Publications

Publications

Hu H, Gu X, Xue L-J, Swamy PS, Harding SA, Tsai C-J (2016) Tubulin C-terminal post-translational modifications do not occur in wood forming tissue of Populus. Frontiers in Plant Science 7, 1493. Full text
 
Xue L-J, Frost CJ, Tsai C-J, Harding SA (2016) Drought response transcriptomes are altered in poplar with reduced tonoplast sucrose transporter expression. Scientific Reports 6, 33655. Full text

Bowsher AW, Ali R, Harding SA, Tsai C-J, Donovan LA (2016) Evolutionary divergences in root exudate composition among ecologically-contrasting Helianthus species. PLoS One 11: e0148280. Full text

Mason CM, Bowsher AW, Crowell BL, Celoy RM, Tsai C-J, Donovan LA (2016) Macroevolution of leaf defenses and secondary metabolites across the genus HelianthusNew Phytologist 209: 1720-1733. Full text

Tsai C-J, Xue L-J (2015) CRISPRing into the woods. GM Crops & Food. DOI: 10.1080/21645698.2015.1091553. Full text

Bowsher AW, Ali R, Harding SA, Tsai C-J, Donovan LA (2015) Analysis of wild sunflower (Helianthus annuus L.) root exudates using gas chromatography‐mass spectrometry. Journal of Plant Nutrition and Soil Science 178: 776-786. Full text

Swamy PS, Hu H, Pattathil S, Maloney VJ, Xiao H, Xue L-J, Chung J-D, Johnson VE, Zhu Y, Peter GF, Hahn MG,  Mansfield SD, Harding SA, Tsai C-J (2015) Tubulin perturbation leads to unexpected cell wall modifications and affects stomatal behavior in Populus. Journal of Experimental Botany 66: 6507-6518.  Full text

Xue L-J, Alabady MS, Mohebbi M, Tsai C-J (2015) Exploiting genome variation to improve next-generation sequencing data analysis and genome editing efficiency in Populus tremula x alba 717-1B4.  Tree Genetics and Genomics 11: 82. Full text

Xue L-J, Tsai C-J (2015) AGEseq: Analysis of genome editing by sequencing. Molecular Plant 8: 1428-1430. Full text

Zhou X, Jacobs TB, Xue L-J, Harding S, Tsai C-J (2015) Exploiting SNPs for biallelic CRISPR mutations in the outcrossing woody perennial Populus reveals 4-coumrate:CoA ligase specificity and redundancy. New Phytologist 208: 298-301. Full text

Harding SA, Xue L-J, Du L, Nyamdari B, Lindroth RL, Sykes R, Davis MF, Tsai C-J (2014) Condensed tannin biosynthesis and polymerization synergistically condition carbon use, defense, sink strength and growth in PopulusTree Physiology 34: 1240-1251. Full text

Peng D, Gu X, Xue L-J, Leebens-Mack JH, Tsai C-J (2014) Bayesian phylogeny of sucrose transporters: Ancient origins, differential expansion and convergent evolution in monocots and dicots.  Frontiers in Plant Science 5: 615.  Full text

Chen H-Y, Babst BA, Nyamdari B, Sykes R, Davis MF, Harding SA, Tsai C-J (2014) Loblolly pine contains phylogenetically divergent 4-coumarate:CoA ligases that confer distinct metabolic phenotypes when over-expressed in Populus. Plant Cell Physiology 55: 1669-1678. Full text

Babst BA, Chen H-Y, Wang H-Q, Payyavula RS, Thomas TP, Harding SA, Tsai C-J (2014) Stress responsive Populus hydroxycinnamate glycosyltransferase modulates phenylpropanoid homeostasis.  Journal of Experimental Botany 65: 4191-4200. Full text

da Silva Taveira JH, Borém FM, Figueiredo LP, Reis N, Franca AS, Harding SA, Tsai C-J (2014) Potential markers of coffee genotypes grown in different Brazilian regions: Metabolomics approach. Food Research International 61: 75-82.  Full text

Xu Y, Chen C-F, Thomas TP, Azadi P, Diehl B, Tsai C-J, Brown N, Carlson JE, Tien M, Liang H (2013) Wood chemistry analysis and expression profiling of a poplar clone expressing a tyrosine-rich peptide.  Plant Cell Reports 32: 1827-1841. Abstract

