Richard B. Meagher

Distinguished Research Professor, Emeritus
  • Fellow, The American Association for the Advancement of Science
  • Fellow, National Academy of Inventors
  • Inventor's Award, University of Georgia
  • Lamar Dodd Award for Research, University of Georgia
  • Creative Research Medal, University of Georgia,
  • Grant Support -
    • "Targeted Pan-Antifungal Lipsomes," NIH
    • "Antifungal Liposomes Targeted to Cell Wall Mannans," NIH
    • "Antifungal Immunoliposomes," NIH
  • Research Interests -
    • Invasive fungal diseases are globally responsible for over 1,350,000 deaths each year, with annual mortality rates ranging from 25 to 50%, in spite of various antifungal drug therapies. I and my research team have designed a new drug delivery system, DectiSomes. We've begun demonstrating the efficacy of DectiSomes against four of the five most life-threatening pathogens causing candidiasis, aspergillosis, cryptococcosis, and mucormycosis. Antifungal drug loaded liposomes are coated with fungal cell binding proteins that concentrate the drugs on fungal cells and their biofilms. In vitro and in vivo in mouse models, DectiSomes lower the effective dose by order(s) of magnitude. We continue to modify and improve or design of DectiSomes to improve their anti-infective properties against diverse pathogens and diseases.
Education:

Ph.D. (1973) Yale University

M. Phil. (1971) Yale University

B.S. with Honors (1969) University of Illinois, Champaign

Research Areas:
Molecular Genetics
Biotechnology
Evolutionary Genetics
Research Interests:

I have very broad biology research interests, having worked on organisms from all four eukaryotic kingdoms and eubacteria and archaea. I have employed diverse scientific methods to study biological problems and I have published in the fields of biochemistry, enzymology, protein chemistry, immunology, cell biology, microbiology, genetics, epigenetics, metabolism, electrochemistry, and anti-infective drug delivery. I have changed fields several times to keep my interests in biology alive and challenging.

Selected Publications:

2019 to 2022 (see Google Scholar for a complete list of peer reviewed publications)

Meagher, R., Lewis, Z., Ambati, S., and Lin, X. (2021). Aiming for a bull’s-eye: Targeting antifungals to fungi with dectin-decorated liposomes. PLoS Pathog 17, 1-7. 10.1371/journal.ppat.1009699. https://www.ncbi.nlm.nih.gov/pubmed/34293050.

Ambati, S., Ellis, E.C., Lin, J., Lin, X., Lewis, Z.A., and Meagher, R.B. (2019a). Dectin-2-Targeted Antifungal Liposomes Exhibit Enhanced Efficacy. mSphere 4, 1-16. https://www.ncbi.nlm.nih.gov/pubmed/31666315.

Ambati, S., Ellis, E.C., Pham, T., Lewis, Z.A., Lin, X., and Meagher, R.B. (2021a). Antifungal Liposomes Directed by Dectin-2 Offer a Promising Therapeutic Option for Pulmonary Aspergillosis. mBio 12, 1-8. https://www.ncbi.nlm.nih.gov/pubmed/33622715.

Ambati, S., Ferarro, A.R., Kang, S.E., Lin, J., Lin, X., Momany, M., Lewis, Z.A., and Meagher, R.B. (2019c). Dectin-1-Targeted Antifungal Liposomes Exhibit Enhanced Efficacy. mSphere 4, 1-15. https://www.ncbi.nlm.nih.gov/pubmed/30760610.

Ambati, S., Pham, T., Lewis, Z.A., Lin, X., and Meagher, R.B. (2021b). DC-SIGN Targets Amphotericin B-Loaded Liposomes to Diverse Pathogenic Fungi. Fungal Biol and Biotech 8, 1-13. https://rdcu.be/cDPZS.

Ambati, S., Pham, T., Lewis, Z.A., Lin, X., and Meagher, R.B. (2022). DectiSomes- Glycan Targeting of Liposomal Amphotericin B Improves the Treatment of Disseminated Candidiasis. Antimicrob Agents Chemother 66, 1-13. https://journals.asm.org/doi/10.1128/AAC.01467-21.

Meagher, R., Ambati, S., Lewis, Z., and Lin, X. (2021a). TARGETED NANOPARTICLES AND THEIR USES RELATED TO INFECTIOUS DISEASES. I. University of Georgia Research Foundation.

