KBase: DOE Systems Biology Knowledgebase

Community-Driven Cyberinfrastructure for Sharing and Integrating Data and Analytical Tools to Accelerate Predictive Biology

kbase logoThe Department of Energy Systems Biology Knowledgebase (KBase) is an open-software FAIR biological data platform that aims to enable researchers to collaboratively drive discovery for prediction, control, and design of function in plants, microbes, and their communities. KBase’s unified data model allows users to perform integrated analyses across plants, microbes, and their communities with a wide range of tools that interoperate across the tree of life, and to publish their data, methods, results, and thoughts in persistent, citable, executable, and reusable electronic narratives that allow scientists to build on the work of others. KBase’s open platform enables external developers to integrate their analysis tools, facilitating distribution, comparative tool analysis, and access to enterprise-class computing.

GSP Science Focus Area (SFA) Collaborations

These collaborations benefit KBase users and SFAs alike through the development and implementation of new and exciting tools. To smooth the process of adding SFA tools to KBase, each collaboration begins with a week-long in-person software development kit (SDK) training session. This is followed by continual developmental support to ensure SFAs are able to build, test, and deploy Apps on the KBase platform.

Omics-Enabled Global Gapfilling (OMEGGA) for Phenotype-Consistent Metabolic Network Reconstruction of Microorganisms and Communities

Building pipelines for long read assembly of microbial isolates and metagenomes in the DOE Systems Biology KnowledgeBase

Improved Protein Annotation in KBase Using Machine Learning, Multi-Omics Data Integration, and Structural Prediction

Design and Omics Exploration of Synthetic Microbial Communities

Probabilistic Annotation and Ensemble Metabolic Modeling in KBase

Microbes Persist: Towards quantitative theory-based predictions of soil microbial fitness, interaction and function in KBase


See additional information about ongoing SFA collaborations on the KBase Website.

