Works (52)
Updated: April 3rd, 2024 18:50
2024 article
Spatiotemporal dynamics of NF-κB/Dorsal inhibitor IκBα/Cactus inDrosophilablastoderm embryos
Schloop, A. E., Hiremath, S., Shaikh, R., Williams, C. M., & Reeves, G. T. (2024, February 27).
TL;DR:
This study uses the CRISPR/Cas9 system to tag Cactus with the recently developed “LlamaTag” (LT), a genetically encodable nanobody from llamas that dynamically binds to GFP in vivo, and estimates biophysical parameters of Cactus dynamics in vivo, including its nuclear transport rate constants and fraction bound to GFP.
(via Semantic Scholar)
doi.org (repository)
Source: ORCID
Added: March 1, 2024
2024 article
The Black American experience: Answering the global challenge of broadening participation in STEM/agriculture
Haverroth, E., Gobble, M., Bradley, L., Harris-Gilliam, K., Fischer, A., Williams, C., … Sozzani, R. (2024, January 29). PLANT CELL, Vol. 1.
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 1, 2024
2023 journal article
Cellular clarity: a logistic regression approach to identify root epidermal regulators of iron deficiency response
BMC GENOMICS, 24(1).
author keywords: Iron deficiency; Epidermis; Arabidopsis; Logistic regression; Gene regulatory network; RNA-seq
TL;DR:
Machine learning approaches combined with additional static data identified putative regulators of -Fe response that would not have been identified solely through transcriptomic profiles and reveal how developmental and general stress responses within the epidermis may act upstream of more specialized -Fe responses for Fe uptake.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: November 27, 2023
2023 review
Compositionality, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies
[Review of ]. CURRENT OPINION IN PLANT BIOLOGY, 71.
author keywords: Machine learning; Deep learning; Plant-associated microbiome; Compositional data analysis
MeSH headings : Microbiota; Algorithms; Machine Learning; Plants
TL;DR:
The analysis is expanded to other fields to quantify the degree to which mitigation approaches improve the performance of ML and describe the mathematical basis for this.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: January 30, 2023
2023 journal article
FER and LecRK show haplotype-dependent cold-responsiveness and mediate freezing tolerance in Lotus japonicus
PLANT PHYSIOLOGY, 191(2), 1138–1152.
MeSH headings : Lotus / metabolism; Haplotypes / genetics; Freezing; Acclimatization / genetics; Adaptation, Physiological / genetics; Gene Expression Regulation, Plant
TL;DR:
This work suggests that recruiting a conserved growth regulator gene, FER, and a receptor-like kinase gene, LecRK, into the set of cold-responsive genes has contributed to freezing tolerance and local climate adaptation in L. japonicus, offering functional genetic insight into perennial herb evolution.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science; OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 21, 2023
2023 journal article
Multiplex CRISPR editing of wood for sustainable fiber production
SCIENCE, 381(6654), 216-+.
TL;DR:
This work demonstrates that genome editing can be harnessed for breeding more efficient trees, which will provide timely opportunities for sustainable forestry and a more efficient bioeconomy.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 9, 2023
2022 article
Dynamics of BMP signaling in the earlyDrosophilaembryo
Asafen, H. Y. A., Beseli, A., Hiremath, S., Williams, C. M., & Reeves, G. T. (2022, October 21).
TL;DR:
The dynamics of the Bone Morphogenetic Protein pathway in Drosophila blastoderm-stage embryos are examined and it is found that dorsal-lateral cells experience only a short transient in BMP signaling, after which the signal is lost completely.
