Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Research Summaries: BER Biological Systems Science Division Annual PI Meeting, April 2023


Abstract Book provided by Oak Ridge Associated Universities (ORAU)

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TitlePIPI InstitutionPresenterResearch Area
A Gene-Editing System for Large-Scale Fungal Phenotyping in a Model Wood DecomposerZhangUniversity of Minnesota–Saint PaulZhangBiosystems Design
Model-Guided Design of Synthetic Microbial Consortia for Next-Generation Biofuel ProductionZenglerUniversity of California–San DiegoThiruppathyBiosystems Design
Reproducible Plant Growth in Fabricated Ecosystems (EcoFAB 2.0) Reveals that Nitrogen Supply Modulates Root ExudationZenglerUniversity of California–San DiegoNorthenBiosystems Design
Microbial Guilds and Niches Enable Targeted Modifications of the Microbiome ZenglerUniversity of California–San DiegoMoyneBiosystems Design
Unraveling Metabolic Interactions in a Rhizosphere Microbial Community Through Genome-Scale ModelingZenglerUniversity of California–San DiegoKumarBiosystems Design
Designing Novel Enzymes for Complete Degradation of Recalcitrant PolyamidesZanghelliniArzeda CorporationSanghaBioenergy
Encapsulin Nanocompartment Systems in Rhodococcus opacus for Compartmentalized Biosynthesis ApplicationsYungLawrence Livermore National LaboratoryYungBiosystems Design
Systems Biology to Enable Modular Metabolic Engineering of Fatty Acid Production in CyanobacteriaYoungUniversity of Wisconsin–Madison ZunigaBioenergy
Inter-Facility Collaboration: Overarching Challenges and Opportunities Identified Through the “Genomes to Structure and Function” Virtual WorkshopAdamsLawrence Berkeley National LaboratoryAdamsStructural Biology
Metabolism in Microbial Communities and the Associated Biochemistry of Polymer DeconstructionYeatesUniversity of California–Los Angeles DOE Institute for Genomics and Proteomics GunsalusStructural Biology
Electron Diffraction for High-Resolution Structure Determination of BiomoleculesYeatesUniversity of California–Los Angeles DOE Institute for Genomics and ProteomicsVlahakisStructural Biology
Investigating Plant and Microbe Systems for Understanding the Formation and Modulation of Amyloid and Amyloid-Like ProteinsEisenbergUniversity of California–Los Angeles DOE Institute for Genomics and ProteomicsLutterStructural Biology
Phenotypic Characterization of Sorghum Nitrogen Responsive Gene Edits Using High-Throughput PhenotypingJinUniversity of Nebraska–Lincoln JinBioenergy
A Leaf-Level Spectral Library to Support High-Throughput Plant Phenotyping: Predictive Accuracy and Model TransferWijewardaneMississippi State UniversityWijewardaneBioenergy
Ghost Imaging of Biological Samples Using Non-Degenerate Entangled PhotonsWernerLos Alamos National Laboratory RyanBioimaging
Biological Imaging of Plant and Fungal Samples Using Infrared LightMoralesLos Alamos National LaboratoryMoralesBioimaging
Putting Microorganisms on the Map: Continental-Scale Context for Thousands of Newly Sampled Microbial Genomes from North American WetlandsWrightonColorado State UniversityWrightonEnvironmental Microbiome
Construction of a Microbial Methane Observatory Reveals Metabolic Dynamics of Freshwater Wetland MicrobiomesWrightonColorado State UniversityOliverioEnvironmental Microbiome
Membrane Potential Dynamics during the Cell Cycle of Single Proliferating and Nonproliferating Bacterial CellsWeissUniversity of California–Los AngelesBharadwajBioimaging
Laboratory for BioMolecular Structure: A DOE-Funded National Cryo-EM CenterMcSweeneyBrookhaven National LaboratoryWangStructural Biology
Phage Engineering for Targeted Editing of Microbial CommunitiesNorthernLawrence Berkeley National LaboratoryAdlerEnvironmental Microbiome
Metabolic Modeling and Genetic Engineering of Enhanced Anaerobic Microbial Ethylene SynthesisNorthThe Ohio State UniversityNorthBioenergy
Using 13CO2 to Track Carbon Flow Mediated by Fungal-Bacterial Interactions in Grassland SoilsNguyenUniversity of Hawaiʻi–MānoaYuanEnvironmental Microbiome
