosis
Collart, FrankFunctional Attributes of ABC Transporter Complexes from P. fluorescens That Mediate the Cellular Response to Changes in Environmental Nutrients
Cseke, LelandNutrient Cycling for Biomass: Biochemical and Proteomic Profiling of a Nutrient Limited Poplar x Laccaria Ectomycorrhizal System
Cseke, LelandNutrient Cycling for Biomass: ChIP Sequencing of Transcriptional Factors to Infer Gene Regulatory Networks for Carbon and Nitrogen Sequestration During Poplar x Laccaria Ectomycorrhizal Interactions
Currie, CameronStreptomyces isolated from herbivorous insects reveal phylogenetically-linked mechanisms for the degradation   of lignocellulose
Currie, CameronHighly Cellulolytic Microbial Communities Enriched from Leaf-Cutter Ant Refuse Dumps
Cushman, JohnTranscriptome sequencing and RNA-seq mRNA expression profiling in the facultative CAM model species Mesembryanthemum crystallinum
Cushman, JohnEngineering Crassulacean Acid Metabolism (CAM) to Improve Water-use Efficiency of Bioenergy Feedstocks
Cushman, JohnComparative Genomics in Support of CAM Engineering

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D
Principal Investigator Abstract Title
Davison, BrianSimulation and Structure of Cel7A during Binding and Hydrolysis of Cellulose
Davison, BrianInvestigation of Pretreatment-specific Changes in Biomass Structure
Davison, BrianProduction and Characterization of Deuterated Switchgrass and Annual Grasses for Neutron Studies
Ding, Shi-You Stimulated Raman Scattering (SRS) and atomic force microscopy (AFM) of enzymatic deconstruction of plant cell walls
Doktycz, MitchelPlant Microbe Interfaces: Proteomic Characterization of Endophyte and Rhizosphere Microorganisms and their Impacts on Plants
Doktycz, MitchelPlant-Microbe  Interfaces:   PMI   Data   Consolidation:   Estimating   Data   Quality   in   Large  Datasets
Doktycz, MitchelPlant-Microbe Interfaces: Tripartite plant-fungal-bacterial interactions
Doktycz, MitchelPlant-Microbe Interfaces: Understanding the factors shaping microbial community structure within root and rhizosphere microbiomes of Populus species
Doktycz, MitchelPlant Microbe Interfaces: Defining the functional diversity of the Populus root microbiome
Doktycz, MitchelPlant-Microbe Interfaces: Probing the Molecular Mechanisms of Plant-Microbe Interactions
Doktycz, MitchelPlant-Microbe Interfaces: Discovery of Small Secreted Proteins in Populusin Response to Symbiotic Fungus Laccaria bicolor
Doktycz, MitchelPlant-Microbe Interfaces: Bacterial Community Effects on Host Plant Biomass Allocation through Experimentation and Modeling
Donohue, TimothyComputational Algorithms for Metabolic Engineering Strain Design
Dueber, JohnRepurposing the Yeast Peroxisome to Compartmentalize Engineered Metabolic Pathways
Dunlop, MaryEngineering Robust Hosts for Microbial Biofuel Production

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E
Principal Investigator Abstract Title
Ecker, JosephNext Generation Protein Interactomes for Plant Systems Biology and Biomass Feedstocks Research

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F
Principal Investigator Abstract Title
Firestone, MaryMapping soil carbon from cradle to grave #3: Plant-microbial interactions regulate soil C cycling
Firestone, MaryMapping soil carbon from cradle to grave #2: Multi-level omics analyses for parameterization of trait-based models of rhizosphere microbial community function
Firestone, MaryMapping soil carbon from cradle to grave #1: drafting a molecular blueprint for C transformation from roots to stabilized soil organic C
Frederickson, JamesCompartmentalization of metabolic functions in microbial communities
Frederickson, JamesFSFA Poster #2: Metabolic Interactions Structuring Microbial Communities
Frederickson, JamesIdentifying environmental state variables governing the assembly of microbial communities

