PAG XXV (2017)

Talks

Sezen, U. U., Neale, D. B., McGuire, P. E., Wheeler, N. C., Stevens, K. A., Crepeau, M. W., Cardeno, C., Zimin, A. V., Puiu, D., Pertea, G. M., Sablok, G., Casola, C., Koralewski, T. E., Paul, R., Gonzalez-Ibeas, D., Cronn, R., Yandell, M., Holt, C., Langley, C. H., Yorke, J. A., Salzberg, S. L., Wegrzyn, J. L. 2017. A reference draft genome for Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco). International Plant and Animal Genome XXV Conference, W352, Forest Tree Workshop, Jan. 15, 2017 San Diego, CA

 

PAG XXIV (2016)

Talks (Presenter name in bold)

Demurjian Jr., S. A., Grau, E., Vasquez-Gross, H., Gessler, D., Neale, D., Wegrzyn, J. 2016. TreeGenes and CartograTree: Community resources for forest tree genomics. International Plant and Animal Genome XXIV Conference, C07 Computer Demonstration, Jan. 9, 2016, San Diego, CA

Grau, E., Demurjian Jr., S. A., Vasquez-Gross, H., Gessler, D., Staton, M., Jung, S., Feltus, A., Main, D., Ficklin, S. P., Neale, D., Wegrzyn, J. 2016. TreeGenes: Enabling visualization and analysis in forest tree genomics. International Plant and Animal Genome XXIV Conference, W970, Tripal Database Network and Initiatives Workshop, Jan. 10, 2016, San Diego, CA

Humann, J. L., Ficklin, S. P., Lee, T., Cheng, C.-H., Jung, S., Wegrzyn, J., Neale, D., Main, D. 2016. GenSAS v4.0: A web-based platform for structural and functional genome annotation and curation. International Plant and Animal Genome XXIV Conference, C25 Computer Demonstration, Jan. 13, 2016, San Diego, CA

Martinez-Garcia, P. J., Gonzalez-Ibeas, D., Famula, R. A., Delfino-Mix, A., Stevens, K. A., Puryear, J. D., Loopstra, C. A., Langley, C. H., Neale, D. B., Wegrzyn, J. L. 2016. A comprehensive study of the sugar pine (Pinus lambertiana) transcriptome implemented through diverse next-generation sequencing approaches. International Plant and Animal Genome XXIV Conference, W321, Forest Tree Workshop, Jan. 10, 2016, San Diego, CA

Paul, R., Stevens, K. A., Gonzalez-Ibeas, D., Pratt, K., Zimin, A., Yorke, J. A., Holtz-Morris, A., Koriabine, M., Crepeau, M., Puiu, D., Salzberg, S. L., deJong, P. J., Langley, C. H., Neale, D. B., Wegrzyn, J. L. 2016. Elucidation of transposable elements in conifers and their effect on conifer evolution. International Plant and Animal Genome XXIV Conference, W959, Transposable Elements Workshop, Jan. 10, 2016, San Diego, CA

Sezen, U. U., Baker, E. A. G., Falk, T., Maloney, P. E., Vogler, D. R., Delfino-Mix, A., Jensen, C. E., Mitton, J. B., Wright, J., Knaus, B., Rai, H. S., Cronn, R., Gonzalez-Ibeas, D., Vasquez-Gross, H., Famula, R., Liu, J.-J., Kueppers, L. M., Salzberg, S. L., Langley, C. H., Stevens, K., Puiu, D., Zimin, A., Yorke, J. A., Crepeau, M., Loopstra, C., Puryear, J., Neale, D., Wegrzyn, J. 2016. Signatures of selection among de novo assembled transcriptomes of four white pine species. International Plant and Animal Genome XXIV Conference, W740, Population and Conservation Genomics Workshop, Jan. 9, 2016, San Diego, CA

Posters

Demurjian Jr., S. A., Grau, E., Vasquez-Gross, H., Gessler, D., Neale, D., Wegrzyn, J. 2016. TreeGenes and CartograTree: Community resources for forest tree genomics. International Plant and Animal Genome XXIV Conference, Poster 0383. Jan. 8-13, 2016, San Diego, CA

Humann, J. L., Ficklin, S. P., Lee, T., Cheng, C.-H., Jung, S., Wegrzyn, J., Neale, D., Main, D. 2016. GenSAS v4.0: An easy-to-use, web-based platform for structural and functional genome annotation and Curation. International Plant and Animal Genome XXIV Conference, Poster 0364. Jan. 8-13, 2016, San Diego, CA