Fungal-Bacterial Interactions: Bridging Soil Niches in Regulating Carbon and Nitrogen ProcessesNguyenUniversity of Hawaiʻi–MānoaNguyenEnvironmental Microbiome
Broadening Aromatic Compound Degradation in Acinetobacter baylyi Using Synthetic Metabolic PathwaysNeidleUniversity of GeorgiaBaughBiosystems Design
Quantify the Impact of Your Data with DOE JGI’s Genome Citation ServiceFagnanJGIFagnanCrosscutting
Engineering Novel Microbes for Upcycling Waste PlasticMoon Washington University–St. LouisDiaoBiosystems Design
HypoRiPPAtlas: an Atlas of Hypothetical Natural Products for Mass Spectrometry Database SearchMohimaniCarnegie Mellon UniversityGulerComputational Biology
Scalable Computational Tools for Inference of Protein Annotation and Metabolic Models in Microbial CommunitiesMillerUniversity of Colorado–DenverDavoudiComputational Biology
Systems Metabolic Engineering of Novosphingobium aromaticivorans for Lignin ValorizationMichenerOak Ridge National LaboratoryMichenerBiosystems Design
Advanced Photon Source Capabilities for Environmental and Biological ScienceMichalskaArgonne National LaboratoryMichalskaStructural Biology
Root-Mediated Impacts of Plant Volatile Organic Compound Emissions on Soil CarbonMeredithUniversity of ArizonaHonekerEnvironmental Microbiome
Direct Routes for Microbial Carbon Stabilization of Volatile Organic Compounds in SoilMeredithUniversity of ArizonaGil-LoaizaEnvironmental Microbiome
Deploying Top-Down and Bottom-Up Strategies for Genetic Engineering of Auxenochlorella protothecoides for the Production of Sustainable BiofuelsMerchantUniversity of California–BerkeleyRothBiosystems Design
Tools and Targets: Engineering Modified Fatty Acids and Improved Photosynthetic Resilience in Auxenochlorella protothecoidesMerchantUniversity of California–BerkeleyMoseleyBiosystems Design
A Gapless and Phased Diploid Genome Assembly for Auxenochlorella protothecoides Facilitates Metabolic Modeling and Proteomics AnalysesMerchantUniversity of California–BerkeleyBoyleBiosystems Design
Ghost Imaging in the X-ray RegimeMcSweeneyNational Synchrotron Light Source IIGoodrichStructural Biology
Development of a CenH3-Based Haploid Inducer in Hexaploid Camelina sativaHenryUniversity of California–DavisHenryBioenergy
Transcriptome and Gene Regulatory Network Analyses in Camelina Nitrogen Response and Seed DevelopmentLuMontana State UniversityCorrerBioenergy
Developing, Understanding, and Harnessing Modular Carbon/Nitrogen-fixing Tripartite Microbial Consortia for Versatile Production of Biofuel and Platform ChemicalsLinUniversity of MichiganLinBiosystems Design
Development of Classically Entangled Light for Depth-Resolved Quantum Mimicry BioimagingLiaoUniversity of Colorado–BoulderLiaoBioimaging
Discovering Transcriptional Regulators of Photosynthesis in Energy Sorghum to Improve ProductivityLongUniversity of Illinois at Urbana–ChampaignPelechBioenergy
Overview of CABBI Conversion ThemeZhaoUniversity of Illinois Urbana–ChampaignShenBioenergy
Integrating Measurements and Models to Improve Projections of Ecosystem Carbon Balance in Bioenergy AgricultureBrzostekCABBIJuiceBioenergy
Increasing the Value of Bioenergy Grasses—Expressing Engineered Traits in the Right Place at the Right TimeMarshall-ColonCenter for Advanced Bioenergy and Bioproducts InnovationFuBioenergy
Pooled Microbial CRISPR Screens using Single-Cell RNA SequencingCarothersUniversity of WashingtonBrandnerBiosystems Design
Uncovering the Microbial Networks that Degrade Plant-Derived Phenolic Compounds and Their Role in Peatland Soil Carbon Sequestration: Revisiting the ‘Enzyme Latch’ HypothesisKostkaGeorgia Institute of TechnologyKostkaEnvironmental Microbiome
Computational Tools for Multiomic Data Standardization and Integration to Represent Whole Microbial CommunitiesKostkaGeorgia Institute of TechnologyKonstantinidisEnvironmental Microbiome
Identification of Regulatory Mechanisms Underlying Cell Differentiation in Sorghum BiomassKirstUniversity of FloridaVermerrisBioenergy
