Curriculum Vitae

Contact

Phone: (415)-265-4321
Email: dbirdseye@gmail.com
LinkedIn: linkedin.com/in/devon-birdseye
GitHub: github.com/devonbirdseye
ORCID: orcid.org/0000-0003-1767-8486

Education

Ph.D., Biology, July 2023
University of California San Diego

B.S., Biology, June 2014
University of California Santa Barbara

Research Experience

UC San Diego, Steven Briggs’ Lab
September 2018 - Present

Identified molecular biomarkers associated with heterosis by analyzing multi-omics datasets and correlating RNA and protein expression to phenotypes
Characterized altered gene regulation and expression networks in hybrids by conducting differential expression analyses, gene ontology enrichment, and pathway mapping
Identified the role of post-transcriptional regulation in heterosis by comparing paired transcriptomics and proteomics datasets
Built a publicly-available web application for interactive data visualization

Joint BioEnergy Institute, Henrik Scheller’s Lab
September 2014 - August 2018

Characterized glycosyltransferases and nucleotide sugar transporters by radioactivity assays, western blot, and RNA-seq of mutants and overexpression lines
Analyzed cell wall phenotypes by high-performance anion-exchange chromatography and size-exclusion chromatography, and conducted data analysis and visualization in R
Performed yeast-one-hybrid assay to identify candidate genes involved in rubber biosynthesis

UC Santa Barbara, Scott Hodges’ Lab
November 2012 - June 2014

Identified genomic loci associated with phenotypes in an F2 population by DNA extraction, genomic library preparation, Illumina sequencing, and QTL mapping

UC Santa Barbara, Thomas Weimbs’ Lab
July 2012 - December 2013

Evaluated conservation of a novel gene implicated in polycystic kidney disease by conducting multiple sequence alignment and phylogenetic analysis

Publications

Birdseye D, de Boer L, Bai H, Zhou P, Shen Z, Schmelz EA, Springer NM, Briggs SP (2021). Plant height heterosis is quantitatively associated with expression levels of plastid ribosomal proteins. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2109332118

Chiniquy D, Underwood W, Corwin J, Ryan A, Szemenyei H, Lim CC, Stonebloom S, Birdseye D, Kliebenstein D, Vogel J, Scheller HV, Somerville S (2019). PMR5, a pectin acetyltransferase, offers trade-offs in fungal disease resistance. The Plant Journal. https://doi.org/tpj.14497

Brandon AG, Birdseye D, Scheller H (2019). A dominant negative approach to reduce xylan in plants. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13198

Ebert B, Birdseye D, Liwanag AJM, Laursen T, Rennie EA, Guo X, Catena M, Rautengarten C, Stonebloom SH, Pidatala V, Andersen MCF, Cheetamun R, Mortimer JC, Bacic A, Heazlewood JL, Clausen MH, Willats WGT, Scheller HV. (2018) The Three Members of the Arabidopsis thaliana Glycosyltransferase Family 92 are Functional beta-1,4-Galactan Synthases. Plant and Cell Physiology. https://doi.org/10.1093/pcp/pcy180

Xu L, Naylor D, Dong Z, Simmons T, Pierroz G, Hixson KK, Kim YM, Zink EM, Engbrecht KM, Wang Y, Gao C, Degraaf S, Madera M, Sievert J, Hollingsworth J, Birdseye D, Scheller HV, Hutmacher R, Dahlberg J, Jansson C, Taylor J, Lemaux P, Coleman-Derr D. (2018) Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1717308115

Stranne M, Ren Y, Fimognari L, Birdseye D, Yan J, Bardor M, Mollet JC, Komatsu T, Kikuchi J, Scheller HV, Sakuragi Y. (2018) TBL 10 is required for O‐acetylation of pectic rhamnogalacturonan‐I in Arabidopsis thaliana. The Plant Journal. https://doi.org/10.1111/tpj.14067

Li G, Jones KC, Eudes A, Pidatala VR, Sun J, Xu F, Zhang C, Wei T, Jain R, Birdseye D, Canlas, PE, Baidoo EEK, Duong PQ, Sharma MK, Singh S, Ruan D, Keasling J, Mortimer J, Loque D, Bartley LE, Scheller HV, Ronald PC. (2018) Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification. BMC Biotechnology. https://doi.org/10.1186/s12896-018-0464-8

