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Hierarchical Transcription-Factor and Chromatin Binding Network for Wood Formation in Populus trichocarpa.

Chen H, Wang JP, Liu H, Li H, Lin YJ, Shi R, Yang C, Gao J, Zhou C, Li Q, Sederoff RR, Li W, Chiang VL.

Plant Cell. 2019 Feb 12. pii: tpc.00620.2018. doi: 10.1105/tpc.18.00620. [Epub ahead of print]


Enzyme-Enzyme Interactions in Monolignol Biosynthesis.

Wang JP, Liu B, Sun Y, Chiang VL, Sederoff RR.

Front Plant Sci. 2019 Jan 11;9:1942. doi: 10.3389/fpls.2018.01942. eCollection 2018. Review.


Flux modeling for monolignol biosynthesis.

Wang JP, Matthews ML, Naik PP, Williams CM, Ducoste JJ, Sederoff RR, Chiang VL.

Curr Opin Biotechnol. 2018 Dec 14;56:187-192. doi: 10.1016/j.copbio.2018.12.003. [Epub ahead of print] Review.


CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa.

Yan X, Liu J, Kim H, Liu B, Huang X, Yang Z, Lin YJ, Chen H, Yang C, Wang JP, Muddiman DC, Ralph J, Sederoff RR, Li Q, Chiang VL.

New Phytol. 2019 Apr;222(1):244-260. doi: 10.1111/nph.15505. Epub 2018 Oct 27.


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

Lin YJ, Chen H, Li Q, Li W, Wang JP, Shi R, Tunlaya-Anukit S, Shuai P, Wang Z, Ma H, Li H, Sun YH, Sederoff RR, Chiang VL.

Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):E9722-E9729. doi: 10.1073/pnas.1714422114. Epub 2017 Oct 23.


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

Shi R, Wang JP, Lin YC, Li Q, Sun YH, Chen H, Sederoff RR, Chiang VL.

Planta. 2017 May;245(5):927-938. doi: 10.1007/s00425-016-2640-1. Epub 2017 Jan 12.


Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa.

Loziuk PL, Parker J, Li W, Lin CY, Wang JP, Li Q, Sederoff RR, Chiang VL, Muddiman DC.

J Proteome Res. 2015 Oct 2;14(10):4158-68. doi: 10.1021/acs.jproteome.5b00233. Epub 2015 Sep 1.


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

Wang JP, Chuang L, Loziuk PL, Chen H, Lin YC, Shi R, Qu GZ, Muddiman DC, Sederoff RR, Chiang VL.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8481-6. doi: 10.1073/pnas.1510473112. Epub 2015 Jun 24.


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.

Lin CY, Wang JP, Li Q, Chen HC, Liu J, Loziuk P, Song J, Williams C, Muddiman DC, Sederoff RR, Chiang VL.

Mol Plant. 2015 Jan;8(1):176-87. doi: 10.1016/j.molp.2014.12.003. Epub 2014 Dec 11.


Populus trichocarpa.

Li Q, Yeh TF, Yang C, Song J, Chen ZZ, Sederoff RR, Chiang VL.

Methods Mol Biol. 2015;1224:357-63. doi: 10.1007/978-1-4939-1658-0_28.


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.

Lin CY, Wang JP, Li Q, Chen HC, Liu J, Loziuk P, Song J, Williams C, Muddiman DC, Sederoff RR, Chiang VL.

Mol Plant. 2014 Oct 20. pii: ssu117. [Epub ahead of print]


Plant biotechnology for lignocellulosic biofuel production.

Li Q, Song J, Peng S, Wang JP, Qu GZ, Sederoff RR, Chiang VL.

Plant Biotechnol J. 2014 Dec;12(9):1174-92. doi: 10.1111/pbi.12273. Epub 2014 Oct 20. Review.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Climate change and the integrity of science.

