Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program
About
About the Program
Overview
Reports and Documents
BSSD Strategic Plan
News
Genomic Science Program Timeline
Research Snapshot
Research Approach
Research Highlights
Research Publications
PI Research Abstracts
BSSD By the Numbers
Research
Research Areas
Bioenergy
Plant Genomics
Microbial Conversion
Sustainable Bioenergy
Biosystems Design
Biosystems Design
Secure Biosystems Design
Environmental Microbiome
Computational Biology
Bioenergy Research Centers
Overview
Center for Advanced Bioenergy and Bioproducts Innovation (CABBI)
Center for Bioenergy Innovation (CBI)
Great Lakes Bioenergy Research Center (GLBRC)
Joint BioEnergy Institute (JBEI)
Bioenergy Research Centers First 10 Years
Science Focus Areas
Overview
µBiospheres
Bacterial-Fungal Interactions
ENIGMA: Ecosystems and Networks Integrated with Genes and Molecular Assemblies
Microbial Secure Biosystems Design
IMAGINE BioSecurity: Integrative Modeling and Genome-Scale Engineering for Biosystems Security
m-CAFEs: Microbial Community Analysis and Functional Evaluation in Soils
Systems Biology of Soil Microbiome
Persistence Control of Soil Microbiomes
Phenotypic Response of Soil Microbiomes
Plant-Microbe Interfaces
QPSI: Quantitative Plant Science Initiative
SEED: Secure Ecosystem Engineering and Design
Biomass Deconstruction
Publications
BER Enabling Capabilities
Cyberinfrastructure
Overview
NMDC
KBase
Biomolecular Characterization and Imaging Science
Overview
Structural Biology and Cryo-EM
Bio- and Quantum Imaging
UCLA-DOE Institute for Genomics and Proteomics
DOE Scientific User Facilities
Overview
JGI
EMSL
Structural Biology and Cryo-EM
Funding
Funding Opportunities
Early Career Awards
Workforce Development for Teachers and Students
SBIR / STTR
Guidance
Contacts
Diversity, Equity, and Inclusion
Information and Data Sharing Policy
Site Citation & Disclaimers
DOE Performance Metrics
Abstract Test
Title
PI
PI Institution
Presenter
Research Area
Project
A Gene-Editing System for Large-Scale Fungal Phenotyping in a Model Wood Decomposer
Zhang
University of Minnesota–Saint Paul
Zhang
Biosystems Design
University
Model-Guided Design of Synthetic Microbial Consortia for Next-Generation Biofuel Production
Zengler
University of California–San Diego
Thiruppathy
Biosystems Design
University
Reproducible Plant Growth in Fabricated Ecosystems (EcoFAB 2.0) Reveals that Nitrogen Supply Modulates Root Exudation
Zengler
University of California–San Diego
Northen
Biosystems Design
University
Microbial Guilds and Niches Enable Targeted Modifications of the Microbiome
Zengler
University of California–San Diego
Moyne
Biosystems Design
University
Unraveling Metabolic Interactions in a Rhizosphere Microbial Community Through Genome-Scale Modeling
Zengler
University of California–San Diego
Kumar
Biosystems Design
University
Designing Novel Enzymes for Complete Degradation of Recalcitrant Polyamides
Zanghellini
Arzeda Corporation
Sangha
Bioenergy
Encapsulin Nanocompartment Systems in
Rhodococcus opacus
for Compartmentalized Biosynthesis Applications
Yung
Lawrence Livermore National Laboratory
Yung
Biosystems Design
Early Career
Systems Biology to Enable Modular Metabolic Engineering of Fatty Acid Production in Cyanobacteria
Young
University of Wisconsin–Madison
Zuniga
Bioenergy
University
Inter-Facility Collaboration: Overarching Challenges and Opportunities Identified Through the “Genomes to Structure and Function” Virtual Workshop
Adams
Lawrence Berkeley National Laboratory
Adams
Structural Biology
Metabolism in Microbial Communities and the Associated Biochemistry of Polymer Deconstruction