2023 Abstracts

TitlePIPI InstitutionPresenter
A Gene-Editing System for Large-Scale Fungal Phenotyping in a Model Wood DecomposerZhangUniversity of Minnesota–Saint PaulZhangUniversity
Model-Guided Design of Synthetic Microbial Consortia for Next-Generation Biofuel ProductionZenglerUniversity of California–San DiegoThiruppathyUniversity
Reproducible Plant Growth in Fabricated Ecosystems (EcoFAB 2.0) Reveals that Nitrogen Supply Modulates Root ExudationZenglerUniversity of California–San DiegoNorthenUniversity
Microbial Guilds and Niches Enable Targeted Modifications of the Microbiome ZenglerUniversity of California–San DiegoMoyneUniversity
Unraveling Metabolic Interactions in a Rhizosphere Microbial Community Through Genome-Scale ModelingZenglerUniversity of California–San DiegoKumarUniversity
Designing Novel Enzymes for Complete Degradation of Recalcitrant PolyamidesZanghelliniArzeda CorporationSangha
Encapsulin Nanocompartment Systems in Rhodococcus opacus for Compartmentalized Biosynthesis ApplicationsYungLawrence Livermore National LaboratoryYungEarly Career
Systems Biology to Enable Modular Metabolic Engineering of Fatty Acid Production in CyanobacteriaYoungUniversity of Wisconsin–Madison ZunigaUniversity
Inter-Facility Collaboration: Overarching Challenges and Opportunities Identified Through the “Genomes to Structure and Function” Virtual WorkshopAdamsLawrence Berkeley National LaboratoryAdams
Metabolism in Microbial Communities and the Associated Biochemistry of Polymer DeconstructionYeatesUniversity of California–Los Angeles DOE Institute for Genomics and Proteomics GunsalusUCLA DOE IGP
Electron Diffraction for High-Resolution Structure Determination of BiomoleculesYeatesUniversity of California–Los Angeles DOE Institute for Genomics and ProteomicsVlahakisUCLA DOE IGP
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 ProteomicsLutterUCLA DOE IGP
Phenotypic Characterization of Sorghum Nitrogen Responsive Gene Edits Using High-Throughput PhenotypingJinUniversity of Nebraska–Lincoln JinUniversity
A Leaf-Level Spectral Library to Support High-Throughput Plant Phenotyping: Predictive Accuracy and Model TransferWijewardaneMississippi State UniversityWijewardaneUniversity
Ghost Imaging of Biological Samples Using Non-Degenerate Entangled PhotonsWernerLos Alamos National Laboratory Ryan
Biological Imaging of Plant and Fungal Samples Using Infrared LightMoralesLos Alamos National LaboratoryMorales
Putting Microorganisms on the Map: Continental-Scale Context for Thousands of Newly Sampled Microbial Genomes from North American WetlandsWrightonColorado State UniversityWrightonUniversity
Construction of a Microbial Methane Observatory Reveals Metabolic Dynamics of Freshwater Wetland MicrobiomesWrightonColorado State UniversityOliverioUniversity
Membrane Potential Dynamics during the Cell Cycle of Single Proliferating and Nonproliferating Bacterial CellsWeissUniversity of California–Los AngelesBharadwaj
Laboratory for BioMolecular Structure: A DOE-Funded National Cryo-EM CenterMcSweeneyBrookhaven National LaboratoryWang
Phage Engineering for Targeted Editing of Microbial CommunitiesNorthernLawrence Berkeley National LaboratoryAdlerm-CAFEs
Metabolic Modeling and Genetic Engineering of Enhanced Anaerobic Microbial Ethylene SynthesisNorthThe Ohio State UniversityNorthUniversity
Using 13CO2 to Track Carbon Flow Mediated by Fungal-Bacterial Interactions in Grassland SoilsNguyenUniversity of Hawaiʻi–MānoaYuanUniversity
Fungal-Bacterial Interactions: Bridging Soil Niches in Regulating Carbon and Nitrogen ProcessesNguyenUniversity of Hawaiʻi–MānoaNguyenUniversity
Broadening Aromatic Compound Degradation in Acinetobacter baylyi Using Synthetic Metabolic PathwaysNeidleUniversity of GeorgiaBaughUniversity
Quantify the Impact of Your Data with DOE JGI’s Genome Citation ServiceFagnanJGIFagnanJGI
Engineering Novel Microbes for Upcycling Waste PlasticMoon Washington University–St. LouisDiaoUniversity
HypoRiPPAtlas: An Atlas of Hypothetical Natural Products for Mass Spectrometry Database SearchMohimaniCarnegie Mellon UniversityGulerUniversity
Scalable Computational Tools for Inference of Protein Annotation and Metabolic Models in Microbial CommunitiesMillerUniversity of Colorado–DenverDavoudiUniversity