(via Semantic Scholar)
Source: ORCID
Added: February 21, 2023
2022 journal article
Identification of Transcription Factors Regulating SARS-CoV-2 Tropism Factor Expression by Inferring Cell-Type-Specific Transcriptional Regulatory Networks in Human Lungs
VIRUSES-BASEL, 14(4).
author keywords: SARS-CoV-2; single-cell RNA-seq; differential network analysis
MeSH headings : COVID-19; Gene Regulatory Networks; Humans; Lung / metabolism; SARS-CoV-2 / genetics; Transcription Factors / genetics; Viral Tropism / genetics
TL;DR:
This work constructed transcriptional regulatory networks (TRNs) controlling SARS-CoV-2 tropism factors for healthy donors and COVID-19 patients using lung single-cell RNA-sequencing (scRNA-seq) data and found that the altered regulatory role of TFs in the same cell types of healthy and Sars-Cov-2-infected networks may be partially responsible for differential tropism factor expression.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: May 2, 2022
2022 article
POPEYE intercellular localization mediates cell-specific iron deficiency responses
Muhammad, D. S., Clark, N. M., Haque, S., Williams, C. M., Sozzani, R., & Long, T. A. (2022, August 3). PLANT PHYSIOLOGY, Vol. 8.
MeSH headings : Iron Deficiencies; Arabidopsis Proteins / metabolism; Gene Expression Regulation, Plant; Basic Helix-Loop-Helix Transcription Factors / metabolism; Arabidopsis / metabolism; Iron / metabolism; Plant Roots / genetics; Plant Roots / metabolism
TL;DR:
The findings indicate that PYE acts as a positive regulator of iron deficiency response by regulating iron bioavailability differentially across cells, which may trigger iron uptake from the surrounding rhizosphere and impact root energy metabolism.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 13, 2022
2022 journal article
Practical spectral photography II: snapshot spectral imaging using linear retarders and microgrid polarization cameras
OPTICS EXPRESS, 30(8), 12337–12352.
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: May 2, 2022
2021 journal article
A multiscale model of lignin biosynthesis for predicting bioenergy traits in Populus trichocarpa
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 19, 168–182.
author keywords: Lignin biosynthesis; Multiscale modeling; Cross-regulatory influences; Random forests
Sources: Web Of Science, NC State University Libraries, ORCID
Added: September 20, 2021
2021 journal article
Computer vision approach to characterize size and shape phenotypes of horticultural crops using high-throughput imagery
Computers and Electronics in Agriculture, 182, 106011.
Contributors: S. Haque n, E. Lobaton n , N. Nelson n , G. Yencho n, K. Pecota n , R. Mierop n, M. Kudenov n, M. Boyette n, n
author keywords: Crop phenotyping; Machine learning; Computer vision
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: March 18, 2021
2021 journal article
Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa
FRONTIERS IN PLANT SCIENCE, 12.
author keywords: protein interaction; monolignol biosynthesis; wood formation; Populus trichocarpa; BiFC; metabolic flux
TL;DR:
It is proposed that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: November 8, 2021
2021 review
High-throughput image segmentation and machine learning approaches in the plant sciences across multiple scales
(J. M. Jez & C. N. Topp, Eds.) [Review of ]. EMERGING TOPICS IN LIFE SCIENCES, 5(2), 239–248.
Ed(s): J. Jez & C. Topp
MeSH headings : Machine Learning; Phenotype; Plant Development; Plants / genetics; Stress, Physiological
TL;DR:
It is shown how the methodologies for segmentation and classification differ due to the diversity of physical characteristics found at these different scales, and how the biological mechanisms by which plants respond to abiotic/biotic stresses or genotypic modifications can be extracted from these approaches.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: June 21, 2021
2021 journal article
Internal defect scanning of sweetpotatoes using interactance spectroscopy
PLOS ONE, 16(2).
MeSH headings : Ipomoea batatas; Plant Diseases; Plant Tubers; Spectroscopy, Near-Infrared
TL;DR:
It is demonstrated that interactance spectroscopy can detect the unique near-infrared optical signatures of necrotic tissues in sweetpotatoes down to a depth of approximately 5±0.5 mm and that light scattering measurement methods will represent a significant improvement over the current destructive analysis methods used to assay for internal defects inSweetpotatoes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: March 22, 2021
2021 article
Multiscale Modeling of Cross-Regulatory Transcript and Protein Influences
MODELING TRANSCRIPTIONAL REGULATION, Vol. 2328, pp. 115–138.