Yeates
University of California–Los Angeles DOE Institute for Genomics and Proteomics
Gunsalus
Structural Biology
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
Structural Biology
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
Structural Biology
UCLA DOE IGP
Phenotypic Characterization of Sorghum Nitrogen Responsive Gene Edits Using High-Throughput Phenotyping
Jin
University of Nebraska–Lincoln
Jin
Bioenergy
University
A Leaf-Level Spectral Library to Support High-Throughput Plant Phenotyping: Predictive Accuracy and Model Transfer
Wijewardane
Mississippi State University
Wijewardane
Bioenergy
University
Ghost Imaging of Biological Samples Using Non-Degenerate Entangled Photons
Werner
Los Alamos National Laboratory
Ryan
Bioimaging
Biological Imaging of Plant and Fungal Samples Using Infrared Light
Morales
Los Alamos National Laboratory
Morales
Bioimaging
Putting Microorganisms on the Map: Continental-Scale Context for Thousands of Newly Sampled Microbial Genomes from North American Wetlands
Wrighton
Colorado State University
Wrighton
Environmental Microbiome
University
Construction of a Microbial Methane Observatory Reveals Metabolic Dynamics of Freshwater Wetland Microbiomes
Wrighton
Colorado State University
Oliverio
Environmental Microbiome
University
Membrane Potential Dynamics during the Cell Cycle of Single Proliferating and Nonproliferating Bacterial Cells
Weiss
University of California–Los Angeles
Bharadwaj
Bioimaging
Laboratory for BioMolecular Structure: A DOE-Funded National Cryo-EM Center
McSweeney
Brookhaven National Laboratory
Wang
Structural Biology
Phage Engineering for Targeted Editing of Microbial Communities
Northern
Lawrence Berkeley National Laboratory
Adler
Environmental Microbiome
m-CAFEs
Metabolic Modeling and Genetic Engineering of Enhanced Anaerobic Microbial Ethylene Synthesis
North
The Ohio State University
North
Bioenergy
University
Using
13
CO
2
to Track Carbon Flow Mediated by Fungal-Bacterial Interactions in Grassland Soils
Nguyen
University of Hawaiʻi–Mānoa
Yuan
Environmental Microbiome
University
Fungal-Bacterial Interactions: Bridging Soil Niches in Regulating Carbon and Nitrogen Processes
Nguyen
University of Hawaiʻi–Mānoa
Nguyen
Environmental Microbiome
University
Broadening Aromatic Compound Degradation in
Acinetobacter baylyi
Using Synthetic Metabolic Pathways
Neidle
University of Georgia
Baugh
Biosystems Design
University
Quantify the Impact of Your Data with DOE JGI’s Genome Citation Service
Fagnan
JGI
Fagnan
Crosscutting
JGI
Engineering Novel Microbes for Upcycling Waste Plastic
Moon
Washington University–St. Louis
Diao
Biosystems Design
University
HypoRiPPAtlas: an Atlas of Hypothetical Natural Products for Mass Spectrometry Database Search
Mohimani
Carnegie Mellon University
Guler
Computational Biology
University
Scalable Computational Tools for Inference of Protein Annotation and Metabolic Models in Microbial Communities
Miller
University of Colorado–Denver
Davoudi
Computational Biology
University
Systems Metabolic Engineering of
Novosphingobium aromaticivorans
for Lignin Valorization
Michener
Oak Ridge National Laboratory
Michener
Biosystems Design
Early Career
Advanced Photon Source Capabilities for Environmental and Biological Science
Michalska
Argonne National Laboratory
Michalska
Structural Biology
Root-Mediated Impacts of Plant Volatile Organic Compound Emissions on Soil Carbon
Meredith
University of Arizona
Honeker
Environmental Microbiome
University
Direct Routes for Microbial Carbon Stabilization of Volatile Organic Compounds in Soil
Meredith
University of Arizona
Gil-Loaiza