Systems Metabolic Engineering of Novosphingobium aromaticivorans for Lignin ValorizationMichenerOak Ridge National LaboratoryMichenerEarly Career
Advanced Photon Source Capabilities for Environmental and Biological ScienceMichalskaArgonne National LaboratoryMichalska
Root-Mediated Impacts of Plant Volatile Organic Compound Emissions on Soil CarbonMeredithUniversity of ArizonaHonekerUniversity
Direct Routes for Microbial Carbon Stabilization of Volatile Organic Compounds in SoilMeredithUniversity of ArizonaGil-LoaizaUniversity
Deploying Top-Down and Bottom-Up Strategies for Genetic Engineering of Auxenochlorella protothecoides for the Production of Sustainable BiofuelsMerchantUniversity of California–BerkeleyRothUniversity
Tools and Targets: Engineering Modified Fatty Acids and Improved Photosynthetic Resilience in Auxenochlorella protothecoidesMerchantUniversity of California–BerkeleyMoseleyUniversity
A Gapless and Phased Diploid Genome Assembly for Auxenochlorella protothecoides Facilitates Metabolic Modeling and Proteomics AnalysesMerchantUniversity of California–BerkeleyBoyleUniversity
Ghost Imaging in the X-ray RegimeMcSweeneyNational Synchrotron Light Source IIGoodrich
Development of a CenH3-Based Haploid Inducer in Hexaploid Camelina sativaHenryUniversity of California–DavisHenryUniversity
Transcriptome and Gene Regulatory Network Analyses in Camelina Nitrogen Response and Seed DevelopmentLuMontana State UniversityCorrerUniversity
Developing, Understanding, and Harnessing Modular Carbon/Nitrogen-fixing Tripartite Microbial Consortia for Versatile Production of Biofuel and Platform ChemicalsLinUniversity of MichiganLinUniversity
Development of Classically Entangled Light for Depth-Resolved Quantum Mimicry BioimagingLiaoUniversity of Colorado–BoulderLiao
Discovering Transcriptional Regulators of Photosynthesis in Energy Sorghum to Improve ProductivityLongUniversity of Illinois at Urbana–ChampaignPelechCABBI
Overview of CABBI Conversion ThemeZhaoUniversity of Illinois Urbana–ChampaignShenCABBI
Integrating Measurements and Models to Improve Projections of Ecosystem Carbon Balance in Bioenergy AgricultureBrzostekCABBIJuiceCABBI
Increasing the Value of Bioenergy Grasses—Expressing Engineered Traits in the Right Place at the Right TimeMarshall-ColonCenter for Advanced Bioenergy and Bioproducts InnovationFuCABBI
Pooled Microbial CRISPR Screens using Single-Cell RNA SequencingCarothersUniversity of WashingtonBrandnerUniversity
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 TechnologyKostkaUniversity
Computational Tools for Multiomic Data Standardization and Integration to Represent Whole Microbial CommunitiesKostkaGeorgia Institute of TechnologyKonstantinidisUniversity
Identification of Regulatory Mechanisms Underlying Cell Differentiation in Sorghum BiomassKirstUniversity of FloridaVermerrisUniversity
Single-Cell Genomics of Poplar Wood DevelopmentKirstUniversity of FloridaPereiraUniversity
Scenario-Based Technoeconomic and Life-Cycle Analyses of Biomass Conversion TechnologiesKeaslingLawrence Berkeley National LaboratorySimmonsJBEI
Characterizing Lignocellulose Breakdown Mechanisms in Anaerobic Gut FungiKeaslingJBEIJinJBEI
Understanding the Role of Lignin in Native Architecture of Engineered Plant Cell Walls via Multi-Dimensional Solid-State NMRKeaslingJBEIGaoJBEI
Evolutionary Engineering is a Versatile Strain Optimization Approach for Sustainable BioproductionKeaslingJBEIFeistJBEI
Domesticating Cyanobacteria Through Development of New Genome Engineering Tools, and Isolation of New Bio-Prospected Model StrainsChurchHarvard UniversitySchubertUniversity
Defining the Influence of Environmental Stress on Bioenergy Feedstocks at Single-Cell ResolutionColeJGIDaoEarly Career
Expression of S-Adenosyl Methionine Hydrolase Modifies Lignin in SorghumKeaslingJBEIEudesJBEI
Development of a Quantum-Optimal Bioimaging System for Plant-Microbiome InteractionsKasevichStanford UniversityReynolds
Development of High-Throughput Light-Sheet Fluorescence Lifetime Microscopy for 3D Functional Imaging of Metabolic Pathways in Plants and MicroorganismsKasevichStanford UniversityBowman
Exploring Switchgrass Genetic Diversity with Multiple Reference GenomesJuengerUniversity of Texas–AustinSchmutzUniversity
