KBase: DOE Systems Biology Knowledgebase

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

The 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

SFA: Phenotypic Response of the Soil Microbiome to Environmental Perturbations
KBase Collaboration: https://www.kbase.us/research/hofmockel-sfa/
PI: Kirsten Hofmockel, PNNL

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

SFA: ENIGMA: Ecosystems and Networks Integrated with Genes and Molecular Assemblies
KBase Collaboration: https://www.kbase.us/research/adams-sfa/
PI: Paul Adams, LBNL

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

SFA: Persistence Control of Engineered Functions in Complex Soil Microbiomes
KBase Collaboration:https://www.kbase.us/research/egbert-sfa/
PI: Robert Egbert, PNNL

Design and Omics Exploration of Synthetic Microbial Communities

SFA: Plant-Microbe Interfaces (PMI)
KBase Collaboration: https://www.kbase.us/research/doktycz-sfa/
PI: Mitch Docktycz, ORNL

Probabilistic Annotation and Ensemble Metabolic Modeling in KBase

SFA: A Systems Biology Approach to Interactions and Resource Allocation in Bioenergy-Relevant Microbial Communities
KBase Collaboration: https://www.kbase.us/research/stuart-sfa/
PI: Rhona Stuart, LLNL

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

SFA: Microbes Persist: Systems Biology of the Soil Microbiome
KBase Collaboration: https://www.kbase.us/research/pett-ridge-sfa/
PI: Jennifer Pett-Ridge, LLNL

