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| | University of Maryland | GEN LI | Assistant Research Professor |
Academic
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Bioenergy
| I am currently an Assistant Research Professor in the Department of Plant Science and Landscape Architecture at the University of Maryland, where I focus on tree genome engineering, particularly in poplar, a model plant for bioenergy crops. My research is dedicated to improving nitrogen use efficiency (NUE) in poplar trees, which directly impacts growth, biomass production, and overall tree health. Nitrogen is a key component of chlorophyll, proteins, and nucleic acids, making it essential for photosynthesis and rapid growth. The seasonal cycling of nitrogen is crucial to determining NUE in perennial plants like poplar, and my previous work has highlighted the significance of bark storage proteins and auxin regulation in this process.
Additionally, I have developed a highly efficient transformation and genome editing system for poplar, which allows for precise genetic manipulation to enhance NUE. By identifying key genes and understanding their regulatory mechanisms, I aim to develop nitrogen-use-efficient poplar varieties that are better suited for bioenergy production. This aligns well with ARPA-E’s program objectives to reduce synthetic nitrogen fertilizer use and mitigate N2O emissions in agriculture while maintaining high biomass yields.
For this proposal, I am particularly interested in applying my expertise in plant genome editing to advance the commercialization of cellulosic nanomaterials (CNs). CNs have the potential to replace greenhouse gas-intensive materials, such as plastics and cement, and provide a sustainable alternative for biofuels, reducing the carbon intensity of bioenergy crops like corn and sorghum. By leveraging my experience with poplar genome engineering, I aim to develop new plant-based technologies that minimize nitrogen inputs while optimizing biomass production, contributing to a 50% reduction in nitrous oxide emissions by 2030, as outlined in the ARPA-E program goals.
My research background positions me to explore the integration of plant breeding and microbial approaches to improve nitrogen delivery and retention, thereby reducing nitrogen losses to the environment. I am confident that my expertise in plant biology, physiology, and metabolic engineering will contribute to ARPA-E’s goal of reducing N2O emissions and advancing bioenergy crop production.
Furthermore, I am eager to collaborate with other researchers in fields such as agronomy, microbiology, and bioinformatics to design innovative solutions for nitrogen mana |
| MD |
| | Climate Foundation | Dr Brian von Herzen | Executive Director |
Non-Profit
|
Bioenergy
| The Climate Foundation (CF) is poised to be a strategic partner for ARPA-E's TEOSYNTE program, offering innovative solutions to enhance nitrogen use efficiency and reduce synthetic fertilizer reliance. For over a decade, CF has led the development of seaweed-based biostimulants and advanced microbiome analysis, aiming to transform agricultural practices sustainably.
Seaweed-Based Biostimulant Technology: Our proprietary biostimulant, applied as a foliar spray, enhances nitrogen uptake by activating plant regulatory pathways. This reduces the need for synthetic fertilizers, minimizes nitrogen runoff, and decreases nitrous oxide emissions. Field trials across 50+ sites, in collaboration with Cornell University and multiple NGOs, have shown yield improvements of 100% to 300%, effectively doubling to quadrupling yield per unit of nitrogen fertilizer.
Microbiome Analysis Expertise: CF collaborates with leading universities to optimize plant and soil microbiomes, enhancing nitrogen fixation and nutrient cycling. This research supports reduced dependence on fossil-derived nitrogen by leveraging beneficial microbial communities in the rhizosphere.
Partnership Opportunities: CF seeks collaboration with teams innovating in plant and microbial bio-design for corn and sorghum. We offer:
1. Biostimulant Formulations: Providing our seaweed-based biostimulant, application protocols, and expertise to maximize efficacy with partner technologies.
2. Microbiome Analysis: Expertise in analyzing microbial communities, assessing partner technology impacts, and identifying synergistic interactions to enhance nitrogen efficiency.
3. Strengthening Applications: By integrating CF's technologies, partners can bolster their proposals to DOE ARPA-E, addressing program goals of reducing nitrogen fertilizer use and emissions while maintaining yields. Our solutions complement bio-design strategies, offering a comprehensive approach to revolutionizing nitrogen management in bioenergy crops.