Environmental Microbiome
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
Biosystems Design
University
Tools and Targets: Engineering Modified Fatty Acids and Improved Photosynthetic Resilience in
Auxenochlorella protothecoides
Merchant
University of California–Berkeley
Moseley
Biosystems Design
University
A Gapless and Phased Diploid Genome Assembly for
Auxenochlorella protothecoides
Facilitates Metabolic Modeling and Proteomics Analyses
Merchant
University of California–Berkeley
Boyle
Biosystems Design
University
Ghost Imaging in the X-ray Regime
McSweeney
National Synchrotron Light Source II
Goodrich
Structural Biology
Development of a CenH3-Based Haploid Inducer in Hexaploid
Camelina sativa
Henry
University of California–Davis
Henry
Bioenergy
University
Transcriptome and Gene Regulatory Network Analyses in Camelina Nitrogen Response and Seed Development
Lu
Montana State University
Correr
Bioenergy
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
Biosystems Design
University
Development of Classically Entangled Light for Depth-Resolved Quantum Mimicry Bioimaging
Liao
University of Colorado–Boulder
Liao
Bioimaging
Discovering Transcriptional Regulators of Photosynthesis in Energy Sorghum to Improve Productivity
Long
University of Illinois at Urbana–Champaign
Pelech
Bioenergy
CABBI
Overview of CABBI Conversion Theme
Zhao
University of Illinois Urbana–Champaign
Shen
Bioenergy
CABBI
Integrating Measurements and Models to Improve Projections of Ecosystem Carbon Balance in Bioenergy Agriculture
Brzostek
CABBI
Juice
Bioenergy
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
Bioenergy
CABBI
Pooled Microbial CRISPR Screens using Single-Cell RNA Sequencing
Carothers
University of Washington
Brandner
Biosystems Design
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
Environmental Microbiome
University
Computational Tools for Multiomic Data Standardization and Integration to Represent Whole Microbial Communities
Kostka
Georgia Institute of Technology
Konstantinidis
Environmental Microbiome
University
Identification of Regulatory Mechanisms Underlying Cell Differentiation in Sorghum Biomass
Kirst
University of Florida
Vermerris
Bioenergy
University
Single-Cell Genomics of Poplar Wood Development
Kirst
University of Florida
Pereira
Bioenergy
University
Scenario-Based Technoeconomic and Life-Cycle Analyses of Biomass Conversion Technologies
Keasling
Lawrence Berkeley National Laboratory
Simmons
Bioenergy
JBEI
Characterizing Lignocellulose Breakdown Mechanisms in Anaerobic Gut Fungi
Keasling
JBEI
Jin
Bioenergy
JBEI
Understanding the Role of Lignin in Native Architecture of Engineered Plant Cell Walls via Multi-Dimensional Solid-State NMR
Keasling
JBEI
Gao
Bioenergy
JBEI
Evolutionary Engineering is a Versatile Strain Optimization Approach for Sustainable Bioproduction
Keasling
JBEI
Feist
Bioenergy
JBEI
Domesticating Cyanobacteria Through Development of New Genome Engineering Tools, and Isolation of New Bio-Prospected Model Strains
Church
Harvard University
Schubert
Biosystems Design
University
Defining the Influence of Environmental Stress on Bioenergy Feedstocks at Single-Cell Resolution
Cole
JGI
Dao
Bioenergy
Early Career
Expression of S-Adenosyl Methionine Hydrolase Modifies Lignin in Sorghum
Keasling
JBEI
Eudes
Bioenergy
JBEI
Development of a Quantum-Optimal Bioimaging System for Plant-Microbiome Interactions
Kasevich
Stanford University
Reynolds
Structural Biology
Development of High-Throughput Light-Sheet Fluorescence Lifetime Microscopy for 3D Functional Imaging of Metabolic Pathways in Plants and Microorganisms
Kasevich
Stanford University
Bowman