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

2023 Abstracts

Title	PI	PI Institution	Presenter	Project
A Gene-Editing System for Large-Scale Fungal Phenotyping in a Model Wood Decomposer	Zhang	University of Minnesota–Saint Paul	Zhang	University
Model-Guided Design of Synthetic Microbial Consortia for Next-Generation Biofuel Production	Zengler	University of California–San Diego	Thiruppathy	University
Reproducible Plant Growth in Fabricated Ecosystems (EcoFAB 2.0) Reveals that Nitrogen Supply Modulates Root Exudation	Zengler	University of California–San Diego	Northen	University
Microbial Guilds and Niches Enable Targeted Modifications of the Microbiome	Zengler	University of California–San Diego	Moyne	University
Unraveling Metabolic Interactions in a Rhizosphere Microbial Community Through Genome-Scale Modeling	Zengler	University of California–San Diego	Kumar	University
Designing Novel Enzymes for Complete Degradation of Recalcitrant Polyamides	Zanghellini	Arzeda Corporation	Sangha
Encapsulin Nanocompartment Systems in Rhodococcus opacus for Compartmentalized Biosynthesis Applications	Yung	Lawrence Livermore National Laboratory	Yung	Early Career
Systems Biology to Enable Modular Metabolic Engineering of Fatty Acid Production in Cyanobacteria	Young	University of Wisconsin–Madison	Zuniga	University
Inter-Facility Collaboration: Overarching Challenges and Opportunities Identified Through the “Genomes to Structure and Function” Virtual Workshop	Adams	Lawrence Berkeley National Laboratory	Adams
Metabolism in Microbial Communities and the Associated Biochemistry of Polymer Deconstruction	Yeates	University of California–Los Angeles DOE Institute for Genomics and Proteomics	Gunsalus	UCLA DOE IGP
Electron Diffraction for High-Resolution Structure Determination of Biomolecules	Yeates	University of California–Los Angeles DOE Institute for Genomics and Proteomics	Vlahakis	UCLA DOE IGP
Investigating Plant and Microbe Systems for Understanding the Formation and Modulation of Amyloid and Amyloid-Like Proteins	Eisenberg	University of California–Los Angeles DOE Institute for Genomics and Proteomics	Lutter	UCLA DOE IGP
Phenotypic Characterization of Sorghum Nitrogen Responsive Gene Edits Using High-Throughput Phenotyping	Jin	University of Nebraska–Lincoln	Jin	University
A Leaf-Level Spectral Library to Support High-Throughput Plant Phenotyping: Predictive Accuracy and Model Transfer	Wijewardane	Mississippi State University	Wijewardane	University
Ghost Imaging of Biological Samples Using Non-Degenerate Entangled Photons	Werner	Los Alamos National Laboratory	Ryan
Biological Imaging of Plant and Fungal Samples Using Infrared Light	Morales	Los Alamos National Laboratory	Morales
Putting Microorganisms on the Map: Continental-Scale Context for Thousands of Newly Sampled Microbial Genomes from North American Wetlands	Wrighton	Colorado State University	Wrighton	University
Construction of a Microbial Methane Observatory Reveals Metabolic Dynamics of Freshwater Wetland Microbiomes	Wrighton	Colorado State University	Oliverio	University
Membrane Potential Dynamics during the Cell Cycle of Single Proliferating and Nonproliferating Bacterial Cells	Weiss	University of California–Los Angeles	Bharadwaj
Laboratory for BioMolecular Structure: A DOE-Funded National Cryo-EM Center	McSweeney	Brookhaven National Laboratory	Wang
Phage Engineering for Targeted Editing of Microbial Communities	Northern	Lawrence Berkeley National Laboratory	Adler	m-CAFEs
Metabolic Modeling and Genetic Engineering of Enhanced Anaerobic Microbial Ethylene Synthesis	North	The Ohio State University	North	University
Using ¹³CO₂ to Track Carbon Flow Mediated by Fungal-Bacterial Interactions in Grassland Soils	Nguyen	University of Hawaiʻi–Mānoa	Yuan	University
Fungal-Bacterial Interactions: Bridging Soil Niches in Regulating Carbon and Nitrogen Processes	Nguyen	University of Hawaiʻi–Mānoa	Nguyen	University
Broadening Aromatic Compound Degradation in Acinetobacter baylyi Using Synthetic Metabolic Pathways	Neidle	University of Georgia	Baugh	University
Quantify the Impact of Your Data with DOE JGI’s Genome Citation Service	Fagnan	JGI	Fagnan	JGI
Engineering Novel Microbes for Upcycling Waste Plastic	Moon	Washington University–St. Louis	Diao	University
HypoRiPPAtlas: An Atlas of Hypothetical Natural Products for Mass Spectrometry Database Search	Mohimani	Carnegie Mellon University	Guler	University