The Influence of Switchgrass Internode Anatomy on Biofuel Production-Relevant TraitsJungerUniversity of Texas–AustinBartleyUniversity
Structural Biology Center at Sector 19 of Advanced Photon SourceJoachimiakArgonne National LaboratoryJoachimiak
Engineered Overlapping Genes Paired with Directed Evolution Prolongs the Evolutionary Stability of a Genetic CircuitParkLawrence Livermore National LaboratoryParkSecure Biosystems Design
Engineering Overlapping Genes in BacteriaJiaoLawrence Livermore National LaboratoryJiaoSecure Biosystems Design
Developing Genome Engineering Technologies in Cupriavidus necator for Carbon-Negative BiomanufacturingIsaacsYale UniversityNakamuraUniversity
A Cell-Free Protein Evolution PlatformJewettNorthwestern UniversityLandwehrUniversity
Plant Methanol Emission at the Interface of the Photosynthetic C1 Pathway, Leaf Water Status, and GrowthJardineLawrence Berkeley National LaboratoryJardineEarly Career
AI/ML for Bioenergy Research in CABBILeakeyCABBIZhaoCABBI
From Strand Design Principles to SNP Detection—Probing Oligonucleotide Hybridization at the Single Molecule LevelChurchHarvard Medical SchoolSteinUniversity
Novel Systems Approach for Rational Engineering of Robust Microbial Metabolic PathwaysJarboeIowa State UniversityJarboeUniversity
A Pipeline for High-Throughput Genomic Recoding in Organisms Beyond E. coliChurchHarvard Medical SchoolTasUniversity
High (School)-Throughput Screening of BAHD TransferasesAchesonUniversity of Wisconsin−MadisonAchesonGLBRC
Chemical Imaging of Plant-Soil-Microbe Systems at the Stanford Synchrotron Radiation LightsourceHodgsonSLAC National Accelerator LaboratoryRichardson
Harnessing Regulatory Variation to Elucidate Drought Resilience Mechanisms in SorghumEvelandDonald Danforth Plant Science CenterEvelandUniversity
Opportunities Linking Omics and Structural Biology at PNNL: Excelling at Cryo-EMEvansPacific Northwest National LaboratoryEvans
Fluorescence Lifetime Measurements using Entangled-Photon CoincidencesLaurenceLawrence Livermore National LaboratoryEshun
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 LaboratoryMurray
Impacts of Altered Climate on Microbial Growth and Nutrient Assimilation in an Ombitrophic Peat BogHungateNorthern Arizona UniversityBellUniversity
Impact of Soil Viruses on Microbial Compositions and FunctionsHofmockelPacific Northwest National LaboratoryWuPhenotypic Response of SOIL Microbes
OMEGGA: A Computationally Efficient Omics-Guided Global Gapfilling Algorithm for Phenotype-Consistent Metabolic Network ReconstructionHofmockelPacific Northwest National LaboratorySongPhenotypic Response of SOIL Microbes
Removal of Primary Nutrient Degraders Reduces Growth and Modifies Functional Pathways of Soil Microbial Communities with Genomic RedundancyHofmockelPacific Northwest National LaboratoryMcClurePhenotypic Response of SOIL Microbes
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 LaboratoryHenryKBase
Integration of Enzyme Function Initiative Tools in the KBase PlatformHenryArgonne National LaboratoryHenryKBase
IMAGINE BioSecurity: Genome-Scale Engineering and Modeling for Secure Biosystems DesignGuarnieriNational Renewable Energy LaboratorySuzukiIMAGINE BioSecurity
IMAGINE BioSecurity: Mesocosm-Based Methods to Evaluate Biocontainment Strategies and Impact of Industrial Microbes Upon Native Ecosystems.GuarnieriBiosciences CenterGuarnieriIMAGINE BioSecurity
The Genetics of Pathogen and Microbiome Control in the Switchgrass LeafLowryGLBRCWallendaelGLBRC
Systems Framework to Enhance the Potential of Camelina as Oilseed CropGrotewoldMichigan State UniversityGrotewoldUniversity
A Temporal Atlas and Response to Nitrate Availability of 3D Root System Architecture in Diverse Pennycress (Thlaspi arvense L.) AccessionsSedbrookIllinois State UniversityGriffithsUniversity
Understanding Plant Signaling via Innovations in Probe Delivery and ImagingGreenbergThe University of ChicagoGreenbergUniversity
Metagenomic Insights into Microbial Traits Influencing Community Dynamics and N Cycling Post-FireGlassmanUniversity of California–RiversideNelsonUniversity
Predicting Post-Fire N Cycling through Traits and Cross-Kingdom InteractionsGlassmanUniversity of California–RiversideGlassmanUniversity