Meagher, R., Lewis, Z., Ambati, S., and Lin, X. (2021b). Aiming for a bull’s-eye: Targeting antifungals to fungi with dectin-decorated liposomes. PLoS Pathog 17, 1-7. https://www.ncbi.nlm.nih.gov/pubmed/34293050.

Meagher, R.B., Lewis, Z.A., Lin, X., Ambati, S., and Momany, M. (2019). Targeted Nanoparticles and Their Uses Related to Fungal Infections. U.S. Patent. WO/2020/146514. 62/913,489. https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2020146514&_cid=P11-KHDI99-36314-1.

Phillips, B.G., Wang, Y., Ambati, S., Ma, P., and Meagher, R.B. (2020). Airways therapy of obstructive sleep apnea dramatically improves aberrant levels of soluble cytokines involved in autoimmune disease. Clinical Immunology 221, 1-10. http://www.sciencedirect.com/science/article/pii/S1521661620307610.

Wang, Y., Meagher, R.B., Ambati, S., Ma, P., and Phillips, B.G. (2020). Patients with obstructive sleep apnea have suppressed levels of soluble cytokine receptors involved in neurodegenerative disease, but normal levels with airways therapy. Sleep Breath April, 1-13. https://www.ncbi.nlm.nih.gov/pubmed/33037528.