PAG XXIII (2015)

Talks (Presenter name in bold)

Ficklin, S. P., Lee T., Humann, J. L., Cheng, C.-H., Wegrzyn, J., Neale, D., Main, D. 2015. GenSAS: A web-based platform for automated and manual curation of genomic sequence.International Plant and Animal Genome XXIII Conference, C03 Computer Demonstration, Jan. 10, 2015, San Diego, CA

Grau, E., Vasquez-Gross, H., Liechty, J., Zieve, J., Gessler, D., Neale, D., Wegrzyn, J. 2015. TreeGenes: a comprehensive resource for forest tree genomics. International Plant and Animal Genome XXIII Conference, W311, Forest Tree Workshop, Jan. 11, 2015, San Diego, CA

Grau, E., Vasquez-Gross, H., Liechty, J., Zieve, J., Gessler, D., Neale, D., Wegrzyn, J. 2015. TreeGenes and CartograTree: tools for forest tree genomics. International Plant and Animal Genome XXIII Conference, C19 Computer Demonstration, Jan. 13, 2015, San Diego, CA

Main, D., Ficklin, S. P., Lee, T., Humann, J. L., Cheng, C.-H., Wegrzyn, J., Neale, D. 2015.0GenSAS. International Plant and Animal Genome XXIII Conference, W571, Pine Genome Reference Sequence Workshop, Jan. 10, 2015, San Diego, CA

Stevens, K., Crepeau, M., Puiu, D., Zimin, A., Wegrzyn, J., Koriabine, M., Cardeno, C., Holtz-Morris, A., deJong, P. J., Salzberg, S. L., Yorke, J. A., Langley, C., Neale, D. B. 2015. A reference genome sequence for sugar pine (Pinus lambertiana). International Plant and Animal Genome XXIII Conference, W568, Pine Genome Reference Sequence Workshop, Jan. 10, 2015, San Diego, CA

Wegrzyn, J., Stevens, K., Paul, R., Gonzalez-Ibeas, D., Martinez-Garcia, P. J., Liechty, J., Vasquez-Gross, H., Kuruganti, S., Grau, E., Loopstra, C., Zimin, A., Yorke, J. A., Crepeau, M., Puiu, D., Holt, C., Yandell, M., Salzberg, S. L., deJong, P. J., Mockaitis, K., Main, D., Langley, C. H., Neale, D. Sugar pine annotation. International Plant and Animal Genome XXIII Conference, W569, Pine Genome Reference Sequence Workshop, Jan. 10, 2015, San Diego, CA

Zimin, A., Marcais, G., Puiu, D., Stevens, K., Roberts, M., Salzberg, S., Yorke, J. 2015. Moving toward loblolly pine 2.0, improvements of assembly techniques for mega-genomes. International Plant and Animal Genome XXIII Conference, W570, Pine Genome Reference Sequence Workshop, Jan. 10, 2015, San Diego, CA

Posters

Ficklin, S. P., Lee T., Humann, J. L., Cheng, C.-H., Wegrzyn, J., Neale, D., Main, D. 2015. GenSAS: A web-based platform for automated and manual curation of genomic sequence. International Plant and Animal Genome XXIII Conference, Poster P1153, Jan. 10-14, 2015, San Diego, CA

Gonzalez-Ibeas, D., Martinez-Garcia, P. J., Famula, R., Loopstra, C. A., Puryear, J., Neale, D. B., Wegrzyn, J. L. 2015. Survey of the sugar pine (Pinus lambertiana) transcriptome by deep sequencing. International Plant and Animal Genome XXIII Conference, Poster P0987, Jan. 10-14, 2015, San Diego, CA

Grau, E., Vasquez-Gross, H., Liechty, J., Zieve, J., Gessler, D., Neale, D., Wegrzyn, J. 2015. TreeGenes and CartograTree: tools for forest tree genomics. International Plant and Animal Genome XXIII Conference, Poster P1232, Jan. 10-14, 2015, San Diego, CA

Paul, R., Stevens, K. A., Martinez-Garcia, P. J., Zimin, A., Holtz-Morris, A., Yorke, J. A., Koriabine, M., Crepeau, M., Puiu, D., Salzberg, S. L., deJong, P. J., Langley, C. H., Kurugunti, S., Neale, D. B., Wegrzyn, J. L. 2015. Repeat sequence characterization in sugar pine (Pinus lambertiana) and loblolly pine (Pinus taeda).International Plant and Animal Genome XXIII Conference, Poster  P0988, Jan. 10-14, 2015, San Diego, CA