Gleick PH, Adams RM, Amasino RM, Anders E, Anderson DJ, Anderson WW, Anselin LE, Arroyo MK, Asfaw B, Ayala FJ, Bax A, Bebbington AJ, Bell G, Bennett MV, Bennetzen JL, Berenbaum MR, Berlin OB, Bjorkman PJ, Blackburn E, Blamont JE, Botchan MR, Boyer JS, Boyle EA, Branton D, Briggs SP, Briggs WR, Brill WJ, Britten RJ, Broecker WS, Brown JH, Brown PO, Brunger AT, Cairns J Jr, Canfield DE, Carpenter SR, Carrington JC, Cashmore AR, Castilla JC, Cazenave A, Chapin FS 3rd, Ciechanover AJ, Clapham DE, Clark WC, Clayton RN, Coe MD, Conwell EM, Cowling EB, Cowling RM, Cox CS, Croteau RB, Crothers DM, Crutzen PJ, Daily GC, Dalrymple GB, Dangl JL, Darst SA, Davies DR, Davis MB, De Camilli PV, Dean C, DeFries RS, Deisenhofer J, Delmer DP, DeLong EF, DeRosier DJ, Diener TO, Dirzo R, Dixon JE, Donoghue MJ, Doolittle RF, Dunne T, Ehrlich PR, Eisenstadt SN, Eisner T, Emanuel KA, Englander SW, Ernst WG, Falkowski PG, Feher G, Ferejohn JA, Fersht A, Fischer EH, Fischer R, Flannery KV, Frank J, Frey PA, Fridovich I, Frieden C, Futuyma DJ, Gardner WR, Garrett CJ, Gilbert W, Goldberg RB, Goodenough WH, Goodman CS, Goodman M, Greengard P, Hake S, Hammel G, Hanson S, Harrison SC, Hart SR, Hartl DL, Haselkorn R, Hawkes K, Hayes JM, Hille B, Hökfelt T, House JS, Hout M, Hunten DM, Izquierdo IA, Jagendorf AT, Janzen DH, Jeanloz R, Jencks CS, Jury WA, Kaback HR, Kailath T, Kay P, Kay SA, Kennedy D, Kerr A, Kessler RC, Khush GS, Kieffer SW, Kirch PV, Kirk K, Kivelson MG, Klinman JP, Klug A, Knopoff L, Kornberg H, Kutzbach JE, Lagarias JC, Lambeck K, Landy A, Langmuir CH, Larkins BA, Le Pichon XT, Lenski RE, Leopold EB, Levin SA, Levitt M, Likens GE, Lippincott-Schwartz J, Lorand L, Lovejoy CO, Lynch M, Mabogunje AL, Malone TF, Manabe S, Marcus J, Massey DS, McWilliams JC, Medina E, Melosh HJ, Meltzer DJ, Michener CD, Miles EL, Mooney HA, Moore PB, Morel FM, Mosley-Thompson ES, Moss B, Munk WH, Myers N, Nair GB, Nathans J, Nester EW, Nicoll RA, Novick RP, O'Connell JF, Olsen PE, Opdyke ND, Oster GF, Ostrom E, Pace NR, Paine RT, Palmiter RD, Pedlosky J, Petsko GA, Pettengill GH, Philander SG, Piperno DR, Pollard TD, Price PB Jr, Reichard PA, Reskin BF, Ricklefs RE, Rivest RL, Roberts JD, Romney AK, Rossmann MG, Russell DW, Rutter WJ, Sabloff JA, Sagdeev RZ, Sahlins MD, Salmond A, Sanes JR, Schekman R, Schellnhuber J, Schindler DW, Schmitt J, Schneider SH, Schramm VL, Sederoff RR, Shatz CJ, Sherman F, Sidman RL, Sieh K, Simons EL, Singer BH, Singer MF, Skyrms B, Sleep NH, Smith BD, Snyder SH, Sokal RR, Spencer CS, Steitz TA, Strier KB, Südhof TC, Taylor SS, Terborgh J, Thomas DH, Thompson LG, Tjian RT, Turner MG, Uyeda S, Valentine JW, Valentine JS, Van Etten JL, van Holde KE, Vaughan M, Verba S, von Hippel PH, Wake DB, Walker A, Walker JE, Watson EB, Watson PJ, Weigel D, Wessler SR, West-Eberhard MJ, White TD, Wilson WJ, Wolfenden RV, Wood JA, Woodwell GM, Wright HE Jr, Wu C, Wunsch C, Zoback ML.

Science. 2010 May 7;328(5979):689-90. doi: 10.1126/science.328.5979.689. No abstract available. Erratum in: Science. 2010 May 14;328(5980):826.


Genomics of growth traits in forest trees.

Grattapaglia D, Plomion C, Kirst M, Sederoff RR.

Curr Opin Plant Biol. 2009 Apr;12(2):148-56. doi: 10.1016/j.pbi.2008.12.008. Epub 2009 Jan 29. Review.


Heterologous array analysis in Pinaceae: hybridization of Pinus taeda cDNA arrays with cDNA from needles and embryogenic cultures of P. Taeda, P. Sylvestris or Picea abies.

van Zyl L, von Arnold S, Bozhkov P, Chen Y, Egertsdotter U, Mackay J, Sederoff RR, Shen J, Zelena L, Clapham DH.

Comp Funct Genomics. 2002;3(4):306-18. doi: 10.1002/cfg.199.


Studying the functional genomics of stress responses in loblolly pine with the Expresso microarray experiment management system.