Michael McEachern

Professor
Ph.D. (1988) University of California, San Diego
  • Director, NIH Graduate Training Grant in Genetics, Department of Genetics, University of Georgia (through 2013)
  • Member, National Institutes of Health Biomedical Research Training B Study Section
  • Grant Support -
    • “Recombinational Telomere Maintanance,” NIH
    • “Searching Genomes for their Non-Coding RNAs by their Structure,” NIH
  • Research Interests -
    • Eukaryotic chromosomes terminate with specific structures known as telomeres which permit the complete replication of chromosome ends and which also provide them with a protective "cap." The former role is achieved by the enzyme telomerase, a specialized reverse transcriptase that synthesizes a short DNA sequence directly onto the chromosomal terminus. Full telomeric function is provided by tandem arrays of this short repeat. There is considerable recent excitement in the possibility that loss of telomere function may often be a crucial event in carcinogenesis. Human somatic cells typically have little or no telomerase and display gradual telomere loss; however, most human cancers emerge with high levels of telomerase. My own work is involved with studying telomeres and telomerase in yeasts. I have found that consequences of altered telomere function can include cellular growth senescence, runaway telomere elongation, greatly increased telomeric recombination, and telomere-telomere fusions. Future aims will include identifying and characterizing other components of telomeres and telomerase and determining other roles they may play within cells.
Research Areas:
Molecular Genetics
Selected Publications:
  • Bechard, L.H., B.D. Butuner,  G.J. Peterson, W. McRae, Z. Topcu and M.J. McEachern. 2009. Mutant telomeric repeats in yeast can disrupt the negative regulation of recombination-mediated telomere maintenance and create an Alternative-Lengthening of Telomeres-like phenotype. Mol. Cell. Biol. 29: 626-639.
  • Cesare, A.J., C. Groff-Vindman, S.A. Compton, M.J. McEachern and J.D. Griffith. 2008. Telomere loops and homologous recombination-dependent telomeric circles in a Kluyveromyces lactis telomere mutant strain. Mol. Cell. Biol. 28: 20-29.
  • Hsu, M., M.J. McEachern, T.A. Sankjinou, Y. Tfzati, E. Orr, E.H. Blackburn and N.F. Lue. 2007. Telomerase core components protect Candida telomeres against aberrant overhang accumulation. Proc Natl. Acad. Sci. USA 104: 11682-11687.
  • McEachern, M.J. 2007. Telomeres: Guardians of genomic integrity or double agents of evolution? In: Origins and evolution of telomeres. J. Noseck, L. Tomaska (eds). Landes Bioscience, Eurekah Press.
  • Carter, S. D., S. Iyer, J. Xu, M.J. McEachern and S.U. Astrom. 2007. The role of NHEJ-components in telomere metabolism in Kluyveromyces lactis. Genetics 175: 1035-1045.
  • McEachern, M.J. and J.E. Haber. 2006. Break-induced replication and recombinational telomere elongation in yeast. Ann. Rev. Biochem. 75: 111-135.
  • Natarajan, S., K. Nickles and M.J. McEachern. 2006. Screening for telomeric recombination in wild-type Kluyveromyces lactis. FEMS Yeast Research 6: 442-448.
  • Iyer, S., A.D. Chadha and M.J. McEachern. 2005. A mutation in the STN1 gene triggers an alternative lengthening of telomere-like runaway recombinational telomere elongation and rapid deletion in yeast. Mol. Cell. Biol. 25: 8064-8073.
  • McEachern, M.J. and J.E. Haber. 2005. Telomerase-independent telomere maintenance in yeast. In: Telomeres, second edition. T. deLange, V. Lundblad, and E. Blackburn (eds). Cold Spring Harbor Laboratory Press.