 

PAG XXII (2014)

Talks (Presenter name in bold)

Langley, C.H., Wegrzyn, J. L., Stevens, K., Zimin, A., Puiu, D., Crepeau, M., Cardeno, C., Koriabine, M., Holtz-Morris, A., Liechty, J., Martinez-Garcia, P. J., Vasquez-Gross, H., Lin, B. Y., Zieve, J. J., Dougherty, M., Fuentes-Soriano, S., Wu, L., Gilbert, D., Marcais, G., Roberts, M., Holt, C., Yandell, M., Davis, J. M., Smith, K., Dean, J. F. D., Lorenz, W. W., Whetten, R. W., Sederoff, R., Wheeler, N., McGuire, P., Main, D., Mockaitis, K., Loopstra, C., deJong, P. J., Yorke, J. A., Salzberg, S. L., Neale, D. B. 2014. The loblolly pine genome, v1.0. International Plant and Animal Genome XXII Conference, W558, Pine Genome Reference Sequence Workshop, Jan. 11, 2014, San Diego, CA

Martinez-Garcia, P. J., Stevens, K., Crepeau, M., Liechty, J., Cardeno, C., Wegrzyn, J. L., Langley, C. H., Neale, D. 2014. Genetic mapping of scaffolds by whole genome shotgun sequencing. International Plant and Animal Genome XXII Conference, W563, Pine Genome Reference Sequence Workshop, Jan. 11, 2014, San Diego, CA

Mockaitis, K., Wu, L.-S., Loopstra, C., Fuentes-Soriano, S., Gilbert, D. 2014. Gene expression in conifers revealed on a comprehensive scale: Sequencing, assembly, and classification of the loblolly pine transcriptome. International Plant and Animal Genome XXII Conference, W561, Pine Genome Reference Sequence Workshop, Jan. 11, 2014, San Diego, CA

Stevens, K., Crepeau, M., Martinez-Garcia, P. J., Zimin, A., Puiu, D., Koriabine, M., Cardeno, C., Holtz-Morris, A., deJong, P. J., Salzberg, S. L., Yorke, J. A., Langley, C., Neale, D. 2014. Recent progress in the shotgun sequencing of conifer mega-genomes. International Plant and Animal Genome XXII Conference, W562, Pine Genome Reference Sequence Workshop, Jan. 11, 2014, San Diego, CA

Wegrzyn, J.L., Liechty, J., Stevens, K., Loopstra, C., Vasquez-Gross, H., Lin, B., Dougherty, M., Zieve, J., Martinez-Garcia, P. J., Holt, C., Yandell, M., Zimin, Yorke, J. A., Crepeau, M., Puiu, D., Salzerberg, S. L., deJong, P. J., Mockaitis, K., Main, D., Langley, C. H., Neale, D. 2014. Annotation of the loblolly pine megagenome. International Plant and Animal Genome XXII Conference, W559, Pine Genome Reference Sequence Workshop, Jan. 12, 2014, San Diego, CA

Wegrzyn, J.L., Liechty, J., Stevens, K., Loopstra, C., Vasquez-Gross, H., Lin, B., Zieve, J., Martinez-Garcia, P. J., Holt, C., Yandell, M., Zimin, Yorke, J. A., Crepeau, M., Puiu, D., Salzberg, S. L., deJong, P. J., Mockaitis, K., Main, D., Langley, C. H., Neale, D. International Plant and Animal Genome XXII Conference, W512, Next Generation Genome Annotation and Analysis Workshop, Jan. 11, 2014, San Diego, CA

Wegrzyn, J., Zieve, J., Vasquez-Gross, H., Lin, D., Zheng, J., Neale, D. 2014. Bioinformatic solutions in forest genomics: Accessing the TreeGenes database. International Plant and Animal Genome XXII Conference, C13 Computer Demonstration, Jan. 13, 2014, San Diego, CA

Zieve, J., Vasquez-Gross, H., Gessler, D., Neale, D., Wegrzyn, J. 2014. Cartogratree: Enabling forest tree genomics through association studies. International Plant and Animal Genome XXII Conference, C11 Computer Demonstration, Jan. 13, 2014, San Diego, CA

Zimin, A., Salzberg, S. L., Puiu, D., Stevens, K., Roberts, M., Yorke, J. A. Marcais, G., Langley, C. 2014. Assembly improvements to move beyond loblolly pine assembly v1.0. International Plant and Animal Genome XXII Conference, W564, Pine Genome Reference Sequence Workshop, Jan. 11, 2014, San Diego, CA