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G
Principal Investigator Abstract Title
Garrity, GeorgeSemantic Index of Phenotypic and Genotypic Data
Gasch, Audrey Comparative fungal genomics for improved biofuel production
Gerstein, MarkA notion before projecting biological networks across species: have the genes co- occurred through evolution?
Ghirardi, Maria Design Principles Controlling Hydrogen Metabolism in Phototrophic Organisms
Gill, RyanA Strategy for Genome-scale Design, Redesign, and Optimization for Ethylene Production in E. coli
Gill, RyanTrackingCombinatorial Engineered(TRACE) librariesatthegenome-scale
Gill, RyanNext Generation Multiplex Genome Engineering
Gill, RyanCRISPR-Assisted Rational Protein Engineering (CARPE) For Biofuel Production
Gilna, PaulFermentation Performance of Field-Grown Natural Variant and Transgenic Feedstocks
Gilna, PaulDirect Conversion of Plant Biomass to Ethanol by Engineered Caldicellulosiruptor bescii
Gilna, PaulDevelopment of a High-throughput Genetic Transformation System for Switchgrass (Panicum virgatum L.)
Gilna, PaulIn vitro Synthesis of Xylan Catalyzed by Purified Plant Xylosyl Transferases
Gilna, PaulDiscovering Naturally Occurring Allelic Variants Associated with Biomass Recalcitrance in Populus trichocarpa
Gilna, PaulFirst Year Field Results of PvMYB4-overexpressing Transgenic Switchgrass and Other Multiple Lines
Gilna, PaulChemical Factors that Control Lignin Polymerization
Gilna, PaulSurface Characterization of Populus during C. bescii Growth: Understanding the Relationship between Biomass Degradation and C. bescii Penetration in Wood Sticks
Gilna, PaulComparative Solubilization of Minimally Pretreated Lignocellulose as Impacted by Choice of Feedstock and Biocatalyst
Gilna, PaulThe D494G Point Mutation in the Bifunctional Alcohol and Aldehyde Dehydrogenase of Clostridium thermocellum Leads to Improved Ethanol Production
Gilna, PaulToward Thermophilic Isobutanol Production in Clostridium thermocellum
Gilna, PaulAlkaline Hydrogen Peroxide Pretreatment Differentially Affects Cell Wall Cross-Linking and Recalcitrance in Diverse Bioenergy Feedstocks
Gilna, PaulElimination of Hydrogenase Post-translational Modification in Clostridium thermocellum Blocks H2 Production and Increases Ethanol Yield
Gilna, PaulCoexistence but Independent Biosynthesis of Catechyl and Guaiacyl/Syringyl Lignin Polymers in Plant Seeds
Gilna, PaulRevealing Nature's Cellulase Diversity: The Digestion Mechanism of the Hyperactive Cellulase Caldicellulosiruptor bescii CelA
Gilna, Paul‘Caldi World’: Unraveling the Mystery and Mechanisms of Plant Biomass Deconstruction by the Bacterial Genus Caldicellulosiruptor
Gilna, PaulMatrix Cell Wall Polysaccharide Synthesis Gene 1 Knockdown in Switchgrass — a BESC TOP Line
Gilna, PaulFundamentals of Aqueous Pretreatment Chemistry and Cell Wall Cellular Structures of Low Recalcitrance Populus Lines for Enhanced Performance
Gilna, PaulDegradation of High Loads of Crystalline Cellulose and of Unpretreated Switchgrass by Caldicellulosiruptor bescii
Goodenough, UrsulaDetermining Eukaryotic Microalgal TAG Yield Using a Commercial Serum Triglyceride Determination Kit
Goodenough, UrsulaUltrastructure and Composition of the Nannochloropsis gaditana Cell Wall
Goodenough, UrsulaThe Path to Triacylglycerol (TAG) Obesity in the sta6 Strain of Chlamydomonas reinhardtii