Optimizing Enzymes for Plastic Upcycling using Machine Learning Design and High Throughput ExperimentsGauthierDana-Farber Cancer InstituteFramUniversity
Structure and Molecular Mechanism of a Bacterial ADP-forming 4-Coumarate CoA LigaseFoxUniversity of Wisconsin−MadisonChaudhuryGLBRC
Extracting Functional Traits from Large Volumes of Field Phenomics DataEvelandDonald Danforth Plant Science CenterGonzalezUniversity
Probing Photoreception with New Quantum-Enabled ImagingEvansPacific Northwest National LaboratoryEvans
Unraveling Spatiotemporal and Physicochemical Constraints on Soil Viral Community Composition and Viral Particle IntegrityEmersonUniversity of California–DavisEmersonUniversity
Community Engagement Strategies of the National Microbiome Data Collaborative (NMDC)Eloe-FadroshLawrence Berkeley National LaboratoryKelliherNMDC
Refactoring Metabolism to Control the Persistence of Genetically Engineered Microorganisms in the EnvironmentEgbertPacific Northwest National LaboratoryElmorePersistence Control of Soil Microbiomes
Development of Synthetic Microbial Communities to Study Consortium Engraftment Dynamics and to Improve the Yield Performance of SorghumEgbertPacific Northwest National LaboratoryEgbertPersistence Control of Soil Microbiomes
EndoPopulus: Elucidating the Molecular Mechanisms of N-Fixation by Populus Endophyte, Burkholderia vietnamiensis WPBDotyUniversity of WashingtonAufrechtUniversity
EndoPopulus: Elucidation of the Roles of Diazotrophic Endophyte Communities in Promoting Productivity and Resilience of Populus Through Systems Biology ApproachesDotyUniversity of WashingtonDotyUniversity
EndoPopulus: Endophyte Inoculation Enhances Populus Physiological Responses to Abiotic StressDotyUniversity of WashingtonBananUniversity
Novosphingobium aromaticivorans for ccMA Production from Lignin BiomassDonohueGLBRCVilbertGLBRC
Defining Transcriptomic Dynamics in Sorghum in Multiple Abiotic StressesDonohueGLBRCKoGLBRC
Plant-Microbe Interfaces: Molecular Insights into the Mutualistic Symbiosis Between Populus and Plant Growth-Promoting BacteriaDoktyczOak Ridge National LaboratoryPiatkowskiPlant-Microbe Interfaces
Plant-Microbe Interfaces: Capturing and Interpreting the Role of Populus’ MicrobiomeDoktyczOak Ridge National LaboratoryPelletierPlant-Microbe Interfaces
Accelerating Carbon-Negative Biomanufacturing Through Systems-Level Biology and Genome OptimizationJewettStanford UniversityFacklerUniversity
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 CenterHubbardUniversity
The Predictive Power of Phylogeny on Growth Rates in Soil Bacterial CommunitiesHungateNorthern Arizona UniversityWalkupUniversity
Agent-Based Algal Modeling for the Rational Engineering of Chlamydomonas reinhardtiiBoyleColorado School of MinesBoyleUniversity
Predicting Gene Functions in Plants with Single-Cell Genomic DataDinnenyStanford UniversityTimilsenaUniversity
Probabilistic Annotation and Ensemble Metabolic Modeling in KBaseD’haeseleerLawrence Livermore National LaboratoryD’haeseleerKBase
NLP for Synthetic Biology: Providing Generalizable Literature Mining Through KBaseDehalLawrence Berkeley National LaboratoryYooKBase
Ultra-Sensitive Protein-SIP to Quantify Activity and Substrate Uptake in Microbiomes with Stable IsotopesKleinerNorth Carolina State UniversityKleinerUniversity
Biofuels Disruption of Membrane Domains: An Unrecognized Mode of Solvent StressDavisonOak Ridge National LaboratoryElkinsBiomass Deconstruction
Visualization of Solvent Disruption of Biomass and Biomembrane Structures in the Production of Advanced Biofuels and BioproductsDavisonOak Ridge National LaboratoryDavisonBiomass Deconstruction
Visualizing Spatial and Temporal Responses of Plant Cells to the EnvironmentDahlbergSLAC National Accelerator LaboratoryJoubert
Understanding the Effects of Populus—Mycorrhizal Associations on Plant Productivity and Resistance to Abiotic StressCreggerOak Ridge National LaboratoryCreggerEarly Career
Elucidating the Genetic Components of the Physiological and Metabolic Processes Governed by the TORC Regulatory Module in PoplarColemanUniversity of MarylandColemanUniversity