author keywords: Multiscale modeling; Cross-regulation; Transcript regulation; Protein regulation
MeSH headings : Algorithms; Computational Biology / methods; Gene Expression Profiling / methods; Gene Expression Regulation / genetics; Gene Regulatory Networks / genetics; Metabolomics / methods; Models, Theoretical; Populus / genetics; Populus / metabolism; Proteins / genetics; Proteins / metabolism; Proteomics / methods; Transcriptome / genetics
TL;DR:
A method is described to model cross-regulatory influences between the transcripts and proteins of a set of genes using abundance data collected from a series of transgenic experiments, using a sparse maximum likelihood algorithm to determine relationships that influence transcript and protein abundance.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: October 4, 2021
2021 article
Snapshot spectral imaging using Solc-based multivariate optical filters and pixelated polarization cameras
POLARIZATION SCIENCE AND REMOTE SENSING X, Vol. 11833.
author keywords: Polarization; imaging; spatial; modulation; snapshot; Solc; birefringence; wave plates
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: March 21, 2022
2020 chapter
BioVision Tracker: A semi-automated image analysis software for spatiotemporal gene expression tracking in Arabidopsis thaliana
In Methods in Cell Biology (Vol. 160, pp. 419–436).
Contributors: E. Buckner n, I. Madison n, C. Melvin n, T. Long n , R. Sozzani n & n
MeSH headings : Arabidopsis / genetics; Automation; Gene Expression Regulation, Plant; Image Processing, Computer-Assisted; Plant Roots / anatomy & histology; Software; Time Factors
TL;DR:
A procedure for analyzing 3D microscopy images to track spatiotemporal gene expression signals using the MATLAB-based BioVision Tracker software, which requires either a fluorescence image or a brightfield image to analyze root geometry and afluorescence image to capture and track temporal changes in gene expression.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: June 17, 2020
2020 article
Computer vision approach to characterize size and shape phenotypes of horticultural crops using high-throughput imagery
Haque, S., Lobaton, E., Nelson, N., Yencho, G. C., Pecota, K. V., Mierop, R., … Williams, C. M. (2020, July 26). (Vol. 7). Vol. 7.
TL;DR:
This work introduces a computer vision algorithm for quantifying shape and size characteristics in a high-throughput manner of sweetpotato (SP) and develops a neural network-based shape classifier that was able to predict Cull vs. No. 1sweetpotato with 84.59% accuracy.
(via Semantic Scholar)
Source: ORCID
Added: February 21, 2023
2020 journal article
Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling
Frontiers in Genetics, 11.
author keywords: gene regulatory network; network properties; network inference; machine learning; experimental methodologies
TL;DR:
This review provides examples of experimental methodologies commonly used to identify regulatory interactions and generate GRNs, and describes network inference techniques that leverage gene expression data to predict regulatory interactions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref, ORCID
Added: July 13, 2020
2020 chapter
MAGIC: Live imaging of cellular division in plant seedlings using lightsheet microscopy
In Methods in Cell Biology (Vol. 160, pp. 405–418).
Contributors: I. Madison n, C. Melvin n, E. Buckner n, n , R. Sozzani n & T. Long n
MeSH headings : Arabidopsis / cytology; Arabidopsis / growth & development; Cell Division; Imaging, Three-Dimensional; Microscopy, Fluorescence / methods; Seedlings / cytology; Seedlings / growth & development
TL;DR:
This chapter describes a detailed method for preparing and imaging Arabidopsis thaliana seedlings for lightsheet microscopy via a Multi-Sample Imaging Growth Chamber (MAGIC), which allows simultaneous imaging of at least four samples.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: June 17, 2020
2020 journal article
Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa
PLOS Computational Biology.
Ed(s): S. Roy
MeSH headings : Computational Biology / methods; Gene Expression Regulation, Plant / genetics; Gene Knockdown Techniques / methods; Lignin / biosynthesis; Lignin / genetics; Lignin / metabolism; Models, Theoretical; Populus / genetics; Wood / genetics
Source: ORCID
Added: April 11, 2020
2019 journal article
Computational prediction of gene regulatory networks in plant growth and development
Current Opinion in Plant Biology, 47, 96–105.