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H
Principal Investigator Abstract Title
Hammel, KennethFluorescent probe selective for hydrogen atom abstraction based on polyethylene glycol cleavage
Hazen, SamuelCell Walls and the Developmental Anatomy of Brachypodium distachyon Stem Biomass
Hazen, SamuelSystems Level Regulation of Rhythmic Growth Rate and Biomass Accumulation in Grasses
Hazen, SamuelCreating a Multi-Functional Library of Grass Transcription Factors for the Energy Crop Model System Brachypodium distachyon
Hazen, SamuelBdMYB48 Regulates Biofuel Feedstock Attributes in the Model Grass Brachypodium distachyon
Heazlewood, JoshuaMining post translational modifications in Arabidopsis using the ModHunter
Hittinger, Chris ToddConstruction and Characterization of Interspecies Yeast Hybrids Using Newly Discovered Species with Native Biofuel Potential
Hofmockel, KirstenComposition and Distribution of Core Carbohydrate-Active Microbial Genes in Biofuel Soils
Hungate, BruceMultiple-Element Isotope Probes, NanoSIMS, and the Functional Genomics of Microbial Carbon Cycling in Soils in Response to Chronic Climatic Change
Hunt, Chris Confocal flourescence microscopy/modeling of lignolytic mechanisms

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J
Principal Investigator Abstract Title
Jackson, RandallSoil Microbial Community Composition as an Indicator of Agroecosystem N2O Emissions
Jansson, JanetHalophilic Communities as a Source for Novel Lignocellulolytic Enzymes
Jiao, YongqinUncovering Uranium Resistance Mechanisms in Caulobacter crescentus

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K
Principal Investigator Abstract Title
Karp, PeterMetabolic RouteSearch in Pathway Databases and Expansion of MetaCyc
Keasling, JayProduction of anteiso-branched fatty acids in Escherichia coli, next generation biofuels with improved cold- flow properties
Keasling, JayA nature inspired platform for production of acetyl-CoA derived mevalonate pathway products in S. cerevisiae
Kirst, MatiasA Systems Biology, Whole-Genome Association Analysis of the Molecular Regulation of Biomass Growth and Composition in Populus deltoides
Konstantinidis, KonstantinosExpanding the toolkit for comparative metagenomics,   implementing   it   in   K-Base,   and applying it to the study of the effects of experimental warming in Midwestern    and Alaskan soils
Kuske, CherylInfluence of shallow soil strata and chronic N deposition on the fungal community in pine and maple forests
Kuske, CherylMolecular tools and databases to monitor and classify soil fungal and bacterial communities
Kuske, CherylSoil carbon cycling communities and their response to climate and land use changes in patchy arid land ecosystems

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L
Principal Investigator Abstract Title
Landick, RobertA functional genomics approach to improving microbial fermentation
Landick, RobertOvercoming barriers for the conversion of lignocellulose to biofuels by E. coli
Langan, Paul Neutron and X-Ray Experiments and Computational Modeling of Pretreatment of Biomass
Lee, Taek SoonEngineering a Balanced MEV Pathway for Biofuels Production
Liao, JamesDynamic Model Building Based on the Ensemble Modeling Approach
Lidstrom, MarySystems Level Insights into Alternate Methane Cycling Modes Phase II: Deciphering Mechanistic Details of Interspecies Cooperation Through Manipulation of Model Microbial Communities
Loffler, FrankLinking Iron and Nitrogen Cycling in Anaeromyxobacter dehalogenans
Loffler, FrankDetecting Nitrous Oxide Reductase (nosZ) Genes in Soil Metagenomes: Method Development and Implications for the Nitrogen Cycle
Loffler, FrankCultivation and PCR-based Approaches Elucidate the Functional Diversity of Soil Fungal Populations Contributing to Nitrogen Cycling in Soils
Loque, DominiqueDeveloping Synthetic Biology Tools to Improve Nutrient Acquisition of Energy Crops
Loque, DominiqueIntroduction of a Transgene Regulation Strategy to Improve Lignin Engineering
Lovely, DerekA New DIET for Methanosarcina barkeri: Direct Interspecies Electron Transfer in a Genetically Tractable Methanogen
Luthey-Schulten, ZaidaHeterogeneity in Protein Expression Induces Metabolic Variability in a Modeled Escherichia coli Population
Luthey-Schulten, ZaidaA Computational Model of Methane Producing Archaea