Posters

Chhatre, V. E., Westbrook, J., Echt, C. S., Gomide Neves, L., Martinez-Garcia, P. J., Munoz, P. R., Kirst, M., Peter, G. F., Neale, D., Davis, J. M., Nelson, C. D. 2014. A high-density, consensus linkage map for loblolly pine. International Plant and Animal Genome XXII Conference, Poster P0490, Jan. 10-14, 2015, San Diego, CA

Wegrzyn, J., Zieve, J., Vasquez-Gross, H., Lin, D., Zheng, J., Neale, D. 2014. Bioinformatic solutions in forest genomics: Accessing the Treegenes database. International Plant and Animal Genome XXII Conference, Poster P1008, Jan. 10-14, 2015, San Diego, CA

Zieve, J., Vasquez-Gross, H., Gessler, D., Neale, D., Wegrzyn, J. 2014. Cartogratree: Enabling forest tree genomics through association studies. International Plant and Animal Genome XXII Conference, Poster P1049, Jan. 10-14, 2015, San Diego, CA

 

PAG XXI (2013)

Talks (Presenter name in bold)

Crepeau, M., Puiu, D., Holtz-Morris, A., Koriabine, M., Cardeno, C., Zimin, A., deJong, P., Langley, C., Salzberg, S. L., Stevens, K. 2013. Sequencing strategies in conifer. International Plant and Animal Genome XXI Conference, W537, Pine Genome Reference Sequence Workshop. Jan. 12, 2013, San Diego CA

Martinez-Garcia, P. J., Stevens, K., Wegrzyn, J., Liechty, J., Crepeau, M., Langley, C., Neale, D. 2013. A comprehensive high-density genetic linkage map for Loblolly pine (Pinus taeda L.). International Plant and Animal Genome XXI Conference, W541, Pine Genome Reference Sequence Workshop. Jan. 12, 2013, San Diego CA

Mockaitis, K., Fuentes-Soriano, S., Loopstra, C., Wegrzyn, J. 2013. Building references for functional genomics of conifer development: deep sequencing and comparative gene expression in reproductive tissues and seeds of Loblolly pine. International Plant and Animal Genome XXI Conference, W540, Pine Genome Reference Sequence Workshop, Jan. 12, 2013, San Diego CA

Wegrzyn J., Lin, B., Zieve, J., Stevens, K., Neale, D., Martinez-Garcia, P. J., Dougherty, M. 2013. Insights into the Loblolly pine genome: Characterization of fosmid sequences. International Plant and Animal Genome XXI Conference, W539, Pine Genome Reference Sequence Workshop. Jan. 12, 2013, San Diego CA

Zimin, A. 2013. Assembly of the 24Gb Loblolly pine genome from WGS short read data. International Plant and Animal Genome XXI Conference, W538, Pine Genome Reference Sequence Workshop. Jan. 12, 2013, San Diego CA

Posters

Main, D., Lee, T., Zheng, P., Jung, S., Ficklin, S. P., Humann, J., Wegrzyn, J., Neale, D. 2013. GenSAS: Genome Sequence Annotation Server, a tool for online annotation and curation. Poster P0985. International Plant and Animal Genome XXI Conference, Jan. 12-16, 2013, San Diego CA

Wegrzyn, J., Figueroa, B., Yu, J., Vasquez-Gross, H., Liechty, J., Lin, B., Zieve, J., Ip, J., Neale, D. 2013. Bioinformatic solutions in forest genomics: Accessing the TreeGenes database. Poster P0948. International Plant and Animal Genome XXI Conference, Jan. 12-16, 2013, San Diego CA

 

PAG XX (2012)

Posters

Neale D, de Jong P, Langley C, Loopstra C, Main D, Mockaitis K, Salzberg SL, Yorke JA, Wegrzyn J, and Wheeler N. 2012. PineRefSeq: Genome sequences for loblolly pine, Douglas-fir, and sugar pine. Poster P0060. Plant & Animal Genome XX Conference. 14–18 January 2012. San Diego CA

Wegrzyn J, Figueroa B, Yu J, Liechty J, Vasquez-Gross H, Lin B, Zieve J, and Neale D. 2012. Bioinformatic solutions in forest genomics: Overview of the resources from the TreeGenes database. Poster P0963. Plant & Animal Genome XX Conference. 14–18 January 2012. San Diego CA