MeSH headings : Computational Biology / methods; Gene Regulatory Networks; Models, Genetic; Plant Development / genetics; Reproducibility of Results
TL;DR:
Computational frameworks integrating large-scale heterogeneous datasets are needed for a more accurate and comprehensive inference of gene regulatory networks, or GRNs, in the context of plant growth and development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
16. Peace, Justice and Strong Institutions
(OpenAlex)
Sources: Crossref, ORCID, NC State University Libraries, Web Of Science
Added: February 8, 2019
2019 journal article
Directions for research and training in plant omics: Big Questions and Big Data
Plant Direct, 3(4), e00133.
author keywords: genomics; metabolomics; proteomics; training; transcriptomics
TL;DR:
It is hoped that this article will inspire beginning and established scientists, corporations, and funding agencies to pursue directions in research and training identified by this workshop, capitalizing on the reference species Arabidopsis thaliana and other valuable plant systems.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Crossref, NC State University Libraries, ORCID
Added: June 25, 2019
2019 journal article
Flux modeling for monolignol biosynthesis
Current Opinion in Biotechnology, 56, 187–192.
Contributors: J. Wang n , M. Matthews n, P. Naik n, n , J. Ducoste n , R. Sederoff n, V. Chiang n
MeSH headings : Biosynthetic Pathways; Kinetics; Lignin / biosynthesis; Metabolic Engineering; Metabolic Flux Analysis; Models, Biological
TL;DR:
This review summarizes the recent progress in flux modeling and its application to lignin engineering for improved plant development and utilization.
(via Semantic Scholar)
Sources: Crossref, ORCID, NC State University Libraries
Added: April 24, 2019
2019 article
Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa
Matthews, M. L., Wang, J. P., Sederoff, R., Chiang, V. L., & Williams, C. M. (2019, June 19). (Vol. 6). Vol. 6.
TL;DR:
A computational model is developed that more accurately estimates transcript and protein abundances in differentiating xylem tissue when individual and families of monolignol genes were perturbed, and is an important addition to current models of lignin biosynthesis.
(via Semantic Scholar)
Source: ORCID
Added: June 20, 2019
2019 journal article
Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks
NATURE COMMUNICATIONS, 10.
MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Asymmetric Cell Division / genetics; Asymmetric Cell Division / physiology; Cell Differentiation; Cell Division; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / growth & development; Stem Cells / cytology; Stem Cells / metabolism; Transcription Factors / metabolism; Transcriptome; Ubiquitination / genetics; Ubiquitins / genetics
TL;DR:
In the Arabidopsis root, a stem-cell-ubiquitous gene, TESMIN-LIKE CXC2 (TCX2), controls stem cell division by regulating stem cell-type specific networks and orchestrates the coordinated division of different stem cell types.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: December 30, 2019
2018 journal article
Assessing the impact of the 4CL enzyme complex on the robustness of monolignol biosynthesis using metabolic pathway analysis
PLOS ONE, 13(3), e0193896.
Contributors: P. Naik n, J. Wang n , R. Sederoff n, V. Chiang n, n & J. Ducoste n
Ed(s): D. Cullen
MeSH headings : Biosynthetic Pathways; Homeostasis; Lignin / biosynthesis; Metabolic Networks and Pathways; Monte Carlo Method; Plant Proteins / metabolism; Populus / enzymology; Populus / metabolism
TL;DR:
Results from robustness and stability analyses suggest that the monolignol biosynthetic pathway is resilient to mild perturbations in the presence of the Ptr4CL3-Ptr4CL5 complex, which increased the stability of the pathway by 22%.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: August 6, 2018
2018 journal article
Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis
Nature Communications, 9(1), 1579.
