Matthew Jones-Rhoades

Years at Knox: 2008 to present

Education
Ph.D., 2005, Massachusetts Institute of Technology.
B.A., 1999, Grinnell College. 

Teaching Interests
Gene regulation in plants and amoeba, genomics, regulatory RNAs.

Selected Professional Accomplishments

Honors/Grants

National Science Foundation Major Research Instrumentation Grant, with Janet Kirkley, Andrew Mehl, Judy Thorn: Acquisition of a Multifunctional Imager for Research, Undergraduate Training, and Curricular Reform, August 2014 - $41,902.

The Pennsylvania State University, sub-award from the National Science Foundation, with Dr. Michael Axtell, Penn State: Reference annotations for sall RNA-producing genes in plants, May 2014 - $61,151.

Helen Hay Whitney Postdoctoral Fellow, in Daphne Preuss' lab at the University of Chicago, 2006-2008.

Publications
"Prediction of Plant miRNA Genes." Methods in Molecular Biology 592 (2010):19-30.

"Mechanistic insights from a quantitative analysis of pollen tube guidance." Stewman, S.F., Jones-Rhoades, M.W., Bhimalapuram, P., Tchernookov, M., Preuss, D., & Dinner, A.R. (2010). In submission.

"Genome-Wide Expression Profiling of the Arabidopsis Female Gametophyte Identifies Families of Small, Secreted Proteins." Jones-Rhoades, M.W., Borevitz, J.O., & Preuss, D. PLoS Genetics 3 (2007): 1848-1861.

"MicroRNAs and their regulatory roles in plants." Jones-Rhoades, M.W., Bartel D.P. and Bartel, B. Annual Review of Plant Biology 57 (2006):19-53.

"The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)." Tuskan, G.A., Jones-Rhoades, M.W., Roksar, D. Science 313 (2006): 1596-604.

"Regulatory mutations of mir-48, a C. elegans let-7 family microRNA, cause developmental timing defects." Li, M., Jones-Rhoades, M.W., Lau, N.C., Bartel, D.P., and Rougvie, A. Developmental Cell 9 (2005): 415-422.

"Computational identification of plant microRNAs and their targets, including a stress-induced miRNA." Jones-Rhoades, M.W., & Bartel D.P. Molecular Cell 6 (2004): 787-99.

"MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region." Mallory A.C., Reinhart B.J., Jones-Rhoades M.W., Tang G., Zamore P.D., Barton M.K., and Bartel D.P. EMBO Journal 16 (2004): 3356-64.

"Prediction of mammalian microRNA targets." Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel, D.P., and Burge, C.B. Cell 115 (2003): 787-798.

"The microRNAs of Caenorhabditis elegans." Lim, L.P., Lau, N.C., Weinstein, E.G., Abdelhakim, A., Yekta, S., Rhoades, M.W., Burge, C.B., and Bartel, D.P. Genes & Development 17 (2003): 991-1008.

"Prediction of plant microRNA targets." Rhoades, M.W., Reinhart, B.J., Lim, L.P., Burge, C.B., Bartel, B., and Bartel, D.P. Cell 110 (2002): 513-520.

"MicroRNAs in plants." Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., and Bartel, D.P. Genes & Development 16 (2002): 1616-1626.

Presentations
"Genome-Wide Expression Profiling of the Arabidopsis Female Gametophyte Identifies Families of Small, Secreted Proteins." With Borevitz, J.O., & Preuss, D., Poster, Plant Biology & Botany Joint Congress, Chicago, Illinois, 2007.

"Genome-Wide Expression Profiling of the Arabidopsis Female Gametophyte Identifies Families of Small, Secreted Proteins." With Borevitz, J.O., & Preuss., Poster, 18th International Conference on Arabidopsis Research, Beijing, China, 2007.

"Genomics of miRNA-mediated regulation in plants and animals." With Lewis B.P., Burge, C.B., & Bartel D.P., CSIRO Emerging Science: Small RNAs, Canberra, Australia, 2005.

"Computational identification of plant microRNAs and their mRNA targets." With Bartel D.P., Poster, Keystone Symposium on siRNAs and miRNAs, Keystone, Colorado, 2004.

"MicroRNAs and plant development." With Reinhart, B.J., Lim, L.P., Burge, C.B., Barton, M.K., Bartel, B., & Bartel D.P., 14th International Conference on Arabidopsis Research, Madison, Wisconsin, 2003.

What Students Say
"Matt is always smiling, laughing, and ready to help. He lives for his students. As my academic adviser, professor, and Honors committee chair, Matt was always there for me. His classes are interactive whether incorporating research discussion in his lectures or designing research project-based labs. He is motivated to help each of us learn and develop our biological interests in and out of class. There is never a silly question, never judgment...just sincerity and dedication to teach. Working with Matt absolutely changed my life: I developed a passion for molecular biology and research, which helped me secure my first job immediately after graduation. Truly, the best mentor I could have ever asked for."
-Shaunak Mulani, Biology Major and Chemistry Minor

"Professor Jones-Rhoades fosters independent thinking. In class, he teaches by demonstrating and explaining, while allowing you to explore and develop your own perspective and understanding. In lab, he cultivates a research mentality in you, honing your ability to logically troubleshoot and to critically analyze your results. All this requires time and patience, and despite his busy schedule, he ensures his availability for the students."
-Ya-Lin Lu, Biology Major and Chemistry Minor

"I approached Professor Jones-Rhoades with ideas for an Honors project that extended outside of his expertise. Instead of being daunted, however, Matt seemed as excited as I was to try something new! We worked together, seeking interdisciplinary advice as needed, to tailor my idea into something that could reasonably be accomplished without compromising my original interests. In courses and as a mentor, Matt successfully and skillfully balances guided instruction with independent exploration, authority with equality, realism with creativity, life off-campus with accessibility, and high expectations with patience and understanding."
-Sara DeMaria, Biology Major and Art History and Environmental Studies Minor