Susan McEvoy, PhD

bioinformatics - computational biology - genomics

Available for contract work:
susanlmcevoy@gmail.com

Experience

Postdoctoral Researcher

University of Helsinki
December 2023 - present

  • Population genetics analysis and modeling for the EU FORGENIUS project
  • Bioinformatic analysis for GENOPIN, a study on the mechanics and evolution of polyembryony in Pinus sylvestris
Conservation Genomics Postdoctoral Scientist

Santa Barbara Botanic Garden
Courtesy Research Fellow, UC Santa Cruz, Dr. Rachel Meyer's lab
July 2022 - November 2023

Landscape and population genomics of the Gaviota tarplant (Deinandra increscens subsp. villosa; Asteraceae) for long term conservation. Assembly of Dittrichia graveolens (Asteraceae).

  • Sample collection, DNA/RNA extraction and library preparation, sequencing design
  • Genome assembly and gene annotation
  • Population, landscape, and conservation genetics
Graduate Research Assistant

Ecology & Evolutionary Biology, University of Connecticut
August 2018 – July 2022

Dissertation: Application of Emerging Computational and Genomic Approaches to Examine Challenges to Forest Health. Conducted plant computational genomics and transcriptomics, specializing in biotic and abiotic stress response in broadleaf and conifer forest tree species.

  • Assembly and annotation
  • Comparative genomics and methylomics
  • Structural and single nucleotide variant analysis,
Graduate Teaching Assistant

Ecology & Evolutionary Biology, University of Connecticut
January – December 2019

Instructor for Principles of Biology II laboratory section

Bioinformatician - Faculty Research Assistant

Oregon State University, Forests, Ecosystems & Society Department
March 2017 - July 2018

Generated a transcriptomic assembly and called variants related to white pine blister rust resistance. Assisted with creation of a SNP genotyping array for Douglas-fir. Assisted with software projects. Wrote scripts and modified software using R, Perl, C#, and Java

Software Developer - Faculty Research Assistant

University of Oregon, Center on Teaching & Learning
April 2014 - March 2017

Working closely with education researchers, designed and developed web applications and tablet-based instruction tools for the purpose of assessing and tracking student learning and the effectiveness of curricular programs.

Library Web Manager - Analyst Programmer 3

Oregon State University, University Libraries & Press
August 2009 - April 2014

Responsible for the web presence of OSU Libraries and Press, including web applications related to resource discovery and access, library instruction, digital collection creation, and supplementary sites for OSU Press books.

Publications

McEvoy, S. L., Grady, P. G. S., Pauloski, N. Wegrzyn, J., (2022). Profiling genome-wide methylation in two maples: fine-scale approaches to detection with nanopore technology. bioRxiv.

Vuruputoor, V. S., Monyak, D., Fetter, K. C., Webster, C., Zaman, S., Bhattarai, A., Bennett, J., McEvoy, S. L., Shrestha, B., Caballero, M., & Wegrzyn, J. (2022). Welcome to the big leaves: best practices for improving genome annotation in non-model plant genomes. bioRxiv.

McEvoy, S. L., Sezen, U. U., Trouern-Trend, A., McMahon, S. M., Schaberg, P. G., Yang, J., Wegrzyn, J., & Swenson, N. G. (2021). Strategies of tolerance reflected in two North American maple genomes. The Plant Journal, 109(6), 1591-1613.

Caballero, M., Lauer, E., Bennett, J., Zaman, S., McEvoy, S., Acosta, J., Jackson, C., Townsend, L., Eckert, A., Whetten, R.W. and Loopstra, C., Holliday, J., Mandal, M., Wegrzyn, J., & Isik, F. (2021). Toward genomic selection in Pinus taeda: Integrating resources to support array design in a complex conifer genome. Applications in plant sciences.

Howe, G. T., Jayawickrama, K., Kolpak, S. E., Kling, J., Trappe, M., Hipkins, V., Ye, T., Guida, S. Cronn, R., Cushman, S., & McEvoy, S. (2020). An Axiom SNP genotyping array for Douglas-fir. BMC genomics, 21(1), 1-17.

Presentations

Investigating beech bark disease resistance: variation and assembly error in two Fagus grandifolia genomes Plant Genomes Online, April 2022.

Genomic characterization and comparison of two maples highlights genes involved in the stress response to acidic soils Botanical Society of America, virtual, July 2021.

Genomic characterization of two maples highlights genes involved in the stress response to acidic soils across seasons Forest Genetics Student and Postdoc Symposium, virtual, May 2021.

Genomic characterization and comparison of two maples highlights genes involved in the stress response to acidic soils Botanical Society of America, virtual, July 2020.

Sweet Genomes: Assembling, Annotating and Comparing Three Maples Plant & Animal Genome Conference, San Diego, CA, USA, January 2020.

Viikki teaching fields Gaviota tarplant Central California coast Sugar maple journal cover