Single-Cell Genomics of Poplar Wood DevelopmentKirstUniversity of FloridaPereiraBioenergy
Scenario-Based Technoeconomic and Life-Cycle Analyses of Biomass Conversion TechnologiesKeaslingLawrence Berkeley National LaboratorySimmonsBioenergy
Characterizing Lignocellulose Breakdown Mechanisms in Anaerobic Gut FungiKeaslingJBEIJinBioenergy
Understanding the Role of Lignin in Native Architecture of Engineered Plant Cell Walls via Multi-Dimensional Solid-State NMRKeaslingJBEIGaoBioenergy
Evolutionary Engineering is a Versatile Strain Optimization Approach for Sustainable BioproductionKeaslingJBEIFeistBioenergy
Domesticating Cyanobacteria Through Development of New Genome Engineering Tools, and Isolation of New Bio-Prospected Model StrainsChurchHarvard UniversitySchubertBiosystems Design
Defining the Influence of Environmental Stress on Bioenergy Feedstocks at Single-Cell ResolutionColeJGIDaoBioenergy
Expression of S-Adenosyl Methionine Hydrolase Modifies Lignin in SorghumKeaslingJBEIEudesBioenergy
Development of a Quantum-Optimal Bioimaging System for Plant-Microbiome InteractionsKasevichStanford UniversityReynoldsStructural Biology
Development of High-Throughput Light-Sheet Fluorescence Lifetime Microscopy for 3D Functional Imaging of Metabolic Pathways in Plants and MicroorganismsKasevichStanford UniversityBowmanStructural Biology
Exploring Switchgrass Genetic Diversity with Multiple Reference GenomesJuengerUniversity of Texas–AustinSchmutzBioenergy
The Influence of Switchgrass Internode Anatomy on Biofuel Production-Relevant TraitsJungerUniversity of Texas–AustinBartleyBioenergy
Structural Biology Center at Sector 19 of Advanced Photon SourceJoachimiakArgonne National LaboratoryJoachimiakStructural Biology
Engineered Overlapping Genes Paired with Directed Evolution Prolongs the Evolutionary Stability of a Genetic CircuitParkLawrence Livermore National LaboratoryParkEnvironmental Microbiome
Engineering Overlapping Genes in BacteriaJiaoLawrence Livermore National LaboratoryJiaoEnvironmental Microbiome
Developing Genome Engineering Technologies in Cupriavidus necator for Carbon-Negative BiomanufacturingIsaacsYale UniversityNakamuraBiosystems Design
A Cell-Free Protein Evolution PlatformJewettNorthwestern UniversityLandwehrBiosystems Design
Plant Methanol Emission at the Interface of the Photosynthetic C1 Pathway, Leaf Water Status, and GrowthJardineLawrence Berkeley National LaboratoryJardineBioenergy
AI/ML for Bioenergy Research in CABBILeakeyCABBIZhaoBioenergy
From Strand Design Principles to SNP Detection—Probing Oligonucleotide Hybridization at the Single Molecule LevelChurchHarvard Medical SchoolSteinBiosystems Design
Novel Systems Approach for Rational Engineering of Robust Microbial Metabolic PathwaysJarboeIowa State UniversityJarboeBiosystems Design
A Pipeline for High-Throughput Genomic Recoding in Organisms Beyond E. coliChurchHarvard Medical SchoolTasBiosystems Design
High (School)-Throughput Screening of BAHD TransferasesAchesonUniversity of Wisconsin−MadisonAchesonBioenergy
Chemical Imaging of Plant-Soil-Microbe Systems at the Stanford Synchrotron Radiation LightsourceHodgsonSLAC National Accelerator LaboratoryRichardsonStructural Biology
Harnessing Regulatory Variation to Elucidate Drought Resilience Mechanisms in SorghumEvelandDonald Danforth Plant Science CenterEvelandBioenergy
Opportunities Linking Omics and Structural Biology at PNNL: Excelling at Cryo-EMEvansPacific Northwest National LaboratoryEvansStructural Biology
Fluorescence Lifetime Measurements using Entangled-Photon CoincidencesLaurenceLawrence Livermore National LaboratoryEshunStructural Biology
Conformational Equilibria Underlying Electron Bifurcation and Transfer in Thermotoga Maritima Fix/EtfABCX: Novel Structural States and Their Correlation to Catalysis by Anaerobic SEC-SAXSHuraLawrence Berkeley National LaboratoryMurrayStructural Biology