4. Commitment to Innovation: CF's track record in soil science innovation, evidenced by successful projects and collaborations, underscores our commitment to advancing food and energy security. Partnering with CF allows teams to leverage our unique technologies and expertise to tackle global challenges, reduce emissions, and promote sustainable agriculture. |
| WA |
| | University of Minnesota | Kathryn Fixen | Assistant Professor |
Academic
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Bioenergy
| My background is in bacterial genetics and biochemistry. My lab is interested in electron transfer to nitrogenase, and we are working to understand how this could work in plants. My lab uses omics-based approaches and adaptive laboratory evolution in addition to classic bacterial genetic and biochemical approaches. |
| MN |
| | Award Advisors | Dan Durst | Principal |
Small Business
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Other Energy Technologies
| Award Advisors is a specialized consulting firm dedicated to helping organizations navigate the complexities of federal grant processes, particularly those offered by the Department of Energy (DOE). As a trusted partner, we bring a wealth of expertise in Federal project budget development and post-award compliance, ensuring that our clients are well-prepared to secure and successfully manage DOE grants.
Expert Budget Development:
Our team excels in the intricacies of federal budget formulation, including the completion of SF 424 and the DOE Budget Justification Worksheet. We work closely with organizations to develop detailed, accurate budgets that align with DOE requirements and maximize funding opportunities. Our deep understanding of cost principles and budgeting regulations ensures that your proposal is not only compliant but also competitive.
Indirect Rate Calculation and Negotiation:
Award Advisors specializes in the calculation and negotiation of indirect cost rates, a critical component for organizations seeking to optimize their funding. We guide our clients through the complex process of determining appropriate rates, negotiating with federal agencies, and applying those rates effectively within their budgets. This service is essential for organizations aiming to recover the full spectrum of allowable costs, thereby enhancing the sustainability and impact of their projects.
Post-Award Compliance Preparation:
Navigating the post-award phase requires a thorough understanding of 2 CFR 200, the "Uniform Guidance" that governs federal awards. Our services extend beyond the pre-award stage to ensure that organizations are fully prepared to meet compliance requirements after securing funding. We provide training, policy development, and ongoing support to help organizations establish robust compliance frameworks, mitigating the risk of audit findings and ensuring project success.
Partnering with Award Advisors means gaining a dedicated ally committed to your success in the DOE grant landscape. Let us help you turn your innovative ideas into funded, compliant, and impactful projects. |
| DC |
| | Utah State University | Yiming Su | Assistant Professor |
Academic
|
Bioenergy
| Background:
Nanofertilizer design, synthesis and efficacy assessment; nanomaterial-plant-microbial community interaction about N cycle;
Interests:
nanofertilizer design and test, and nano-agent application technology (foliar vs soil application) development;
Capabilities:
Nanomaterial design, synthesis and characterization;
Greenhouse study on N cycle assessment;
Plant metabolites analysis; |
| UT |
| | University of Missouri | Gary Stacey | Professor |
Academic
|
Bioenergy
| Gary Stacey is Curators’ Distinguished Professor and Professor of Plant Science and Technology at the University of Missouri-Columbia. His research focuses generally on molecular aspects of plant-microbe interactions, including studies of the beneficial nitrogen fixing symbioses and plant-fungal pathogen interactions. He has also been instrumental in the development of genomic resources for the study of soybean. He has mentored 51 postdoctoral fellows and 36 Ph.D. and 8 M.S. graduate students. Past postdocs have gone on to start independent careers in academia (e.g., Michigan State Univ., Washington State Univ.), industry, as well as winning the 2005 USA National Medal of Technology, which was presented to Dr. Puvanesarajah by Pres. Bush. Past graduate students (Dr. Jeongmin Choi) have won the 2015 distinguished dissertation award in Life Sciences/ Biology presented by the National Council of Graduate Study/Proquest, while others have started successful, multimillion-dollar businesses (e.g., Seegene.com). Dr. Stacey has authored or co-authored more than 300 peer-reviewed research articles (33601 citations, h index=101), 79 book chapters, and 13 patents. Two of his patents support the product OptimizeTM sold by Novozymes, Inc., to enhance rhizobial inoculant performance on soybean. He has edited or co-edited 17 books/reports. He has served on