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Conferences

2017

Wegrzyn, J. (2017, June). Computational Approaches to decode megagenomes and develop database resources for the forest tree community. Presentation for the 34th Southern Forest Tree Improvement Conference, Melbourne, FL.

Wegrzyn, J. (2017, March). Computational approaches to decode megagenomes and understand adaptation in forest trees. Presentation for the University of Georgia, Department of Plant Biology, Athens, GA.

Wegrzyn, J. (2017, March). Computational approaches to decode megagenomes and understand adaptation in forest trees. Presentation for the University of Toronto, Department of Biology Seminar, Mississauga, ON.

Chen, M., Henry, N., Lane, T., Zhou, X., Wegrzyn, J., Ficklin, S. P., & Staton, M. (2017, January). C26 Elasticsearch Indexing/Search and Expression Data Visualization with Two New Tripal Extension Modules. Presentation for the Plant and Animal Genome XXV Conference, San Diego, CA.

Grau, E., Herndon, N., Demurjian Jr., S. A., Lin, Q., Wynne, M., Gessler, D., Feltus, A., Staton, M., Ficklin, S. P., Main, D., & Wegrzyn, J. (2017, January). P0358 TreeGenes and CartograTree: Genetic and Genomic Resources for Forest Trees. Poster for the Plant and Animal Genome XXV Conference, San Diego, CA.

Grau, E., Herndon, N., Demurjian Jr., S. A., Lin, Q., Wynne, M., Gessler, D., Feltus, A., Staton, M., Ficklin, S. P., Main, D., & Wegrzyn, J. (2017, January). P0360 TreeGenes: Genetic and Genomic Resources for Forest Trees. Poster for the Plant and Animal Genome XXV Conference, San Diego, CA.

Zaman, S., Wegrzyn, J., Whalen, J., Cronn, R., Jogdeo, S., & Lawrence, C. (2017, January). P0398 Bioinformatic Evaluation of Transcriptomic Frame Selection Methods in Non-Model Species. Poster for the Plant and Animal Genome XXV Conference, San Diego, CA.

Humann, J. L., Ficklin, S. P., Lee, T., Cheng, C.-H., Hough, H., Jung, S., Wegrzyn, J., Neale, D. B., & Main, D. (2017, January). P0467 GenSAS v5.0: Structural and Functional Annotation Using a Web-Based Platform for Model and Non-Model Organisms. Poster for the Plant and Animal Genome XXV Conference, San Diego, CA.

Chen, M., Henry, N., Lane, T., Zhou, X., Bretaudeau, A., Wegrzyn, J., Ficklin, S. P., & Staton, M. (2017, January). P0473 Enhancement of Data Searching, Visualization and Exploration in the Hardwood Genomics Database (HGD) by Integration of New Tripal Extensions and Galaxy. Poster for the Plant and Animal Genome XXV Conference, San Diego, CA.

Lin, Q., Herndon, N., Grau, E., Ficklin, S. P., Staton, M., Jung, S., Main, D., Feltus, A., & Wegrzyn, J. (2017, January). P0479 A Novel Tripal Database Module and Workflow to Facilitate Variant Mapping and Detection in Non-Model Plant Species. Poster for the Plant and Animal Genome XXV Conference, San Diego, CA.

Acosta, J. J., Walker, T., Wegrzyn, J., Eckert, A. J., Sniezko, R., & Isik, F. (2017, January). P0582 Towards Genomic Selection in Pine Breeding. Poster for the Plant and Animal Genome XXV Conference, San Diego, CA.

Humann, J. L., Ficklin, S. P., Lee, T., Cheng, C.-H., Hough, H., Jung, S., Wegrzyn, J., Neale, D. B., & Main, D. (2017, January). W080 Structural and Functional Annotation of Model and Non-Model Organisms with GenSAS v5.0, a Web-Based Annotation Platform. Presentation for the Plant and Animal Genome XXV Conference, San Diego, CA.

