# positions[].organizations[].parent[].label
College of Agriculture and Life Sciences

# positions[].organizations[].parent[].label
Texas A&M Engineering Experiment Station (TEES)

# overview
Our lab aims to employ design-based engineering to address the challenges in energy, environment, and health. The design-based engineering strategies focused on chemical, computational, and systems biology analyses to understand the fundamental mechanisms and to guide the design of enzymes, processes, microorganisms, and plant for various applications. While the principle can be broadly applied, our research primarily focused on increasing biorefinery waste utilization, enhancing photosynthetic terpene production, and improving enzymes based on structure dynamics.

# keywords[]
Basic Helix-loop-helix Leucine Zipper Transcription Factors

# keywords[]
12 Responsible Consumption And Production

# keywords[]
Reverse Transcriptase Polymerase Chain Reaction

# keywords[]
National Alliance For Advanced Biofuels And Bioproducts

# keywords[]
Reverse Transcriptase Polymerase Chain Reaction

# keywords[]
Reverse Transcriptase Polymerase Chain Reaction

# keywords[]
Reverse Transcriptase Polymerase Chain Reaction

# keywords[]
Reverse Transcriptase Polymerase Chain Reaction

# keywords[]
Reverse Transcriptase Polymerase Chain Reaction

# keywords[]
1.1 Normal Biological Development And Functioning

# keywords[]
Reverse Transcriptase Polymerase Chain Reaction

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12 Responsible Consumption And Production

# keywords[]
Reverse Transcriptase Polymerase Chain Reaction

# educationAndTraining[].organization.label
University of Tennessee at Knoxville - (Knoxville, Tennessee, United States)

# educationAndTraining[].field
Plants, Insects, and Soils with Focus on Functional Genomics

# publications[].label
Functional Genomics Analysis of Horseweed (Conyza canadensis) with Special Reference to the Evolution of NonTarget-Site Glyphosate Resistance

# publications[].label
Application of an Improved Proteomics Method for Abundant Protein Cleanup: Molecular and Genomic Mechanisms Study in Plant Defense*

# publications[].label
Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses.

# publications[].label
Altered Carbon Partitioning Enhances CO2 to Terpene Conversion in Cyanobacteria.

# publications[].publisher
American Association for the Advancement of Science (AAAS)

# publications[].tags
12 Responsible Consumption and Production

# publications[].label
Transcriptome analysis of the digestive system of a wood-feeding termite (Coptotermes formosanus) revealed a unique mechanism for effective biomass degradation.

# publications[].label
Simultaneous conversion of all cell wall components by an oleaginous fungus without chemi-physical pretreatment

# publications[].label
Sensitivity of a real-time PCR method for the detection of transgenes in a mixture of transgenic and non-transgenic seeds of papaya (Carica papaya L.).

# publications[].label
Identification and analysis of an efficient dicot constitutive promoter from tomato

# publications[].label
Molecular and genomic basis of volatile-mediated indirect defense against insects in rice.

# publications[].label
Exploration of Natural Biomass Utilization Systems (NBUS) for advanced biofuel--from systems biology to synthetic design.

# publications[].label
Enhanced medium chain length-polyhydroxyalkanoate production by co-fermentation of lignin and holocellulose hydrolysates

# publications[].label
Phytoestrogens and Mycoestrogens Induce Signature Structure Dynamics Changes on Estrogen Receptor .

# publications[].label
Statistical tools for transgene copy number estimation based on real-time PCR.

# publications[].label
Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function.

# publications[].label
Comparative genomics of Pseudomonas syringae pv. syringae strains B301D and HS191 and insights into intrapathovar traits associated with plant pathogenesis.

# publications[].label
Toward the development of performance-related specification for bio-rejuvenators

# publications[].label
Conversion of corn stover alkaline pre-treatment waste streams into biodiesel via Rhodococci

# publications[].label
Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum.

# publications[].label
Phototunable Lignin Plastics to Enable Recyclability.

# publications[].label
Lignin Conversion: Opportunities and Challenges for the Integrated Biorefinery

# publications[].label
Characterization of the horseweed (Conyza canadensis) transcriptome using GS-FLX 454 pyrosequencing and its application for expression analysis of candidate non-target herbicide resistance genes.

# publications[].label
Molecular approaches to study the insect gut symbiotic microbiota at the 'omics' age

# publications[].label
Discovery of potential pathways for biological conversion of poplar wood into lipids by co-fermentation of Rhodococci strains.

# publications[].label
Elucidation of the genomic basis of indirect plant defense against insects.

# publications[].label
Statistical methods for efficiency adjusted real-time PCR quantification.

# publications[].label
Reply to Dong and Zhao: Plant stress via Raman spectroscopy.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Identifying and creating pathways to improve biological lignin valorization

# publications[].label
Defining lignin nanoparticle properties through tailored lignin reactivity by sequential organosolv fragmentation approach (SOFA)

# publications[].label
In vivo diagnostics of early abiotic plant stress response via Raman spectroscopy.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
USChina collaborative biofuel research: towards a global solution for petroleum replacement

# publications[].label
Comparative analysis of insect gut symbionts for compositionfunction relationships and biofuel application potential

# publications[].label
Early, in vivo, Detection of Abiotic Plant Stress Responses via Raman Spectroscopy

# publications[].label
Synergistic maximization of the carbohydrate output and lignin processability by combinatorial pretreatment

# publications[].label
Statistical analysis of real-time PCR data.

# publications[].label
Medicago truncatula (E)-beta-ocimene synthase is induced by insect herbivory with corresponding increases in emission of volatile ocimene.