various advisory/editorial boards and, from 2010 to 2013, served as Editor-in-Chief of the journal Molecular Plant-Microbe Interactions. He founded the journal series “Current Protocols in Plant Biology”, published by Wiley, and served as the editor-in-chief through Fall, 2021. He chaired the Public Affairs Committee of the American Society for Plant Biologists (ASPB) from 2006 to 2011. From 2009-2018 he was chair of the DOE, Biological and Environmental Research Advisory Committee. In 2008, he founded a not-for-profit corporation, Missouri Energy Initiative (MEI; www.moenergy.org), and served as its Acting Executive Director until 2011. In 2021, he cofounded the biotechnology company, Viosimos Agricuture LLC. He has received a variety of honors, including being named Fellow of the American Association for the Advancement of Science. American Academy of Microbiology, American Society for Plant Biology, St. Louis Academy of Science and, most recently, National Academy of Inventors. |
| MO |
| | University of California, Irvine | Markus Ribbe | Professor |
Academic
|
Bioenergy
| Background:
Nitrogen fixation, microbiology, protein biochemistry, spectroscopy
Interests:
Nitrogenase assembly
Nitrogenase mechanism
Engineering of nitrogenase hybrids/equivalents
Heterologous expression of nitrogenase
Capabilities:
Large scale fermentation of diazotrophic microbes
Anaerobic protein expression and purification
Analysis of nitrogenase reaction products (e.g., ammonia, hydrocarbons, hydrogen)
Analysis of isotopically labeled nitrogenase reaction products
Spectroscopic and structural approaches for nitrogenase analysis |
| CA |
| | University of California, Irvine | Yilin Hu | Professor |
Academic
|
Bioenergy
| Background:
Nitrogen fixation, microbiology, protein biochemistry, spectroscopy
Interests:
Nitrogenase mechanism
Nitrogenase assembly
Engineering of nitrogenase hybrids/equivalents
Heterologous expression of nitrogenase
Molecular biology
Synthetic Biology
Capabilities:
Large scale fermentation of diazotrophic microbes
Anaerobic protein expression and purification
Analysis of nitrogenase reaction products (e.g., ammonia, hydrocarbons, hydrogen)
Analysis of isotopically labeled nitrogenase reaction products
Spectroscopic and structural approaches for nitrogenase analysis |
| CA |
| | Lawrence Berkeley National Lab | Dr. Vivek Mutalik | Staff Scientist |
Federally Funded Research and Development Center (FFRDC)
|
Bioenergy
| I am a Staff Scientist and lead Principal Investigator at the DOE BRaVE Phage Foundry, Biosciences Division at the Lawrence Berkeley National Laboratory, Berkeley, CA. My research group is focused on developing tools and technologies to study and engineer diverse bacteria, phages and their interactions. We are passionate about isolating non-model phages and use them for applications such as studying and manipulating microbial communities involved in carbon and nitrogen cycling. Our expertise are in regulation of bacterial and phage gene expression, developing genetic tools, high-throughput genetic screens, functional genomics of phages and bacteria, study of biotic and abiotic conditions on phage infectivity pathways, genetic basis of phage host range, engineering phages with genetic payload, study of horizontal gene transfers, development of biosensors, bacterial stress responses, genotype-phenotype relationships, and modeling. |
| CA |
| | University of Illinois at Urbana-Champaign | Steve Moose | Alexander Professor of Maize Breeding and Genetics |
Academic
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Bioenergy
| As cited in reference 40 in the FOA, my research group and collaborators have discovered and evaluated genetic variation for maize nitrogen use efficiency traits. We have a field site with 20-year history of fertility management to produce consistent responses to N fertilizer, and have performed trials with both maize and sorghum. We have developed a "NUE panel" of maize hybrids representing natural variation in different components of NUE, such as root architecture, N-sensing and transport, amnio acid cycling and transport, late-season senescence or "staygreen", and kernel N accumulation. Learnings from our predictive modeling using transcriptome data have informed approaches to improve maize NUE using CRISPR mutagenesis, for which 3 years of trials of CRISPR hybrids have demonstrated increased yields with lower N fertilizer. We also have prototyped a living "nitrate sensor" where maize N status is visualized using N-responsive expression of reporter genes. For TEOSYNTE, we are looking to partner with experts in rhizhosphere biology and N dynamics, to discover and characterize expected changes in microbe-maize interactions and NO emissions associated with growing our maize hybrids with improved NUE. We are willing to host research of potential collaborators at our Illinois field site, and share our maize NUE panel with other researchers, including our CRISPR hybrids where we have confirmed exemption from USDA-APHIS. |