Heath LS, Ramakrishnan N, Sederoff RR, Whetten RW, Chevone BI, Struble CA, Jouenne VY, Chen D, van Zyl L, Grene R.

Comp Funct Genomics. 2002;3(3):226-43. doi: 10.1002/cfg.169.


High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome.

Novaes E, Drost DR, Farmerie WG, Pappas GJ Jr, Grattapaglia D, Sederoff RR, Kirst M.

BMC Genomics. 2008 Jun 30;9:312. doi: 10.1186/1471-2164-9-312.


Genetic architecture of transcript-level variation in differentiating xylem of a eucalyptus hybrid.

Kirst M, Basten CJ, Myburg AA, Zeng ZB, Sederoff RR.

Genetics. 2005 Apr;169(4):2295-303. Epub 2005 Jan 31.


Variation in transcript abundance during somatic embryogenesis in gymnosperms.

Stasolla C, Bozhkov PV, Chu TM, Van Zyl L, Egertsdotter U, Suarez MF, Craig D, Wolfinger RD, Von Arnold S, Sederoff RR.

Tree Physiol. 2004 Oct;24(10):1073-85.


Microarray analyses of gene expression during adventitious root development in Pinus contorta.

Brinker M, van Zyl L, Liu W, Craig D, Sederoff RR, Clapham DH, von Arnold S.

Plant Physiol. 2004 Jul;135(3):1526-39. Epub 2004 Jul 9.


Metabolic profiling: a new tool in the study of wood formation.

Morris CR, Scott JT, Chang HM, Sederoff RR, O'Malley D, Kadla JF.

J Agric Food Chem. 2004 Mar 24;52(6):1427-34.



Whetten RW, MacKay JJ, Sederoff RR.

Annu Rev Plant Physiol Plant Mol Biol. 1998 Jun;49:585-609.


Characterisation of Pt MYB1, an R2R3-MYB from pine xylem.

Patzlaff A, Newman LJ, Dubos C, Whetten RW, Smith C, McInnis S, Bevan MW, Sederoff RR, Campbell MM.

Plant Mol Biol. 2003 Nov;53(4):597-608.


The effect of reduced glutathione on morphology and gene expression of white spruce (Picea glauca) somatic embryos.

Stasolla C, Belmonte MF, van Zyl L, Craig DL, Liu W, Yeung EC, Sederoff RR.

J Exp Bot. 2004 Mar;55(397):695-709. Epub 2004 Feb 13.


An auxin-inducible gene from loblolly pine (Pinus taeda L.) is differentially expressed in mature and juvenile-phase shoots and encodes a putative transmembrane protein.

Busov VB, Johannes E, Whetten RW, Sederoff RR, Spiker SL, Lanz-Garcia C, Goldfarb B.

Planta. 2004 Apr;218(6):916-27. Epub 2004 Jan 13.


Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine.

Watkinson JI, Sioson AA, Vasquez-Robinet C, Shukla M, Kumar D, Ellis M, Heath LS, Ramakrishnan N, Chevone B, Watson LT, van Zyl L, Egertsdotter U, Sederoff RR, Grene R.

Plant Physiol. 2003 Dec;133(4):1702-16.


Characterisation of a pine MYB that regulates lignification.

Patzlaff A, McInnis S, Courtenay A, Surman C, Newman LJ, Smith C, Bevan MW, Mansfield S, Whetten RW, Sederoff RR, Campbell MM.

Plant J. 2003 Dec;36(6):743-54.


NMR analysis of lignins in CAD-deficient plants. Part 1. Incorporation of hydroxycinnamaldehydes and hydroxybenzaldehydes into lignins.

Kim H, Ralph J, Lu F, Ralph SA, Boudet AM, MacKay JJ, Sederoff RR, Ito T, Kawai S, Ohashi H, Higuchi T.

Org Biomol Chem. 2003 Jan 21;1(2):268-81.


Comparative genetic linkage maps of Eucalyptus grandis, Eucalyptus globulus and their F1 hybrid based on a double pseudo-backcross mapping approach.

Myburg AA, Griffin AR, Sederoff RR, Whetten RW.

Theor Appl Genet. 2003 Oct;107(6):1028-42. Epub 2003 Jul 1.


An arabinogalactan protein associated with secondary cell wall formation in differentiating xylem of loblolly pine.

Zhang Y, Brown G, Whetten R, Loopstra CA, Neale D, Kieliszewski MJ, Sederoff RR.

Plant Mol Biol. 2003 May;52(1):91-102.


Up, down and up again is a signature global gene expression pattern at the beginning of gymnosperm embryogenesis.

van Zyl L, Bozhkov PV, Clapham DH, Sederoff RR, von Arnold S.

Gene Expr Patterns. 2003 Mar;3(1):83-91.


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