Structural Biology
Exploring Switchgrass Genetic Diversity with Multiple Reference Genomes
Juenger
University of Texas–Austin
Schmutz
Bioenergy
University
The Influence of Switchgrass Internode Anatomy on Biofuel Production-Relevant Traits
Junger
University of Texas–Austin
Bartley
Bioenergy
University
Structural Biology Center at Sector 19 of Advanced Photon Source
Joachimiak
Argonne National Laboratory
Joachimiak
Structural Biology
Engineered Overlapping Genes Paired with Directed Evolution Prolongs the Evolutionary Stability of a Genetic Circuit
Park
Lawrence Livermore National Laboratory
Park
Environmental Microbiome
Secure Biosystems Design
Engineering Overlapping Genes in Bacteria
Jiao
Lawrence Livermore National Laboratory
Jiao
Environmental Microbiome
Secure Biosystems Design
Developing Genome Engineering Technologies in
Cupriavidus necator
for Carbon-Negative Biomanufacturing
Isaacs
Yale University
Nakamura
Biosystems Design
University
A Cell-Free Protein Evolution Platform
Jewett
Northwestern University
Landwehr
Biosystems Design
University
Plant Methanol Emission at the Interface of the Photosynthetic C
1
Pathway, Leaf Water Status, and Growth
Jardine
Lawrence Berkeley National Laboratory
Jardine
Bioenergy
Early Career
AI/ML for Bioenergy Research in CABBI
Leakey
CABBI
Zhao
Bioenergy
CABBI
From Strand Design Principles to SNP Detection—Probing Oligonucleotide Hybridization at the Single Molecule Level
Church
Harvard Medical School
Stein
Biosystems Design
University
Novel Systems Approach for Rational Engineering of Robust Microbial Metabolic Pathways
Jarboe
Iowa State University
Jarboe
Biosystems Design
University
A Pipeline for High-Throughput Genomic Recoding in Organisms Beyond
E. coli
Church
Harvard Medical School
Tas
Biosystems Design
University
High (School)-Throughput Screening of BAHD Transferases
Acheson
University of Wisconsin−Madison
Acheson
Bioenergy
GLBRC
Chemical Imaging of Plant-Soil-Microbe Systems at the Stanford Synchrotron Radiation Lightsource
Hodgson
SLAC National Accelerator Laboratory
Richardson
Structural Biology
Harnessing Regulatory Variation to Elucidate Drought Resilience Mechanisms in Sorghum
Eveland
Donald Danforth Plant Science Center
Eveland
Bioenergy
University
Opportunities Linking Omics and Structural Biology at PNNL: Excelling at Cryo-EM
Evans
Pacific Northwest National Laboratory
Evans
Structural Biology
Fluorescence Lifetime Measurements using Entangled-Photon Coincidences
Laurence
Lawrence Livermore National Laboratory
Eshun
Structural Biology
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
Structural Biology
Impacts of Altered Climate on Microbial Growth and Nutrient Assimilation in an Ombitrophic Peat Bog
Hungate
Northern Arizona University
Bell
Environmental Microbiome
University
Impact of Soil Viruses on Microbial Compositions and Functions
Hofmockel
Pacific Northwest National Laboratory
Wu
Environmental Microbiome
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
Environmental Microbiome
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
Environmental Microbiome
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
Computational Biology
KBase
Integration of Enzyme Function Initiative Tools in the KBase Platform
Henry
Argonne National Laboratory
Henry
Computational Biology
KBase
IMAGINE BioSecurity: Genome-Scale Engineering and Modeling for Secure Biosystems Design
Guarnieri
National Renewable Energy Laboratory
Suzuki
Biosystems Design
IMAGINE BioSecurity
IMAGINE BioSecurity: Mesocosm-Based Methods to Evaluate Biocontainment Strategies and Impact of Industrial Microbes Upon Native Ecosystems.