Sezen, U. U., Neale, D. B., McGuire, P., Wheeler, N., Stevens, K. A., Crepeau, M., Cardeno, C., Zimin, A., Puiu, D., Pertea, M., Sablok, G., Casola, C., Koralewski, T., Paul, R., Gonzalez-Ibeas, D., Zaman, S., Cronn, R., Yandell, M., Holt, C., Langley, C. H., Yorke, J. A., Salzberg, S. L., & Wegrzyn, J. (2017, January). W352: A Reference Draft Genome for Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco). Presentation for the Plant and Animal Genome XXV Conference, San Diego, CA.

Ficklin, S. P., Cheng, C.-H., Watts, N., Chen, M., Wytko, C., Soto, B., Sanderson, L.-A., Jung, S., Wang, K.-C., Staton, M., Main, D., Feltus, A., & Wegrzyn, J. (2017, January). W956 Tripal Introduction and Core Development Efforts. Presentation for the Plant and Animal Genome XXV Conference, San Diego, CA.

Herndon, N., Lin, Q., Wynne, M., Grau, E., Ficklin, S. P., Staton, M., Jung, S., Main, D., Feltus, A., Gessler, D., & Wegrzyn, J. (2017, January). W959 CartograTree Workflows with Tripal API for Association Mapping in Forest Trees. Presentation for the Plant and Animal Genome XXV Conference, San Diego, CA.

2016

Wegrzyn, J. (2016, November). Computational tools for conservation genomics in forest trees. Presentation for the University of California Davis, Department of Plant Biology, Davis, CA.

Lind, B., Friedline, C., Wegrzyn, J., Maloney, P., Vogler, D., & Eckert, A. (2016, June). When local means local: Polygenic signatures of local adaptation within whitebark pine (Pinus albicaulis Englm.) across the Lake Tahoe Basin, USA. Presentation for the Evolution 2016 Conference, Austin, TX.

Wegrzyn, J. (2016, May). Applications of TreeGenes and CartograTree. Presentation for the US Forest Service: Gene Conservation of Forest Species Conference, Chicago, IL.

Wegrzyn, J., & Grau, E. (2016, May). TreeGenes: Enabling visualization and analysis in forest tree genomics. Presentation for the Gene Conservation in Forest Trees: Banking on the Future Meeting, Chicago, IL.

Martinez-Garcia, P. J., Gonzalez-Ibeas, D., & Wegrzyn, J. (2016, January). A Comprehensive Study of the Sugar Pine (Pinus lambertiana) Transcriptome Implemented through Diverse Next-Generation Sequencing Approaches. Presentation for the Plant and Animal Genome XXIV Conference, San Diego, CA.

Dolan, P., Cronn, R., & Wegrzyn, J. (2016, January). Does Douglas-fir Celebrate the Solstice? Circadian and Circannual Cycles of Gene Expression Variation in Douglas-fir Needles. Presentation for the Plant and Animal Genome XXIV Conference, San Diego, CA.

Paul, R., Stevens, K., Gonzalez-Ibeas, D., Pratt, K., & Wegrzyn, J. (2016, January). Elucidation of Transposable Elements in Conifers and their Effect on Conifer Evolution. Presentation for the Plant and Animal Genome XXIV Conference, San Diego, CA.

Humann, J. L., Ficklin, S. P., Lee, T., Cheng, C., Jung, S., Wegrzyn, J., Neale, D. B., & Main, D. (2016, January). GenSAS v4.0: An Easy-to-Use, Web-Based Platform for Structural and Functional Genome Annotation and Curation. Presentation for the Plant and Animal Genome XXIV Conference, San Diego, CA.

Sezen, U. U., Baker, E. A., Falk, T., & Wegrzyn, J. (2016, January). Signatures of Selection Among de novo Assembled Transcriptomes of Four White Pine Species. Presentation for the Plant and Animal Genome XXIV Conference, San Diego, CA.