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M
Principal Investigator Abstract Title
Magnuson, JohnDevelopment of Aspergillus niger as a host   for hyperproduction of   thermophilic cellulases
Mansfield, BettyBiological and Environmental Research Information System: A Multifaceted Approach to DOE Systems Research Communication
Maranas, Costas Using MetRxn for metabolic model reconstruction, flux elucidation and redesign
Marx, ChristopherLive-cell Micropatterning for Analysis of Inter-cellular Behavior in Multi-species Systems
Marx, ChristopherMechanisms leading to the evolution of novel glucose utilization by Shewanella oneidensis MR-1
McKinlay, JamesEnhancing H2-Production and Nutrient Exchange in a Symbiotic Bacterial Coculture
Methe, BarbaraGenome-scale Reconstruction of Metabolic Networks from Microbial Communities at Sites Undergoing Natural Attenuation of Uranium
Methe, BarbaraThe Study of Microbial Communities using ‘Metaomic’ Approaches at Naturally Reducing Subsurface Sites
Myrold, DavidMicrobial Community and Functional Responses to Rainfall Manipulations in a Prairie Soil

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N
Principal Investigator Abstract Title
Northen, TrentRapid Kinetic Characterization of Glycosyl Hydrolases (GHs) Based on Oxime Derivatization and Nanostructure-Initiator Mass Spectrometry (NIMS)
Northern, TrentHigh-Throughput Nanostructure-Initiator Mass Spectrometry (HT-NIMS) Metabolite Screening at JBEI

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O
Principal Investigator Abstract Title
O’Malley, MichelleEngineering Anaerobic Gut Fungi for Lignocellulose Breakdown
Onstott, TullisMicrobial community structure and activity during thawing of mineral cryosols of the Canadian High Arctic: meta genomics, transcriptomic and proteomics
Onstott, TullisAn Atmospheric CH4 Sink in the High Arctic and its Implication for Global Warming
Onstott, TullisMetaproteomics reveals key aspects of microbial community mediated carbon cycling in thawing Arctic Permafrost
Orphan, VictoriaSystems-level dissection of anaerobic methane cycling: single cell ecophysiology, genetic mechanisms, and microbial interactions

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P
Principal Investigator Abstract Title
Pakrasi, HimadriUse of Systems Biology Approaches to Develop Advanced Biofuel-Synthesizing Cyanobacterial Strains
Palsson, BernhardParametrizing a Genome-Scale Model of Metabolism and Expression in E. coli with Multi-omic Data
Palsson, BernhardDetermining the control circuitry of redox metabolism at the genome-scale
Palsson, BernhardReconstruction of Protein Translocation in Escherichia coli Allows For Bottom-Up Predictions of Compartmentalization Properties
Papoutsakis, EleftheriosThe small RNome of Clostridium acetobutylicum that orchestrates metabolite stress response
Papoutsakis, EleftheriosExperimental Systems-Biology Approaches for Clostridia-Based Bioenergy Production: The Metabolite Stress-Response System in Solventogenic Clostridia
Payne, SamielAlgorithms Enabling Metaproteomics
Peers, GrahamIntegrating energy transduction from light absorption to biofuel precursors in the alga Phaeodactylum tricornutum
Pett-Ridge, JenniferA Systems Biology Characterization of the Biotechnological Potential Stored in the Wood-Feeding Beetle Odontotaenius disjunctus
Pett-Ridge, JenniferUnderstanding the carbon and hydrogen flow in constructed H2-producing co-cultures
Pett-Ridge, JenniferBioenergy and Biogeochemical Cycling in Elkhorn Slough Hypersaline Microbial mats
Pfelger, BrianApplication of Next-Generation Sequencing to Engineering mRNA Turnover in Cyanobacteria
Podar, MirceaFrom Genomes to Metabolomes: Interspecies Interaction in the Archaeal System Ignicoccus-Nanoarchaeum and in other Nanoarchaeota