Guarnieri
Biosciences Center
Guarnieri
Biosystems Design
IMAGINE BioSecurity
The Genetics of Pathogen and Microbiome Control in the Switchgrass Leaf
Lowry
GLBRC
Wallendael
Bioenergy
GLBRC
Systems Framework to Enhance the Potential of
Camelina
as Oilseed Crop
Grotewold
Michigan State University
Grotewold
Bioenergy
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
Bioenergy
University
Understanding Plant Signaling via Innovations in Probe Delivery and Imaging
Greenberg
The University of Chicago
Greenberg
Bioimaging
University
Metagenomic Insights into Microbial Traits Influencing Community Dynamics and N Cycling Post-Fire
Glassman
University of California–Riverside
Nelson
Environmental Microbiome
University
Predicting Post-Fire N Cycling through Traits and Cross-Kingdom Interactions
Glassman
University of California–Riverside
Glassman
Environmental Microbiome
University
Optimizing Enzymes for Plastic Upcycling using Machine Learning Design and High Throughput Experiments
Gauthier
Dana-Farber Cancer Institute
Fram
Bioenergy
University
Structure and Molecular Mechanism of a Bacterial ADP-forming 4-Coumarate CoA Ligase
Fox
University of Wisconsin−Madison
Chaudhury
Bioenergy
GLBRC
Extracting Functional Traits from Large Volumes of Field Phenomics Data
Eveland
Donald Danforth Plant Science Center
Gonzalez
Bioenergy
University
Probing Photoreception with New Quantum-Enabled Imaging
Evans
Pacific Northwest National Laboratory
Evans
Bioimaging
Unraveling Spatiotemporal and Physicochemical Constraints on Soil Viral Community Composition and Viral Particle Integrity
Emerson
University of California–Davis
Emerson
Environmental Microbiome
University
Community Engagement Strategies of the National Microbiome Data Collaborative (NMDC)
Eloe-Fadrosh
Lawrence Berkeley National Laboratory
Kelliher
Environmental Microbiome
NMDC
Refactoring Metabolism to Control the Persistence of Genetically Engineered Microorganisms in the Environment
Egbert
Pacific Northwest National Laboratory
Elmore
Biosystems Design
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
Biosystems Design
Persistence Control of Soil Microbiomes
EndoPopulus: Elucidating the Molecular Mechanisms of N-Fixation by
Populus
Endophyte,
Burkholderia vietnamiensis
WPB
Doty
University of Washington
Aufrecht
Bioenergy
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
Bioenergy
University
EndoPopulus: Endophyte Inoculation Enhances Populus Physiological Responses to Abiotic Stress
Doty
University of Washington
Banan
Bioenergy
University
Novosphingobium aromaticivorans
for
cc
MA Production from Lignin Biomass
Donohue
GLBRC
Vilbert
Bioenergy
GLBRC
Defining Transcriptomic Dynamics in Sorghum in Multiple Abiotic Stresses
Donohue
GLBRC
Ko
Bioenergy
GLBRC
Plant-Microbe Interfaces: Molecular Insights into the Mutualistic Symbiosis Between
Populus
and Plant Growth-Promoting Bacteria
Doktycz
Oak Ridge National Laboratory
Piatkowski
Environmental Microbiome
Plant-Microbe Interfaces
Plant-Microbe Interfaces: Capturing and Interpreting the Role of
Populus’
Microbiome
Doktycz
Oak Ridge National Laboratory
Pelletier
Environmental Microbiome
Plant-Microbe Interfaces
Accelerating Carbon-Negative Biomanufacturing Through Systems-Level Biology and Genome Optimization
Jewett
Stanford University
Fackler
Biosystems Design
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
Biosystems Design
University
The Predictive Power of Phylogeny on Growth Rates in Soil Bacterial Communities
Hungate
Northern Arizona University
Walkup
Environmental Microbiome
University
Agent-Based Algal Modeling for the Rational Engineering of
Chlamydomonas reinhardtii
Boyle
Colorado School of Mines
Boyle
Biosystems Design
University
Predicting Gene Functions in Plants with Single-Cell Genomic Data
Dinneny
Stanford University
Timilsena
Bioenergy
University
Probabilistic Annotation and Ensemble Metabolic Modeling in KBase
D’haeseleer
Lawrence Livermore National Laboratory
D’haeseleer
Computational Biology
KBase
NLP for Synthetic Biology: Providing Generalizable Literature Mining Through KBase
Dehal
Lawrence Berkeley National Laboratory
Yoo
Computational Biology
KBase
Ultra-Sensitive Protein-SIP to Quantify Activity and Substrate Uptake in Microbiomes with Stable Isotopes
Kleiner
North Carolina State University
Kleiner
Environmental Microbiome
University
Biofuels Disruption of Membrane Domains: An Unrecognized Mode of Solvent Stress
Davison
Oak Ridge National Laboratory
Elkins
Bioenergy