Yan J, Aznar A, Chalvin C, Birdseye D, Baidoo E, Eudes A, Shih P, Loque D, Zhang A, Scheller HV. (2018) Increased drought tolerance in plants engineered for low lignin and low xylan content. Biotechnology for biofuels. https://doi.org/10.1186/s13068-018-1196-7

Laursen T, Stonebloom S, Pidatala V, Birdseye D, Clausen M, Mortimer J, Scheller HV. (2018) Bi-functional glycosyltransferases catalyze both extension and termination of pectic galactan oligosaccharides. The Plant Journal. https://doi.org/10.1111/tpj.13860

Aznar A, Chalvin C, Shih P, Maimann M, Ebert B, Birdseye D, Loque D, Scheller H. (2018) Gene stacking of multiple traits for high yield of fermentable sugars in plant biomass. Biotechnology for Biofuels. https://doi.org/10.1186/s13068-017-1007-6

Rautengarten C, Birdseye D, Pattathil S, McFarlane HE, Saez-Aguayo S, Orellana A, Persson S, Hahn MG, Scheller HV, Heazlewood JL, Ebert B. (2017) The elaborate route for UDP-arabinose delivery into the Golgi of plants. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1701894114

Stonebloom S, Ebert B, Xiong G, Pattathil S, Birdseye D, Lao J, Pauly M, Hahn MG, Heazlewood JL Scheller HV. (2016) A DUF-246 family glycosyltransferase-like gene affects male fertility and the biosynthesis of pectic arabinogalactans. BMC plant biology. https://doi.org/10.1186/s128709-016-0780-x

Conference Presentations

Maize Genetics Meeting, virtual, 2020
Proteomic analyses reveal a molecular phenotype in maize hybrids and a correlation between ribosomal protein abundance and growth heterosis, Birdseye D, Shen Z, Gates L, Zhou P, Springer NM, Schmelz EA, Bai H, Briggs SP. (Oral)

American Society of Plant Biologists, virtual, 2020
Proteomic analyses reveal a molecular phenotype in maize hybrids and a correlation between ribosomal protein abundance and growth heterosis, Birdseye D, Shen Z, Gates L, Zhou P, Springer NM, Schmelz EA, Bai H, Briggs SP. (Poster)

Cell Wall Research Conference, Asilomar, California, 2018
Characterization of a glycosyltransferase involved in beta-1,4-galactan biosynthesis in Arabidopsis, Birdseye D, Stonebloom S, Scheller HV. (Poster)

Plant Cell Wall Biology Conference, Dalian, China, 2017
Beta-1,4-galactan biosynthesis and engineering to improve biomass for biofuels, Birdseye D, Ebert B, Laursen T, Pidatala V, Aznar A, Chalvin C, Eudes A, Scheller HV. (Oral)

Cell Wall Biology Conference, Crete, Greece, 2016
Characterization of beta-1,4-galactan synthases in Arabidopsis; plants devoid of beta-1,4-galactan have normal growth and development, Birdseye D, Ebert B, Birdseye D, Liwanag A, Laursen T, Rennie E, Xiaoyuan G, Catena M, Rautengarten C, Stonebloom S, Pidatala V, Andersen MCF, Cheetamun R, Mortimer J, Bacic A, Heazlewood J, Clausen M, Willats WGT, Scheller HV. (Poster)

American Society of Plant Biologists Conference, Portland, OR, 2014
Identification of the genetic basis of compound leaf variation in columbines, Birdseye, D, Ballerini, E, Hodges, S. (Poster)

Awards and Fellowships

National Science Foundation Graduate Research Fellowship, 2019

C.H. Muller Award for Excellence in the Plant Sciences, 2014

Distinction in the Major, University of California Santa Barbara, 2014

Teaching Experience

December 2019 - Present: Mentored undergraduate students in Steven Briggs’ Lab at UC San Diego

January - March 2022: Served as a teaching assistant for the Cellular Biology course at UC San Diego

January - March 2021: Served as a teaching assistant for the Bioinformatics course at UC San Diego

January - March 2020: Served as a teaching assistant for the Metabolic Biochemistry course at UC San Diego

March 2015 - May 2016: Mentored an undergraduate student in the laboratory at the Joint Bioenergy Institute

March — June 2016: Tutored high school students in math and science at the Tutoring and Learning Center, Fairfax, CA