@article{wang_matthews_williams_shi_yang_tunlaya-anukit_chen_li_liu_lin_et al._2018, title={Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-018-03863-z}, DOI={10.1038/s41467-018-03863-z}, abstractNote={Abstract}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Wang, Jack P. and Matthews, Megan L. and Williams, Cranos M. and Shi, Rui and Yang, Chenmin and Tunlaya-Anukit, Sermsawat and Chen, Hsi-Chuan and Li, Quanzi and Liu, Jie and Lin, Chien-Yuan and et al.}, year={2018}, month={Apr}, pages={1579} }
 @article{luo_maity_wu_smith_duan_li_tzeng_2018, title={On the substructure controls in rare variant analysis: Principal components or variance components?}, volume={42}, ISSN={["1098-2272"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85039155216&partnerID=MN8TOARS}, DOI={10.1002/gepi.22102}, abstractNote={Abstract}, number={3}, journal={GENETIC EPIDEMIOLOGY}, author={Luo, Yiwen and Maity, Arnab and Wu, Michael C. and Smith, Chris and Duan, Qing and Li, Yun and Tzeng, Jung-Ying}, year={2018}, month={Apr}, pages={276–287} }
 @article{nguyen_reuter_gaikwad_rotroff_kucera_motsinger-reif_smith_nieman_rubinow_kaddurah-daouk_et al._2017, title={The steroid metabolome in women with premenstrual dysphoric disorder during GnRH agonist-induced ovarian suppression: Effects of estradiol and progesterone addback}, volume={7}, journal={Translational Psychiatry}, author={Nguyen, T. V. and Reuter, J. M. and Gaikwad, N. W. and Rotroff, D. M. and Kucera, H. R. and Motsinger-Reif, A. and Smith, C. P. and Nieman, L. K. and Rubinow, D. R. and Kaddurah-Daouk, R. and et al.}, year={2017} }
 @article{kubisiak_nelson_staton_zhebentyayeva_smith_olukolu_fang_hebard_anagnostakis_wheeler_et al._2012, title={A transcriptome-based genetic map of Chinese chestnut (Castanea mollissima) and identification of regions of segmental homology with peach (Prunus persica)}, volume={9}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/S11295-012-0579-3}, DOI={10.1007/s11295-012-0579-3}, abstractNote={The Chinese chestnut (Castanea mollissima) carries resistance to Cryphonectria parasitica, the fungal pathogen inciting chestnut blight. The pathogen, introduced from Asia, devastated the American chestnut (Castanea dentata) throughout its native range early in the twentieth century. A highly informative genetic map of Chinese chestnut was constructed to extend genomic studies in the Fagaceae and to aid the introgression of Chinese chestnut blight resistance genes into American chestnut. Two mapping populations were established with three Chinese chestnut parents, ‘Mahogany’, ‘Nanking’, and ‘Vanuxem’, totaling 337 progeny. The transcriptome-based genetic map was created with 329 simple sequence repeat and 1,064 single nucleotide polymorphism markers all derived from expressed sequence tag sequences. Genetic maps for each parent were developed and combined to establish 12 consensus linkage groups spanning 742 cM, providing the the most comprehensive genetic map for a Fagaceae species to date. Over 75 % of the mapped markers from the Chinese chestnut consensus genetic map were placed on the physical map using overgo hybridization, providing a fully integrated genetic and physical map resource for Castanea spp. About half (57 %) of the Chinese chestnut genetic map could be assigned to regions of segmental homology with 58 % of the peach (Prunus persica) genome assembly. A three quantitative trait loci (QTL) model for blight resistance was verified using the new genetic markers and an existing interspecies (C. mollissima × C. dentata) F2 mapping population. Two of the blight resistance QTLs in chestnut shared synteny with two QTLs for powdery mildew resistance in peach, indicating the potential conservation of disease resistance genes at these loci.}, number={2}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Kubisiak, T. L. and Nelson, C. D. and Staton, M. E. and Zhebentyayeva, T. and Smith, C. and Olukolu, B. A. and Fang, G.-C. and Hebard, F. V. and Anagnostakis, S. and Wheeler, N. and et al.}, year={2012}, month={Nov}, pages={557–571} }