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
Bioenergy
Biomass Deconstruction
Visualizing Spatial and Temporal Responses of Plant Cells to the Environment
Dahlberg
SLAC National Accelerator Laboratory
Joubert
Structural Biology
Understanding the Effects of Populus—Mycorrhizal Associations on Plant Productivity and Resistance to Abiotic Stress
Cregger
Oak Ridge National Laboratory
Cregger
Bioenergy
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
Bioenergy
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
Biosystems Design
University
Expanding Knowledge of Bacterial-Fungal Interactions in Environmental Microbiomes
Chain
Los Alamos National Laboratory
Robinson
Bioenergy
Bacterial-Fungal Interactions
An Online Public Resource for Bacterial-Fungal Interaction Research
Chain
Los Alamos National Laboratory
Chain
Bioenergy
Bacterial-Fungal Interactions
Multiomics-Driven Microbial Model Optimization
Carothers
University of Washington
Shin
Biosystems Design
University
Genome-Wide Gene Regulation by Transcriptional CRISPRa/i Tools in Non-Model Bacteria
Carothers
University of Washington
Kiattisewee
Biosystems Design
University
FatPlants: A Comprehensive Information System for Lipid-Related Genes and Metabolic Pathways in Plants
Cahoon
University of Nebraska
Durrett
Biosystems Design
University
B5: Bigger Better Brassicaceae Biofuels and Bioproducts—An Overview
Cahoon
University of Nebraska–Lincoln
Cahoon
Biosystems Design
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
Bioimaging
Metabolome-Informed Proteome Imaging of Lignocellulose Decomposition by a Naturally Evolved Fungal Garden Microbial Consortium
Burnum-Johnson
Pacific Northwest National Laboratory
Burnum-Johnson
Environmental Microbiome
Early Career
BioPoplar: A Tunable Chassis for Diversified Bioproduct Production
Buell
University of Georgia
Buell
Biosystems Design
University
Synthetic Membrane Biology of Microbial Cell Factories: Lipid Interactions that Shape the Inner Mitochondrial Membrane
Budin
University of California–San Diego
Budin
Bioenergy
Early Career
Developing Chassis for LDPE Upcycling from Microbes Native to the Gut Microbiome of Yellow Mealworms
Blenner
University of Delaware
Klauer
Biosystems Design
University
Analysis of the Beneficial Associations of Sorghum with Arbuscular Mycorrhizal Fungi Studied with Genetics, Genomics, and Microbiomics
Bennetzen
University of Georgia
Bennetzen
Bioenergy
University
Understanding and Engineering Crown Root Development to Improve Water-Use Efficiency in Bioenergy Grasses
Baxter
Donald Danforth Plant Science Center
Goudinho Viana
Biosystems Design
University
Accelerating Discovery of Genes Regulating Stomatal Patterning and Water Use Efficiency in C
4
Crops with Novel High-Throughput Methods for Mutagenesis and Phenotyping
Baxter
Donald Danforth Plant Science Center
Tan
Biosystems Design
University
Quantum Optical Microscopy of Biomolecules near Interfaces and Surfaces (QuOMBIS)
Backlund
University of Illinois Urbana–Champaign
Backlund
Bioimaging
Optical and X-ray Multimodal-Hybrid Microscope Systems for Imaging of Plant Stress Response and Microbial Interactions
Wakatsuki
SLAC National Accelerator Laboratory
Dowlatshahi
Bioimaging
Diffraction-Free Beams in Light-Sheet Microcopy
Vasdekis
University of Idaho
Luo
Bioimaging
University
Gatekeepers of Arctic Carbon Loss: Landscape-Scale Metabolites-to-Ecosystems Profiling to Mechanistically Map Climate Feedbacks
Varner
University of New Hampshire
Kuhn
Environmental Microbiome
University
Populus
Secondary Cell Walls: Atomistic Models and Natural Variability in Architecture Informed by Solid-State Nuclear Magnetic Resonance
Tuskan
CBI
Harman-Ware
Bioenergy
CBI
AI-Informed Systems Biology: The Discovery of Cryptic Phenotypes and the Functional Networks that Control Them
Tuskan
CBI
Lagergren
Bioenergy
CBI
Metaproteomic Insights into Mechanisms Enabling Anaerobic, Thermophilic Microbiomes to Achieve Undiminished Fractional Carbohydrate Solubilization at High Solids Loading
Tuskan
CBI
Holwerda
Bioenergy
CBI
Comprehensive Genome-Wide CRISPR Interference Library for High-Throughput Functional Genomic Studies in
Pseudomonas putida
Tuskan
CBI
Eckert
Bioenergy
CBI
Deciphering the Genetic Basis of S/G Lignin Variation in Switchgrass through QTL Mapping and Transgenic Approaches
Tuskan
CBI
Devos
Bioenergy
CBI
Engineering Bacterial Microcompartments in
Clostridium autoethanogenum
to Overcome Bottlenecks in Sustainable Production of Synthetic Rubber
