CORY D. HIRSCH, PH.D.
CONTACT INFORMATION
Department of Plant Biology
University of Minnesota
360 Biological Science Center
1445 Gortner Avenue
St. Paul, MN 55108
EDUCATION
2011
2005
APPOINTMENTS
2015 - pres.
2012 - 2015
2011 - 2012
2006 - 2011
2006
608.239.1953
cdhirsch@umn.edu
@HirschCory
University of Wisconsin-Madison
Ph.D. Plant Breeding and Plant Genetics
University of Wisconsin-Madison
B.S. Biochemistry
University of Minnesota
Postdoctoral Associate
Mentor: Nathan Springer
University of Minnesota & Michigan State University
NSF National Plant Genome Initiative Postdoctoral Research Fellow in
Biology
Mentors: C. Robin Buell, Dave Douches, Nathan Springer
Michigan State University
Visiting Research Associate
Mentor: C. Robin Buell
University of Wisconsin-Madison
Graduate Research Assistant
Advisor: Jiming Jiang
Thesis: “Structure and evolution of the centromere of chromosome 8 in
three Oryza species”
University of Wisconsin-Madison
Research Technician
GRANTS AND AWARDS
USDA National Food and Agriculture (Agriculture and Food Research Initiative
Foundational Program) “Understanding the role of transposable elements in maize
abiotic stress response” (12/15 to 11/18) $408,000 (PI: Nathan Springer, Co PI: Cory
Hirsch)
NSF National Plant Genome Initiative Postdoctoral Research Fellow in Biology “A
systems biology approach to understanding anthocyanin biosynthesis and regulation in
potato” (8/12 to 7/15) $197,400 (PI: Cory Hirsch)
NSF Research Experience for Undergraduates (REU) (6/05 - 8/05) $3,000
NSF Research Experience for Undergraduates (REU) (6/04 - 8/04) $3,000
PUBLICATIONS
Journal Articles
1. Hirsch CD, Buell CR, Hirsch CN. 2015. A toolbox of potato genetic and genomic
resources. American Journal of Potato Research. doi: 10.1007/s12230-015-9486-0
CORY D. HIRSCH, PH.D.
2
2. Li Q, Gent J, Zynda G, Song J, Makarevitch I, Hirsch CD, Hirsch CN, Dawe RK,
McGinnis K, Lisch D, Schmitz R, Vaughn M, Springer N. 2015. RNA-directed DNA
methylation enforces boundaries between heterochromatin and euchromatin in the maize
genome. Proc. of the National Academy of Sciences. 112: 14728-14733.
3. Hirsch CD, Springer N, Hirsch CN. 2015. Genomic limitations to RNAseq expression
profiling. The Plant Journal. 84: 491-503.
4. Hirsch CD, Evans J, Buell CR, Hirsch, CN. 2014. Reduced representation approaches to
interrogate genome diversity in large, repetitive plant genomes. Briefings in Functional
Genomics. 13: 257-267.
5. Hirsch CD, Hamilton J, Childs K, Cepela J, Crisovan E, Vaillancourt B, Hirsch CN,
Habermann M, Neal B, Buell CR. 2014. Spud DB: A resource for mining sequences,
genotypes, and phenotypes to accelerate potato breeding. The Plant Genome 7: 1-.
6. Hirsch CN, Hirsch CD, Felcher K, Coombs J, Zarka D, Van Deynze A, De Jong W,
Veilleux R, Jansky S, Bethke P, Douches D, Buell CR. 2013. Retrospective view of
North American potato breeding in the 20th and 21st centuries. Genes, Genomes, Genetics
3: 1003-1013. (on cover)
7. Fan C, Walling J, Zhang J, Hirsch C, Jiang J, Wing R. 2011. Conservation and purifying
selection of transcribed genes located in a rice centromere. Plant Cell 23: 2821-2830.