Impacts of Altered Climate on Microbial Growth and Nutrient Assimilation in an Ombitrophic Peat BogHungateNorthern Arizona UniversityBellEnvironmental Microbiome
Impact of Soil Viruses on Microbial Compositions and FunctionsHofmockelPacific Northwest National LaboratoryWuEnvironmental Microbiome
OMEGGA: A Computationally Efficient Omics-Guided Global Gapfilling Algorithm for Phenotype-Consistent Metabolic Network ReconstructionHofmockelPacific Northwest National LaboratorySongEnvironmental Microbiome
Removal of Primary Nutrient Degraders Reduces Growth and Modifies Functional Pathways of Soil Microbial Communities with Genomic RedundancyHofmockelPacific Northwest National LaboratoryMcClureEnvironmental Microbiome
Crosslinking The Department of Energy Systems Biology Knowledgebase (DOE-KBase) and the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RSCB PDB) to Support Protein Function DiscoveryHenryArgonne National LaboratoryHenryComputational Biology
Integration of Enzyme Function Initiative Tools in the KBase PlatformHenryArgonne National LaboratoryHenryComputational Biology
IMAGINE BioSecurity: Genome-Scale Engineering and Modeling for Secure Biosystems DesignGuarnieriNational Renewable Energy LaboratorySuzukiBiosystems Design
IMAGINE BioSecurity: Mesocosm-Based Methods to Evaluate Biocontainment Strategies and Impact of Industrial Microbes Upon Native Ecosystems.GuarnieriBiosciences CenterGuarnieriBiosystems Design
The Genetics of Pathogen and Microbiome Control in the Switchgrass LeafLowryGLBRCWallendaelBioenergy
Systems Framework to Enhance the Potential of Camelina as Oilseed CropGrotewoldMichigan State UniversityGrotewoldBioenergy
A Temporal Atlas and Response to Nitrate Availability of 3D Root System Architecture in Diverse Pennycress (Thlaspi arvense L.) AccessionsSedbrookIllinois State UniversityGriffithsBioenergy
Understanding Plant Signaling via Innovations in Probe Delivery and ImagingGreenbergThe University of ChicagoGreenbergBioimaging
Metagenomic Insights into Microbial Traits Influencing Community Dynamics and N Cycling Post-FireGlassmanUniversity of California–RiversideNelsonEnvironmental Microbiome
Predicting Post-Fire N Cycling through Traits and Cross-Kingdom InteractionsGlassmanUniversity of California–RiversideGlassmanEnvironmental Microbiome
Optimizing Enzymes for Plastic Upcycling using Machine Learning Design and High Throughput ExperimentsGauthierDana-Farber Cancer InstituteFramBioenergy
Structure and Molecular Mechanism of a Bacterial ADP-forming 4-Coumarate CoA LigaseFoxUniversity of Wisconsin−MadisonChaudhuryBioenergy
Extracting Functional Traits from Large Volumes of Field Phenomics DataEvelandDonald Danforth Plant Science CenterGonzalezBioenergy
Probing Photoreception with New Quantum-Enabled ImagingEvansPacific Northwest National LaboratoryEvansBioimaging
Unraveling Spatiotemporal and Physicochemical Constraints on Soil Viral Community Composition and Viral Particle IntegrityEmersonUniversity of California–DavisEmersonEnvironmental Microbiome
Community Engagement Strategies of the National Microbiome Data Collaborative (NMDC)Eloe-FadroshLawrence Berkeley National LaboratoryKelliherEnvironmental Microbiome
Refactoring Metabolism to Control the Persistence of Genetically Engineered Microorganisms in the EnvironmentEgbertPacific Northwest National LaboratoryElmoreBiosystems Design
Development of Synthetic Microbial Communities to Study Consortium Engraftment Dynamics and to Improve the Yield Performance of SorghumEgbertPacific Northwest National LaboratoryEgbertBiosystems Design
EndoPopulus: Elucidating the Molecular Mechanisms of N-Fixation by Populus Endophyte, Burkholderia vietnamiensis WPBDotyUniversity of WashingtonAufrechtBioenergy
EndoPopulus: Elucidation of the Roles of Diazotrophic Endophyte Communities in Promoting Productivity and Resilience of Populus Through Systems Biology ApproachesDotyUniversity of WashingtonDotyBioenergy
EndoPopulus: Endophyte Inoculation Enhances Populus Physiological Responses to Abiotic StressDotyUniversity of WashingtonBananBioenergy
