@article{zhang_franks_liu_kang_keebler_schaff_huang_xiang_2013, title={De novo Sequencing, Characterization, and Comparison of Inflorescence Transcriptomes of Cornus canadensis and C. florida (Cornaceae)}, volume={8}, ISSN={1932-6203}, url={https://dx.plos.org/10.1371/journal.pone.0082674}, DOI={10.1371/journal.pone.0082674}, abstractNote={Background Transcriptome sequencing analysis is a powerful tool in molecular genetics and evolutionary biology. Here we report the results of de novo 454 sequencing, characterization, and comparison of inflorescence transcriptomes of two closely related dogwood species, Cornus canadensis and C. florida (Cornaceae). Our goals were to build a preliminary source of genome sequence data, and to identify genes potentially expressed differentially between the inflorescence transcriptomes for these important horticultural species. Results The sequencing of cDNAs from inflorescence buds of C. canadensis (cc) and C. florida (cf), and normalized cDNAs from leaves of C. canadensis resulted in 251799 (ccBud), 96245 (ccLeaf) and 114648 (cfBud) raw reads, respectively. The de novo assembly of the high quality (HQ) reads resulted in 36088, 17802 and 21210 unigenes for ccBud, ccLeaf and cfBud. A reference transcriptome for C. canadensis was built by assembling HQ reads of ccBud and ccLeaf, containing 40884 unigenes. Reference mapping and comparative analyses found 10926 sequences were putatively specific to ccBud, and 6979 putatively specific to cfBud. Putative differentially expressed genes between ccBud and cfBud that are related to flower development and/or stress response were identified among 7718 shared sequences by ccBud and cfBud. Bi-directional BLAST found 87 (41.83% of 208) of Arabidopsis genes related to inflorescence development had putative orthologs in the dogwood transcriptomes. Comparisons of the shared sequences by ccBud and cfBud yielded 65931 high quality SNPs between two species. The twenty unigenes with the most SNPs are listed as potential genetic markers for evolutionary studies. Conclusions The data provide an important, although preliminary, information platform for functional genomics and evolutionary developmental biology in Cornus. The study identified putative candidates potentially involved in the genetic regulation of inflorescence evolution and/or disease resistance in dogwoods for future analyses. Results of the study also provide markers useful for dogwood phylogenomic studies.}, number={12}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Zhang, Jian and Franks, Robert G. and Liu, Xiang and Kang, Ming and Keebler, Jonathan E. M. and Schaff, Jennifer E. and Huang, Hong-Wen and Xiang, Qiu-Yun (Jenny)}, editor={Wang, TingEditor}, year={2013}, month={Dec}, pages={e82674} }
 @article{myers_casals_gauthier_hamdan_keebler_boyko_bustamante_piton_spiegelman_henrion_et al._2011, title={A population genetic approach to mapping neurological disorder genes using deep resequencing}, volume={7}, number={2}, journal={PLoS Genetics}, author={Myers, R. A. and Casals, F. and Gauthier, J. and Hamdan, F. F. and Keebler, J. and Boyko, A. R. and Bustamante, C. D. and Piton, A. M. and Spiegelman, D. and Henrion, E. and et al.}, year={2011} }
 @article{conrad_keebler_depristo_lindsay_zhang_casals_idaghdour_hartl_torroja_garimella_et al._2011, title={Variation in genome-wide mutation rates within and between human families}, volume={43}, number={7}, journal={Nature Genetics}, author={Conrad, D. F. and Keebler, J. E. M. and DePristo, M. A. and Lindsay, S. J. and Zhang, Y. J. and Casals, F. and Idaghdour, Y. and Hartl, C. L. and Torroja, C. and Garimella, K. V. and et al.}, year={2011}, pages={712–137} }
 @article{awadalla_gauthier_myers_casals_hamdan_griffing_cote_henrion_spiegelman_tarabeux_et al._2010, title={Direct measure of the de novo mutation rate in autism and schizophrenia cohorts}, volume={87}, number={3}, journal={American Journal of Human Genetics}, author={Awadalla, P. and Gauthier, J. and Myers, R. A. and Casals, F. and Hamdan, F. F. and Griffing, A. R. and Cote, M. and Henrion, E. and Spiegelman, D. and Tarabeux, J. and et al.}, year={2010}, pages={316–324} }
 @article{prugnolle_mcgee_keebler_awadalla_2008, title={Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents}, volume={8}, journal={BMC Evolutionary Biology}, author={Prugnolle, F. and Mcgee, K. and Keebler, J. and Awadalla, P.}, year={2008} }