| IL |
| | University of Florida | Jianping Wang | Professor |
Academic
|
Bioenergy
| Background: Crop genetics and genomics
Interests:
-Molecular and cellular mechanisms of peanut symbiosis,
-Biological N fixation,
-Bradyrhizobial crack entry invasion process into plant host,
-epigenetic gene expression regulation
Lab capacity:
-Biological N fixation efficiency test,
-Single cell RNAseq,
-Spatial RNAseq,
-Whole genome wide methylation analysis
-Hair root transformation,
-CRISPR-Cas9 genome editing |
Website: http://wanglabuf.com
Email: wangjp@ufl.edu
Phone: 3522738104
Address: 337 Mowry Road, Cancer and Genetics Research Complex, UF, Gainesville, FL, 32610, United States
| FL |
| | Stanford | Phillip Kyriakakis | Senior Research Scientist |
Academic
|
Bioenergy
| My background is in synthetic biology most generally. I have recently begun to build off of my work on optogenetics where we used ferredoxins to produce plant and cyanobacterial molecules in other types of cells. I have begun to dive into engineering nitrogenases to be functional in Eukaryotes, which can help to produce biofuels or for carbon capture, as well as many other things. |
| CA |
| | Lawrence Berkeley National Laboratory | Hans Carlson | Research Scientist |
Federally Funded Research and Development Center (FFRDC)
|
Other Energy Technologies
| Expertise: Microbial physiology, high-throughput chemical screening to identify controls on microbial element cycling, mechanistic biogeochemistry, mechanistic biochemistry and enzymology, geochemistry of the nitrogen cycle, bioinformatics, metagenomics
Contributions in this area: Identification of selective controls on nitrate respiratory end-products using high-throughput laboratory approaches. Found phage/carbon/inhibitor formulations to control nitrogen oxide respiratory products including nitrous oxide
Characterization of the mechanism of anaerobic nitrate dependent iron oxidation by bacteria and consequences for nitrous oxide fluxes. |
| CA |
| | North Carolina State University | Rubén Rellán Álvarez | Associate Professor |
Academic
|
Bioenergy
| We are interested in understanding the metabolic, physiological and molecular processes that allow crops to adapt to their local environment and in particular adaptation to low temperature and to soils with low nitrogen, phosphorus availability Our work has focused on maize traditional varieties and maize wild relatives (teosintes). We use genome wide environmental associations to identify candidate genes involved in adaptation to the mentioned abiotic stresses. Using georeferenced materials, we have developed large panels of introgressions using teosinte species and hundreds of maize traditional varieties into temperate maize. These introgression lines offer an unparallel collection of teosinte alleles providing allelic series of candidate genes involved on traits of interest to this RFP including: nitrogen recycling, exudation of compounds with BNI activity and others. |
| NC |
| | Boundless Impact Research & Analytics | Maria Jaramillo., M.S., | Senior Research Analyst |
Small Business
|
Bioenergy
| Boundless is a Federal and New York State-certified women-owned business specializing in industry research and environmental impact analytics. Our approach, grounded in the proven Life Cycle Assessment (LCA) methodology, produces highly accurate and actionable industry and company analytics that are used to de-risk clean technologies, inform operational decisions, and differentiate products. The scores and metrics derived from our assessments are unbiased and validated by our extensive network of +1,000 industry and/or scientific experts. Boundless has completed assessments of hundreds of clean-tech products and technologies renewable energy, circular economy, food and ag, bioenergy, bioestimulants, biofertilizers and pesticides, and advanced materials.
Boundless can provide teaming partners with our extensive and customizable LCA services that align with all three Vision OPEN goals, including:
ISO-Compliant LCA: Follows rigorous ISO standards (14040 & 14044) for LCA modeling and reporting, involving three independent experts for peer review, competitor analysis, sensitivity analysis, and complete source documentation. It results in a 60-80 pages report that gives full visibility on a product upstream and downstream performance.
1-4 environmental metrics (4-6 months)
Best suited for projects ≥TRL 4
Baseline LCA: ISO-guided and performed at a reduced time and cost, it is a data-driven impact analysis that enables smarter operational and investment decisions. This LCA includes independent modeling, competitor analysis, and an independent industry expert review.
Full: 7-8 environmental metrics (6-8 weeks)
Basic: 4 environmental metrics (4-6 weeks)
Techno-Economic Assessment: Evaluates companies’ financial performance and helps them leverage their cost of production to gain strategic and competitive advantage. The report analyzes scalability potential and how the product compares to market dynamics.
