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Results: 1 to 20 of 114

1.

Establishing ion ratio thresholds based on absolute peak area for absolute protein quantification using protein cleavage isotope dilution mass spectrometry.

Loziuk PL, Sederoff RR, Chiang VL, Muddiman DC.

Analyst. 2014 Aug 26. [Epub ahead of print]

PMID:
25154770
[PubMed - as supplied by publisher]
2.

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

Lin YC, Li W, Chen H, Li Q, Sun YH, Shi R, Lin CY, Wang JP, Chen HC, Chuang L, Qu GZ, Sederoff RR, Chiang VL.

Nat Protoc. 2014 Sep;9(9):2194-205. doi: 10.1038/nprot.2014.147. Epub 2014 Aug 21.

PMID:
25144270
[PubMed - in process]
3.

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

Li W, Lin YC, Li Q, Shi R, Lin CY, Chen H, Chuang L, Qu GZ, Sederoff RR, Chiang VL.

Nat Protoc. 2014 Sep;9(9):2180-93. doi: 10.1038/nprot.2014.146. Epub 2014 Aug 21.

PMID:
25144269
[PubMed - in process]
4.

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.

Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JF, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg SL, Langley CH.

Genome Biol. 2014 Mar 4;15(3):R59. doi: 10.1186/gb-2014-15-3-r59.

PMID:
24647006
[PubMed - in process]
Free PMC Article
5.

Systems Biology of Lignin Biosynthesis in Populus trichocarpa: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling.

Chen HC, Song J, Wang JP, Lin YC, Ducoste J, Shuford CM, Liu J, Li Q, Shi R, Nepomuceno A, Isik F, Muddiman DC, Williams C, Sederoff RR, Chiang VL.

Plant Cell. 2014 Mar;26(3):876-93. doi: 10.1105/tpc.113.119685. Epub 2014 Mar 11.

PMID:
24619612
[PubMed - in process]
6.

Complete proteomic-based enzyme reaction and inhibition kinetics reveal how monolignol biosynthetic enzyme families affect metabolic flux and lignin in Populus trichocarpa.

Wang JP, Naik PP, Chen HC, Shi R, Lin CY, Liu J, Shuford CM, Li Q, Sun YH, Tunlaya-Anukit S, Williams CM, Muddiman DC, Ducoste JJ, Sederoff RR, Chiang VL.

Plant Cell. 2014 Mar;26(3):894-914. doi: 10.1105/tpc.113.120881. Epub 2014 Mar 11.

PMID:
24619611
[PubMed - in process]
7.

SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa.

Lin YC, Li W, Sun YH, Kumari S, Wei H, Li Q, Tunlaya-Anukit S, Sederoff RR, Chiang VL.

Plant Cell. 2013 Nov;25(11):4324-41. doi: 10.1105/tpc.113.117697. Epub 2013 Nov 26.

PMID:
24280390
[PubMed - in process]
8.

Understanding the role of proteolytic digestion on discovery and targeted proteomic measurements using liquid chromatography tandem mass spectrometry and design of experiments.

Loziuk PL, Wang J, Li Q, Sederoff RR, Chiang VL, Muddiman DC.

J Proteome Res. 2013 Dec 6;12(12):5820-9. doi: 10.1021/pr4008442. Epub 2013 Nov 1.

PMID:
24144163
[PubMed - indexed for MEDLINE]
9.

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

Shi R, Shuford CM, Wang JP, Sun YH, Yang Z, Chen HC, Tunlaya-Anukit S, Li Q, Liu J, Muddiman DC, Sederoff RR, Chiang VL.

Planta. 2013 Sep;238(3):487-97. doi: 10.1007/s00425-013-1905-1. Epub 2013 Jun 14.

PMID:
23765265
[PubMed - indexed for MEDLINE]
10.

Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa.

Lu S, Li Q, Wei H, Chang MJ, Tunlaya-Anukit S, Kim H, Liu J, Song J, Sun YH, Yuan L, Yeh TF, Peszlen I, Ralph J, Sederoff RR, Chiang VL.

Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):10848-53. doi: 10.1073/pnas.1308936110. Epub 2013 Jun 10.

PMID:
23754401
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Genomics: A spruce sequence.

Sederoff R.

Nature. 2013 May 30;497(7451):569-70. doi: 10.1038/nature12250. Epub 2013 May 22. No abstract available.

PMID:
23698364
[PubMed - indexed for MEDLINE]
12.

Monolignol pathway 4-coumaric acid:coenzyme A ligases in Populus trichocarpa: novel specificity, metabolic regulation, and simulation of coenzyme A ligation fluxes.

Chen HC, Song J, Williams CM, Shuford CM, Liu J, Wang JP, Li Q, Shi R, Gokce E, Ducoste J, Muddiman DC, Sederoff RR, Chiang VL.

Plant Physiol. 2013 Mar;161(3):1501-16. doi: 10.1104/pp.112.210971. Epub 2013 Jan 23.

PMID:
23344904
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa.

Li Q, Lin YC, Sun YH, Song J, Chen H, Zhang XH, Sederoff RR, Chiang VL.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14699-704. doi: 10.1073/pnas.1212977109. Epub 2012 Aug 22.

PMID:
22915581
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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

Liu J, Shi R, Li Q, Sederoff RR, Chiang VL.

Planta. 2012 Sep;236(3):879-85. doi: 10.1007/s00425-012-1688-9. Epub 2012 Jun 24.

PMID:
22729823
[PubMed - indexed for MEDLINE]
15.

Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC-MS/MS based protein quantification and metabolic flux analysis.

Wang JP, Shuford CM, Li Q, Song J, Lin YC, Sun YH, Chen HC, Williams CM, Muddiman DC, Sederoff RR, Chiang VL.

Planta. 2012 Sep;236(3):795-808. doi: 10.1007/s00425-012-1663-5. Epub 2012 May 25.

PMID:
22628084
[PubMed - indexed for MEDLINE]
16.

Peptide production and decay rates affect the quantitative accuracy of protein cleavage isotope dilution mass spectrometry (PC-IDMS).

Shuford CM, Sederoff RR, Chiang VL, Muddiman DC.

Mol Cell Proteomics. 2012 Sep;11(9):814-23. doi: 10.1074/mcp.O112.017145. Epub 2012 May 17.

PMID:
22595788
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Comprehensive quantification of monolignol-pathway enzymes in populus trichocarpa by protein cleavage isotope dilution mass spectrometry.

Shuford CM, Li Q, Sun YH, Chen HC, Wang J, Shi R, Sederoff RR, Chiang VL, Muddiman DC.

J Proteome Res. 2012 Jun 1;11(6):3390-404. doi: 10.1021/pr300205a. Epub 2012 May 9.

PMID:
22524869
[PubMed - in process]
18.

Chestnut resistance to the blight disease: insights from transcriptome analysis.

Barakat A, Staton M, Cheng CH, Park J, Yassin NB, Ficklin S, Yeh CC, Hebard F, Baier K, Powell W, Schuster SC, Wheeler N, Abbott A, Carlson JE, Sederoff R.

BMC Plant Biol. 2012 Mar 19;12:38. doi: 10.1186/1471-2229-12-38.

PMID:
22429310
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

MicroRNAs in trees.

Sun YH, Shi R, Zhang XH, Chiang VL, Sederoff RR.

Plant Mol Biol. 2012 Sep;80(1):37-53. doi: 10.1007/s11103-011-9864-z. Epub 2011 Dec 8. Review.

PMID:
22161564
[PubMed - indexed for MEDLINE]
20.

Membrane protein complexes catalyze both 4- and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis.

Chen HC, Li Q, Shuford CM, Liu J, Muddiman DC, Sederoff RR, Chiang VL.

Proc Natl Acad Sci U S A. 2011 Dec 27;108(52):21253-8. doi: 10.1073/pnas.1116416109. Epub 2011 Dec 12.

PMID:
22160716
[PubMed - indexed for MEDLINE]
Free PMC Article

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