Novosphingobium aromaticivorans for ccMA Production from Lignin BiomassDonohueGLBRCVilbertBioenergy
Defining Transcriptomic Dynamics in Sorghum in Multiple Abiotic StressesDonohueGLBRCKoBioenergy
Plant-Microbe Interfaces: Molecular Insights into the Mutualistic Symbiosis Between Populus and Plant Growth-Promoting BacteriaDoktyczOak Ridge National LaboratoryPiatkowskiEnvironmental Microbiome
Plant-Microbe Interfaces: Capturing and Interpreting the Role of Populus’ MicrobiomeDoktyczOak Ridge National LaboratoryPelletierEnvironmental Microbiome
Accelerating Carbon-Negative Biomanufacturing Through Systems-Level Biology and Genome OptimizationJewettStanford UniversityFacklerBiosystems Design
Combining GWAS of Metabolomic and Transcriptomic Datasets to Accelerate Discovery of Genes Regulating the Effect of Drought on Plant Growth and Metabolism in Sorghum and SetariaBaxterDonald Danforth Plant Science CenterHubbardBiosystems Design
The Predictive Power of Phylogeny on Growth Rates in Soil Bacterial CommunitiesHungateNorthern Arizona UniversityWalkupEnvironmental Microbiome
Agent-Based Algal Modeling for the Rational Engineering of Chlamydomonas reinhardtiiBoyleColorado School of MinesBoyleBiosystems Design
Predicting Gene Functions in Plants with Single-Cell Genomic DataDinnenyStanford UniversityTimilsenaBioenergy
Probabilistic Annotation and Ensemble Metabolic Modeling in KBaseD’haeseleerLawrence Livermore National LaboratoryD’haeseleerComputational Biology
NLP for Synthetic Biology: Providing Generalizable Literature Mining Through KBaseDehalLawrence Berkeley National LaboratoryYooComputational Biology
Ultra-Sensitive Protein-SIP to Quantify Activity and Substrate Uptake in Microbiomes with Stable IsotopesKleinerNorth Carolina State UniversityKleinerEnvironmental Microbiome
Biofuels Disruption of Membrane Domains: An Unrecognized Mode of Solvent StressDavisonOak Ridge National LaboratoryElkinsBioenergy
Visualization of Solvent Disruption of Biomass and Biomembrane Structures in the Production of Advanced Biofuels and BioproductsDavisonOak Ridge National LaboratoryDavisonBioenergy
Visualizing Spatial and Temporal Responses of Plant Cells to the EnvironmentDahlbergSLAC National Accelerator LaboratoryJoubertStructural Biology
Understanding the Effects of Populus—Mycorrhizal Associations on Plant Productivity and Resistance to Abiotic StressCreggerOak Ridge National LaboratoryCreggerBioenergy
Elucidating the Genetic Components of the Physiological and Metabolic Processes Governed by the TORC Regulatory Module in PoplarColemanUniversity of MarylandColemanBioenergy
Construction of a Synthetic 57-Codon E. coli Chromosome to Achieve Resistance to All Natural Viruses, Prevent Horizontal Gene Transfer, and Enable BiocontainmentChurchHarvard Medical SchoolNyergesBiosystems Design
Expanding Knowledge of Bacterial-Fungal Interactions in Environmental MicrobiomesChainLos Alamos National LaboratoryRobinsonBioenergy
An Online Public Resource for Bacterial-Fungal Interaction ResearchChainLos Alamos National LaboratoryChainBioenergy
Multiomics-Driven Microbial Model OptimizationCarothersUniversity of WashingtonShinBiosystems Design
Genome-Wide Gene Regulation by Transcriptional CRISPRa/i Tools in Non-Model BacteriaCarothersUniversity of WashingtonKiattiseweeBiosystems Design
FatPlants: A Comprehensive Information System for Lipid-Related Genes and Metabolic Pathways in PlantsCahoonUniversity of NebraskaDurrettBiosystems Design
B5: Bigger Better Brassicaceae Biofuels and Bioproducts—An OverviewCahoonUniversity of Nebraska–LincolnCahoonBiosystems Design
Changes in Amino Acid Distribution Across Populus trichocarpa Roots with and Without Microbes in a Rhizosphere-on-a-Chip HabitatCahillOak Ridge National LaboratoryCahillBioimaging
Metabolome-Informed Proteome Imaging of Lignocellulose Decomposition by a Naturally Evolved Fungal Garden Microbial ConsortiumBurnum-JohnsonPacific Northwest National LaboratoryBurnum-JohnsonEnvironmental Microbiome