8. Torres G, Gong Z, Iovene M, Hirsch C, Buell CR, Bryan G, Novak P, Macas J, Jiang J.
2011. Organization and evolution of subtelomeric satellite repeats in the potato genome.
Genes, Genomes, Genetics 1: 85-92. (on cover)
9. Hirsch C, Wu Y, Yan H, Jiang J. 2009. Lineage-specific adaptive evolution of the
centromeric protein CENH3 in diploid and allotetraploid Oryza species. Mol Biol Evol
26: 2877-2885.
Manuscripts currently under review or in preparation (available upon request):
1. Hirsch CN, Hirsch CD, Brohammer A, Bowman, M, Soifer I, Barad O, Shem-Tov D,
Baruch K, Lu F, Hernandez A, Fields C, Wright C, Koehler K, Buckler E, Buell CR, de
Leon N, Kaeppler S, Childs K, Mikel M. De novo assembly of the genome of elite inbred
PH207 documents extensive natural genome and transcriptome variation including widespread presence-absence variation. (in prep target journal Genome Biology)
2. Hirsch C, Tong C. Genomic variation between Norland potato and its sports. (in prep
target journal Plant Genome)
Book Chapters
1. Hirsch, C and Jiang, J. 2012. Centromeres: sequences, structure, and biology. Plant
Genome Diversity, Volume 1: Plant Genomes, Their Residents, and Their Evolutionary
Dynamics. 59-70.
2. Nagaki K, Walling J, Hirsch C, Jiang J, Murata M. 2009. Structure and evolution of
plant centromeres. Prog Mol Subcell Biol 48: 153-179.
Conference Abstracts
1. Laimbeer P, Holt S, Peterson B, Coombs J, Hamilton J, Hirsch C, Buell CR, Douches D,
Veilleux R. 2015. Residual heterozygosity cycles of inbreeding in diploid potatoes.
Solanaceae Conference. October 25-29.
2. Hirsch CN, Hirsch CD, Brohammer A, Bowman M, Childs K, Soifer I, Barad O, Buell
CR, de Leon N, Kaeppler S, Mikel M. 2015. Insights into the relationship between
structural diversity and transcriptional diversity in maize. Plant Biology, July 26-30.
CORY D. HIRSCH, PH.D.
3
3. Hirsch CD, West P, Springer N, Hirsch CN. 2015. Improving our biological
understanding of RNAseq. 57th Maize Genetics Conference, March 12-15.
4. Hirsch CN, Hirsch CD, Brohammer A, Bowman M, Childs K, Soifer I, Barad O, Buell
CR, de Leon N, Kaeppler S, Mikel M. 2015. Insights into the relationship between
structural diversity and transcriptional diversity in maize. 57th Maize Genetics Conference.
March 12-15.
5. Waters A, Makarevitch I, Hirsch CN, Hirsch CD, Hermanson P, Vaughn M, Springer N.
2015. Exploring allelic variation for response to abiotic stress. 57th Maize Genetics
Conference, March 12-15
6. Hirsch C, Hume R, Cepela J, Douches D, Springer N, Buell CR. 2015. A systems
biology approach to understanding anthocyanin biosynthesis and regulation in potato.
23rd International Plant & Animal Genome Conference. January 10-14.
7. Hirsch CN, Hirsch CD, Brohammer A, Bowman M, Childs K, Soifer I, Barad O, de
Leon N, Buell CR, Mikel M, Kaeppler S. 2015. Comprehensive de novo genome
assemblies and resequencing of diverse individuals provides insights into structural
diversity and the relationship with transcriptional diversity in maize. 23rd International
Plant & Animal Genome Conference. January 10-14.
8. Waters A, Makarevitch I, Hirsch CN, Hirsch CD, Springer N. 2015. Maize Exhibits
Differential Expression and Allelic Regulatory Variation in Response to Abiotic Stress.
23rd International Plant & Animal Genome Conference. January 10-14.
9. Hamilton J, Hirsch C, Crisovan E, Vaillancourt B, Arnold B, Veilleux R, Buell CR.
2014. Haplotype Discovery in a highly heterozygous 850 Mb potato genome using LongRead Sequencing. 14th Genome Informatics Conference. September 21-24.