Wang H-Q, Tsai C-J (2013) CorSig: A general framework for estimating statistical significance of correlation and its applciation to gene co-expression analysis.  PLoS ONE 8(10): e77429.  Full text

Xue L-J, Guo W, Yuan Y, Anino EO, Nyamdari B, Wilson MC, Frost CJ, Chen H-Y, Babst BA, Harding SA, Tsai CJ (2013) Constitutively elevated salicylic acid levels alter photosynthesis and oxidative state but not growth in transgenic Populus. Plant Cell 25: 2714-2730.  Full text

Tsai C-J (2013) Next-generation sequencing for next-generation breeding, and more.  New Phytologist 198: 635-637.  Full text

Molina-Rueda JJ, Tsai C-J, Kirby EG (2013) The Populus superoxide dismutase gene family and its responses to drought stress in transgenic poplar overexpressing a pine cytosolic glutamine synthetase (GS1a).  PLoS ONE 8(2): e56421.  Full text

Tsai C-J and Harding SA (2013) In situ hybridization.  Methods in Cell Biology 113: 339-359.  Full text

Frost CJ, Nyamdari B, Tsai C-J, Harding SA (2012) The tonoplast-localized sucrose transporter in Populus (PtaSUT4) regulates whole-plant water relations, responses to water stress, and photosynthesis.  PLoS ONE 7(8): e44467.  Full text

Tuominen LK, Johnson VE, Tsai C-J (2011) Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues.  BMC Genomics 12: 236. Full text

Payyavula RS, Tay KHC, Tsai C-J, Harding SA (2011) The sucrose transporter family in Populus: The importance of a tonoplast PtaSUT4 to bioamss and carbon partitioning. Plant Journal 65: 757-770.  Full text

Wang H-Q, Tuominen LK, Tsai C-J (2011) SLIM: A sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures.  Bioinformatics 27:225-231. Abstract

Wegrzyn JL, Eckert AJ, Choi M, Lee JM, Stanton BJ, Sykes R, Davis MF, Tsai C-J, Neale DB (2010) Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem. New Phytologist 188: 515-532. Abstract

Tsai C-J, Ranjan P, DiFazio SP, Tuskan GA, Johnson V (2011) Poplar genome microarrays. In: Joshi CP, DiFazio SP and Kole C (eds), Genetics, Genomics and Breeding of Poplars. Science Publishers, Enfield, NH. pp. 112-127.

Douglas CJ, Ehlting J, Harding SA (2010) Phenylpropanoid and phenolic metabolism in Populus: Gene family structure and comparative and functional genomics. In: Joshi CP, DiFazio SP and Kole C (eds), Genetics, Genomics and Breeding of Poplars. Science Publishers, Enfield,NH. pp. 304-326.

Gou J, Strauss SH, Tsai C-J, Fang K, Chen Y, Jiang X, Busov VB (2010) Gibberellins regulate lateral root formation in Populus through interaction with auxin and other hormones.  Plant Cell 22: 623-639. Abstract

Babst BA, Harding SA, Tsai C-J (2010) Biosynthesis of phenolic glycosides from phenylpropanoid and benzenoid precursors in Populus. Journal of Chemical Ecology 36: 286-297. Abstract

Barron MJ, Tsai C-J, Donahue SW (2010) Mechanical stimulation mediates gene expression in MC3T3 osteoblastic cells differently in 2D and 3D environments.  Journal of Biomedical Engineering 132: 041005. Abstract

Huang Z, Tsai C-J, Harding S, Meilan R, Woeste K (2010) A cross-species transcriptional profile analysis of heartwood formation in black walnut. Plant Molecular Biology Reporter 28: 222-230. Reprint

Street N, Tsai C-J (2010) Populus resources and bioinformatics. In: Jansson S, Bhalerao R, and Groover AT (eds), Genetics and Genomics of Populus. Plant Genetics and Genomics: Crops and Models book series. Springer, New York, pp. 135-152.