  • Groff-Vindman, C., S. Natarajan, A. Cesare, J.D. Griffith and M.J. McEachern. 2005. Recombination at dysfunctional long telomeres forms tiny double and single stranded t-circles. Mol. Biol. Cell 25: 4406-4412.
  • Topcu, Z., K. Nickles, C. Davis and M.J. McEachern. 2005. Abrupt disruption of capping and a single source for recombinationally elongated telomeres in Kluyveromyces lactis. Proc Natl. Acad. Sci. USA 102: 3348-3353.
  • Askree, S.H., T. Yehuda, S. Smolikov, R. Gurevich, J. Hawk, C. Coker, A. Krauskopf, M. Kupiec and M.J. McEachern. 2004. A genome-wide screen for Saccharomyces cerevisiae deletion mutants that affect telomere length. Proc Natl. Acad. Sci. USA 101: 8658-8663.
  • Tomaska, L., M.J. McEachern and J. Nosek 2004. Alternatives to telomerase: Keeping linear chromosomes via telomeric circles. FEBS Lets. 567: 142-146.
  • Nickles, K. and M.J. McEachern. 2004. Characterization of K. lactis Subtelomeric Sequences Including a Distal Element with Strong Purine/Pyrimidine Strand Bias. Yeast 21: 813-830.
  • Underwood, D. H., C. Carroll and M.J. McEachern. 2004. Genetic dissection of the K. lactis telomere and evidence for telomere capping defects in TER1 mutants with long telomeres. Eukaryotic Cell 3:369-384.
  • Underwood, D. H., R. Zinzen and M.J. McEachern. 2004. Template requirements for telomerase translocation in the yeast K. lactis. Mol. Cell Biol. 24: 912-923.
  • Natarajan, S., C. Groff-Vindman and M.J. McEachern. 2003. Factors influencing the recombinational expansion and spread of telomeric tandem arrays in Kluyveromyces lactis. Eukaryotic Cell 2: 1115-1127.
  • Natarajan, S. and M.J. McEachern. 2002. Recombinational telomere elongation promoted by DNA circles. Mol. Cell Biol. 22: 4512-4521.
  • McEachern, M.J., D.H. Underwood and E.H. Blackburn. 2002. Dynamics of telomeric DNA turnover in yeast. Genetics 16: 63-73.
  • Underwood, D.H. and M.J. McEachern. 2001. Totally mutant telomeres: singe-step mutagenesis of tandem repeat DNA sequences. BioTechniques 30: 934-938.
  • McEachern, M.J. and S. Iyer. 2001. Short telomeres in yeast are highly recombinogenic. Molecular Cell 7: 695-704.
  • McEachern, M.J., A. Krausfopf and E.H. Blackburn. 2000. Telomeres and their control. Annu. Rev. Genet. 34: 331-358.
  • McEachern, M.J., S. Iyer, T.B. Fulton and E.H. Blackburn. 2000. Telomere fusions caused by mutating the terminal region of telomeric DNA. Proc. Natl. Acad. Sci. USA 97: 11409-11414.
  • Cohn, M., M.J. McEachern and E.H. Blackburn. 1998. Telomeric sequence diversity within the genus Saccharomyces. Current Genetics 33: 83-91.
  • McEachern, M.J. and E.H. Blackburn. 1997. Consequences of mutations that alter telomeres in the yeast K. lactis. Pp. 111-127 In: Pezcoller Foundation Symposia No. 8: Genomic Instability and Immortality in Cancer. E. Mihich and L. Hartwell (eds). Plenum Press, New York.
  • Blackburn, E., A. Bhattacharyya, D. Gilley, K. Kirk, A. Krauskopf, M. McEachern, J. Prescott and T. Ware. 1997. The telomere and telomerase: how do they interact? Ciba Foundation Symposia 211: 2-13.
  • McEachern, M.J. and E.H. Blackburn. 1996. Cap-prevented recombination between terminal telomeric repeat arrays (telomere CPR) maintains telomeres in K. lactis lacking telomerase. Genes and Dev. 10: 1822-1834.
  • McEachern, M.J. and E.H. Blackburn. 1995. Runaway telomere elongation caused by telomerase RNA gene mutations. Nature 376: 403-409.
  • McEachern, M.J. and E.H. Blackburn. 1994. A conserved motif within the exceptionally diverse telomeric sequences of budding yeasts. Proc. Natl. Acad. Sci. USA 91: 3453-3457.
  • McEachern, M.J. and J.B. Hicks. 1993. Unusually large telomeric repeats in the yeast Candida albicans. Mol. Cell Biol. 13: 551-560.