Construction of a Synthetic 57-Codon E. coli Chromosome to Achieve Resistance to All Natural Viruses, Prevent Horizontal Gene Transfer, and Enable BiocontainmentChurchHarvard Medical SchoolNyergesUniversity
Expanding Knowledge of Bacterial-Fungal Interactions in Environmental MicrobiomesChainLos Alamos National LaboratoryRobinsonBacterial-Fungal Interactions
An Online Public Resource for Bacterial-Fungal Interaction ResearchChainLos Alamos National LaboratoryChainBacterial-Fungal Interactions
Multiomics-Driven Microbial Model OptimizationCarothersUniversity of WashingtonShinUniversity
Genome-Wide Gene Regulation by Transcriptional CRISPRa/i Tools in Non-Model BacteriaCarothersUniversity of WashingtonKiattiseweeUniversity
FatPlants: A Comprehensive Information System for Lipid-Related Genes and Metabolic Pathways in PlantsCahoonUniversity of NebraskaDurrettUniversity
B5: Bigger Better Brassicaceae Biofuels and Bioproducts—An OverviewCahoonUniversity of Nebraska–LincolnCahoonUniversity
Changes in Amino Acid Distribution Across Populus trichocarpa Roots with and Without Microbes in a Rhizosphere-on-a-Chip HabitatCahillOak Ridge National LaboratoryCahill
Metabolome-Informed Proteome Imaging of Lignocellulose Decomposition by a Naturally Evolved Fungal Garden Microbial ConsortiumBurnum-JohnsonPacific Northwest National LaboratoryBurnum-JohnsonEarly Career
BioPoplar: A Tunable Chassis for Diversified Bioproduct ProductionBuellAgricultural Research Service, U.S. Department of AgricultureBuellUniversity
Synthetic Membrane Biology of Microbial Cell Factories: Lipid Interactions that Shape the Inner Mitochondrial MembraneBudinUniversity of California–San DiegoBudinEarly Career
Developing Chassis for LDPE Upcycling from Microbes Native to the Gut Microbiome of Yellow MealwormsBlennerUniversity of DelawareKlauerUniversity
Analysis of the Beneficial Associations of Sorghum with Arbuscular Mycorrhizal Fungi Studied with Genetics, Genomics, and MicrobiomicsBennetzenUniversity of GeorgiaBennetzenUniversity
Understanding and Engineering Crown Root Development to Improve Water-Use Efficiency in Bioenergy GrassesBaxterDonald Danforth Plant Science CenterGoudinho VianaUniversity
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 CenterTanUniversity
Quantum Optical Microscopy of Biomolecules near Interfaces and Surfaces (QuOMBIS)BacklundUniversity of Illinois Urbana–ChampaignBacklund
Optical and X-ray Multimodal-Hybrid Microscope Systems for Imaging of Plant Stress Response and Microbial InteractionsWakatsukiSLAC National Accelerator LaboratoryDowlatshahi
Diffraction-Free Beams in Light-Sheet MicrocopyVasdekisUniversity of IdahoLuoUniversity
Gatekeepers of Arctic Carbon Loss: Landscape-Scale Metabolites-to-Ecosystems Profiling to Mechanistically Map Climate FeedbacksVarnerUniversity of New HampshireKuhnUniversity
Populus Secondary Cell Walls: Atomistic Models and Natural Variability in Architecture Informed by Solid-State Nuclear Magnetic ResonanceTuskanCBIHarman-WareCBI
AI-Informed Systems Biology: The Discovery of Cryptic Phenotypes and the Functional Networks that Control ThemTuskanCBILagergrenCBI
Metaproteomic Insights into Mechanisms Enabling Anaerobic, Thermophilic Microbiomes to Achieve Undiminished Fractional Carbohydrate Solubilization at High Solids LoadingTuskanCBIHolwerdaCBI
Comprehensive Genome-Wide CRISPR Interference Library for High-Throughput Functional Genomic Studies in Pseudomonas putidaTuskanCBIEckertCBI
Deciphering the Genetic Basis of S/G Lignin Variation in Switchgrass through QTL Mapping and Transgenic ApproachesTuskanCBIDevosCBI
Engineering Bacterial Microcompartments in Clostridium autoethanogenum to Overcome Bottlenecks in Sustainable Production of Synthetic RubberTullman-ErcekNorthwestern UniversityPalmeroUniversity
WINTR: Winter Transcriptome Regulation in PoplarTsaiUniversity of GeorgiaTsaiUniversity
Harnessing Robustness of Thermophilic Bacillus coagulans for Conversion of Switchgrass Hydrolysates to Designer Bioesters at Elevated TemperaturesTrinhUniversity of TennesseeRyuUniversity
From Bulk Organic Matter Profiling to Specific Metabolite Identification: Improving Metabolomics Data Analysis, Annotation, Interpretation, and Integration TfailyUniversity of Arizona Ayala-OrtizUniversity