Scalable Computational Tools for Inference of Protein Annotation and Metabolic Models in Microbial Communities	Miller	University of Colorado–Denver	Davoudi	University
Systems Metabolic Engineering of Novosphingobium aromaticivorans for Lignin Valorization	Michener	Oak Ridge National Laboratory	Michener	Early Career
Advanced Photon Source Capabilities for Environmental and Biological Science	Michalska	Argonne National Laboratory	Michalska
Root-Mediated Impacts of Plant Volatile Organic Compound Emissions on Soil Carbon	Meredith	University of Arizona	Honeker	University
Direct Routes for Microbial Carbon Stabilization of Volatile Organic Compounds in Soil	Meredith	University of Arizona	Gil-Loaiza	University
Deploying Top-Down and Bottom-Up Strategies for Genetic Engineering of Auxenochlorella protothecoides for the Production of Sustainable Biofuels	Merchant	University of California–Berkeley	Roth	University
Tools and Targets: Engineering Modified Fatty Acids and Improved Photosynthetic Resilience in Auxenochlorella protothecoides	Merchant	University of California–Berkeley	Moseley	University
A Gapless and Phased Diploid Genome Assembly for Auxenochlorella protothecoides Facilitates Metabolic Modeling and Proteomics Analyses	Merchant	University of California–Berkeley	Boyle	University
Ghost Imaging in the X-ray Regime	McSweeney	National Synchrotron Light Source II	Goodrich
Development of a CenH3-Based Haploid Inducer in Hexaploid Camelina sativa	Henry	University of California–Davis	Henry	University
Transcriptome and Gene Regulatory Network Analyses in Camelina Nitrogen Response and Seed Development	Lu	Montana State University	Correr	University
Developing, Understanding, and Harnessing Modular Carbon/Nitrogen-fixing Tripartite Microbial Consortia for Versatile Production of Biofuel and Platform Chemicals	Lin	University of Michigan	Lin	University
Development of Classically Entangled Light for Depth-Resolved Quantum Mimicry Bioimaging	Liao	University of Colorado–Boulder	Liao
Discovering Transcriptional Regulators of Photosynthesis in Energy Sorghum to Improve Productivity	Long	University of Illinois at Urbana–Champaign	Pelech	CABBI
Overview of CABBI Conversion Theme	Zhao	University of Illinois Urbana–Champaign	Shen	CABBI
Integrating Measurements and Models to Improve Projections of Ecosystem Carbon Balance in Bioenergy Agriculture	Brzostek	CABBI	Juice	CABBI
Increasing the Value of Bioenergy Grasses—Expressing Engineered Traits in the Right Place at the Right Time	Marshall-Colon	Center for Advanced Bioenergy and Bioproducts Innovation	Fu	CABBI
Pooled Microbial CRISPR Screens Using Single-Cell RNA Sequencing	Carothers	University of Washington	Brandner	University
Uncovering the Microbial Networks that Degrade Plant-Derived Phenolic Compounds and Their Role in Peatland Soil Carbon Sequestration: Revisiting the ‘Enzyme Latch’ Hypothesis	Kostka	Georgia Institute of Technology	Kostka	University
Computational Tools for Multiomic Data Standardization and Integration to Represent Whole Microbial Communities	Kostka	Georgia Institute of Technology	Konstantinidis	University
Identification of Regulatory Mechanisms Underlying Cell Differentiation in Sorghum Biomass	Kirst	University of Florida	Vermerris	University
Single-Cell Genomics of Poplar Wood Development	Kirst	University of Florida	Pereira	University
Scenario-Based Technoeconomic and Life-Cycle Analyses of Biomass Conversion Technologies	Keasling	Lawrence Berkeley National Laboratory	Simmons	JBEI
Characterizing Lignocellulose Breakdown Mechanisms in Anaerobic Gut Fungi	Keasling	JBEI	Jin	JBEI
Understanding the Role of Lignin in Native Architecture of Engineered Plant Cell Walls via Multi-Dimensional Solid-State NMR	Keasling	JBEI	Gao	JBEI
Evolutionary Engineering is a Versatile Strain Optimization Approach for Sustainable Bioproduction	Keasling	JBEI	Feist	JBEI
Domesticating Cyanobacteria Through Development of New Genome Engineering Tools, and Isolation of New Bio-Prospected Model Strains	Church	Harvard University	Schubert	University
Defining the Influence of Environmental Stress on Bioenergy Feedstocks at Single-Cell Resolution	Cole	JGI	Dao	Early Career
Expression of S-Adenosyl Methionine Hydrolase Modifies Lignin in Sorghum	Keasling	JBEI	Eudes	JBEI
Development of a Quantum-Optimal Bioimaging System for Plant-Microbiome Interactions	Kasevich	Stanford University	Reynolds
Development of High-Throughput Light-Sheet Fluorescence Lifetime Microscopy for 3D Functional Imaging of Metabolic Pathways in Plants and Microorganisms	Kasevich	Stanford University	Bowman