Rodney Mauricio

Josiah Meigs Distinguished Teaching Professor of Genetics
Ph.D. (1995) Duke University
  • Associate Editor, PLoS Genetics
  • Associate Editor, BMC Genetics
  • Member, University of Georgia Teaching Academy
  • Excellence in Undergraduate Research Mentoring Award, Center for Undergraduate Research Opportunities, University of Georgia, 2006
  • Richard B. Russell Teaching Award, University of Georgia, 2005
  • Sandy Beaver Excellence in Teaching Award, Franklin College, University of Georgia, 2004
  • Outstanding Advisor Award, Franklin College, University of Georgia, 2003
  • Lilly Teaching Fellow, 2000-2002
  • American Society of Naturalists’ Young Investigators’ Prize, 1998
  • Grant Support -
    • “Evolutionary Genetics of Senna," Traditional Medicinals Foundation 
    • "Evolutionary Genetics of a Sinai Desert Endemic," Egyptian Cultural and Educational Bureau
  • Research Interests -
    • Ecological genetics sits at the crossroads of evolutionary biology, ecology, field biology, experimental design, molecular genetics, natural history and genomics. A significant and exciting challenge in this new world of "-omics sciences" is understanding how genetic variation is relevant to organisms living their lives out in Nature. The students in my lab and I are interested in an array of topics in ecological genetics, although we are mainly interested in the evolutionary genetics of invasive plants and in basic questions on the evolution of traits that we can show are ecologically relevant to organisms in the field. Our approach is to integrate field experiments with genetic techniques to learn the fitness effects of traits and the selective histories of the genes that underlie these traits. Our work on invasives focuses on species exchanged between the U.S. and Asia, particularly China. Students in my lab are intellectually independent and encouraged to explore any variety of interesting questions.
Research Areas:
Evolutionary Genetics
Selected Publications:
  • Bentley, K.E. and R. Mauricio. 2016. High degree of clonal reproduction and lack of large-scale geographic patterning mark the introduced range of the invasive vine, kudzu (Pueraria montana var. lobata), in North America. American Journal of Botany 103:  1499-1507.
  • Hoffberg, S.L., T. Kieran, J. Catchen, A. Devault, B. Faircloth, R. Mauricio and T. Glenn. 2016. RADcap: Sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data. Molecular Ecology Resources 16:  1264-1278.
  • Zaghloul, M.S., A. A. Moustafa, R. Mauricio and H.M.H. Mansour. 2016. Evolution and conservation of Sinai's primrose (Primula boveana): an endangered pre-glacial relict species growing on Sinai Mountain, Egypt. Bio-Genetics Journal 4:  56-72.
  • Bentley, K.E., K.R. Berryman, M. Hopper, S.L. Hoffberg, K.E. Myhre, K. Iwao, J.B. Lee, T.C. Glenn and R. Mauricio. 2015. Eleven microsatellites for an emerging invader, Phytolacca americana (Phytolaccaceae), from its native and introduced ranges. Applications in Plant Sciences 3(3): 1500002. doi:10.3732/apps.1500002.
  • Dahn, H.A., J.B. Lee, K.E. Bentley, T.C. Glenn and R. Mauricio. 2015. Development of 12 novel microsatellite loci for invasive Chinese privet (Ligustrum sinense) from its introduced range. Conservation Genetics Resources 7:  467-469.
  • Hoffberg, S.L., K.E. Bentley, J.B. Lee, K.E. Myhre, K. Iwao, T.C. Glenn and R. Mauricio. 2015. Characterization of 15 microsatellite loci in kudzu (Pueraria montana var. lobata) from the native and introduced ranges. Conservation Genetics Resources 7:  403-405.
  • Koelling, V., J.L. Hamrick and R. Mauricio. Genetic diversity and structure in two species of Leavenworthia with self-incompatible and self-compatible populations. Heredity 106: 310-318.
  • Koelling, V. and R. Mauricio. 2010. Genetic factors associated with mating system cause a partial reproductive barrier between two parapatric species of Leavenworthia (Brassicaceae). American Journal of Botany 97: 412-422.
  • Richards, C.L., S.N. White, M.A. McGuire, S.J. Franks, L.A. Donovan and R. Mauricio. 2009. Plasticity, not adaptation to salt level, explains variation along a salinity gradient in a salt marsh perennial. Estuaries and Coasts. DOI 10.1007/s12237-009-9186-4.
  • Baucom, R.S. and R. Mauricio. 2008. Constraints on the evolution of tolerance to herbicide in the common morning glory: resistance and tolerance are mutually exclusive. Evolution 68: 2842-2854.
  • Baucom, R.S. and R. Mauricio. 2008. The evolution of novel herbicide tolerance in a noxious weed: the geographic mosaic of selection. Evolutionary Ecology 22: 85-101.
  • Mauricio, R. (editor), 2005. The Genetics of Adaptation. Springer, Dordrecht.
  • Mauricio, R. 2005. Ontogenetics of QTL: the genetic architecture of trichome density over time in Arabidopsis thaliana. Genetica 123: 75-85.
  • Malmberg, R.L., S. Held, A. Waits and R. Mauricio. 2005. Epistasis for fitness-related quantitative traits in Arabidopsis thaliana grown in the field and greenhouse. Genetics 171: 2013-2027.
  • Mauricio, R. 2005. Can ecology help genomics: the genome as ecosystem? Genetica 123: 205-209.
  • Malmberg, R.L. and R. Mauricio. 2005. QTL-based evidence for the role of epistasis in evolution. Genetical Research 86: 89-95.
  • Jörgensen, S. and R. Mauricio. 2005. Hybridization as a source of evolutionary novelty: leaf shape in a Hawaiian composite. Genetica 123: 171-179.
  • Richards, C.L., J.L. Hamrick, L.A. Donovan and R. Mauricio. 2004. Unexpectedly high clonal diversity of two salt marsh perennials across a severe environmental gradient. Ecology Letters 7: 1155-1162.
  • Baucom, R.S. and R. Mauricio. 2004. Fitness costs and benefits of novel herbicide tolerance in a noxious weed. Proceedings of the National Academy of Sciences, USA 101: 13386-13390.
  • Jörgensen, S. and R. Mauricio. 2004. Neutral genetic variation among wild North American populations of the weedy plant Arabidopsis thaliana is not geographically structured. Molecular Ecology 13: 3403-3413.
  • Mauricio, R., E.A. Stahl, T. Korves, D. Tian, M. Kreitman and J. Bergelson. 2003. Natural selection for polymorphism in the disease resistance gene Rps2 of Arabidopsis thaliana. Genetics 163: 735-746.
  • Stinchcombe, J.R., M.T. Rutter, D.S. Burdick, P. Tiffin, M.D. Rausher, and R. Mauricio. 2002. Testing for environmentally induced bias in phenotypic estimates of natural selection: theory and practice. American Naturalist 160: 511-523.
  • Mauricio, R. 2001. Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology. Nature Reviews Genetics 2: 370-381.
  • Mauricio, R. 2000. Natural selection and the joint evolution of tolerance and resistance as plant defenses. Evolutionary Ecology 14: 491-507.
  • Stahl, E.A., G. Dwyer, R. Mauricio, M. Kreitman and J. Bergelson. 1999. Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis. Nature 400: 667-671.
  • Mauricio, R. 1998. Costs of resistance to natural enemies in field populations of the annual plant, Arabidopsis thaliana. American Naturalist 151: 20-28.
  • Mauricio, R. and M.D. Rausher. 1997. Experimental manipulation of putative selective agents provides evidence for the role of natural enemies in the evolution of plant defense. Evolution 51: 1435-1444.
  • Mauricio, R., M.D. Rausher and D.S. Burdick. 1997. Variation in the defense strategies of plants: are resistance and tolerance mutually exclusive? Ecology 78: 1301-1310.