Demurjian Jr., S. A., Grau, E., Vasquez-Gross, H., Gessler, D., Neale, D. B., & Wegrzyn, J. (2016, January). TreeGenes and CartograTree: Community Resources for Forest Tree Genomics. Presentation for the Plant and Animal Genome XXIV Conference, San Diego, CA.

Grau, E., Demurjian Jr., S. A., Vasquez-Gross, H., Gessler, D., & Wegrzyn, J. (2016, January). TreeGenes: Enabling Visualization and Analysis in Forest Tree Genomics. Presentation for the Plant and Animal Genome XXIV Conference, San Diego, CA.

2015

Wegrzyn, J. (2015, November). Evolution of conifer gene families. Presentation for the ProCoGen Final Open Conference and Workshops Promoting Conifer Genomic Resources, Orléans, France.

Wegrzyn, J. (2015, September). Assembly and annotation of complex genomes. Presentation for the Conifer Genome Summit, Gysinge, Sweden.

Hoffman, M. L., Peck, K. N., Wegrzyn, J., Reed, S. A., Zinn, S., & Govoni, K. (2015, July). The effects of maternal under- and over-feeding on muscle development of lambs as determined by RNA-Seq analysis. Poster for the ASAS/ADSA Joint Annual Meeting, Orlando, FL.

Wegrzyn, J., Grau, E., Vasquez-Gross, H., Lee, T., Humann, J., Ficklin, S., Staton, M., Henry, N., & Main, D. (2015, June). Computational tools and resources for comparative tree genomics. Presentation for the New Phytologist Symposium: The genomes of forest trees: new frontiers of forest biology, Boston, MA.

Wegrzyn, J. (2015, June). Comparative Genomics of Conifers. Presentation for the IUFRO: Tree Biotechnology: Forests and their importance to the planet and society, Florence, Italy.

Ficklin, S. P., Lee, T., Humann, J. L., Cheng, C.-H., Wegrzyn, J., Neale, D. B., & Main, D. (2015, January). C03 GenSAS: A Web-Based Platform for Automated and Manual Curation of Genomic Sequence. Presentation for the Plant and Animal Genome XXIII Conference, San Diego, CA.

Grau, E., Vasquez-Gross, H., Liechty, J., Zieve, J., Gessler, D., Neale, D. B., & Wegrzyn, J. (2015, January). C19 TreeGenes and CartograTree: Tools for Forest Tree Genomics. Presentation for the Plant and Animal Genome XXIII Conference, San Diego, CA.

Gonzalez-Ibeas, D., Martinez-Garcia, P. J., Famula, R., Loopstra, C., Puryear, J., Neale, D. B., & Wegrzyn, J. (2015, January). P0987 Survey of the Sugar Pine (Pinus lambertiana) Transcriptome By Deep Sequencing. Presentation for the Plant and Animal Genome XXIII Conference, San Diego, CA.

Paul, R., Kuruganti, S., Stevens, K., Gonzalez-Ibeas, D., Martinez-Garcia, P. J., Liechty, J., Vasquez-Gross, H., Grau, E., Loopstra, C., Zimin, A., Holtz-Morris, A., Koriabine, M., Yorke, J. A., Crepeau, M., Puiu, D., Salzberg, S. L., deJong, P. J., Mockaitis, K., Main, D., Langley, C. H., Neale, D. B., & Wegrzyn, J. (2015, January). P0988 Genome Annotation and Repeat Sequence Characterization in Sugar Pine (Pinus lambertiana). Presentation for the Plant and Animal Genome XXIII Conference, San Diego, CA.

Ficklin, S. P., Lee, T., Humann, J. L., Cheng, C.-H., Wegrzyn, J., Neale, D. B., & Main, D. (2015, January). P1153 GenSAS: A Web-Based Platform for Automated and Manual Curation of Genomic Sequence. Presentation for the Plant and Animal Genome XXIII Conference, San Diego, CA.

Grau, E., Vasquez-Gross, H., Liechty, J., Zieve, J., Gessler, D., Neale, D. B., & Wegrzyn, J. (2015, January). W311 TreeGenes: A Comprehensive Resource for Forest Tree Genomics. Presentation for the Plant and Animal Genome XXIII Conference, San Diego, CA.