# publications[].label
Methods for suspension culture, protoplast extraction, and transformation of high-biomass yielding perennial grass Arundo donax.

# publications[].label
Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis.

# publications[].label
Synergistic enzymatic and microbial lignin conversion

# publications[].label
HDX-analyzer: a novel package for statistical analysis of protein structure dynamics.

# publications[].label
Biomass feedstock: diversity as a solution

# publications[].label
Comparison of Insect Gut Cellulase and Xylanase Activity Across Different Insect Species with Distinct Food Sources

# publications[].label
Plant Protein-Protein Interaction Network and Interactome

# publications[].label
Lignin as Renewable and Superior Asphalt Binder Modifier

# publications[].label
An Arabidopsis thaliana methyltransferase capable of methylating farnesoic acid.

# publications[].label
Transcriptional responses of Arabidopsis thaliana plants to As (V) stress.

# publications[].label
Non-target-site herbicide resistance: a family business.

# publications[].label
Microstructure defines the electroconductive and mechanical performance of plant-derived renewable carbon fiber.

# publications[].label
Mechanism-Guided Design of Highly Efficient Protein Secretion and Lipid Conversion for Biomanufacturing and Biorefining.

# publications[].tags
12 Responsible Consumption and Production

# publications[].label
Enhanced limonene production in cyanobacteria reveals photosynthesis limitations.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].tags
12 Responsible Consumption and Production

# publications[].label
Directed bioconversion of Kraft lignin to polyhydroxyalkanoate by Cupriavidus basilensis B-8 without any pretreatment

# publications[].label
Combinatorial pretreatment and fermentation optimization enabled a record yield on lignin bioconversion.

# publications[].label
Kinetic understanding of nitrogen supply condition on biosynthesis of polyhydroxyalkanoate from benzoate by Pseudomonas putida KT2440.

# publications[].label
Omics Platforms: Importance of Twenty-First Century Genome-Enabled Technologies in Seed Developmental Research for Improved Seed Quality and Crop Yield

# publications[].label
JAZ7 negatively regulates dark-induced leaf senescence in Arabidopsis.

# publications[].label
Cooperative valorization of lignin and residual sugar to polyhydroxyalkanoate (PHA) for enhanced yield and carbon utilization in biorefineries

# publications[].label
Phosphorylation of trihelix transcriptional repressor ASR3 by MAP KINASE4 negatively regulates Arabidopsis immunity.

# publications[].label
Enhancement of Environmental Hazard Degradation in the Presence of Lignin: a Proteomics Study.

# publications[].label
Co-Compartmentation of Terpene Biosynthesis and Storage via Synthetic Droplet.

# publications[].label
Lignin carbon fiber: The path for quality

# publications[].label
Utilization of simultaneous saccharification and fermentation residues as feedstock for lipid accumulation in Rhodococcus opacus.

# publications[].label
Genomic and molecular mechanisms for efficient biodegradation of aromatic dye.

# publications[].label
Belowground ABA boosts aboveground production of DIMBOA and primes induction of chlorogenic acid in maize.

# publications[].label
Novel software package for cross-platform transcriptome analysis (CPTRA).

# publications[].label
Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

# publications[].label
Discovering Biomass Structural Determinants Defining the Properties of Plant-Derived Renewable Carbon Fiber.

# publications[].label
Policy Update: Biomass utilization toward energy independence and sustainable economic development in China

# publications[].label
Production of single cell protein from agro-waste using Rhodococcus opacus.

# publications[].tags
12 Responsible Consumption and Production

# publications[].label
Molecular and Genomic Mechanisms of Non-Target-Site Herbicide Resistance

# publications[].label
Effects of Seawater on Carotenoid Production and Lipid Content of Engineered Saccharomyces cerevisiae

# publications[].label
Redesigning photosynthesis to sustainably meet global food and bioenergy demand.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Transforming biorefinery designs with 'Plug-In Processes of Lignin' to enable economic waste valorization.

# publications[].label
Gene alterations by peroxisome proliferator-activated receptor gamma agonists in human colorectal cancer cells.

# publications[].label
Microarray analysis reveals selenium down-regulates glucosinolate biosynthesis in Arabidopsis shoots

# publications[].label
Tuning hydroxyl groups for quality carbon fiber of lignin

# publications[].label
Selenium regulates gene expression for glucosinolate and carotenoid biosynthesis in arabidopsis

# publications[].label
Four terpene synthases produce major compounds of the gypsy moth feeding-induced volatile blend of Populus trichocarpa.