Tullman-Ercek
Northwestern University
Palmero
Bioenergy
University
WINTR: Winter Transcriptome Regulation in Poplar
Tsai
University of Georgia
Tsai
Bioenergy
University
Harnessing Robustness of Thermophilic
Bacillus coagulans
for Conversion of Switchgrass Hydrolysates to Designer Bioesters at Elevated Temperatures
Trinh
University of Tennessee
Ryu
Bioenergy
University
From Bulk Organic Matter Profiling to Specific Metabolite Identification: Improving Metabolomics Data Analysis, Annotation, Interpretation, and Integration
Tfaily
University of Arizona
Ayala-Ortiz
Environmental Microbiome
University
Deciphering Virocell Metabolic Dynamics and Ecosystem Outputs Using a Novel Integration of Machine Learning and Metabolomics
Sullivan
The Ohio State University
Rajakaruna
Environmental Microbiome
University
Diversity Patterns and Ecological Footprint of RNA Viruses Along a Permafrost Thaw Gradient
Sullivan
The Ohio State University
Pratama
Environmental Microbiome
University
Genetic Determinants of
Klebsiella
Phage Infection
Sullivan
The Ohio State University
Gittrich
Environmental Microbiome
University
Portals of Discovery: The NMDC Infrastructure and Products for Microbiome Research
Eloe-Fadrosh
Lawrence Berkeley National Laboratory
Smith
Environmental Microbiome
NMDC
The Context-Dependency of Plant-Microbial Interactions in the Bioenergy Resource Economy
Stuart
Lawrence Livermore National Laboratory
Hestrin
Bioenergy
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
Bioenergy
Microbial Systems Biology for Bioenergy
Improving Bioprocess Robustness by Cellular Noise Engineering
Stephanopoulos
Massachusetts Institute of Technology
Daletos
Bioenergy
University
Developing Anaerobic Fungal Tools for Efficient Upgrading of Lignocellulosic Feedstocks
Solomon
University of Delaware
Pareek
Biosystems Design
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
Bioimaging
Optogenetic Control of a Dual Yeast-Yeast Consortia for Chemical Production
Avalos
Princeton University
Garcia Echauri
Bioenergy
University
KBase Science and Infrastructure Updates
Arkin
Lawrence Berkeley National Laboratory
Wood-Charlson
Computational Biology
KBase
The KBase Knowledge Engine: Ecosystem Classification Prototype
Arkin
Lawrence Berkeley National Laboratory
Dehal
Computational Biology
KBase
Learning and Training with KBase
Arkin
Lawrence Berkeley National Laboratory
Allen
Computational Biology
KBase
Probing Lignin Deconstruction and Catabolism in Soil
Pseudomonas
Species
Aristilde
Northwestern University
Aristilde
Bioenergy
University
A Systems Understanding of Nitrogen-Fixation on the Aerial Roots of Sorghum
Ané
University of Wisconsin–Madison
Vermerris
Bioenergy
University
Plastic Degradation by the Gut Microbiome of Yellow Mealworms
Solomon
University of Delaware
Klauer
Bioenergy
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
Biosystems Design
University
Predicting and Modeling Protein-Protein Complexes at Large-Scale with Deep Learning
Skolnick
Georgia Institute of Technology
Gao
Computational Biology
University
Feedstocks-to-Fuels Pipeline Demonstration: End-to-End Process Synthesis
Singh
CABBI
Banerjee
Bioenergy
CABBI
Functional Analysis of Genes Encoding Ubiquitin Proteasome System Components Affecting Poplar Wood Traits
Shabek
University of California–Davis
Rodriguez-Zaccaro
Bioenergy
University
532 Genomes Reveal Natural Variation and Local Adaptation History in Pennycress
Sedbrook
Illinois State University
Toro Arana
Bioenergy
University
Comparison of Physiological and Metabolomic Responses to Drought Across Pennycress CRISPR Mutants and Natural Accessions
Sedbrook
Illinois State University
Thomas
Bioenergy
University
Optimizing Biological Nitrogen Fixation on Sorghum by Manipulating Microbial Communities
Ané
University of Wisconsin–Madison
Palmer
Bioenergy
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
Bioenergy
University
Developing a National Virtual Biosecurity for Bioenergy Crops Center
Schoonen
Brookhaven National Laboratory
Freimuth
Bioenergy
NVBBCC
Lipid Membrane Remodeling and Metabolic Response During Ethanol and Isobutanol Stress in
Zymomonas mobilis
Donohue
GLBRC
Rivera Vazquez
Bioenergy
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
Bioenergy
Early Career
Integrases on Demand
Schoeniger
Sandia National Laboratories
Williams
Biosystems Design
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
Bioenergy
Early Career
RNA Phages: Under-Estimated Players in Soil Ecosystems?