Exploring Switchgrass Genetic Diversity with Multiple Reference Genomes	Juenger	University of Texas–Austin	Schmutz	University
The Influence of Switchgrass Internode Anatomy on Biofuel Production-Relevant Traits	Junger	University of Texas–Austin	Bartley	University
Structural Biology Center at Sector 19 of Advanced Photon Source	Joachimiak	Argonne National Laboratory	Joachimiak
Engineered Overlapping Genes Paired with Directed Evolution Prolongs the Evolutionary Stability of a Genetic Circuit	Park	Lawrence Livermore National Laboratory	Park	Secure Biosystems Design
Engineering Overlapping Genes in Bacteria	Jiao	Lawrence Livermore National Laboratory	Jiao	Secure Biosystems Design
Developing Genome Engineering Technologies in Cupriavidus necator for Carbon-Negative Biomanufacturing	Isaacs	Yale University	Nakamura	University
A Cell-Free Protein Evolution Platform	Jewett	Northwestern University	Landwehr	University
Plant Methanol Emission at the Interface of the Photosynthetic C₁ Pathway, Leaf Water Status, and Growth	Jardine	Lawrence Berkeley National Laboratory	Jardine	Early Career
AI/ML for Bioenergy Research in CABBI	Leakey	CABBI	Zhao	CABBI
From Strand Design Principles to SNP Detection—Probing Oligonucleotide Hybridization at the Single Molecule Level	Church	Harvard Medical School	Stein	University
Novel Systems Approach for Rational Engineering of Robust Microbial Metabolic Pathways	Jarboe	Iowa State University	Jarboe	University
A Pipeline for High-Throughput Genomic Recoding in Organisms Beyond E. coli	Church	Harvard Medical School	Tas	University
High (School)-Throughput Screening of BAHD Transferases	Acheson	University of Wisconsin−Madison	Acheson	GLBRC
Chemical Imaging of Plant-Soil-Microbe Systems at the Stanford Synchrotron Radiation Lightsource	Hodgson	SLAC National Accelerator Laboratory	Richardson
Harnessing Regulatory Variation to Elucidate Drought Resilience Mechanisms in Sorghum	Eveland	Donald Danforth Plant Science Center	Eveland	University
Opportunities Linking Omics and Structural Biology at PNNL: Excelling at Cryo-EM	Evans	Pacific Northwest National Laboratory	Evans
Fluorescence Lifetime Measurements using Entangled-Photon Coincidences	Laurence	Lawrence Livermore National Laboratory	Eshun
Conformational Equilibria Underlying Electron Bifurcation and Transfer in Thermotoga Maritima Fix/EtfABCX: Novel Structural States and Their Correlation to Catalysis by Anaerobic SEC-SAXS	Hura	Lawrence Berkeley National Laboratory	Murray
Impacts of Altered Climate on Microbial Growth and Nutrient Assimilation in an Ombitrophic Peat Bog	Hungate	Northern Arizona University	Bell	University
Impact of Soil Viruses on Microbial Compositions and Functions	Hofmockel	Pacific Northwest National Laboratory	Wu	Phenotypic Response of SOIL Microbes
OMEGGA: A Computationally Efficient Omics-Guided Global Gapfilling Algorithm for Phenotype-Consistent Metabolic Network Reconstruction	Hofmockel	Pacific Northwest National Laboratory	Song	Phenotypic Response of SOIL Microbes
Removal of Primary Nutrient Degraders Reduces Growth and Modifies Functional Pathways of Soil Microbial Communities with Genomic Redundancy	Hofmockel	Pacific Northwest National Laboratory	McClure	Phenotypic 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 Discovery	Henry	Argonne National Laboratory	Henry	KBase
Integration of Enzyme Function Initiative Tools in the KBase Platform	Henry	Argonne National Laboratory	Henry	KBase
IMAGINE BioSecurity: Genome-Scale Engineering and Modeling for Secure Biosystems Design	Guarnieri	National Renewable Energy Laboratory	Suzuki	IMAGINE BioSecurity
IMAGINE BioSecurity: Mesocosm-Based Methods to Evaluate Biocontainment Strategies and Impact of Industrial Microbes Upon Native Ecosystems.	Guarnieri	Biosciences Center	Guarnieri	IMAGINE BioSecurity
The Genetics of Pathogen and Microbiome Control in the Switchgrass Leaf	Lowry	GLBRC	Wallendael	GLBRC
Systems Framework to Enhance the Potential of Camelina as Oilseed Crop	Grotewold	Michigan State University	Grotewold	University
A Temporal Atlas and Response to Nitrate Availability of 3D Root System Architecture in Diverse Pennycress (Thlaspi arvense L.) Accessions	Sedbrook	Illinois State University	Griffiths	University
Understanding Plant Signaling via Innovations in Probe Delivery and Imaging	Greenberg	The University of Chicago	Greenberg	University
Metagenomic Insights into Microbial Traits Influencing Community Dynamics and N Cycling Post-Fire	Glassman	University of California–Riverside	Nelson	University