10. Hirsch C, Douches D, Springer N, Buell CR. 2014. A systems biology approach to
understanding anthocyanin biosynthesis and regulation in potato. 17th Annual NSF
Awardee Meeting. September 3-5.
11. Hirsch C, Douches D, Springer N, Buell CR. 2013. A systems biology approach to
understanding anthocyanin biosynthesis and regulation in potato. 16th Annual NSF
Awardee Meeting. September 5-6.
12. Hirsch CN, Hirsch CD, Kimberly F, Coombs J, Zarka D, Van Deynze A, De Jong W,
Veilleux R, Jansky S, Bethke P, Douches D, Buell CR. 2013. Retrospective View of
North American Potato Breeding In The 20th and 21st Centuries. 21st International Plant
& Animal Genome Conference. January 12-16.
13. Fan C, Walling J, Zhang J, Hirsch C, Jiang J, Wing R. 2011. Conservation and purifying
selection of transcribed genes located in a rice centromere. Plant Biology. August 6-10.
14. Walling J, Hirsch C, Fan C, Wu Y, Gao D, Gill N, Jackson S, Wing R, Jiang J. 2011.
Comparative genomics of a rice centromere. 19th International Plant & Animal Genome
Conference. January 15-19.
15. Hirsch C, Wu Y, Yan H, Jiang J. 2010. Adaptive evolution of the centromeric histone
CENH3 in Oryza species. 18th International Plant & Animal Genome Conference.
January 9-13.
16. Walling J, Wu Y, Hirsch C, Gao D, Fan C, Wing R, Jackson S, Jiang J. 2010.
Comparative genomics of a rice centromere. 18th International Plant & Animal Genome
Conference. January 9-13.
CORY D. HIRSCH, PH.D.
INVITED TALKS
2015
2014
2014
2012
4
University of Minnesota
Plant Biological Sciences Seminar Series
A systems biology approach to understand pigmentation in potato
17th Annual NSF Awardee Meeting
A systems biology approach to understanding anthocyanin biosynthesis
and regulation in potato.
University of Minnesota
The Microbial & Plant Genomics Institute 8th Annual Retreat
From genomics to phenomics: Elucidating potato pigmentation
biosynthesis.
15th Annual NSF Awardee Meeting
A systems biology approach to understanding anthocyanin biosynthesis
and regulation in potato.
TEACHING AND MENTORING
2015
ULearn Training Workshops, University of Minnesota
Learning Management System Courses Completed:
- Active Learning 101: A Whirlwind Tour
- Developing Memorable Presentations: Strategies to Make Teaching Stick
- Engaging Quiet Students
2014, 2015
Guest Lecturer, University of Minnesota
Applied Plant Genomics and Bioinformatics, AGRO 5431
2013
Instructor, Michigan State University
Beginner Applied Bioinformatics Workshop
Intermediate Applied Bioinformatics Workshop
2012, 2013 Mentor, Michigan State University
High School Honors Science/Mathematics/Engineering Program
2012
Guest Lecturer, Michigan State University
Principles and Applications of Plant Genomics, Plant Biology 812
2012
Instructor, Michigan State University
Plant Breeding, Genetics, and Biotechnology Program Bioinformatics
Workshop
2009
Instructor, University of Wisconsin-Madison
Plant Cytogenetic Training Workshop
Directly mentored 4 High School, 4 undergraduate, and numerous graduate students in: plant
science, computational biology, bioinformatics, and molecular biology
PROFESSIONAL ACTIVITIES
Ad hoc reviewer for:
BMC Plant Biology, Genome Research, Genomics, Journal of Genetics and Genomics,
Molecular Biology and Evolution, PLoS One
2014
2010
Microbial & Plant Genomics Institute Retreat Graduate Student Poster Judge,
University of Minnesota
Plant Science Graduate Student Council, University of Wisconsin-Madison