Deciphering Virocell Metabolic Dynamics and Ecosystem Outputs Using a Novel Integration of Machine Learning and MetabolomicsSullivanThe Ohio State UniversityRajakarunaUniversity
Diversity Patterns and Ecological Footprint of RNA Viruses Along a Permafrost Thaw GradientSullivanThe Ohio State UniversityPratamaUniversity
Genetic Determinants of Klebsiella Phage InfectionSullivanThe Ohio State UniversityGittrichUniversity
Portals of Discovery: The NMDC Infrastructure and Products for Microbiome ResearchEloe-FadroshLawrence Berkeley National LaboratorySmithNMDC
The Context-Dependency of Plant-Microbial Interactions in the Bioenergy Resource EconomyStuartLawrence Livermore National LaboratoryHestrinMicrobial Systems Biology for Bioenergy
Identifying Genomic and Metabolic Underpinnings of Algal-Bacterial Interactions via Metatranscriptomics, NanoSIMS Isotope Tracing, and Genome-Scale Metabolic ModelingStuartLawrence Livermore National LaboratoryMayaliMicrobial Systems Biology for Bioenergy
Improving Bioprocess Robustness by Cellular Noise EngineeringStephanopoulosMassachusetts Institute of TechnologyDaletosUniversity
Developing Anaerobic Fungal Tools for Efficient Upgrading of Lignocellulosic FeedstocksSolomonUniversity of DelawarePareekUniversity
Developing a High-Throughput Functional Bioimaging Capability for Rhizosphere Interactions Utilizing Sensor Cells, Microfluidics, Automation, and AI-Guided AnalysesBabniggArgonne National LaboratoryBabnigg
Optogenetic Control of a Dual Yeast-Yeast Consortia for Chemical ProductionAvalosPrinceton UniversityGarcia EchauriUniversity
KBase Science and Infrastructure UpdatesArkinLawrence Berkeley National LaboratoryWood-CharlsonKBase
The KBase Knowledge Engine: Ecosystem Classification PrototypeArkinLawrence Berkeley National LaboratoryDehalKBase
Learning and Training with KBaseArkinLawrence Berkeley National LaboratoryAllenKBase
Probing Lignin Deconstruction and Catabolism in Soil Pseudomonas SpeciesAristildeNorthwestern UniversityAristildeUniversity
A Systems Understanding of Nitrogen-Fixation on the Aerial Roots of SorghumAnéUniversity of Wisconsin–MadisonVermerrisUniversity
Plastic Degradation by the Gut Microbiome of Yellow MealwormsSolomonUniversity of DelawareKlauerUniversity
The MoonTag Programmable Transcription Activator and Synthetic Promoters: Tools for Engineering Oil Biosynthesis in Camelina and PennycressSmanskiUniversity of Minnesota–Saint PaulCasas MollanoUniversity
Predicting and Modeling Protein-Protein Complexes at Large-Scale with Deep LearningSkolnickGeorgia Institute of TechnologyGaoUniversity
Feedstocks-to-Fuels Pipeline Demonstration: End-to-End Process SynthesisSinghCABBIBanerjeeCABBI
Functional Analysis of Genes Encoding Ubiquitin Proteasome System Components Affecting Poplar Wood TraitsShabekUniversity of California–DavisRodriguez-ZaccaroUniversity
532 Genomes Reveal Natural Variation and Local Adaptation History in PennycressSedbrookIllinois State UniversityToro AranaUniversity
Comparison of Physiological and Metabolomic Responses to Drought Across Pennycress CRISPR Mutants and Natural AccessionsSedbrookIllinois State UniversityThomasUniversity
Optimizing Biological Nitrogen Fixation on Sorghum by Manipulating Microbial CommunitiesAnéUniversity of Wisconsin–MadisonPalmerUniversity
Single-Cell Omics to Examine the Cell Type-Specific Gene Regulatory Programs of Mucilage Production in Sorghum bicolorAnéUniversity of Wisconsin–MadisonAnéUniversity
Developing a National Virtual Biosecurity for Bioenergy Crops CenterSchoonenBrookhaven National LaboratoryFreimuth NVBBCC
Lipid Membrane Remodeling and Metabolic Response During Ethanol and Isobutanol Stress in Zymomonas mobilisDonohueGLBRCRivera VazquezEarly Career
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-NoguezEarly Career
Integrases on DemandSchoenigerSandia National LaboratoriesWilliamsInCoGenTEC 
Genomic Analyses and Enzyme Characterization Provide Insights into the Catabolism of Lignin-Related Aromatic Compounds in White-Rot FungiSalvachúaNational Renewable Energy LaboratorySalvachúaEarly Career
RNA Phages: Under-Estimated Players in Soil Ecosystems?RouxJGIRouxJGI
Quantum Diamond EcoFAB Microscope for In Situ NMR of Root Exudate MoleculesAjoyUniversity of California–BerkeleyGilbert