2014

Wegrzyn, J. (2014, November). Strategies for annotating conifer genomes. Presentation for the Seminar at Scion, Rotorua, New Zealand.

Wegrzyn, J. (2014, November). Approaches to sequencing and assembling complex genomes. Presentation for the Seminar at Virginia Commonwealth University, Richmond, VA.

Wegrzyn, J. (2014, June). Sequencing the sugar pine transcriptome. Presentation for the IUFRO Challenges and Opportunities in the Genetics of Five-Needle Pines, Fort Collins, CO.

Wegrzyn, J., Liechty, J., Stevens, K., Loopstra, C., Vasquez-Gross, H., Lin, B., Dougherty, M., Zieve, J., Martinez-Garcia, P. J., Holt, C., Yandell, M., Zimin, A., Yorke, J. A., Crepeau, M., Puiu, D., Salzberg, S. L., deJong, P. J., Mockaitis, K., Main, D., Langley, C., & Neale, D. B. (2014, January). Annotation of the Lobolly Pine Megagenome. Presentation for the Plant and Animal Genome XXII Conference, San Diego, CA.

Wegrzyn, J., Zieve, J., Vasquez-Gross, H., Lin, D., Zheng, J., & Neale, D. B. (2014, January). Bioinformatic Solutions in Forest Genomics: Accessing the Treegenes Database. Presentation for the Plant and Animal Genome XXII Conference, San Diego, CA.

Zieve, J., Vasquez-Gross, H., Gessler, D., Neale, D. B., & Wegrzyn, J. (2014, January). Cartogratree: Enabling Forest Tree Genomics through Association Studies. Presentation for the Plant and Animal Genome XXII Conference, San Diego, CA.

Vasquez-Gross, H., Zieve, J., Gessler, D., Neale, D. B., & Wegrzyn, J. (2014, January). Case Study: Enabling Forest Tree Genomics through Association Studies with the use of SSWAP. Presentation for the Plant and Animal Genome XXII Conference, San Diego, CA.

Martinez-Garcia, P. J., Stevens, K., Crepeau, M., Liechty, J., Cardeno, C., Wegrzyn, J., Langley, C. H., & Neale, D. B. (2014, January). Genetic Mapping of Scaffolds By Whole Genome Shotgun Sequencing. Presentation for the Plant and Animal Genome XXII Conference, San Diego, CA.

Krutovsky, K. V., Chhatre, V. E., Lu, M., Bryam, T. D., Wegrzyn, J., Neale, D. B., & Loopstra, C. (2014, January). High-Throughput Genome-Wide Genotyping, Targeted Sequencing and Association Mapping of Adaptive and Breeding Traits in Loblolly Pine (Pinus taeda L.) Populations. Presentation for the Plant and Animal Genome XXII Conference, San Diego, CA.

Wegrzyn, J., Liechty, J., Stevens, K., Loopstra, C., Vasquez-Gross, H., Lin, B., Zieve, J., Martinez-Garcia, P. J., Holt, C., Yandell, M., Zimin, A., Yorke, J. A., Crepeau, M., Puiu, D., Salzberg, S. L., deJong, P. J., Mockaitis, K., Main, D., Langley, C., & Neale, D. B. (2014, January). Introns, Ancient Transposable Elements and Gene Families Revealed in the Annotation of the Loblolly Pine (Pinus taeda L.) Megagenome. Presentation for the Plant and Animal Genome XXII Conference, San Diego, CA.

Cronn, R., Dolan, P., Jogdeo, S., Wegrzyn, J., Denver, D., & St. Clair, B. (2014, January). Transcriptome Dynamics of the Dormancy - Growth Transition in Douglas-Fir Needles. Presentation for the Plant and Animal Genome XXII Conference, San Diego, CA.