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Q
Principal Investigator Abstract Title
Qian, Wei-JunQuantitative Site-Specific Redox Proteomics on Protein Thiols and Broad Light/Dark Modulation of Thiol Oxidation in Cyanobacteria

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R
Principal Investigator Abstract Title
Rabinowitz, JoshuaA Fully Reversible, Highly Energy Efficient Glycolysis with Unique Cofactor Utilization in C. cellulolyticum
Rabinowitz, JoshuaAn integrated ‘omics approach to large-scale quantitative analysis of cellular metabolic regulation
Ralph, JohnDevelopment of Crucial Tools for Lignin Research
Rao, ChristopherCloning and Initial Characterization of the Laminarinases from Vibrio breoganii 1C10
Rao, ChristopherCloning and Characterization of the Alginate Lyases from Vibrio splendidus 12B01 and 13B01
Reed, JenniferSystems Approaches for Engineering Cyanobacteria for Biofuel Production
Richardson, RuthIdentification of Iron Reductases Using Top-down Proteomics and Heterologous Expression
Richardson, RuthDevelopment of Quantitative Protein Biomarker Assays for Enzymes Involved in Bacterial Iron and Uranium Reduction
Richardson, RuthInvestigations into the Proteome of Gram-positive Metal-reducing Bacterium Desulfotomaculum reducens MI-1
Ronald, PamelaImproving lignocellulose saccharification by high throughput mutant screening and whole-genome sequencing of the mutants
Rose, JocelynDefining Determinants and Dynamics of Cellulose Microfibril Biosynthesis, Assembly and Degradation
Rosen, GailFizzyQIIME: Feature Selection for Metagenomics