BioPoplar: A Tunable Chassis for Diversified Bioproduct ProductionBuellUniversity of GeorgiaBuellBiosystems Design
Synthetic Membrane Biology of Microbial Cell Factories: Lipid Interactions that Shape the Inner Mitochondrial MembraneBudinUniversity of California–San DiegoBudinBioenergy
Developing Chassis for LDPE Upcycling from Microbes Native to the Gut Microbiome of Yellow MealwormsBlennerUniversity of DelawareKlauerBiosystems Design
Analysis of the Beneficial Associations of Sorghum with Arbuscular Mycorrhizal Fungi Studied with Genetics, Genomics, and MicrobiomicsBennetzenUniversity of GeorgiaBennetzenBioenergy
Understanding and Engineering Crown Root Development to Improve Water-Use Efficiency in Bioenergy GrassesBaxterDonald Danforth Plant Science CenterGoudinho VianaBiosystems Design
Accelerating Discovery of Genes Regulating Stomatal Patterning and Water Use Efficiency in C4 Crops with Novel High-Throughput Methods for Mutagenesis and PhenotypingBaxterDonald Danforth Plant Science CenterTanBiosystems Design
Quantum Optical Microscopy of Biomolecules near Interfaces and Surfaces (QuOMBIS)BacklundUniversity of Illinois Urbana–ChampaignBacklundBioimaging
Optical and X-ray Multimodal-Hybrid Microscope Systems for Imaging of Plant Stress Response and Microbial InteractionsWakatsukiSLAC National Accelerator LaboratoryDowlatshahiBioimaging
Diffraction-Free Beams in Light-Sheet MicrocopyVasdekisUniversity of IdahoLuoBioimaging
Gatekeepers of Arctic Carbon Loss: Landscape-Scale Metabolites-to-Ecosystems Profiling to Mechanistically Map Climate FeedbacksVarnerUniversity of New HampshireKuhnEnvironmental Microbiome
Populus Secondary Cell Walls: Atomistic Models and Natural Variability in Architecture Informed by Solid-State Nuclear Magnetic ResonanceTuskanCBIHarman-WareBioenergy
AI-Informed Systems Biology: The Discovery of Cryptic Phenotypes and the Functional Networks that Control ThemTuskanCBILagergrenBioenergy
Metaproteomic Insights into Mechanisms Enabling Anaerobic, Thermophilic Microbiomes to Achieve Undiminished Fractional Carbohydrate Solubilization at High Solids LoadingTuskanCBIHolwerdaBioenergy
Comprehensive Genome-Wide CRISPR Interference Library for High-Throughput Functional Genomic Studies in Pseudomonas putidaTuskanCBIEckertBioenergy
Deciphering the Genetic Basis of S/G Lignin Variation in Switchgrass through QTL Mapping and Transgenic ApproachesTuskanCBIDevosBioenergy
Engineering Bacterial Microcompartments in Clostridium autoethanogenum to Overcome Bottlenecks in Sustainable Production of Synthetic RubberTullman-ErcekNorthwestern UniversityPalmeroBioenergy
WINTR: Winter Transcriptome Regulation in PoplarTsaiUniversity of GeorgiaTsaiBioenergy
Harnessing Robustness of Thermophilic Bacillus coagulans for Conversion of Switchgrass Hydrolysates to Designer Bioesters at Elevated TemperaturesTrinhUniversity of TennesseeRyuBioenergy
From Bulk Organic Matter Profiling to Specific Metabolite Identification: Improving Metabolomics Data Analysis, Annotation, Interpretation, and Integration TfailyUniversity of Arizona Ayala-OrtizEnvironmental Microbiome
Deciphering Virocell Metabolic Dynamics and Ecosystem Outputs Using a Novel Integration of Machine Learning and MetabolomicsSullivanThe Ohio State UniversityRajakarunaEnvironmental Microbiome
Diversity Patterns and Ecological Footprint of RNA Viruses Along a Permafrost Thaw GradientSullivanThe Ohio State UniversityPratamaEnvironmental Microbiome
Genetic Determinants of Klebsiella Phage InfectionSullivanThe Ohio State UniversityGittrichEnvironmental Microbiome
Portals of Discovery: The NMDC Infrastructure and Products for Microbiome ResearchEloe-FadroshLawrence Berkeley National LaboratorySmithEnvironmental Microbiome
The Context-Dependency of Plant-Microbial Interactions in the Bioenergy Resource EconomyStuartLawrence Livermore National LaboratoryHestrinBioenergy
Identifying Genomic and Metabolic Underpinnings of Algal-Bacterial Interactions via Metatranscriptomics, NanoSIMS Isotope Tracing, and Genome-Scale Metabolic ModelingStuartLawrence Livermore National LaboratoryMayaliBioenergy