Predicting Post-Fire N Cycling through Traits and Cross-Kingdom Interactions	Glassman	University of California–Riverside	Glassman	University
Optimizing Enzymes for Plastic Upcycling using Machine Learning Design and High Throughput Experiments	Gauthier	Dana-Farber Cancer Institute	Fram	University
Structure and Molecular Mechanism of a Bacterial ADP-forming 4-Coumarate CoA Ligase	Fox	University of Wisconsin−Madison	Chaudhury	GLBRC
Extracting Functional Traits from Large Volumes of Field Phenomics Data	Eveland	Donald Danforth Plant Science Center	Gonzalez	University
Probing Photoreception with New Quantum-Enabled Imaging	Evans	Pacific Northwest National Laboratory	Evans
Unraveling Spatiotemporal and Physicochemical Constraints on Soil Viral Community Composition and Viral Particle Integrity	Emerson	University of California–Davis	Emerson	University
Community Engagement Strategies of the National Microbiome Data Collaborative (NMDC)	Eloe-Fadrosh	Lawrence Berkeley National Laboratory	Kelliher	NMDC
Refactoring Metabolism to Control the Persistence of Genetically Engineered Microorganisms in the Environment	Egbert	Pacific Northwest National Laboratory	Elmore	Persistence Control of Soil Microbiomes
Development of Synthetic Microbial Communities to Study Consortium Engraftment Dynamics and to Improve the Yield Performance of Sorghum	Egbert	Pacific Northwest National Laboratory	Egbert	Persistence Control of Soil Microbiomes
EndoPopulus: Elucidating the Molecular Mechanisms of N-Fixation by Populus Endophyte, Burkholderia vietnamiensis WPB	Doty	University of Washington	Aufrecht	University
EndoPopulus: Elucidation of the Roles of Diazotrophic Endophyte Communities in Promoting Productivity and Resilience of Populus Through Systems Biology Approaches	Doty	University of Washington	Doty	University
EndoPopulus: Endophyte Inoculation Enhances Populus Physiological Responses to Abiotic Stress	Doty	University of Washington	Banan	University
Novosphingobium aromaticivorans for ccMA Production from Lignin Biomass	Donohue	GLBRC	Vilbert	GLBRC
Defining Transcriptomic Dynamics in Sorghum in Multiple Abiotic Stresses	Donohue	GLBRC	Ko	GLBRC
Plant-Microbe Interfaces: Molecular Insights into the Mutualistic Symbiosis Between Populus and Plant Growth-Promoting Bacteria	Doktycz	Oak Ridge National Laboratory	Piatkowski	Plant-Microbe Interfaces
Plant-Microbe Interfaces: Capturing and Interpreting the Role of Populus’ Microbiome	Doktycz	Oak Ridge National Laboratory	Pelletier	Plant-Microbe Interfaces
Accelerating Carbon-Negative Biomanufacturing Through Systems-Level Biology and Genome Optimization	Jewett	Stanford University	Fackler	University
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 Setaria	Baxter	Donald Danforth Plant Science Center	Hubbard	University
The Predictive Power of Phylogeny on Growth Rates in Soil Bacterial Communities	Hungate	Northern Arizona University	Walkup	University
Agent-Based Algal Modeling for the Rational Engineering of Chlamydomonas reinhardtii	Boyle	Colorado School of Mines	Boyle	University
Predicting Gene Functions in Plants with Single-Cell Genomic Data	Dinneny	Stanford University	Timilsena	University
Probabilistic Annotation and Ensemble Metabolic Modeling in KBase	D’haeseleer	Lawrence Livermore National Laboratory	D’haeseleer	KBase
NLP for Synthetic Biology: Providing Generalizable Literature Mining Through KBase	Dehal	Lawrence Berkeley National Laboratory	Yoo	KBase
Ultra-Sensitive Protein-SIP to Quantify Activity and Substrate Uptake in Microbiomes with Stable Isotopes	Kleiner	North Carolina State University	Kleiner	University
Biofuels Disruption of Membrane Domains: An Unrecognized Mode of Solvent Stress	Davison	Oak Ridge National Laboratory	Elkins	Biomass Deconstruction
Visualization of Solvent Disruption of Biomass and Biomembrane Structures in the Production of Advanced Biofuels and Bioproducts	Davison	Oak Ridge National Laboratory	Davison	Biomass Deconstruction
Visualizing Spatial and Temporal Responses of Plant Cells to the Environment	Dahlberg	SLAC National Accelerator Laboratory	Joubert
Understanding the Effects of Populus—Mycorrhizal Associations on Plant Productivity and Resistance to Abiotic Stress	Cregger	Oak Ridge National Laboratory	Cregger	Early Career
Elucidating the Genetic Components of the Physiological and Metabolic Processes Governed by the TORC Regulatory Module in Poplar	Coleman	University of Maryland	Coleman	University
