Rui Shi

Works (30)

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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.

By: C. Lin, Y. Sun *, J. Song, H. Chen, R. Shi, C. Yang, J. Liu  n, S. Tunlaya-Anukit ...

author keywords: protein interaction; monolignol biosynthesis; wood formation; Populus trichocarpa; BiFC; metabolic flux
Sources: Web Of Science, ORCID
Added: November 8, 2021

2021 article

Homoeologous chromosome exchange explains the creation of a QTL affecting soil-borne pathogen resistance in tobacco

Shi, R., Jin, J., Nifong, J. M., Shew, D., & Lewis, R. S. (2021, October 22). PLANT BIOTECHNOLOGY JOURNAL.

By: R. Shi, J. Jin, J. Nifong, D. Shew & R. Lewis

author keywords: homoeologous exchange; QTL; resistance; SAR8; 2; tobacco; Phytophthora
Source: Web Of Science
Added: November 1, 2021

2021 journal article

RNAseq Reveals Differential Gene Expression Contributing to Phytophthora nicotianae Adaptation to Partial Resistance in Tobacco

AGRONOMY-BASEL, 11(4).

By: J. Jin, R. Shi, R. Lewis & H. Shew

author keywords: RNAseq; Phytophthora nicotianae; adaptation; partial resistance; tobacco
Source: Web Of Science
Added: May 10, 2021

2019 journal article

Genetic Control of Facultative Parthenocarpy in Nicotiana tabacum L.

JOURNAL OF HEREDITY, 110(5), 610–617.

By: A. Dexter-Boone n, M. Humphry *, R. Shi & R. Lewis

author keywords: Genomics and gene mapping; haploids; Nicotiana; parthenocarpy; QTL mapping; tobacco
Source: Web Of Science
Added: September 16, 2019

2019 journal article

Identification and validation of SNP markers associated with Wz-mediated Phytophthora nicotianae resistance in Nicotiana tabacum L.

MOLECULAR BREEDING, 39(7).

By: R. Shi, H. Hubert n, A. Dexter-Boone n, J. Zeng*, S. Kernodle & R. Lewis

author keywords: Nicotiana; Tobacco; RNA-seq; Black shank; Phytophthora nicotianae
Source: Web Of Science
Added: July 22, 2019

2018 journal article

Filter paper-based spin column method for cost-efficient DNA or RNA purification

PLOS ONE, 13(12).

By: R. Shi, R. Lewis & D. Panthee 

Sources: Web Of Science, ORCID
Added: December 31, 2018

2018 journal article

Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis

Nature Communications, 9(1), 1579.

By: J. Wang , M. Matthews  n, C. Williams , R. Shi, C. Yang  n, S. Tunlaya-Anukit  n, H. Chen  n, Q. Li * ...

Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2017 journal article

A novel plant DNA extraction method using filter paper-based 96-well spin plate

Planta, 246(3), 579–584.

By: R. Shi & D. Panthee 

author keywords: Filter paper; DNA extraction; Inexpensive; Safe; High throughput; Solanum lycopersicum; Ph-3 gene
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2017 journal article

Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(45), E9722–E9729.

By: Y. Lin *, H. Chen, Q. Li *, W. Li, J. Wang , R. Shi, S. Tunlaya-Anukit, P. Shuai n ...

author keywords: reciprocal cross-regulation; NAC transcription factors; alternative splicing; wood formation; Populus trichocarpa
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa

PLANTA, 245(5), 927–938.

By: R. Shi, J. Wang , Y. Lin, Q. Li *, Y. Sun*, H. Chen, R. Sederoff, V. Chiang

author keywords: Wood formation; Transcriptome; Fiber cells; Vessel elements; Cell wall biosynthesis; Co-expression network
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

A cell wall-bound anionic peroxidase, PtrPO21, is involved in lignin polymerization in Populus trichocarpa

Tree Genetics & Genomes, 12(2).

By: C. Lin  n, Q. Li *, S. Tunlaya-Anukit *, R. Shi, Y. Sun*, J. Wang , J. Liu  n, P. Loziuk n ...

author keywords: Lignin polymerization; Populus trichocarpa; Lignin peroxidase; LC-MS/MS; Lignin systems biology
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2015 journal article

Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis

Proceedings of the National Academy of Sciences, 112(27), 8481–8486.

By: J. Wang , L. Chuang, P. Loziuk n, H. Chen, Y. Lin, R. Shi, G. Qu*, D. Muddiman , R. Sederoff, V. Chiang

author keywords: AldOMT; COMT; lignin; phosphoproteomics; phosphoregulation
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2014 journal article

A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue

NATURE PROTOCOLS, 9(9), 2180–2193.

By: W. Li, Y. Lin, Q. Li, R. Shi, C. Lin  n, H. Chen, L. Chuang, G. Qu*, R. Sederoff, V. Chiang

Source: Web Of Science
Added: August 6, 2018

2014 journal article

A simple improved-throughput xylem protoplast system for studying wood formation

NATURE PROTOCOLS, 9(9), 2194–2205.

By: Y. Lin, W. Li, H. Chen, Q. Li, Y. Sun*, R. Shi, C. Lin, J. Wang  ...

Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Growth under field conditions affects lignin content and productivity in transgenic Populus trichocarpa with altered lignin biosynthesis

BIOMASS & BIOENERGY, 68, 228–239.

By: A. Stout n, A. Davis , J. Domec, C. Yang, R. Shi & J. King

author keywords: Populus; Lignin; Field trial; Transgenic; Bioenergy
Sources: Web Of Science, ORCID
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.

