Joseph E. Flaherty, Ph.D.

Professor of Biology; Director of Undergraduate Research; Coordinator of the Biology Education Program

  • Ph.D., Purdue University
  • M.S., North Carolina State University
  • B.S., North Carolina State University

“I enjoy teaching and discovery in the life sciences, especially through the hands and minds of students. My highly rewarding career at Coker extends from the opportunity to engage students both inside and outside the classroom, sharing my experiences and abilities to foster the next generation of future scientists, teachers, and scholars.”

My passion centers on understanding the fundamental characteristics of life and applying tools to expand our knowledge of biological processes. I enjoy teaching introductory biology courses, beginning and advanced courses in molecular biology, genetics, and biochemistry.

In addition to my teaching and service responsibilities, I engage students who participate in research projects both in summertime and during the academic year. Typically, 8-10 students participate in my laboratory during the semester. Students may be supported by grant funds or receive academic credit for taking on a research project. Recent graduates who have performed a research project in my lab that have continued to pursue advanced degrees (or gained permanent employment) include:

  • Sara Atkinson (’14) – MUSC, Occupational Therapy Program
  • Megan Sexton (’13) – North Carolina State University, PhD program in Plant Pathology
  • Rebecca Armentrout (’12) – McLeod Medical Hospital, Medical Technology Program
  • Mandi J. Warner (’11) – Southern Illinois University, PhD program Plant, Soil and Agricultural Systems
  • Bryan Musungu (‘11) – Southern Illinois University, PhD program Plant, Soil and Agricultural Systems
  • Elizabeth Stamey (’10) – Biology teacher, Chesterfield High School, SC
  • Kayla M. Gerberich (’10) – Senior Biological Scientist at the University of Florida, awarded MS in Plant Pathology from Purdue University
  • Andrew J. Shychuk (’10) – awarded MD from the University of South Carolina School of Medicine
  • Shelly M. Catlett (’09) – awarded DDS from The Medical University of South Carolina, College of Dental Medicine
  • A. Michele Burnham (’09) – awarded MS in Plant Pathology from University of Georgia, currently USDA research scientist, Exotic and Emerging Avian Disease Research Unit, Athens, GA.
  • Ashley D. Zearfoss (’08) – awarded MS in Plant Pathology from North Carolina State University, awarded PhD program in Biochemistry at Clemson University
  • Amber B. Rayfield (’08) – University of Arkansas, awarded MS in Animal Science/Genetics
  • Jessica L. Winburn (’07) – The Ohio State University, awarded MS in Plant Biotechnology



Independent laboratory research is an essential educational component for students aspiring to become future scientists, medical doctors and science teachers. The research program that I have developed at Coker University focuses on gene discovery in filamentous fungi, with particular emphasis on elucidation of regulatory networks controlling development in foliar plant pathogens. The research conducted at Coker University is synergistic with both Drs. Jin-Rong Xu’s and Larry Dunkle’s respective programs at Purdue University and Dr. Burton Bluhm’s program at the University of Arkansas, providing opportunities for undergraduate students at Coker University to participate in University-level research projects.

Genomic approaches and field studies are being used in my program to understand fungal biology. We employ real-time qPCR and microarray analysis of gene expression to characterize developmental mutants of Fusarium graminearum. Field studies are focused on understanding the effects of crop selection on Fusarium populations. Student-driven projects are facilitated by collaborations with scientists from government (USDA-ARS), industry (Monsanto), and academia (Purdue University).

Together with Coker University’s institutional commitment to providing resources to stimulate research experiences for undergraduates, my research program has benefitted from extramural support from the SC-EPSCoR Collaborative Research Program (CRP), IDeA Network of Biomedical Research Excellence (INBRE), the South Carolina Independent Colleges and Universities (SCICU), and the National Science Foundation (NSF-CAREER award no. 0845324). Student-driven projects are facilitated by collaborations with scientists from government (USDA-ARS), industry (Monsanto), and academia (Purdue University and University of Arkansas).

For more information: Combating Crop Diseases (US News & World Report, 6/4/12)


  • Bluhm, BH, X Zhao, JE Flaherty, J-R Xu and LD Dunkle. 2007. RAS2 regulates growth and pathogenesis in Fusarium graminearum. Molecular Plant-Microbe Interactions 20:627-636.
  • Flaherty, JE and LD Dunkle. 2005. Identification and expression analysis of regulatory genes induced during conidiation in Exserohilum turcicum. Fungal Genetics and Biology 42:471-481.
  • Flaherty, JE and CP Woloshuk. 2004. Regulation of fumonisin biosynthesis in Fusarium verticilliodes by a zinc binuclear cluster-type gene, ZFR1. Applied and Environmental Microbiology 70:2653-2659.
  • Shim, W-B, JE Flaherty (equal contributors) and CP Woloshuk. 2003. Comparison of fumonisin B1 biosynthesis in maize germ and degermed kernels by Fusarium verticillioides. Journal of Food Protection 66:2116-2122.
  • Flaherty, JE, AM Pirtilla, BH Bluhm and CP Woloshuk. 2003. Role of PAC1, a pH regulatory gene from Fusarium verticillioides, in growth and fumonisin biosynthesis. Applied and Environmental Microbiology 69:5222-5227.
  • Bluhm, BH, JE Flaherty, M Cousin and CP Woloshuk. 2002. PCR detection of fumonisin and trichothecence producing Fusarium species. Journal of Food Protection 65:1955-1961.
  • Flaherty, JE, BK Harbaugh, JB Jones, GC Somodi and LE Jackson. 2001. Use of H-mutant bacteriophages to control bacterial blight of geranium. HortScience 36:98-100.
  • Flaherty, JE, JB Jones, BK Harbaugh, GC Somodi and LE Jackson. 2000. Control of bacterial spot on tomato in the greenhouse and field with bacteriophages. HortScience 35:882-884.
  • Du, W-L, Z-Y Huang, K Wells, JE Flaherty (equal contributors) and GA Payne. 1999. Green fluorescent protein as a reporter to monitor gene expression and food colonization by Aspergillus flavus. Applied and Environmental Microbiology 65:834-836.
  • Liu, BH, JF Brewer, JE Flaherty, GA Payne, D Bhatnagar and FS Chu. 1998. Immunochemical identification of AFLR, a regulatory protein involved in aflatoxin biosynthesis. Food and Agricultural Immunology 9:289-298.
  • Flaherty, JE and GA Payne. 1997. Overexpression of AFLR leads to upregulation of pathway gene transcription and increased aflatoxin production in Aspergillus flavus. Applied Environmental Microbiology 63:3995-4000.
  • Flaherty, JE, MA Weaver, GA Payne and CP Woloshuk. 1995. A beta-glucuronidase reporter gene construct for monitoring aflatoxin biosynthesis in Aspergillus flavus. Applied and Environmental Microbiology 61:2482-2486.

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