Nancy Manley

Adjunct Faculty
Ph.D. (1989) Massachusetts Institute of Technology
  • 2015 Distinguished Research Professor
  • Fellow, American Academy of Arts and Sciences
  • Grant Support -
    • “Molecular mechanisms and epigenetic signatures that specify thymus fate” NIH/NIAID
    • “A pilot forward genetic screen for genes affecting thymus involution” NIH/NIAID
    • “Phenotypic and functional investigation of early stage thymic involution” NIH/NIA
  • Research Interests -

    • My lab is primarily focused on studying the "life history" of the thymus, the primary lymphoid organ responsible for the generation of T cells. This approach encompasses the evolution, fetal development, postnatal function, and aging of this critical organ. Our basic hypothesis is that these diverse aspects of the biology of the organ are controlled by common regulatory networks, cellular dynamics, and physiological processes. We also study the parathyroid, which is required for calcium homeostasis, and has a shared developmental ontogeny with the thymus. We use a variety of approaches to accomplish these goals, including genetic analysis of tissue-specific and inducible mutant mouse strains, comparative and experimental embryology, and immunological techniques. Several of our current projects include natural and induced cellular fate transformations to generate thymic epithelial cells from heterologous cell types, that are either natural sources of ectopic T cell generation, or may be sources of thymus organs for transplant.



      Organogenesis and morphogenesis: Projects include the molecular and cellular control of thymus and parathyroid organogenesis, the generation and maintenance of tissue-specific stem cells, and crosstalk between thymic epithelial cells and the multiple cell types in the fetal and postnatal thymus for the development of a functional organ.

      Thymic epithelial cell development and function: Projects are focused primarily on the role of the Foxn1 transcription factor in thymic epithelial cell differentiation and function, during both fetal development and in the postnatal thymus. Current interests include understaning the molecular mechanisms controlling the switch from fetal growth to postnatal homeostasis.

      Thymic involution and immunosenescence: The thymus is the earliest organ to degenerate, losing much of its structural and functional integrity by early adulthood. This process of involution is a major contributor to immunosenescence. Our work to date suggests that the molecular mechanisms regulating fetal development may provide insight into the mechanisms regulating thymic involution. We are also using this knowledge to develop methods for generating cells and organs that may ultimately be used for therapeutic purposes. These insights are leading to developing new approaches to rejuvenating the old thymus, or replacing the old thymus with organs generated in culture.

Research Areas:
Developmental Biology
Molecular Genetics
Selected Publications:
  • A Sornborger, J Li, C Timmons, Y Takahama, and NR Manley. (2017) “MiCASA: A new method for quantifying tissue organization.” Nature Communications, in press
  • V Bain, J Gordon, JD O’Neil, I Ramos, ER Richie, and NR Manley. (2016) “Tissue-specific roles for Sonic hedgehog signaling in establishing thymus and parathyroid organ fate.” Development, 143(21):4027-4037. PMID:27633995JL Chojnowski, K Masuda, HA Trau, K Thomas, M Capecchi, and NR Manley. (2014) Multiple roles for Hoxa3 in regulating thymus and parathyroid differentiation and morphogenesis. Development, Aug;141(15):2950-8. PMID:25053428
  • N Bredenkamp, S Ulyanchenko, K O'Neill, NR Manley, H Vaidya, and CC Blackburn. (2014) An organized and functional thymus generated from FOXN1-reprogrammed fibroblasts. Nature Cell Biology, Sep;16(9):902-8 PMID:24990082
  • K Reeh, K Cardenas, V Bain, Z. Liu, M Laurent, NR Manley, and ER Richie. (2014) Ectopic TBX1 suppresses thymic epithelial cell differentiation and proliferation during thymus organogenesis. Development, Aug;141(15):2950-8 PMID:25053428
  • Li, J, Z Liu, S. Xiao, and NR Manley. (2013) Transdifferentiation of parathyroid cells into cervical thymi promotes atypical T cell development. Nature Communications, Dec 17;4:2959.  PMID:24343363
  • Bryson, J.L., A.V. Griffith, B. Hughes III, F. Saito, Y. Takahama, E.R. Richie and N.R. Manley. Cell-autonomous defects in thymic epithelial cells disrupt endothelial - perivascular cell crosstalk. PLoS One, in press.
  • Garfin, P.M., M. Dullei, J.L. Bryson, T. Serwold, E. Badreddin, C.C. Blackburng, E.R. Richie, K. Weinberg, N.R. Manley, J. Sage and P. Viatour. 2013. Inactivation of the RB family prevents thymus involution and promotes thymic function by direct control of Foxn1 expression. J. Exp. Med., in press.
  • Gardiner, J.R., A.L. Jackson, J. Gordon, H. Lickert, N.R. Manley and M.A. Basson. 2012. Localized inhibition of FGF signalling in thV Bain, J Gordon, JD O’Neil, I Ramos, ER Richie, and NR Manley. (2016) “Tissue-specific roles for Sonic hedgehog signaling in establishing thymus and parathyroid organ fate.” Development, 143(21):4027-4037. PMID:27633995e third pharyngeal pouch is required for normal thymus and parathyroid organogenesis. Development 139(18): 3456-66.
  • Wei, Q., N.R. Manley and B.G. Condie. 2011. Whole mount in situ hybridization of E8.5 to E11.5 mouse embryos. J. Vis Exp. 56: 2797.
  • Bryson, J.L., M. Coles and N.R. Manley. 2011. A method for labeling vasculature in embryonic mice. J Vis Exp. 56: e327.
  • Liu, Z., L. Chen and N.R. Manley. 2010. Thymus-associated parathyroid hormone has two cellular origins with distinct endocrine and immunological functions. PLoS Genetics 6(12): e1001251.
  • Xiao, S. and N.R. Manley. 2010. Impaired thymic selection and abnormal antigen-specific T cell responses in Foxn1Δ/Δ mutant mice. PLoS One 4;5(11): e15396.
  • Foster, K., J. Gordon, K. Cardenas, H. Veiga-Fernandes, T. Makinen, V. Pachnis, D. Wilkinson, E. Richie, C.C. Blackburn, N.R. Manley, R. Adams, D. Kioussis and M. Coles. 2010. EphB-Ephrin B2 interactions in the collective migration of thymic primordium during organogenesis. PNAS 107: 13414-9.
  • Chen, L., P. Zhao, L. Wells, C.T. Amemiya, B.G. Condie and N.R. Manley. 2010. Mouse and zebrafish Hoxa3 orthologs have non-equivalent in vivo protein function. PNAS 107: 10555-60.
  • Gordon, J., S.R. Patel, Y. Mishina and N.R. Manley. 2010. Evidence for an early role for Bmp4 signaling in thymus and parathyroid morphogenesis. Developmental Biology 339: 141-54.
  • Fraser, G.J., C.D. Hulsey, R.F. Bloomquist, K. Uyesugi, N.R. Manley and J.T. Streelman. 2009. An ancient gene network is co-opted for teeth on old and new jaws. PLoS Biology 7: e31.
  • Griffith, A.V., C. Carter, J. Gordon, A. Iberg, N.R. Manley and E.R. Richie. 2009. Increased thymus- and decreased parathyroid-fated organ domains in Splotch mutant embryos. Developmental Biology 327: 216-27.