Construction of a Synthetic 57-Codon E. coli Chromosome to Achieve Resistance to All Natural Viruses, Prevent Horizontal Gene Transfer, and Enable Biocontainment	Church	Harvard Medical School	Nyerges	University
Expanding Knowledge of Bacterial-Fungal Interactions in Environmental Microbiomes	Chain	Los Alamos National Laboratory	Robinson	Bacterial-Fungal Interactions
An Online Public Resource for Bacterial-Fungal Interaction Research	Chain	Los Alamos National Laboratory	Chain	Bacterial-Fungal Interactions
Multiomics-Driven Microbial Model Optimization	Carothers	University of Washington	Shin	University
Genome-Wide Gene Regulation by Transcriptional CRISPRa/i Tools in Non-Model Bacteria	Carothers	University of Washington	Kiattisewee	University
FatPlants: A Comprehensive Information System for Lipid-Related Genes and Metabolic Pathways in Plants	Cahoon	University of Nebraska	Durrett	University
B5: Bigger Better Brassicaceae Biofuels and Bioproducts—An Overview	Cahoon	University of Nebraska–Lincoln	Cahoon	University
Changes in Amino Acid Distribution Across Populus trichocarpa Roots with and Without Microbes in a Rhizosphere-on-a-Chip Habitat	Cahill	Oak Ridge National Laboratory	Cahill
Metabolome-Informed Proteome Imaging of Lignocellulose Decomposition by a Naturally Evolved Fungal Garden Microbial Consortium	Burnum-Johnson	Pacific Northwest National Laboratory	Burnum-Johnson	Early Career
BioPoplar: A Tunable Chassis for Diversified Bioproduct Production	Buell	Agricultural Research Service, U.S. Department of Agriculture	Buell	University
Synthetic Membrane Biology of Microbial Cell Factories: Lipid Interactions that Shape the Inner Mitochondrial Membrane	Budin	University of California–San Diego	Budin	Early Career
Developing Chassis for LDPE Upcycling from Microbes Native to the Gut Microbiome of Yellow Mealworms	Blenner	University of Delaware	Klauer	University
Analysis of the Beneficial Associations of Sorghum with Arbuscular Mycorrhizal Fungi Studied with Genetics, Genomics, and Microbiomics	Bennetzen	University of Georgia	Bennetzen	University
Understanding and Engineering Crown Root Development to Improve Water-Use Efficiency in Bioenergy Grasses	Baxter	Donald Danforth Plant Science Center	Goudinho Viana	University
Accelerating Discovery of Genes Regulating Stomatal Patterning and Water Use Efficiency in C₄ Crops with Novel High-Throughput Methods for Mutagenesis and Phenotyping	Baxter	Donald Danforth Plant Science Center	Tan	University
Quantum Optical Microscopy of Biomolecules near Interfaces and Surfaces (QuOMBIS)	Backlund	University of Illinois Urbana–Champaign	Backlund
Optical and X-ray Multimodal-Hybrid Microscope Systems for Imaging of Plant Stress Response and Microbial Interactions	Wakatsuki	SLAC National Accelerator Laboratory	Dowlatshahi
Diffraction-Free Beams in Light-Sheet Microcopy	Vasdekis	University of Idaho	Luo	University
Gatekeepers of Arctic Carbon Loss: Landscape-Scale Metabolites-to-Ecosystems Profiling to Mechanistically Map Climate Feedbacks	Varner	University of New Hampshire	Kuhn	University
Populus Secondary Cell Walls: Atomistic Models and Natural Variability in Architecture Informed by Solid-State Nuclear Magnetic Resonance	Tuskan	CBI	Harman-Ware	CBI
AI-Informed Systems Biology: The Discovery of Cryptic Phenotypes and the Functional Networks that Control Them	Tuskan	CBI	Lagergren	CBI
Metaproteomic Insights into Mechanisms Enabling Anaerobic, Thermophilic Microbiomes to Achieve Undiminished Fractional Carbohydrate Solubilization at High Solids Loading	Tuskan	CBI	Holwerda	CBI
Comprehensive Genome-Wide CRISPR Interference Library for High-Throughput Functional Genomic Studies in Pseudomonas putida	Tuskan	CBI	Eckert	CBI
Deciphering the Genetic Basis of S/G Lignin Variation in Switchgrass through QTL Mapping and Transgenic Approaches	Tuskan	CBI	Devos	CBI
Engineering Bacterial Microcompartments in Clostridium autoethanogenum to Overcome Bottlenecks in Sustainable Production of Synthetic Rubber	Tullman-Ercek	Northwestern University	Palmero	University
WINTR: Winter Transcriptome Regulation in Poplar	Tsai	University of Georgia	Tsai	University
Harnessing Robustness of Thermophilic Bacillus coagulans for Conversion of Switchgrass Hydrolysates to Designer Bioesters at Elevated Temperatures	Trinh	University of Tennessee	Ryu	University
From Bulk Organic Matter Profiling to Specific Metabolite Identification: Improving Metabolomics Data Analysis, Annotation, Interpretation, and Integration	Tfaily	University of Arizona	Ayala-Ortiz	University