Improving Bioprocess Robustness by Cellular Noise EngineeringStephanopoulosMassachusetts Institute of TechnologyDaletosBioenergy
Developing Anaerobic Fungal Tools for Efficient Upgrading of Lignocellulosic FeedstocksSolomonUniversity of DelawarePareekBiosystems Design
Developing a High-Throughput Functional Bioimaging Capability for Rhizosphere Interactions Utilizing Sensor Cells, Microfluidics, Automation, and AI-Guided AnalysesBabniggArgonne National LaboratoryBabniggBioimaging
Optogenetic Control of a Dual Yeast-Yeast Consortia for Chemical ProductionAvalosPrinceton UniversityGarcia EchauriBioenergy
KBase Science and Infrastructure UpdatesArkinLawrence Berkeley National LaboratoryWood-CharlsonComputational Biology
The KBase Knowledge Engine: Ecosystem Classification PrototypeArkinLawrence Berkeley National LaboratoryDehalComputational Biology
Learning and Training with KBaseArkinLawrence Berkeley National LaboratoryAllenComputational Biology
Probing Lignin Deconstruction and Catabolism in Soil Pseudomonas SpeciesAristildeNorthwestern UniversityAristildeBioenergy
A Systems Understanding of Nitrogen-Fixation on the Aerial Roots of SorghumAnéUniversity of Wisconsin–MadisonVermerrisBioenergy
Plastic Degradation by the Gut Microbiome of Yellow MealwormsSolomonUniversity of DelawareKlauerBioenergy
The MoonTag Programmable Transcription Activator and Synthetic Promoters: Tools for Engineering Oil Biosynthesis in Camelina and PennycressSmanskiUniversity of Minnesota–Saint PaulCasas MollanoBiosystems Design
Predicting and Modeling Protein-Protein Complexes at Large-Scale with Deep LearningSkolnickGeorgia Institute of TechnologyGaoComputational Biology
Feedstocks-to-Fuels Pipeline Demonstration: End-to-End Process SynthesisSinghCABBIBanerjeeBioenergy
Functional Analysis of Genes Encoding Ubiquitin Proteasome System Components Affecting Poplar Wood TraitsShabekUniversity of California–DavisRodriguez-ZaccaroBioenergy
532 Genomes Reveal Natural Variation and Local Adaptation History in PennycressSedbrookIllinois State UniversityToro AranaBioenergy
Comparison of Physiological and Metabolomic Responses to Drought Across Pennycress CRISPR Mutants and Natural AccessionsSedbrookIllinois State UniversityThomasBioenergy
Optimizing Biological Nitrogen Fixation on Sorghum by Manipulating Microbial CommunitiesAnéUniversity of Wisconsin–MadisonPalmerBioenergy
Single-Cell Omics to Examine the Cell Type-Specific Gene Regulatory Programs of Mucilage Production in Sorghum bicolorAnéUniversity of Wisconsin–MadisonAnéBioenergy
Developing a National Virtual Biosecurity for Bioenergy Crops CenterSchoonenBrookhaven National LaboratoryFreimuth Bioenergy
Lipid Membrane Remodeling and Metabolic Response During Ethanol and Isobutanol Stress in Zymomonas mobilisDonohueGLBRCRivera VazquezBioenergy
The Use of Deuterated Water as a Substrate-Agnostic and Cost-Effective Isotope Tracer for Investigating Reversibility and Thermodynamics of Reactions in Central Carbon MetabolismAmador-NoguezUniversity of Wisconsin–MadisonAmador-NoguezBioenergy
Integrases on DemandSchoenigerSandia National LaboratoriesWilliamsBiosystems Design
Genomic Analyses and Enzyme Characterization Provide Insights into the Catabolism of Lignin-Related Aromatic Compounds in White-Rot FungiSalvachúaNational Renewable Energy LaboratorySalvachúaBioenergy
RNA Phages: Under-Estimated Players in Soil Ecosystems?RouxJGIRouxCrosscutting
Quantum Diamond EcoFAB Microscope for In Situ NMR of Root Exudate MoleculesAjoyUniversity of California–BerkeleyGilbertBioimaging
Improving Candidate Gene Discovery by Combining Multiple Genetic Mapping DatasetsRellán-ÁlvarezNorth Carolina State UniversityRellán-ÁlvarezBioenergy
The Use of Synthetic Communities Reveals Disturbance of Process Partitioning Among Denitrifying Microbes Leads to Increased Nitrous Oxide EmissionsAdamsLawrence Berkeley National LaboratoryValenzuelaEnvironmental Microbiome