2013

Wegrzyn, J., Stevens, K. A., Langley, C., Salzberg, S., Yorke, J., Zimin, A., Main, D., Loopstra, C., Mockaitis, K. M., & Neale, D. B. (2013, May). Sequencing Strategies and Annotation of the Loblolly Pine Genome. Presentation for the IUFRO Tree Biotechnology 2013, Asheville, NC.

Vasquez-Gross, H., Yu, J., Figueroa, B., Gessler, D., Neale, D. B., & Wegrzyn, J. (2013, January). Case Study: TreeGenes Uses SSWAP To Serve Semantic Data To Existing Web Applications, New Web Applications, and Semantic Pipelines. Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.

Wegrzyn, J., Vasquez-Gross, H., Figueroa, B., Yu, J., Gessler, D., & Neale, D. B. (2013, January). iPlant Collaborator: CartograTree for Tree Biology. Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.

Wegrzyn, J., Figueroa, B., Yu, J., Vasquez-Gross, H., Liechty, J., Lin, B., Zieve, J., Ip, J., & Neale, D. B. (2013, January). Bioinformatic Solutions in Forest Genomics: Accessing the TreeGenes Database. Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.

Vasquez-Gross, H., Figueroa, B., Yu, J., Gessler, D., Neale, D. B., & Wegrzyn, J. (2013, January). CartograTree: Connecting Forest Tree Genomes, Phenotypes, and Environment. Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.

Chhatre, V. E., Byram, T. D., Neale, D. B., Wegrzyn, J., & Krutovsky, K. V. (2013, January). Landscape Genomics of East Texas Loblolly Pine (Pinus taeda L.). Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.

Kaya, Z., Gulsoy, A. D., Ulug, A., Wegrzyn, J., & Neale, D. B. (2013, January). SNP Diversity of Candidate Genes Encoding Cellulose and Lignin Biosynthetic Enzymes in Populus nigra Clone Bank in Turkey: Its Implications for Conservation and Breeding. Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.

Wegrzyn, J., Loopstra, C., Harry, D. E., & Kinlaw, C. S. (2013, January). Transcriptome Assembly and SNP Identification in Pongamia pinnata (L.) Pierre using RNA-seq. Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.

Vasquez-Gross, H., Yu, J., Figueroa, B., Gessler, D., Neale, D. B., & Wegrzyn, J. (2013, January). Use of CartograTree to Explore Forest Tree Genomes, Phenotypes, and Environment. Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.

Guerra, F., Davis, M., Eckert, A. J., Fiehn, O., Gonzalez-Martinez, S., Holliday, J., Liechty, J., Macaya-Sanz, D., Richards, J., Shuren, R., Stanton, B., Sykes, R., Thompson, S., Tsai, C.-J., Vendramin, G., Wegrzyn, J., Yu, J., & Neale, D. B. (2013, January). Association Genetics of Wood Chemical Properties in Populus Species. Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.

Main, D., Lee, T., Zheng, P., Jung, S., Ficklin, S. P., Humann, J., Wegrzyn, J., & Neale, D. B. (2013, January). GenSAS: Genome Sequence Annotation Server, a Tool for Online Annotation and Curation. Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.

Martinez-Garcia, P. J., Stevens, K., Wegrzyn, J., Liechty, J., Crepeau, M., Langley, C., & Neale, D. B. (2013, January). A Comprehensive High-Density Genetic Linkage Map For Loblolly Pine (Pinus taeda L.). Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.

Mockaitis, K., Fuentes-Soriano, S., Loopstra, C., & Wegrzyn, J. (2013, January). Building References For Functional Genomics Of Conifer Development: Deep Sequencing and Comparative Gene Expression In Reproductive Tissues and Seeds Of Loblolly Pine. Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.

Wegrzyn, J., Lin, B., Zieve, J., Stevens, K., Neale, D. B., Martinez-Garcia, P. J., & Dougherty, M. (2013, January). Insights Into The Loblolly Pine Genome: Characterization Of Fosmid Sequences. Presentation for the Plant and Animal Genome XXI Conference, San Diego, CA.