Cost of production assessment with competitor analysis (4-6 weeks)
GHG Calculator: An Excel-based tool allowing companies to alter inputs and quantify environmental outcomes to inform and de-risk their decision-making process.
Includes 8 input categories and 2-3 subcategories per input (4-6 weeks)
Valuable at all TRLs
GHG Assessment: Independent GHG Footprint modeling with competitor analysis and expert review, resulting in an impact report showing environmental performance and emission hot-spots.
Single metric (GHG Footprint) (3-4 weeks) |
| NY |
| | Bayer | Dan Ruzicka | External Innovation and Partnerships Lead |
Large Business
|
Bioenergy
| Background:
Bayer is a global enterprise with core competencies in the life science fields of health care and nutrition. In line with its mission, “Health for all, Hunger for none,” the company’s products and services are designed to help people and the planet thrive by supporting efforts to master the major challenges presented by a growing and aging global population. Bayer is committed to driving sustainable development and generating a positive impact with its businesses. With an unparalleled R&D product pipeline and transformative technologies, promoting and scaling regenerative agricultural practices are key to producing more while supporting food security and mitigating impacts of climate change.
Interest:
The Crop Science division of Bayer is vested in improving the economic and environmental sustainability of crop production. With a proven track record of technical and business know-how, Bayer aims to partner to design and develop future solutions for bioenergy and regenerative agriculture challenges.
Capabilities:
• Commodity and specialty crop germplasm and associated product portfolios
• Expertise and research in crop and microbial nitrogen utilization and soil nitrogen dynamics
• Science at large scale – field and controlled environment testing capacity and capabilities
• Seeds and traits – plant breeding, biotech, and gene editing
• Crop protection – chemistry and biologicals
• Digital science – data and modeling
• Proven record – bridging foundational research and product development
• Commercial scale-up experience – global customer and collaborator network
To learn more about our R&D portfolio and commitments to develop more sustainable solutions for agriculture:
www.bayer.com/en/agriculture/advances-agriculture |
| MO |
| | Pacific Northwest National Laboratory | Vanessa Bailey | Lab Fellow |
Federally Funded Research and Development Center (FFRDC)
|
Bioenergy
| My expertise is in soil microbiology and the processes they mediate. |
| WA |
| | University of California - Davis | Jorge Mazza Rodrigues | Professor |
Academic
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Other Energy Technologies
| BACKGROUND: I am a soil microbial ecologist with experience in measuring greenhouse gas emissions in agricultural and pristine ecosystems.
INTERESTS: Research in my laboratory aims to respond how the soil microbiome responds to man-made alterations and its consequences to biogeochemical processes such as greenhouse gas emissions, carbon sequestration and nutrient modulation.
LAB CAPABILITIESs: 1) Soil 'Omics Technologies (Metagenomics, Metatranscriptomics, Metaproteomics, and Metabolomics)
2) Bioinformatics
3) Stable Isotopes
4) Soil Biological Measurements (Biomass, Enzymatic Activity, Carbon Use Efficiency) |
| CA |
| | Raleigh Biosciences | Eric Rogers | Director of Research |
Small Business
|
Bioenergy
| We are leveraging spatial transcriptomics, single-cell gene expression analysis, and advanced machine learning, to explore dynamic changes in key developmental genes impacting nitrogen management. By precisely identifying when and where these key genes are expressed, we can bypass the normal pathways and redirect nitrogen in a tunable way, optimizing its utilization where and when it is needed most. This innovative approach allows us to shift nitrogen from kernels and leaves to roots, enhancing soil organic nitrogen and drastically reducing the environmental impact of corn production. We bring the expertise in high resolution genomic data acquisition and analysis and a strong understanding of root biology. |
| NC |
| | Nikira Labs Inc. | Manish Gupta | Chief Technology Officer |
Small Business
|
Other Energy Technologies
| Nikira Labs Inc. is ideally suited to develop, fabricate, and deliver a suite of N2O analyzers ranging from battery-operated, portable units to fast-response, high-flow systems for eddy flux. We have extensive expertise in developing field-deployable gas analyzers and utilizing them for soil and air measurements. Likewise, the Nikira Labs team has experience with N2O and N2O isotope measurements. In addition to N2O, the technology can be extended to other nitrogen-containing gases as necessary.