Sidney Kushner

Distinguished Research Professor
Ph.D. (1970) Brandeis University
  • Who's Who in America
  • 2013 Lamar Dodd Award Recipient, University of Georgia
  • 2013 Division H Lecturer by the American Society for Microbiology
  • Chair-Elect of Division H, American Society of Microbiology, 2012-2013
  • Fellow, American Academy for the Advancement of Science
  • American Men and Women in Science
  • Fellow, American Academy of Microbiology
  • Excellence in Undergraduate Research Mentoring Award, Center for Undergraduate Research Opportunities, University of Georgia, 2005
  • SREB Faculty Mentor of the Year, 2004
  • Creative Research Medal, University of Georgia, 1987
  • Grant Support -
    • "Analysis of E. coli Ribonucleases and RNA Metabolism," NIH
  • Research Interests -
    • We are using a combination of genetic, biochemical, bioinformatics and RNA-seq approaches to analyze the post-transcriptional control of gene expression in the model prokaryote, Escherichia coli. These studies include examining the biological role of polyadenylation in bacteria, determining the multiple pathways by which primary transfer RNA (tRNA) transcripts are processed into their mature forms, outlining the enzymatic steps in converting primary 30S ribosomal RNA (rRNA) transcripts into their mature 16S, 23S and 5S components, examining the mechanisms of mRNA decay and processing, and understanding how small regulatory RNAs (sRNAs) help control gene expression.  Other research interests include various aspects of using Escherichia coli as a host for expressing eukaryotic proteins and DNA repair. 
Research Areas:
Biotechnology
Molecular Genetics
Selected Publications:

  • Mohanty, B. K. and S. R. Kushner. 2019.  Analysis of post-transcriptional RNA metabolism in prokaryotes.  Methods, 155:124-130.

  • Mohanty, B.K. and S. R. Kushner. 2019.  New insights into the relationship between tRNA processing and polyadenylation in Escherichia coli.  Trends in Genetics, 35:434-445.

  • Kushner, Sidney R.  2018. Messenger RNA in Prokaryotes. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0000874.pub4.