Payyavula RS, Babst BA, Nelsen MP, Harding SA, Tsai C-J (2009) Glycosylation-mediated phenylpropanoid partitioning in Populus tremuloides cell cultures. BMC Plant Biology 9: 151. Reprint

Yuan Y, Chung J-D, Fu X, Johnson VE, Ranjan P, Booth SL, Harding SA, Tsai C-J (2009) Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis. Proceedings of the National Academy of Sciences USA 106: 22020-22025. Reprint

Harding SA, Jarvie MM, Lindroth RL, Tsai C-J (2009) A comparative analysis of phenylpropanoid metabolism, N utilization, and carbon partitioning in fast- and slow-growing Populus hybrid clones. Journal of Experimental Botany 60: 3443-3452. Reprint

Cseke LJ, Tsai C-J, Rogers A, Nelsen MP, White HL, Karnosky DF, Podila GK (2009) Transcriptomic comparison in the leaves of two aspen genotypes having similar carbon assimilation rates but different partitioning patterns under elevated [CO2]. New Phytologist 182: 891-911. Reprint

Qin H, Feng T, Harding SA, Tsai C-J, Zhang S (2008) An efficient method to identify differentially expressed genes in microarray experiments. Bioinformatics 24: 1583-1589. Reprint

Luo K, Harding SA, Tsai C-J (2008) A modified T-vector for simplified assembly of hairpin RNAi constructs. Biotechnology Letters 30: 1271-1274. Reprint

Joshi CP, Brunner A, Busov V, Meilan R, Thammanagowda S, Tsai C-J (2008) Poplars. In: Kole C and Hall TC (eds) Compendium of Transgenic Crop Plants, Vol. IX. Blackwell Publishing. pp. 1-33.

Donahue SW, McGee ME, Bradford RM, Tsai C-J, Nelsen MP, Simoni K (2008) American black bear parathyroid hormone as therapy for osteoporosis. In: Lovegrove BG and Mckechnie AE (eds) Hypometabolism In Animals: Hibernation, Torpor And Cryobiology. University of KwaZulu-Natal, Pietermaritzburg. pp. 25-36.

Busov V and Tsai C-J (2007) Perennial challenges and opportunities. New Phytologist 176: 3-6. Reprint

Oakley RV, Wang Y-S, Ramakrishna W, Harding SA, Tsai C-J (2007) Differential expansion and expression of alpha- and beta-tubulin gene families in Populus. Plant Physiology 145: 961-973. Reprint

Lin J, Gunter LE, Harding SA, Kopp RF, McCord RP, Tsai C-J, Tuskan GA, Smart LB (2007) Development of AFLP and RAPD markers linked to a locus associated with twisted growth in corkscrew willow (Salix matsudana ‘Tortuosa’). Tree Physiology 27: 1575-1583. Reprint

Tiimonen H, Häggman H, Tsai C-J, Chiang VL, Aronen T (2007) The seasonal activity and the effect of mechanical bending and wounding on the PtCOMT promoter in Betula pendula Roth. Plant Cell Reports 26: 1205-1214. Reprint

Rajinikanth M, Harding SA, Tsai C-J (2007) The glycine decarboxylase complex multienzyme family in Populus. Journal of Experimental Botany 58: 1761-1770. Reprint

Tsai C-J, El Kayal W, Harding SA (2006) Populus, the new model system for investigating phenylpropanoid complexity (invited review). International Journal of Applied Science and Engineering 4: 221-233. Reprint

Brodeur-Campbell SE, Vucetich JA, Richter DL, Waite TA, Rosemier JN, Tsai C-J (2006) Insect herbivory on low-lignin transgenic aspen. Environmental Entomology 35: 1696-1701. Reprint

Tuskan GA, DiFazio S et al. (107 authors including Tsai C-J), Rokhsar D (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604. Reprint

Tsai C-J, Harding SA, Tschaplinski TJ, Lindroth RL, Yuan Y (2006) Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus. New Phytologist 172: 47-62. Reprint

Harding SA, Jiang H, Jeong ML, Casado FL, Lin H-W, Tsai C-J (2005) Functional genomics analysis of foliar condensed tannin and phenolic glycoside regulation in natural cottonwood hybrids. Tree Physiology 25: 1475-1486. Reprint

Godin LM, McCabe LR, Tsai C-J, Donahue SW (2005) The time course of shear stress induced changes in bone protein and transcription factor mRNA levels in osteocyte-like MLO-Y4 cells. Proceedings of the 2005 Summer Bioengineering Conference, Paper 0360120, Vail, CO, June 22-26, 2005 (refereed).