We look forward to teaming with scientist who are interested in making in-situ N2O measurements to assess the impact of bioenergy crops and efficacy of remediation measures. |
| CA |
| | Texas A&M AgriLIfe research | Sakiko Okumoto | Associate Professor |
Academic
|
Bioenergy
| My long-term research goal is to make crops more nitrogen-efficient. The impact of nitrogen-efficient crops can be very large: At the current price of > $500 per ton, even one % saving of N fertilizer amounts to around 600 billion dollars. Moreover, plants efficient in nitrogen acquisition will result in less run-off and greenhouse gas emission from agricultural fields, decreasing the environmental impacts. As the need to address nitrogen pollution from agricultural fields more dire than ever, I am focusing my research on several traits that would promote either the retention or efficiency of nitrogen for plants.
One of our current research focus is to discovering and enhancing the innate ability of crops to increase N-use efficiency through root secretion. In collaboration with Dr. Nithya Rajan (climate-smart agriculture specialist and agronomist) and Dr. William Rooney (the PI of Texas A&M sorghum breeding program) at Texas A&M, we have worked to increase nitrogen use efficiency and decrease nitrogen pollution (i.e. nitrous oxide emission and nitrate production) in sorghum. Sorghum is known to secrete a chemical called sorgoleone that inhibits the conversion from ammonium and nitrate (nitrification), the entry point for N pollution. By enhancing sorghum’s innate ability to prevent nitrification (termed biological nitrification inhibition, BNI), we aim to make sorghum cultivation more N-efficient and sustainable. This interdisciplinary project has been extremely exciting; so far, we have been able to identify the cell site of sorgoleone synthesis (Maharajan, 2023) and a novel gene required for secretion. These results give us the targets to increase BNI through biotechnology. In addition, we established the heritability of sorgoleone secretion using genotypes representing the TAMU sorghum breeding program. Lastly, our preliminary data from field emission measurement shows that high-sorgoleone genotypes significantly reduce nitrous oxide emission. We are looking to build upon our current success. Our ultimate goal is to make certified high BNI grain and energy sorghum available on the market, and create a system that directly benefits the growers and other stakeholders through the climate-smart practice by simply planting them. This goal requires not only our team, but also emission modeling, policy and marketing strategies.
References
Maharjan, B., Vitha, S., & Okumoto, S. (2023). The Plant Journal, 115(3), 820-832. |
| TX |
| | The Pennsylvania State University, College of Agricultural Sciences | Aaron Cook | Research Development Associate |
Academic
|
Bioenergy
| We are a multidisciplinary team of scientists at the Pennsylvania State University who are exploring strategies to enhance crop nitrogen use and reduce nitrous oxide emissions and other nitrogen loss pathways from cropland. We conduct research on crop genotypes, mycorrhizae, soil microbial communities, microbe genetic engineering, biochemistry, and products identified as reducing nitrous oxide emissions such as nitrification inhibitors. In addition, we are identifying cropping system strategies that integrate reduced and no-till, cover crops, and nitrogen amendment practices and tools to assist farmers to avoid over-application of nitrogen in corn, as well as agroecosystem models to simulate and evaluate crop and nutrient management scenarios that sustain crop yield while reducing nitrous emissions. Our team includes researchers with expertise in agronomy and crop science (Daniela Carrijo, Heather Karsten, Guojie Wang) biological and agricultural engineering (Armen Kemanian, Howard Salis), crop genetics (Ruairidh Sawers), soil microbiology (Estelle Couradeau), and soil fertility, nutrient management and biogeochemistry (Charlie White, Jason Kaye). |
Website: https://agsci.psu.edu/safes/people
Email: cook@psu.edu
Phone: 814-863-6886
Address: Institute for Sustainable Agricultural, Food, and Environmental Science, 386 Shortlidge Road | Ferguson Building, Room 111C, University Park, PA, 16802, United States
| PA |
| | New York University, Center for Genomics & Systems Biology | Gloria M Coruzzi | Carroll & Milton Petrie Professor of Biology |
Academic
|
Bioenergy
| Our Plant Systems Biology studies reside in Pasteur’s Quadrant – the scientific space where investigations of basic processes aim ultimately to be beneficial to society. Our studies of Nitrogen Regulatory Networks exploit time-series genomic datasets and machine-learning approaches to infer regulatory networks affecting genes-of-importance to Nitrogen Use Efficiency (NUE). To rapidly validate such networks, we developed TARGET: Transient Assay Reporting Genome-wide Expression Targets which enables us to perform high through-put transcription factor perturbation in isolated plant cells to prioritize testing genes-of-importance to NUE for in planta. Our recent model-to-crop studies which combine genomics, systems biology, machine learning have identified and validated genes-of-importance to improving NUE in field-grown maize, a trait which will impact on the environment, energy and human nutrition.