Improving Candidate Gene Discovery by Combining Multiple Genetic Mapping DatasetsRellán-ÁlvarezNorth Carolina State UniversityRellán-ÁlvarezUniversity
The Use of Synthetic Communities Reveals Disturbance of Process Partitioning Among Denitrifying Microbes Leads to Increased Nitrous Oxide EmissionsAdamsLawrence Berkeley National LaboratoryValenzuelaENIGMA
Design and Omics Exploration of Synthetic Microbial Communities in KBaseRanjanOak Ridge National LaboratoryRanjanKBase
Microbes Persist: Towards Quantitative Theory-Based Predictions of Soil Microbial Fitness, Interaction and Function in KBasePett-RidgeLawrence Livermore National LaboratoryKimbrelMicrobes Persist SFA
ENIGMA Long Read Sequencing and Assembly for Microbial Genomes: KBase Integration for Assembly and LISA WorkshopAdamsLawrence Berkeley National LaboratoryLuiENIGMA
Three-Dimensional High Spatial Resolution Simulation for Groundwater Flow and Nitrogen Transport Under Rainfall Perturbations in the Subsurface of Area 3AdamsLawrence Berkeley National LaboratoryImENIGMA
The Path from Root Input to Mineral-Associated Soil Carbon is Dictated by Habitat-Specific Microbial TraitsPett-RidgeLawrence Livermore National LaboratoryFoleyMicrobes Persist SFA
ENIGMA Environmental Atlas: An Integrated Approach to Linking Microbial Genotype to Phenotype in a Dynamic Subsurface EcosystemAdamsLawrence Berkeley National LaboratoryChakrabortyENIGMA
Functional Succession of Growing Soil Microorganisms and Virus-Driven Mortality Following Rewetting in a California Grassland SoilPett-RidgeLawrence Livermore National LaboratoryBlazewiczMicrobes Persist SFA
Conversion of Lignocellulosic Plant Biomass into Industrial Chemicals via Metabolic Engineering of Two Extreme Thermophiles, Caldicellulosiruptor bescii and Pyrococcus furiosusAdamsUniversity of GeorgiaBingUniversity
Towards Generalized Platforms for Functional Genomics in α-ProteobacteriaPetersGLBRCHallGLBRC
Improved Biofuel Production Through Discovery and Engineering of Terpene Metabolism in SwitchgrassZerbeUniversity of California–DavisWyattEarly Career
Enhanced Resistance Pines for Improved Renewable Biofuel and Chemical ProductionPeterUniversity of FloridaMorganUniversity
Functional Characterization of Glycosyltransferases in Duckweed to Enable Predictive BiologyUrbanowiczUniversity of GeorgiaUrbanowiczUniversity
Secure Ecosystem Engineering and Design (SEED) to Enable Safe Biodesign of Novel Plant-Microbe InteractionsAbrahamOak Ridge National LaboratoryYangSEED
The Root Microbiome of Camelina in the Dryland Wheat Production Areas of Eastern WashingtonPaulitzWashington State UniversityPengUniversity
Integrating Functional Genomics with Molecular-Level Experimentation to Understand Adaptation to Nutrient Stress in Poplar and SorghumPaapeBrookhaven National LaboratoryPaapeQPSI
Functional Characterization of bHLH Transcription Factors Coordinating Abiotic Stress Response, Secondary Cell Wall Biosynthesis, and Metal Homeostasis in PopulusXieBrookhaven National LaboratoryXieQPSI
Recent Developments at the Center for Structural Molecular Biology at Oak Ridge National LaboratoryO’NeillOak Ridge National LaboratoryPingali
Cell Free Conversion of Pyruvate to 2,3-Butanediol Using Co-Substrate Feed as pH Control StrategyOlsonDartmouth CollegeJilaniUniversity
Engineering Synthetic Anaerobic Consortia Inspired by the Rumen for Biomass Breakdown and ConversionO’MalleyUniversity of California–Santa BarbaraBlairUniversity
Crosstalk: Interkingdom Interactions in the Mycorrhizal Hyphosphere and Ramifications for Soil Carbon CyclingNuccioLawrence Livermore National LaboratoryNuccioEarly Career
The Twin Ecosystems Project: A New Capability for Field and Laboratory Ecosystems Coupled by Sensor Networks and Autonomous ControlsNorthenLawrence Berkeley National LaboratoryTringeOther
Examine Plant-Microbe-Soil Interactions Using Fabricated Ecosystems Across ScalesNorthenLawrence Berkeley National LaboratoryLinm-CAFEs
Secure Ecosystem Engineering and Design (SEED) to Mitigate the Impacts of Non-Native Fungal Pathogens on Managed EcosystemsAbrahamOak Ridge National Laboratory TannousSEED


Introduction to DOE Systems Biology Knowledgebase

An brief introduction to KBase.