MeSH headings : Gene Expression Regulation, Plant; Lignin / biosynthesis; Lignin / genetics; Plants, Genetically Modified / genetics; Populus / genetics; Populus / metabolism; Transcriptome / genetics; Trees / genetics; Trees / metabolism; Wood / chemistry; Wood / physiology; Xylem / metabolism
TL;DR:
A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels and may lead to greater understanding of other pathways for improved growth and adaptation.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: August 6, 2018
2017 journal article
Design of digital filters
Digital Signal Processing: Principles, Algorithms and System Design, 205–275.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
Digital signal processing systems design
Digital Signal Processing: Principles, Algorithms and System Design, 455–517.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
Digital signal processing: principles, algorithms and system design preface
Digital Signal Processing: Principles, Algorithms and System Design, XXVII-.
Source: NC State University Libraries
Added: August 6, 2018
2017 article
Finite Word Length Effects
DIGITAL SIGNAL PROCESSING: PRINCIPLES, ALGORITHMS AND SYSTEM DESIGN, pp. 351–388.
TL;DR:
Chapter 6 covers methods used to represent numbers and the impact of the use of finite precision arithmetic for the implementation of discrete time systems and presents a concept for statistical analysis of rounding errors due to word length effects.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2017 journal article
Frequency domain analysis
Digital Signal Processing: Principles, Algorithms and System Design, 159–204.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
Fundamental DSP concepts
Digital Signal Processing: Principles, Algorithms and System Design, 19–157.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
Hardware implementation
Digital Signal Processing: Principles, Algorithms and System Design, 519–561.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
Implementation of discrete time systems
Digital Signal Processing: Principles, Algorithms and System Design, 277–350.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
Introduction to digital signal processing
Digital Signal Processing: Principles, Algorithms and System Design, 1–17.
Source: NC State University Libraries
Added: August 6, 2018
2017 review
More than meets the eye: Emergent properties of transcription factors networks in Arabidopsis
[Review of ]. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS, 1860(1), 64–74.
Contributors: D. Muhammad n, S. Schmittling n, n & T. Long n
author keywords: Transcription factor networks (TFNs); Emergent properties; Mathematical modeling
MeSH headings : Arabidopsis / genetics; Arabidopsis / growth & development; Computational Biology / methods; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Plant Development / genetics; Stress, Physiological / genetics; Transcription Factors / genetics
TL;DR:
This review highlights literature that provides, in part, experimental and computational techniques for characterizing Transcription Factor Networks and outlines methodologies that have been used to mathematically model the dynamic characteristics of TFNs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2017 journal article
Multirate digital signal processing
Digital Signal Processing: Principles, Algorithms and System Design, 389–454.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(36), E7632–E7640.
author keywords: root stem cell; root development; cell-type expression profile; gene regulatory network; modeling
MeSH headings : Algorithms; Arabidopsis / genetics; Bayes Theorem; Cluster Analysis; Computational Biology / methods; Gene Expression Profiling / methods; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Plant Roots / genetics; Stem Cells / metabolism; Transcription Factors / genetics; Transcriptome / genetics
TL;DR:
A computational pipeline that uses gene expression datasets for inferring relationships among genes and predicting their importance and a gene regulatory network inference algorithm that combines clustering with dynamic Bayesian network inference that identified PERIANTHIA as an important molecular regulator of quiescent center function.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2015 journal article
4-Coumaroyl and Caffeoyl Shikimic Acids Inhibit 4-Coumaric Acid: Coenzyme A Ligases and Modulate Metabolic Flux for 3-Hydroxylation in Monolignol Biosynthesis of Populus trichocarpa
MOLECULAR PLANT, 8(1), 176–187.
author keywords: monolignol biosynthesis; Populus trichocarpa; metabolic flux; reaction and inhibition kinetics; LC-MS/MS; 4-coumaroyl and caffeoyl shikimic acids
MeSH headings : Acyl Coenzyme A / metabolism; Coenzyme A Ligases / metabolism; Coumaric Acids / metabolism; Coumaric Acids / pharmacology; Hydroxylation / drug effects; Plant Proteins / metabolism; Populus / drug effects; Populus / enzymology; Populus / metabolism; Propionates; Shikimic Acid / pharmacology
TL;DR:
4-coumaroyl and caffeoyl shikimic acids are inhibitors of Ptr4CL3 and Ptr 4CL5, which can reduce lignin content in a number of plant species and play significant regulatory roles when these inhibitors accumulate.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2015 journal article
Clustering and Differential Alignment Algorithm: Identification of Early Stage Regulators in the Arabidopsis thaliana Iron Deficiency Response
PLOS ONE, 10(8).