 @article{mu_awadalla_duan_mcgee_keebler_seydel_mcvean_su_2007, title={Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome}, volume={39}, ISSN={["1546-1718"]}, DOI={10.1038/ng1924}, abstractNote={One goal in sequencing the Plasmodium falciparum genome, the agent of the most lethal form of malaria, is to discover vaccine and drug targets. However, identifying those targets in a genome in which approximately 60% of genes have unknown functions is an enormous challenge. Because the majority of known malaria antigens and drug-resistant genes are highly polymorphic and under various selective pressures, genome-wide analysis for signatures of selection may lead to discovery of new vaccine and drug candidates. Here we surveyed 3,539 P. falciparum genes ( approximately 65% of the predicted genes) for polymorphisms and identified various highly polymorphic loci and genes, some of which encode new antigens that we confirmed using human immune sera. Our collections of genome-wide SNPs ( approximately 65% nonsynonymous) and polymorphic microsatellites and indels provide a high-resolution map (one marker per approximately 4 kb) for mapping parasite traits and studying parasite populations. In addition, we report new antigens, providing urgently needed vaccine candidates for disease control.}, number={1}, journal={NATURE GENETICS}, author={Mu, Jianbing and Awadalla, Philip and Duan, Junhui and McGee, Kate M. and Keebler, Jon and Seydel, Karl and McVean, Gilean A. T. and Su, Xin-zhuan}, year={2007}, month={Jan}, pages={126–130} }
 @article{bockhorst_lu_janes_keebler_gamain_awadalla_su_samudrala_jojica_smith_2007, title={Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA}, volume={155}, ISSN={["0166-6851"]}, DOI={10.1016/j.molbiopara.2007.06.007}, abstractNote={VAR2CSA is the main candidate for a pregnancy malaria vaccine, but vaccine development may be complicated by sequence polymorphism. Here, we obtained partial or full-length var2CSA sequences from 106 parasites and applied novel computational methods and three-dimensional modeling to investigate VAR2CSA geographic variation and selection pressure. Our analysis reveals structural patterns of VAR2CSA sequence variation in which polymorphic sites group into segments of limited diversity. Within these segments, two or three basic types characterize a substantial majority of the parasite samples. Comparison to the primate malaria Plasmodium reichenowi shows that these basic types have ancient origins. Globally, var2CSA genes are comprised of a mosaic of these ancestral polymorphic segments that have recombined extensively between var2CSA alleles. Three-dimensional modeling reveals that polymorphic segments concentrate in flexible loops at characteristic locations in the six VAR2CSA Duffy binding-like (DBL) adhesion domains. Individual DBL domain surfaces have distinct patterns of diversifying selection, suggesting that limited and differing portions of each DBL domain are targeted by host antibody. Since standard phylogenetic tree analysis is inadequate for highly recombining genes like var2CSA, we developed a novel phylogenetic approach that incorporates recombination and tracks new mutations in segment types. In the resulting tree, P. reichenowi is confirmed as an outlier and African and Asian P. falciparum isolates have slightly diverged. These findings validate a new approach to modeling protein evolution in the presence of frequent recombination and provide a clearer understanding of how var gene products function as immunoevasive binding ligands.}, number={2}, journal={MOLECULAR AND BIOCHEMICAL PARASITOLOGY}, author={Bockhorst, Joseph and Lu, Fangli and Janes, Joel H. and Keebler, Jon and Gamain, Benoit and Awadalla, Philip and Su, Xin-zhuan and Samudrala, Ram and Jojica, Nebojsa and Smith, Joseph D.}, year={2007}, month={Oct}, pages={103–112} }
 @article{jackson_watt_gautier_gilchrist_driehaus_graham_keebler_prugnolle_awadalla_forrester_2006, title={A murine specific expansion of the Rhox cluster involved in embryonic stem cell biology is under natural selection}, volume={7}, journal={BMC Genomics}, author={Jackson, M. and Watt, A. J. and Gautier, P. and Gilchrist, D. and Driehaus, J. and Graham, G. J. and Keebler, J. and Prugnolle, F. and Awadalla, P. and Forrester, L. M.}, year={2006} }