Ho C-K, Chang S-H, Lung J, Tsai C-J, Chen K-P (2005) The strategies to increase taxol production by using Taxus mairei cells transformed with TS and DBAT genes. International Journal of Applied Science and Engineering 3: 179-185. Reprint

Jeong ML, Jiang H, Chen H-S, Tsai C-J, Harding SA (2004) Metabolic profiling the sink to source transition in developing leaves of quaking aspen (Populus tremuloides). Plant Physiology 136: 3364-3375. Reprint

Tsai C-J, Hubscher SL (2004) Cryopreservation in Populus functional genomics. New Phytologist 164: 73-81. Reprint

Ranjan P, Kao Y-Y, Jiang H, Joshi CP, Harding SA, Tsai C-J (2004) Suppression subtractive hybridization-mediated transcriptome analysis from multiple tissues of aspen (Populus tremuloides) trees altered in phenylpropanoid metabolism. Planta 219: 694-704. Reprint

Jiang H, Deng Y, Chen H-S, Tao L, Sha Q, Chen J, Tsai C-J, Zhang S (2004) Joint analysis of two microarray gene-expression data sets to select lung adenocarcinoma marker genes. BMC Bioinformatics 5: 81. Reprint

Wang Y-S, Harding SA, Tsai C-J (2004) Expression of a glycine decarboxylase complex H-protein in non-photosynthetic tissues of Populus tremuloides. Biochimica Biophysica Acta 1676: 267-273. Reprint

Cseke LJ, Wu W, Tsai C-J (2003) Isolation and purification of DNA. In: Cseke LJ, Kaufman PB, Podila GK, Tsai C-J (eds) Handbook of Molecular and Cellular Methods in Biology and Medicine. 2nd ed. CRC Press, Boca Raton, FL. pp. 1-24.

Tsai C-J, Cseke LJ, Harding SA (2003) Isolation and purification of RNA. In: Cseke LJ, Kaufman PB, Podila GK, Tsai C-J (eds) Handbook of Molecular and Cellular Methods in Biology and Medicine. 2nd ed. CRC Press, Boca Raton, FL. pp. 25-44.

Tsai C-J, Cseke LJ (2003) Southern hybridization. In: Cseke LJ, Kaufman PB, Podila GK, Tsai C-J (eds) Handbook of Molecular and Cellular Methods in Biology and Medicine. 2nd ed. CRC Press, Boca Raton, FL. pp. 85-104.

Touchell DH, Wang Y-S, Harding SA, Tsai C-J (2003) Differential display. In: Cseke LJ, Kaufman PB, Podila GK, Tsai C-J (eds) Handbook of Molecular and Cellular Methods in Biology and Medicine, 2nd ed. CRC Press, Boca Raton, FL. pp. 305-317.

Harding SA, Tsai C-J, Cseke LJ, Chang SC, Chen F (2003) In situ hybridization. In: Cseke LJ, Kaufman PB, Podila GK, Tsai C-J (eds) Handbook of Molecular and Cellular Methods in Biology and Medicine. 2nd ed. CRC Press, Boca Raton, FL. pp. 487-508.

Aronen T, Tiimonen H, Tsai C-J, Jokipii S, Chen X, Chiang VL, Häggman H (2003) Altered lignin in transgenic silver birch (Betula pendula) expressing PtCOMT gene. In: Espinel S, Barredo Y, Ritter E (eds) Sustainable Forestry, Wood Products & Biotechnology. DFA-AFA Press. Vitoria-Gasteiz, Spain, pp. 149-161.

Harding SA, Kao Y-Y, Tsai C-J (2003) Phenylalanine ammonia-lyase gene expression in condensed tannin-accumulating and lignifying cells of quaking aspen. In: Plant Biotechnology 2002 and beyond, Vasil IK (ed), Kluwer Academic Publishers, Dordrecht, Netherlands, pp. 457-459.