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S
Principal Investigator Abstract Title
Sale, KenHigh-throughput cellulase activity profiling on ionic liquid pretreated biomass
Saleska, ScottPathways to Carbon Liberation: a Systems Approach to Understanding Carbon Transformations and Losses from Thawing Permafrost
Sato, TreyDirected Engineering and Evolution for Xylose Fermentation and Lipid Biofuels from AFEX-Pretreated Corn Stover Hydrolysate by Saccharomyces cerevisiae
Scheller, HenrikIdentification of six Golgi localized bi-functional UDP-Rhamnose/UDP-Galactose transporters in Arabidopsis
Scheller, HenrikGUX and IPUT Members of Arabidopsis Glycosyltransferase Family 8 are Glucuronosyltransferases Involved in Cell Wall and Glycosphingolipid Synthesis
Schilling, JonathanSpatially co-localizing the incompatible oxidative and enzymatic steps during fungal brown rot wood degradation - Early Career Program
Schuur, EdwardMetagenomics-Enabled Predictive Understanding of Microbial Communities to Climate Warming: Results from Long Term Soil Incubations
Segre, DanielModeling metabolic dynamics in 3D: applications to synthetic microbial ecosystems
Semrau, Jeremy Metal Uptake by Methanotrophs: Genetic Basis for the Biosyntehsis of A Novel Chalkophore and Molecular Spectroscopic Analysis of Mercury Detoxification
Semrau, JeremyMechanism of Mercury Binding by Methanobactin from Methylocystis strain SB2
Semrau, JeremyMetal Uptake by Methanotrophs: Genetic Basis for the Biosynthesis of A Novel Chalkophore and Molecular Spectroscopic Analyses of Mercury Detoxification
Singer, StevenUsing Chemical Pretreatment to Understand Bacterial Biomass Deconstruction
Singh, AnupHigh-throughput Microfluidic Platforms for Bioenergy Research
Singh, SeemaEfficient Biomass Pretreatment using renewable Ionic Liquids derived from Lignin and Hemicellulose
Sjolander, KimmenPhyloFacts FAT-CAT Ortholog Identification and Functional Annotation
Smith, RichardIntegrated Pan-omics Measurements for Systems Level Characterization of Biological Systems
Stahl, DavidLand management alters N-cycling metabolic potential in Pacific Northwest soils
Stahl, DavidDiversity of ammonia-oxidizing archaea in soils under managed and native conditions
Stephanopoulos, GregoryIntegrated Biological Conversion of Gaseous Substrate into Lipids
Stephanopoulos, GregoryFunctional overexpressions and characterizations of lipogenesis-related genes in oleaginous yeast Yarrowia lipolytica
Stephanopoulos, GregoryResolving central metabolism of wild type and engineered Yarrowia lipolytica by 13 C- metablic flux analysis with multiple isotopic tracers
Stephanopoulos, GregoryNext generation of the Yeast Genome-Scale Model: Reformulation and Improvement for Future Data Integration
Stephanopoulos, GregoryRegulation of lipid metabolism in Yarrowia lipolytica
Stephanopoulos, GregoryPredicting Gene Targets for Optimizing Oil Production in Yarrowia lipolytica by Cell-Wide Ensemble Modeling
Strand, StuartGreenhouse gas emissions from fertilized plots of bioenergy crops in Eastern  Washington
Suen, GarretAnalysis of Three Ruminal-associated Bacteria Reveal Different Mechanisms for Cellulose Degradation

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T
Principal Investigator Abstract Title
Thelen, MichaelNovel Mechanisms for Ionic Liquid Resistance in Microbial Biofuel Production
Tiedje, JamesMetagenomic Insight into the Rhizospheres of Three Biofuel Crops
Tringe, SusannahMicrobial Communities and Carbon Cycling in California Coastal Wetlands

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W
Principal Investigator Abstract Title
Wolfe, AmyRisk and Escape Policies, Perspectives, and Practices: Issues and Implications for Biosystems Design R&D on Microbes, Algae, and Plants
Worden, AlexandraExamining the post-transcriptional program governing the metabolic proteome of Micromonas pusilla
Worden, AlexandraPhytochromes in widespread photosynthetic algae reveal origins of plant signaling proteins
Worden, AlexandraResponses of the Widespread Green Alga Micromonas to Elevated CO2 at Different Levels of Phosphorus Availability
Wu, CathyThe Core Regulons Orchestrating the Response of Clostridium acetobutylicum to Butanol and Butyrate Stress

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Y
Principal Investigator Abstract Title
Yang, HawDevelopment of Quantum Dot Probes for Studies of Synergy Between Components of the Wood-Degrading Fungal Enzymes
Yang, Haw 3D Multi-resolution visualization of the early stages of cellular uptake of peptide-coated nanoparticles
Young, JameyIsotopically nonstationary 13C flux analysis of isobutyraldehyde production in Synechococcus elongatus

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Z
Principal Investigator Abstract Title
Zak, DonaldA Bacterial Role in Lignin Decomposition Under Future Rates of Nitrogen Deposition
Zhou, JizhongFrom Structure to Function: Metagenomics-Enabled Predictive Understanding of Soil Microbial Feedbacks to Climate Warming

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Featuring

Carbon Cycling Projects Awarded [10/16]


Plant Feedstock Genomics for Bioenergy Abstracts [9/16]


Bioenergy Research Centers
Key Advances Update: 2014-2016 [06/16]


BER Biological Systems Science Division Strategic Plan [10/15]

BER BSSD funds the Genomic Science Program


Research

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