Deciphering Virocell Metabolic Dynamics and Ecosystem Outputs Using a Novel Integration of Machine Learning and Metabolomics	Sullivan	The Ohio State University	Rajakaruna	University
Diversity Patterns and Ecological Footprint of RNA Viruses Along a Permafrost Thaw Gradient	Sullivan	The Ohio State University	Pratama	University
Genetic Determinants of Klebsiella Phage Infection	Sullivan	The Ohio State University	Gittrich	University
Portals of Discovery: The NMDC Infrastructure and Products for Microbiome Research	Eloe-Fadrosh	Lawrence Berkeley National Laboratory	Smith	NMDC
The Context-Dependency of Plant-Microbial Interactions in the Bioenergy Resource Economy	Stuart	Lawrence Livermore National Laboratory	Hestrin	Microbial Systems Biology for Bioenergy
Identifying Genomic and Metabolic Underpinnings of Algal-Bacterial Interactions via Metatranscriptomics, NanoSIMS Isotope Tracing, and Genome-Scale Metabolic Modeling	Stuart	Lawrence Livermore National Laboratory	Mayali	Microbial Systems Biology for Bioenergy
Improving Bioprocess Robustness by Cellular Noise Engineering	Stephanopoulos	Massachusetts Institute of Technology	Daletos	University
Developing Anaerobic Fungal Tools for Efficient Upgrading of Lignocellulosic Feedstocks	Solomon	University of Delaware	Pareek	University
Developing a High-Throughput Functional Bioimaging Capability for Rhizosphere Interactions Utilizing Sensor Cells, Microfluidics, Automation, and AI-Guided Analyses	Babnigg	Argonne National Laboratory	Babnigg
Optogenetic Control of a Dual Yeast-Yeast Consortia for Chemical Production	Avalos	Princeton University	Garcia Echauri	University
KBase Science and Infrastructure Updates	Arkin	Lawrence Berkeley National Laboratory	Wood-Charlson	KBase
The KBase Knowledge Engine: Ecosystem Classification Prototype	Arkin	Lawrence Berkeley National Laboratory	Dehal	KBase
Learning and Training with KBase	Arkin	Lawrence Berkeley National Laboratory	Allen	KBase
Probing Lignin Deconstruction and Catabolism in Soil Pseudomonas Species	Aristilde	Northwestern University	Aristilde	University
A Systems Understanding of Nitrogen-Fixation on the Aerial Roots of Sorghum	Ané	University of Wisconsin–Madison	Vermerris	University
Plastic Degradation by the Gut Microbiome of Yellow Mealworms	Solomon	University of Delaware	Klauer	University
The MoonTag Programmable Transcription Activator and Synthetic Promoters: Tools for Engineering Oil Biosynthesis in Camelina and Pennycress	Smanski	University of Minnesota–Saint Paul	Casas Mollano	University
Predicting and Modeling Protein-Protein Complexes at Large-Scale with Deep Learning	Skolnick	Georgia Institute of Technology	Gao	University
Feedstocks-to-Fuels Pipeline Demonstration: End-to-End Process Synthesis	Singh	CABBI	Banerjee	CABBI
Functional Analysis of Genes Encoding Ubiquitin Proteasome System Components Affecting Poplar Wood Traits	Shabek	University of California–Davis	Rodriguez-Zaccaro	University
532 Genomes Reveal Natural Variation and Local Adaptation History in Pennycress	Sedbrook	Illinois State University	Toro Arana	University
Comparison of Physiological and Metabolomic Responses to Drought Across Pennycress CRISPR Mutants and Natural Accessions	Sedbrook	Illinois State University	Thomas	University
Optimizing Biological Nitrogen Fixation on Sorghum by Manipulating Microbial Communities	Ané	University of Wisconsin–Madison	Palmer	University
Single-Cell Omics to Examine the Cell Type-Specific Gene Regulatory Programs of Mucilage Production in Sorghum bicolor	Ané	University of Wisconsin–Madison	Ané	University
Developing a National Virtual Biosecurity for Bioenergy Crops Center	Schoonen	Brookhaven National Laboratory	Freimuth	NVBBCC
Lipid Membrane Remodeling and Metabolic Response During Ethanol and Isobutanol Stress in Zymomonas mobilis	Donohue	GLBRC	Rivera Vazquez	Early 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 Metabolism	Amador-Noguez	University of Wisconsin–Madison	Amador-Noguez	Early Career
Integrases on Demand	Schoeniger	Sandia National Laboratories	Williams	InCoGenTEC
Genomic Analyses and Enzyme Characterization Provide Insights into the Catabolism of Lignin-Related Aromatic Compounds in White-Rot Fungi	Salvachúa	National Renewable Energy Laboratory	Salvachúa	Early Career
RNA Phages: Under-Estimated Players in Soil Ecosystems?	Roux	JGI	Roux	JGI
Quantum Diamond EcoFAB Microscope for In Situ NMR of Root Exudate Molecules	Ajoy	University of California–Berkeley	Gilbert