 @article{counterman_araujo-perez_hines_baxter_morrison_lindstrom_papa_ferguson_joron_ffrench-constant_et al._2010, title={Genomic hotspots for adaptation: The population genetics of Mullerian mimicry in Heliconius erato}, volume={6}, number={4}, journal={PLoS Genetics}, author={Counterman, B. A. and Araujo-Perez, F. and Hines, H. M. and Baxter, S. W. and Morrison, C. M. and Lindstrom, D. P. and Papa, R. and Ferguson, L. and Joron, M. and Ffrench-Constant, R. H. and et al.}, year={2010} }
 @article{barakat_diloreto_zhang_smith_baier_powell_wheeler_sederoff_carlson_2009, title={Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection}, volume={9}, ISSN={["1471-2229"]}, DOI={10.1186/1471-2229-9-51}, abstractNote={American chestnut (Castanea dentata) was devastated by an exotic pathogen in the beginning of the twentieth century. This chestnut blight is caused by Cryphonectria parasitica, a fungus that infects stem tissues and kills the trees by girdling them. Because of the great economic and ecological value of this species, significant efforts have been made over the century to combat this disease, but it wasn't until recently that a focused genomics approach was initiated. Prior to the Genomic Tool Development for the Fagaceae project, genomic resources available in public databases for this species were limited to a few hundred ESTs. To identify genes involved in resistance to C. parasitica, we have sequenced the transcriptome from fungal infected and healthy stem tissues collected from blight-sensitive American chestnut and blight-resistant Chinese chestnut (Castanea mollissima) trees using ultra high throughput pyrosequencing. We produced over a million 454 reads, totaling over 250 million bp, from which we generated 40,039 and 28,890 unigenes in total from C. mollissima and C. dentata respectively. The functions of the unigenes, from GO annotation, cover a diverse set of molecular functions and biological processes, among which we identified a large number of genes associated with resistance to stresses and response to biotic stimuli. In silico expression analyses showed that many of the stress response unigenes were expressed more in canker tissues versus healthy stem tissues in both American and Chinese chestnut. Comparative analysis also identified genes belonging to different pathways of plant defense against biotic stresses that are differentially expressed in either American or Chinese chestnut canker tissues. Our study resulted in the identification of a large set of cDNA unigenes from American chestnut and Chinese chestnut. The ESTs and unigenes from this study constitute an important resource to the scientific community interested in the discovery of genes involved in various biological processes in Chestnut and other species. The identification of many defense-related genes differentially expressed in canker vs. healthy stem in chestnuts provides many new candidate genes for developing resistance to the chestnut blight and for studying pathways involved in responses of trees to necrotrophic pathogens. We also identified several candidate genes that may underline the difference in resistance to Cryphonectria parasitica between American chestnut and Chinese chestnut.}, journal={BMC PLANT BIOLOGY}, author={Barakat, Abdelali and DiLoreto, Denis S. and Zhang, Yi and Smith, Chris and Baier, Kathleen and Powell, William A. and Wheeler, Nicholas and Sederoff, Ron and Carlson, John E.}, year={2009}, month={May} }
 @article{nielsen_suchindran_smith_2008, title={Does strong linkage disequilibrium guarantee redundant association results?}, volume={32}, ISSN={0741-0395 1098-2272}, url={http://dx.doi.org/10.1002/gepi.20328}, DOI={10.1002/gepi.20328}, abstractNote={Abstract}, number={6}, journal={Genetic Epidemiology}, publisher={Wiley}, author={Nielsen, Dahlia M. and Suchindran, Sunil and Smith, Christopher P.}, year={2008}, month={Sep}, pages={546–552} }
 @article{schaff_nielsen_smith_scholl_bird_2007, title={Comprehensive Transcriptome Profiling in Tomato Reveals a Role for Glycosyltransferase in Mi-Mediated Nematode Resistance}, volume={144}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.106.090241}, DOI={10.1104/pp.106.090241}, abstractNote={Abstract}, number={2}, journal={Plant Physiology}, publisher={American Society of Plant Biologists (ASPB)}, author={Schaff, Jennifer E. and Nielsen, Dahlia M. and Smith, Chris P. and Scholl, Elizabeth H. and Bird, David McK.}, year={2007}, month={Apr}, pages={1079–1092} }