1

Cory D. Hirsch, Ph.D.

Contact Information

Department of Plant Biology608.239.1953

University of

360 Biological Science Center@HirschCory

1445 Gortner Avenue

St. Paul, MN 55108

Education

2011University of Wisconsin-Madison

Ph.D. Plant Breeding and Plant Genetics

2005University of Wisconsin-Madison

B.S. Biochemistry

Appointments

2015 - pres.University of Minnesota

Postdoctoral Associate

Mentor: Nathan Springer

2012 - 2015University of Minnesota & Michigan State University

NSF National Plant Genome Initiative Postdoctoral Research Fellow in Biology

Mentors: C. Robin Buell, Dave Douches, Nathan Springer

2011 - 2012Michigan State University

Visiting Research Associate

Mentor: C. Robin Buell

2006 - 2011University of Wisconsin-Madison

Graduate Research Assistant

Advisor: Jiming Jiang

Thesis: “Structure and evolution of the centromere of chromosome 8 in three Oryza species”

2006University 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
  1. 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.
  2. Hirsch CD, Springer N, Hirsch CN. 2015. Genomic limitations to RNAseq expression profiling. The Plant Journal. 84: 491-503.
  3. 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.
  4. 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-.
  5. 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)
  6. 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.
  7. 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)
  8. 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 wide-spread 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.

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 Long-Read 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.

Invited Talks

2015University of Minnesota

Plant Biological Sciences Seminar Series

A systems biology approach to understand pigmentation in potato

201417th Annual NSF Awardee Meeting

A systems biology approach to understanding anthocyanin biosynthesis and regulation in potato.

2014University of Minnesota

The Microbial & Plant Genomics Institute 8th Annual Retreat

From genomics to phenomics: Elucidating potato pigmentation biosynthesis.

201215th Annual NSF Awardee Meeting

A systems biology approach to understanding anthocyanin biosynthesis and regulation in potato.

Teaching and Mentoring

2015ULearn 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, 2015Guest Lecturer, University of Minnesota

Applied Plant Genomics and Bioinformatics, AGRO 5431

2013Instructor, Michigan State University

Beginner Applied Bioinformatics Workshop

Intermediate Applied Bioinformatics Workshop

2012, 2013Mentor, Michigan State University

High School Honors Science/Mathematics/Engineering Program

2012Guest Lecturer, Michigan State University

Principles and Applications of Plant Genomics, Plant Biology 812

2012Instructor, Michigan State University

Plant Breeding, Genetics, and Biotechnology Program Bioinformatics Workshop

2009Instructor, 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

2014Microbial & Plant Genomics Institute Retreat Graduate Student Poster Judge, University of Minnesota

2010Plant Science Graduate Student Council, University of Wisconsin-Madison