Roux
JGI
Roux
Crosscutting
JGI
Quantum Diamond EcoFAB Microscope for
In Situ
NMR of Root Exudate Molecules
Ajoy
University of California–Berkeley
Gilbert
Bioimaging
Improving Candidate Gene Discovery by Combining Multiple Genetic Mapping Datasets
Rellán-Álvarez
North Carolina State University
Rellán-Álvarez
Bioenergy
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
Environmental Microbiome
ENIGMA
Design and Omics Exploration of Synthetic Microbial Communities in KBase
Ranjan
Oak Ridge National Laboratory
Ranjan
Computational Biology
KBase
Microbes Persist: Towards Quantitative Theory-Based Predictions of Soil Microbial Fitness, Interaction and Function in KBase
Pett-Ridge
Lawrence Livermore National Laboratory
Kimbrel
Environmental Microbiome
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
Environmental Microbiome
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
Environmental Microbiome
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
Environmental Microbiome
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
Environmental Microbiome
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
Environmental Microbiome
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
Environmental Microbiome
University
Towards Generalized Platforms for Functional Genomics in α-Proteobacteria
Peters
GLBRC
Hall
Bioenergy
GLBRC
Improved Biofuel Production Through Discovery and Engineering of Terpene Metabolism in Switchgrass
Zerbe
University of California–Davis
Wyatt
Bioenergy
Early Career
Enhanced Resistance Pines for Improved Renewable Biofuel and Chemical Production
Peter
University of Florida
Morgan
Bioenergy
University
Functional Characterization of Glycosyltransferases in Duckweed to Enable Predictive Biology
Urbanowicz
University of Georgia
Urbanowicz
Bioenergy
University
Secure Ecosystem Engineering and Design (SEED) to Enable Safe Biodesign of Novel Plant-Microbe Interactions
Abraham
Oak Ridge National Laboratory
Yang
Biosystems Design
SEED
The Root Microbiome of
Camelina
in the Dryland Wheat Production Areas of Eastern Washington
Paulitz
Washington State University
Peng
Bioenergy
University
Integrating Functional Genomics with Molecular-Level Experimentation to Understand Adaptation to Nutrient Stress in Poplar and Sorghum
Paape
Brookhaven National Laboratory
Paape
Bioenergy
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
Bioenergy
QPSI
Recent Developments at the Center for Structural Molecular Biology at Oak Ridge National Laboratory
O’Neill
Oak Ridge National Laboratory
Pingali
Structural Biology
Cell Free Conversion of Pyruvate to 2,3-Butanediol Using Co-Substrate Feed as pH Control Strategy
Olson
Dartmouth College
Jilani
Bioenergy
University
Engineering Synthetic Anaerobic Consortia Inspired by the Rumen for Biomass Breakdown and Conversion
O’Malley
University of California–Santa Barbara
Blair
Biosystems Design
University
Crosstalk: Interkingdom Interactions in the Mycorrhizal Hyphosphere and Ramifications for Soil Carbon Cycling
Nuccio
Lawrence Livermore National Laboratory
Nuccio
Environmental Microbiome
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
Environmental Microbiome
Other
Examine Plant-Microbe-Soil Interactions Using Fabricated Ecosystems Across Scales
Northen
Lawrence Berkeley National Laboratory
Lin
Environmental Microbiome
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
Biosystems Design
SEED