# publications[].label
Plants to power: bioenergy to fuel the future.

# publications[].label
Synergistic reaction of silver nitrate, silver nanoparticles, and methylene blue against bacteria.

# publications[].publisher
Proceedings of the National Academy of Sciences

# publications[].label
Deletion analysis of susy-Sl promoter for the identification of optimal promoter sequence

# publications[].label
Advanced Chemical Design for Efficient Lignin Bioconversion

# publications[].label
Fractionation of Organosolv Lignin Using Acetone:Water and Properties of the Obtained Fractions

# publications[].label
Gene expression analysis in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow) in an early growth stage.

# publications[].label
Molecular weight and uniformity define the mechanical performance of lignin-based carbon fiber

# publications[].label
Synergistic maximization of the carbohydrate output and lignin processability by combinatorial pretreatment

# publications[].label
The endo-beta-mannanase gene families in Arabidopsis, rice, and poplar.

# publications[].label
Ecological Functions of Terpenoids in Changing Climates

# publications[].label
A type IV P-type ATPase affects insulin-mediated glucose uptake in adipose tissue and skeletal muscle in mice.

# publications[].label
Machine learning-informed and synthetic biology-enabled semi-continuous algal cultivation to unleash renewable fuel productivity.

# publications[].label
Cover Feature: Phototunable Lignin Plastics to Enable Recyclability (ChemSusChem 19/2021)

# publications[].label
A guanidine-degrading enzyme controls genomic stability of ethylene-producing cyanobacteria

# publications[].label
The rice terpene synthase gene OsTPS19 functions as an (S)‐limonene synthase in planta, and its overexpression leads to enhanced resistance to the blast fungus Magnaporthe oryzae

# publications[].label
Quality carbon fibers from fractionated lignin

# publications[].label
Terpene metabolic engineering via nuclear or chloroplast genomes profoundly and globally impacts off-target pathways through metabolite signalling.

# publications[].label
Chapter 12. Systems Biology Analyses of Lignin Conversion

# publications[].label
Comparative genomic analysis of the microbiome [corrected] of herbivorous insects reveals eco-environmental adaptations: biotechnology applications.

# publications[].label
Systems biology-guided biodesign of consolidated lignin conversion

# publications[].tags
12 Responsible Consumption and Production

# publications[].label
Smelling global climate change: mitigation of function for plant volatile organic compounds.

# publications[].label
Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom.

# publications[].label
Enhancing the multi-functional properties of renewable lignin carbon fibers via defining the structure–property relationship using different biomass feedstocks

# publications[].label
Non-Solvent Fractionation of Lignin Enhances Carbon Fiber Performance.

# publications[].label
Advanced genetic tools for plant biotechnology.

# publications[].label
Differential expression of genes in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow) is soybean growth stage-specific.

# publications[].label
Photosynthetic terpene hydrocarbon production for fuels and chemicals.

# researcherOn[].label
Development of a continuous genome shuffling approach to expedite adaptive laboratory evolution

# researcherOn[].awardedBy.label
National Science Foundation - (Arlington, Virginia, United States)

# researcherOn[].label
Multi-Product Biomass Processing to Enhance Agriculture Output and Competiveness

# researcherOn[].awardedBy.label
National Institute of Food and Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Synthetic Microorganisms to Enable Lignin to Fuel Conversion

# researcherOn[].awardedBy.label
United States Department of Energy - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Use of Algae in the Production of Biofuels - Bulgaria

# researcherOn[].awardedBy.label
United States Department of Agriculture - (Washington D.C., District of Columbia, United States)

# researcherOn[].label
Synthetic Crop for Direct Drop In Biofuel Production Through Photorespiration Intermediates and Engineering Terpenoid Pathways

# researcherOn[].awardedBy.label
United States Department of Energy - (Washington D.C., District of Columbia, United States)

# researcherOn[].awardedBy.label
United States Department of Energy - (Washington D.C., District of Columbia, United States)

# researcherOn[].awardedBy.preferredLabel
DOE-Office of Energy Efficiency and Renewable Energy-EERE

# streetAddress
Texas A&M University; Plant Pathology & Microbiology; 2132 TAMU

# organizations[]
College of Agriculture and Life Sciences

# organizations[]
Texas A&M Engineering Experiment Station (TEES)

# schools[]
Texas A&M Engineering Experiment Station (TEES)

# schools[]
College of Agriculture and Life Sciences

# inTheNews[].label
New ‘plug-in’ process generates environmentally friendly bioplastics

# etdChairOf[].label
Xie, Shangxian (2016-08). Biological and Chemical Design for Lignin Conversion. Doctoral Dissertation.

# etdChairOf[].label
Syrenne, Ryan Douglas (2016-08). Autotrophic Production of Limonene in Engineered Microalgae Chlamydomonas reinhardtii. Master's Thesis.

# etdChairOf[].label
Uzuner, Ugur (2013-06). Structure Dynamics Guided Enzyme Improvement of ENDO-BETA-1, 4-XYLANASE I. Doctoral Dissertation.