Collaborations: I have experience in leading large multi-institutional projects (funded by NIH, DOE and NSF) which involve lab-to-field experiments conducted collaboratively in the US and internationally. Computationally, Dr. Dennis Shasha (NYU Courant Institute of Computer Science) is my long-standing collaborator in the development and deployment of network inference and machine learning approaches to uncover transcription factor-->target gene--> NUE trait relationships for functional validation in planta.
Experimental and Computational Approaches Developed:
TARGET: A rapid and high-through method for validating TF-target regulation genome-wide in plant cells.
ConnecTF: A platform to integrate transcription factor–gene interactions and validate regulatory networks.
OutPredict: Multiple datasets improve prediction of expression and inference of causality.
Relevant Patents & Publications
US Patent 15/548,326/2018: Transgenic plants & a transient transformation system for genome-wide transcription factor target discovery.
US Patent 11,414,715/2022: Nutrient sensing in crop production.
US Patent Publication 0078124/2023 Compositions & methods for improving plant nitrogen utilization efficiency (NUE) & increasing plant biomass.
Cheng … Moose & Coruzzi et al (2021) Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships”. Nature Communications 12 (1) Article No; 5627. DOI https://doi.org/10.1038/s41467-021-25893-w |
| NY |
| | New York University, Center for Genomics & Systems Biology | Gloria M Coruzzi | Carroll & Milton Petrie Professor of Biology |
Academic
|
Bioenergy
| Our Plant Systems Biology studies reside in Pasteur’s Quadrant – the scientific space where investigations of basic processes aim ultimately to be beneficial to society. Our studies of Nitrogen Regulatory Networks exploit time-series genomic datasets and machine-learning approaches to infer regulatory networks affecting genes-of-importance to Nitrogen Use Efficiency (NUE). To rapidly validate such networks, we developed TARGET: Transient Assay Reporting Genome-wide Expression Targets which enables us to perform high through-put transcription factor perturbation in isolated plant cells to prioritize testing genes-of-importance to NUE for in planta.
This systems biology approach has enabled us to predictively model and manipulate gene regulatory networks affecting Nitrogen-Use Efficiency (NUE) in planta, a trait with impact on the environment, energy and human nutrition. Our work bridges bench-to-field on the improvement of nitrogen use in models-to-crops, the latter of which include maize and rice. Our recent model-to-crop studies which combine genomics, systems biology, machine learning have identified and validated genes-of-importance to improving NUE in field-grown maize.
Collaborations: I have experience in leading large multi-institutional projects (funded by NIH, DOE and NSF) which involve lab-to-field experiments conducted collaboratively in the US and internationally. Computationally, Dr. Dennis Shasha (NYU Courant Institute of Computer Science) is my long-standing collaborator in the development and deployment of network inference and machine learning approaches to uncover transcription factor-->target gene--> NUE trait relationships for functional validation in planta.
Traits of Interest
Nitrogen U
Genomic and Systems Biology Approaches Developed:
TARGET: A rapid and high-through method for validating TF-target regulation genome-wide in plant cells.
ConnecTF: A platform to integrate transcription factor–gene interactions and validate regulatory networks.
OutPredict: Multiple datasets improve prediction of expression and inference of causality.
Relevant Patents
US Patent 15/548,326 (2018): Transgenic plants & a transient transformation system for genome-wide transcription factor target discovery.
US Patent 11,414,715 (2022) Nutrient sensing in crop production.
US Patent Application Publication 0078124 (2023) Compositions and methods for improving plant nitrogen utilization efficiency (NUE) and increasing plant biomass. |
| NY |
| | Stanford University | Jenn Brophy | Assistant Professor |
Academic
|
Bioenergy
| Background: I am a plant and microbial synthetic biologist.
Capabilities/Interests:
1) Plant synthetic biology - primarily gene expression control tools for Arabidopsis and bioenergy grasses
2) Non-model microbe engineering
3) Plant phenotyping of above and below ground traits
4) In vitro and soil-based plant microbiome analysis - amplicon sequencing, metabolomics
5) Horizontal gene transfer in the microbiome
6) In vitro PGPB trait analysis |
| CA |
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