Contributors: A. Koryachko n, A. Matthiadis n, D. Muhammad n, J. Foret*, S. Brady *, J. Ducoste n , J. Tuck n , T. Long n , n
MeSH headings : Algorithms; Arabidopsis / genetics; Arabidopsis / metabolism; Databases, Genetic; Gene Expression Regulation, Plant; Iron Deficiencies; Sequence Alignment; Software; Transcriptome
TL;DR:
It is proposed that this tool can be used successfully for similar time course datasets to extract additional information and infer reliable regulatory connections for individual genes, and served as a proof of concept emphasizing the utility of the CDAA for identifying unknown or missing nodes in regulatory cascades.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2015 journal article
Computational approaches to identify regulators of plant stress response using high-throughput gene expression data
Current Plant Biology, 3-4, 20–29.
Contributors: A. Koryachko n, A. Matthiadis n, J. Ducoste n , J. Tuck n , T. Long n & n
author keywords: Stress response; Transcription factors; Gene regulatory networks; Algorithms; Arabidopsis thaliana
TL;DR:
This review conceptually organizes a wide variety of developed algorithms into a classification system based on desired type of output predictions to describe completed approaches in the literature, with a focus on project goals, overall path of implemented algorithms, and biological insight gained.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Crossref, NC State University Libraries, ORCID
Added: December 14, 2019
2014 journal article
Hierarchical Modularization Of Biochemical Pathways Using Fuzzy-C Means Clustering
IEEE TRANSACTIONS ON CYBERNETICS, 44(8), 1473–1484.
author keywords: Clustering algorithms; functional analysis; fuzzy systems; systems biology; time series analysis
MeSH headings : Algorithms; Cluster Analysis; Fuzzy Logic; Humans; MAP Kinase Signaling System; Metabolic Networks and Pathways; Models, Biological; Photosynthesis; Reproducibility of Results; Spatio-Temporal Analysis; Systems Biology / methods
TL;DR:
A method to identify relationships between components of dynamic models of biochemical pathways that reside in different functional groups is presented, which provides the hierarchy of the relationships among components, which can help to understand the low level functional structure of the system and to elucidate potential hierarchical control.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2014 journal article
Systems Biology of Lignin Biosynthesis in Populus trichocarpa: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling
The Plant Cell, 26(3), 876–893.
Contributors: H. Chen n, J. Song n, J. Wang n , Y. Lin n, J. Ducoste n , C. Shuford n, J. Liu n, Q. Li n
MeSH headings : Coenzyme A Ligases / genetics; Coenzyme A Ligases / metabolism; Coumaric Acids / metabolism; Immunoprecipitation; Lignin / biosynthesis; Mass Spectrometry; Models, Biological; Populus / metabolism; Propionates; RNA, Messenger / genetics; Substrate Specificity; Systems Biology
TL;DR:
This work shows that 4CL, an enzyme in monolignol biosynthesis, is found as a heterotetrameric complex of two isoforms in Populus trichocarpa, where the two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact in vivo and in vitro to form a heterosymmetric protein complex.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: August 6, 2018
2013 journal article
Monolignol Pathway 4-Coumaric Acid: Coenzyme A Ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes
PLANT PHYSIOLOGY, 161(3), 1501–1516.