By: H. Chen, J. Song n, J. Wang , Y. Lin  n, J. Ducoste , C. Shuford, J. Liu  n, Q. Li ...

Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2014 journal article

Vibrational sum-frequency-generation (SFG) spectroscopy study of the structural assembly of cellulose microfibrils in reaction woods

CELLULOSE, 21(4), 2219–2231.

By: K. Kafle*, R. Shi, C. Lee *, A. Mittal *, Y. Park *, Y. Sun, S. Park , V. Chiang, S. Kim *

author keywords: Reaction wood; Tension wood; Compression wood; Cellulose microfibril assembly; Sum; frequency; generation spectroscopy; X-ray; diffraction
Sources: Web Of Science, ORCID
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.

By: H. Chen, J. Song n, C. Williams , C. Shuford, J. Liu  n, J. Wang , Q. Li, R. Shi ...

Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa

Planta, 238(3), 487–497.

By: R. Shi, C. Shuford, J. Wang , Y. Sun, Z. Yang n, H. Chen, S. Tunlaya-Anukit, Q. Li ...

Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2013 journal article

The elucidation of the lignin structure effect on the cellulase-mediated saccharification by genetic engineering poplars (Populus nigra L. x Populus maximowiczii A.)

BIOMASS & BIOENERGY, 58, 52–57.

By: D. Min, C. Yang, R. Shi, H. Jameel, V. Chiang & H. Chang

author keywords: Transgenic hybrid poplar; Pretreatment; S to V Ratio; Delignification; Enzymatic saccharification
Source: Web Of Science
Added: August 6, 2018

2012 journal article

A standard reaction condition and a single HPLC separation system are sufficient for estimation of monolignol biosynthetic pathway enzyme activities

PLANTA, 236(3), 879–885.

By: J. Liu  n, R. Shi, Q. Li, R. Sederoff & V. Chiang

author keywords: Monolignols; Enzyme activity; Populus trichocarpa; Pinus taeda; Angiosperm; Gymnosperm
Source: Web Of Science
Added: August 6, 2018

2012 journal article

Comprehensive Quantification of Monolignol-Pathway Enzymes in Populus trichocarpa by Protein Cleavage Isotope Dilution Mass Spectrometry

Journal of Proteome Research, 11(6), 3390–3404.

By: C. Shuford  n, Q. Li, Y. Sun, H. Chen, J. Wang , R. Shi, R. Sederoff, V. Chiang, D. Muddiman 

author keywords: quantification; isotope dilution mass spectrometry; selected reaction monitoring; filter-aided sample preparation; monolignol biosynthesis
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2012 journal article

MicroRNAs in trees

PLANT MOLECULAR BIOLOGY, 80(1), 37–53.

By: Y. Sun, R. Shi, X. Zhang  n, V. Chiang & R. Sederoff

author keywords: MicroRNA; Woody plant; Gene regulation; Plant development; Plant stress response; Artificial microRNA
Source: Web Of Science
Added: August 6, 2018

2010 journal article

Specific down-regulation of PAL genes by artificial microRNAs in Populus trichocarpa

PLANTA, 232(6), 1281–1288.

By: R. Shi, C. Yang, S. Lu, R. Sederoff & V. Chiang

author keywords: Artificial microRNA; Phenylalanine ammonia-lyase; Populus trichocarpa transformation; Down-regulation; PolyA tailing-based real time RT-PCR; Quantitation
Source: Web Of Science
Added: August 6, 2018

2010 review

Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes

[Review of ]. PLANT AND CELL PHYSIOLOGY, 51(1), 144–163.

By: R. Shi, Y. Sun, Q. Li  n, S. Heber , R. Sederoff & V. Chiang

author keywords: Lignin systems biology; Monolignol biosynthesis; Populus trichocarpa; Promoter motifs; Transcript abundance; Xylem-specific expression
Sources: Web Of Science, ORCID
Added: August 6, 2018

2009 journal article

Isolation of expressed sequences from a specific chromosome of Thinopyrum intermedium infected by BYDV

GENOME, 52(1), 68–76.

By: S. Jiang*, W. Yin*, J. Hu *, R. Shi, R. Zhou *, Y. Chen *, G. Zhou*, R. Wang *, L. Song*, Z. Hu*

author keywords: TAi-27; Thinopyrum intermedium; chromosome microdissection; hybridization-specific amplification (HSA); expressed sequences; barley yellow dwarf virus (BYDV)
Source: Web Of Science
Added: August 6, 2018

2008 journal article

Rapid EST isolation from chromosome IR of rye

BMC PLANT BIOLOGY, 8.

By: R. Zhou *, R. Shi, S. Jiang*, W. Yin*, H. Wang*, Y. Chen *, J. Hu *, R. Wang *, X. Zhang*, Z. Hu*

Source: Web Of Science
Added: August 6, 2018

2005 journal article

Facile means for quantifying microRNA expression by real-time PCR

BIOTECHNIQUES, 39(4), 519–525.

By: R. Shi & V. Chiang

Source: Web Of Science
Added: August 6, 2018

2005 journal article

Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis

Plant Cell, 17(8), 2186–2203.

By: S. Lu, Y. Sun, R. Shi, C. Clark, L. Li & V. Chiang

Source: NC State University Libraries
Added: August 6, 2018

2004 journal article

RNA silencing in plants by the expression of siRNA duplexes

NUCLEIC ACIDS RESEARCH, 32(21).

By: S. Lu, R. Shi, C. Tsao, X. Yi, L. Li & V. Chiang

Source: Web Of Science
Added: August 6, 2018