Kao Y-Y, Harding SA, Tsai C-J (2002) Differential expression of two distinct phenylalanine ammonia-lyase genes in condensed tannin-accumulating and lignifying cells of quaking aspen. Plant Physiology 130: 796-807. Reprint

Harding SA, Leshkevich J, Chiang VL, Tsai C-J (2002) Differential substrate inhibition couples kinetically distinct 4-coumarate:CoA ligases with spatially distinct structural and metabolic roles in quaking aspen. Plant Physiology 128: 428-438. Reprint

Touchell DH, Chiang VL, Tsai C-J (2002) Cryopreservation of embryonic cultures of Picea mariana (black spruce) using a vitrification protocol. Plant Cell Reports 21: 118-124. Reprint

Hu W-J, Harding SA, Lung J, Popko JL, Ralph J, Stokke DD, Tsai C-J, Chiang VL (1999) Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees. Nature Biotechnology 17: 808-812. Abstract

Tsai C-J, Popko JL, Mielke MR, Hu W-J, Podila GK, Chiang VL (1998) Suppression of O-methyltransferase gene by homologous sense transgene in quaking aspen cause red-brown wood phenotypes. Plant Physiology 117: 101-112. Reprint

Ho C-K, Chang S-H, Tsay J-Y, Tsai C-J, Chiang VL, Chen Z-Z (1998) Agrobacterium tumefaciens-mediated transformation of Eucalyptus camaldulensis and production of transgenic plants. Plant Cell Reports 17: 675-680. Reprint

Hu W-J, Kawaoka A, Tsai C-J, Lung J, Osakabe K, Ebinuma H, Chiang VL (1998) Compartmentalized expression of two structurally and functionally distinct 4-coumaric acid:coenzyme A ligase (4CL) genes in aspen (Populus tremuloides). Proceedings of the National Academy of Science USA 95: 5407-5412. Abstract

Li L, Popko JL, Zhang X-H, Osakabe K, Tsai C-J, Joshi CP, Chiang VL (1997) A novel multifunctional O-methyltransferase implicated in a dual methylation pathway associated with lignin biosynthesis in loblolly pine. Proceedings of the National Academy of Science USA 94: 5461-5466. Abstract

Boerjan W, Baucher M, Chabbert B, Petit-Conil M, Leple JC, Pilate G, Cornu D, Monties B, Van Montagu M, Van Doorsselaere J, Inze D, Jouanin L, Tsai C-J, Podila GP, Chiang VL (1997) Genetic modification of lignin biosynthesis in quaking aspen (Populus tremuloides) and poplar (Populus tremula × Populus alba). In: Klopfenstein N.B., eds., Micropropagation, Genetic Engineering, and Molecular Biology of Populus. USDA Forest Service, Rocky Mountain Forest and Range Experiment Station. Fort Collins, Colorado, pp. 193-205.

Tsai C-J, Mielke MR, Podila GK, Chiang VL (1996) 3' cycle-labeled oligonucleotides with predictable length and their application in primer extension and transgene analysis. Nucleic Acids Research 24: 5060-5061. Reprint

Tsai C-J, Podila GK, Chiang VL (1995) Nucleotide sequence of a Populus tremuloides gene encoding bispecific caffeic acid/5-hydroxyferulic acid O-methyltransferase. Plant Physiology 107: 1459. Reprint

Tsai C-J, Podila GK, Chiang VL (1994) Agrobacterium-mediated transformation of quaking aspen (Populus tremuloides) and regeneration of transgenic plants. Plant Cell Reports 14: 94-97.

Tsai C-J, Wang Y-N, Chiang C-H (1994) Protoplast isolation from suspension cultures of Eucalyptus saligna. Quarterly Journal of Chinese Forestry 27: 19-24.

Tsai C-J, Wang Y-N, Chiang C-H (1992) Tissue culture propagation of Eucalyptus saligna. Quarterly Journal of the Experimental Forest of National Taiwan University 6: 33-50.

Tsai C-J, Wang Y-N, Chiang C-H (1992) Multiple shoot induction from 8-year-old trees of Eucalyptus saligna. Quarterly Journal of the Experimental Forest of NationalTaiwan University 6: 29-36.

Tsai C-J, Wang Y-N, Chiang C-H (1992) Callus induction and plant regeneration from embryos of Eucalyptus saligna. Quarterly Journal of Chinese Forestry 25: 3-14.

 

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