Design and Omics Exploration of Synthetic Microbial Communities in KBaseRanjanOak Ridge National LaboratoryRanjanComputational Biology
Microbes Persist: Towards Quantitative Theory-Based Predictions of Soil Microbial Fitness, Interaction and Function in KBasePett-RidgeLawrence Livermore National LaboratoryKimbrelEnvironmental Microbiome
ENIGMA Long Read Sequencing and Assembly for Microbial Genomes: KBase Integration for Assembly and LISA WorkshopAdamsLawrence Berkeley National LaboratoryLuiEnvironmental Microbiome
Three-Dimensional High Spatial Resolution Simulation for Groundwater Flow and Nitrogen Transport Under Rainfall Perturbations in the Subsurface of Area 3AdamsLawrence Berkeley National LaboratoryImEnvironmental Microbiome
The Path from Root Input to Mineral-Associated Soil Carbon is Dictated by Habitat-Specific Microbial TraitsPett-RidgeLawrence Livermore National LaboratoryFoleyEnvironmental Microbiome
ENIGMA Environmental Atlas: An Integrated Approach to Linking Microbial Genotype to Phenotype in a Dynamic Subsurface EcosystemAdamsLawrence Berkeley National LaboratoryChakrabortyEnvironmental Microbiome
Functional Succession of Growing Soil Microorganisms and Virus-Driven Mortality Following Rewetting in a California Grassland SoilPett-RidgeLawrence Livermore National LaboratoryBlazewiczEnvironmental Microbiome
Conversion of Lignocellulosic Plant Biomass into Industrial Chemicals via Metabolic Engineering of Two Extreme Thermophiles, Caldicellulosiruptor bescii and Pyrococcus furiosusAdamsUniversity of GeorgiaBingEnvironmental Microbiome
Towards Generalized Platforms for Functional Genomics in α-ProteobacteriaPetersGLBRCHallBioenergy
Improved Biofuel Production Through Discovery and Engineering of Terpene Metabolism in SwitchgrassZerbeUniversity of California–DavisWyattBioenergy
Enhanced Resistance Pines for Improved Renewable Biofuel and Chemical ProductionPeterUniversity of FloridaMorganBioenergy
Functional Characterization of Glycosyltransferases in Duckweed to Enable Predictive BiologyUrbanowiczUniversity of GeorgiaUrbanowiczBioenergy
Secure Ecosystem Engineering and Design (SEED) to Enable Safe Biodesign of Novel Plant-Microbe InteractionsAbrahamOak Ridge National LaboratoryYangBiosystems Design
The Root Microbiome of Camelina in the Dryland Wheat Production Areas of Eastern WashingtonPaulitzWashington State UniversityPengBioenergy
Integrating Functional Genomics with Molecular-Level Experimentation to Understand Adaptation to Nutrient Stress in Poplar and SorghumPaapeBrookhaven National LaboratoryPaapeBioenergy
Functional Characterization of bHLH Transcription Factors Coordinating Abiotic Stress Response, Secondary Cell Wall Biosynthesis, and Metal Homeostasis in PopulusXieBrookhaven National LaboratoryXieBioenergy
Recent Developments at the Center for Structural Molecular Biology at Oak Ridge National LaboratoryO’NeillOak Ridge National LaboratoryPingaliStructural Biology
Cell Free Conversion of Pyruvate to 2,3-Butanediol Using Co-Substrate Feed as pH Control StrategyOlsonDartmouth CollegeJilaniBioenergy
Engineering Synthetic Anaerobic Consortia Inspired by the Rumen for Biomass Breakdown and ConversionO’MalleyUniversity of California–Santa BarbaraBlairBiosystems Design
Crosstalk: Interkingdom Interactions in the Mycorrhizal Hyphosphere and Ramifications for Soil Carbon CyclingNuccioLawrence Livermore National LaboratoryNuccioEnvironmental Microbiome
The Twin Ecosystems Project: A New Capability for Field and Laboratory Ecosystems Coupled by Sensor Networks and Autonomous ControlsNorthenLawrence Berkeley National LaboratoryTringeEnvironmental Microbiome
Examine Plant-Microbe-Soil Interactions Using Fabricated Ecosystems Across ScalesNorthenLawrence Berkeley National LaboratoryLinEnvironmental Microbiome
Secure Ecosystem Engineering and Design (SEED) to Mitigate the Impacts of Non-Native Fungal Pathogens on Managed EcosystemsAbrahamOak Ridge National Laboratory TannousBiosystems Design