MeSH headings : Allosteric Regulation / drug effects; Binding Sites; Biosynthetic Pathways / drug effects; Blotting, Western; Caffeic Acids / pharmacology; Coenzyme A / metabolism; Coenzyme A Ligases / antagonists & inhibitors; Coenzyme A Ligases / metabolism; Computer Simulation; Coumaric Acids / chemistry; Coumaric Acids / metabolism; Coumaric Acids / pharmacology; Kinetics; Lignin / biosynthesis; Lignin / chemistry; Phenylpropionates / metabolism; Phosphoproteins / metabolism; Phosphorylation / drug effects; Plant Extracts; Populus / drug effects; Populus / enzymology; Propionates; Proteomics; Recombinant Fusion Proteins / metabolism; Sequence Homology, Amino Acid; Substrate Specificity / drug effects; Xylem / drug effects; Xylem / metabolism
TL;DR:
Evidence is presented of two monolignol 4CLs, Ptr4CL3 and P tr4CL5, in Populus trichocarpa that act to mitigate the inhibition by caffeic acid to maintain a proper ligation flux and coenzyme A flux with novel specificity.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2012 conference paper
A novel cost function for parameters estimation in oscillatory biochemical systems
2012 Proceedings of IEEE Southeastcon.
TL;DR:
A cost function is proposed to address issues with estimating kinetic parameters in oscillatory systems by integrating temporal information with periodic information embedded in the measurements, which results in an increased ability to estimate accurate kinetic parameters as compared to the traditional LS cost function.
(via Semantic Scholar)
Sources: NC State University Libraries, NC State University Libraries
Added: August 6, 2018
2012 journal article
Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC-MS/MS based protein quantification and metabolic flux analysis
PLANTA, 236(3), 795–808.
author keywords: Lignin; Syringyl lignin; Angiosperm; Kinetics; Subcellular localization
MeSH headings : Cloning, Molecular; Gene Expression Regulation, Enzymologic; Gene Expression Regulation, Plant; Hydroxylation; Kinetics; Lignin / analysis; Lignin / biosynthesis; Mixed Function Oxygenases / metabolism; Plants, Genetically Modified; Populus / metabolism; Xylem / enzymology; Yeasts / metabolism
TL;DR:
The combination of genetic analysis, absolute protein quantitation-based enzyme kinetics, homologous CPR specificity, SNP characterization, and ER localization provides a more rigorous basis for a comprehensive systems understanding of 5-hydroxylation in lignin biosynthesis.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2012 conference paper
Region of attraction estimation of biological continuous Boolean models
Ieee international conference on systems man and cybernetics conference, 1700–1705.
TL;DR:
Assessment of the applicability of a state of the art ROA estimation technique based on interval arithmetic to a subnetwork of the Rb-E2F signaling pathway modeled using continuous Boolean functions shows that this method can successfully be used to provide an estimate of the ROA for dynamic models described using Hillcube continuous Boolean approximations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Sources: NC State University Libraries, NC State University Libraries
Added: August 6, 2018
2012 journal article
Set membership experimental design for biological systems
BMC SYSTEMS BIOLOGY, 6.
MeSH headings : Models, Biological; Research Design; Uncertainty
TL;DR:
A bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available that is able to identify candidate measurement time points that maximize information corresponding to biologically relevant metrics and determine the number at which additional measurements begin to provide insignificant information.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2012 conference paper
Set membership state and parameter estimation for nonlinear differential equations with sparse discrete measurements
Ieee international conference on systems man and cybernetics conference, 72–77.
TL;DR:
This paper presents a method to perform parameter and state estimation in a bounded-error context for nonlinear continuous-time systems with sparse, discrete measurements and demonstrates how preprocessing the measurements through the addition of application specific stabilizing bounds vastly improves bounded parameters and state estimations.
(via Semantic Scholar)
Sources: NC State University Libraries, NC State University Libraries
Added: August 6, 2018
Employment
Updated: December 6th, 2022 12:16
2021 - present
North Carolina State University Raleigh, North Carolina, US
Goodnight Distinguished Professor of Agricultural Analytics
Electrical and Computer Engineering
Education
Updated: December 6th, 2022 12:18
North Carolina State University Raleigh, North Carolina, US
Ph.D.
Electrical and Computer Engineering
North Carolina State University Raleigh, North Carolina, US
M.S.
Electrical and Computer Engineering
North Carolina Agricultural and Technical State University Greensboro, NC, US
B.S.
Electrical and Computer Engineering
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