Improving Candidate Gene Discovery by Combining Multiple Genetic Mapping Datasets	Rellán-Álvarez	North Carolina State University	Rellán-Álvarez	University
The Use of Synthetic Communities Reveals Disturbance of Process Partitioning Among Denitrifying Microbes Leads to Increased Nitrous Oxide Emissions	Adams	Lawrence Berkeley National Laboratory	Valenzuela	ENIGMA
Design and Omics Exploration of Synthetic Microbial Communities in KBase	Ranjan	Oak Ridge National Laboratory	Ranjan	KBase
Microbes Persist: Towards Quantitative Theory-Based Predictions of Soil Microbial Fitness, Interaction and Function in KBase	Pett-Ridge	Lawrence Livermore National Laboratory	Kimbrel	Microbes Persist SFA
ENIGMA Long Read Sequencing and Assembly for Microbial Genomes: KBase Integration for Assembly and LISA Workshop	Adams	Lawrence Berkeley National Laboratory	Lui	ENIGMA
Three-Dimensional High Spatial Resolution Simulation for Groundwater Flow and Nitrogen Transport Under Rainfall Perturbations in the Subsurface of Area 3	Adams	Lawrence Berkeley National Laboratory	Im	ENIGMA
The Path from Root Input to Mineral-Associated Soil Carbon is Dictated by Habitat-Specific Microbial Traits	Pett-Ridge	Lawrence Livermore National Laboratory	Foley	Microbes Persist SFA
ENIGMA Environmental Atlas: An Integrated Approach to Linking Microbial Genotype to Phenotype in a Dynamic Subsurface Ecosystem	Adams	Lawrence Berkeley National Laboratory	Chakraborty	ENIGMA
Functional Succession of Growing Soil Microorganisms and Virus-Driven Mortality Following Rewetting in a California Grassland Soil	Pett-Ridge	Lawrence Livermore National Laboratory	Blazewicz	Microbes Persist SFA
Conversion of Lignocellulosic Plant Biomass into Industrial Chemicals via Metabolic Engineering of Two Extreme Thermophiles, Caldicellulosiruptor bescii and Pyrococcus furiosus	Adams	University of Georgia	Bing	University
Towards Generalized Platforms for Functional Genomics in α-Proteobacteria	Peters	GLBRC	Hall	GLBRC
Improved Biofuel Production Through Discovery and Engineering of Terpene Metabolism in Switchgrass	Zerbe	University of California–Davis	Wyatt	Early Career
Enhanced Resistance Pines for Improved Renewable Biofuel and Chemical Production	Peter	University of Florida	Morgan	University
Functional Characterization of Glycosyltransferases in Duckweed to Enable Predictive Biology	Urbanowicz	University of Georgia	Urbanowicz	University
Secure Ecosystem Engineering and Design (SEED) to Enable Safe Biodesign of Novel Plant-Microbe Interactions	Abraham	Oak Ridge National Laboratory	Yang	SEED
The Root Microbiome of Camelina in the Dryland Wheat Production Areas of Eastern Washington	Paulitz	Washington State University	Peng	University
Integrating Functional Genomics with Molecular-Level Experimentation to Understand Adaptation to Nutrient Stress in Poplar and Sorghum	Paape	Brookhaven National Laboratory	Paape	QPSI
Functional Characterization of bHLH Transcription Factors Coordinating Abiotic Stress Response, Secondary Cell Wall Biosynthesis, and Metal Homeostasis in Populus	Xie	Brookhaven National Laboratory	Xie	QPSI
Recent Developments at the Center for Structural Molecular Biology at Oak Ridge National Laboratory	O’Neill	Oak Ridge National Laboratory	Pingali
Cell Free Conversion of Pyruvate to 2,3-Butanediol Using Co-Substrate Feed as pH Control Strategy	Olson	Dartmouth College	Jilani	University
Engineering Synthetic Anaerobic Consortia Inspired by the Rumen for Biomass Breakdown and Conversion	O’Malley	University of California–Santa Barbara	Blair	University
Crosstalk: Interkingdom Interactions in the Mycorrhizal Hyphosphere and Ramifications for Soil Carbon Cycling	Nuccio	Lawrence Livermore National Laboratory	Nuccio	Early Career
The Twin Ecosystems Project: A New Capability for Field and Laboratory Ecosystems Coupled by Sensor Networks and Autonomous Controls	Northen	Lawrence Berkeley National Laboratory	Tringe	Other
Examine Plant-Microbe-Soil Interactions Using Fabricated Ecosystems Across Scales	Northen	Lawrence Berkeley National Laboratory	Lin	m-CAFEs
Secure Ecosystem Engineering and Design (SEED) to Mitigate the Impacts of Non-Native Fungal Pathogens on Managed Ecosystems	Abraham	Oak Ridge National Laboratory	Tannous	SEED

Introduction to DOE Systems Biology Knowledgebase

An brief introduction to KBase.

KBase: DOE Systems Biology Knowledgebase

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

GSP Science Focus Area (SFA) Collaborations

2023 Abstracts

Videos

Introduction to DOE Systems Biology Knowledgebase