  • Mohanty, B.K. and S. R. Kushner.  2018. Enzymes Involved in Post-transcriptional RNA Metabolism in Gram-negative bacteria. Microbiology Spectrum, 6:RWR-0011-2017. Doi:10.1128/microbiolspec.RWR-0011-2017.

  • Bowden, K. E., Wiese, N.S., Perwez, T., Mohanty, B.K., and S.R. Kushner.  2017.  The rph-1 encoded truncated RNase PH protein inhibits RNase P maturation of pre-tRNAs with short leader sequences in the absence of RppH.  Journal of Bacteriology, 199: UNSP e00301-17.

  • Mildenhall, K.B., Wiese, N., Chung, D., Maples, V.F., Mohanty, B. K., and S. R. Kushner. 2016.  RNase E-based degradosome modulates polyadenylation of mRNAs after Rho-independent transcription terminators in Escherichia coli.  Molecular Microbiology, 101:645-655

  • Mohanty, B. K., Petree, J. R., and S. R. Kushner.  2016.  Endonucleolytic cleavages by RNase E generate the mature 3' termini of the three proline tRNAs in Escherichia coli.  Nucleic Acids Res., 44:6350-62

  • Mohanty, B. K. and S. R. Kushner.  2016.  Regulation of mRNA decay in bacteria.  Annual Review of Microbiology, 70, 25-44.

  • Kushner, S.R. 2016.  Poly(A) tails.  Reference Module in Life Sciences, Elsevier Press,  http://dx.doi.org/10.1016/B978-0-12-809633-8.06925-9.

  • Neidhardt, F. C., and S. R. Kushner.  Escherichia coli.  Reference Module in Life Sciences, Elsevier Press. http://dx.doi.org/10.1016/B978-0-12-809633-8.06393-7.

  • Kushner, S. R.  2015.  Polyadenylation in E. coli: A 20 year odyssey.  RNA, 21:673-674.
  • Agrawal, A., Mohanty, B. K., and S. R. Kushner. 2014.  Processing of the seven valine tRNAs in Escherichia coli involves novel features of RNase P.  Nucleic Acids Res., 42:11166-11179.
  • Mohanty, B. K. and S.R. Kushner.  2014.  In vivo Analysis of Polyadenylation in Prokaryotes. Methods in Molecular Biology 1125, Polyadenylation: Methods and Protocols, J. Rorbach and A. J. Bobrowicz, eds., Humana Press, pp. 229-249.
  • Mohanty, B. K. and S. R. Kushner.  2013.  Deregulation of poly(A) polymerase I in Escherichia coli inhibits protein synthesis and leads to cell death.  Nucleic Acids Res., 41:1757-1766.
  • Mohanty, B. K., Maples, V. F., and S. R. Kushner.  2012. Polyadenylation helps regulate functional tRNA levels in Escherichia coli. Nucleic Acids Res., 40:4589-4603.
  • Stead, M.B., Agrawal, A., Bowden, K.E., Nasir, R., Mohanty, B.K., Meagher, R.B., and S.R. Kushner. 2012.  RNAsnap™: a rapid, quantitative and inexpensive method for isolating total RNA from bacteria. Nucleic Acids Res., 40:e156.
  • Stead, M.B., S. Marshburn, J. Mitra, L.P. Castillo, D. Ray, H. van Bakel, T.R. Hughes and S. R. Kushner. 2011. Analysis of Escherichia coli RNase E and RNase III activity using tiling microarrays. Nucleic Acids Res. 39:3188-3203.
  • Mohanty, B.K. and S.R. Kushner. 2010. Bacterial/archaeal/organellar polyadenylation. WIREs RNA 2: 256-276.
  • Mohanty, B.K. and S.R. Kushner. 2010. Processing of the Escherichia coli leuX tRNA transcript, encoding tRNALeu5, requires either the 3’ - 5’ exoribonucleases polynucleotide phosphorylase or RNase P to remove the Rho-independent transcription terminator. Nucleic Acids Research 38: 597-607.
  • Chung, D.-H., Z. Min, B.-C. Wang and S.R. Kushner. 2010. Single amino acid changes in the predicted RNase H domain of coli RNase G lead to complementation of RNase E deletion mutants. RNA 16: 1371-1385.
  • Tran, T.T., F. Zhou, S. Marshburn, M. Stead, S.R. Kushner and Z. Xu. 2009. De novo computational prediction of non-coding RNA genes in prokaryotic genomes. Bioinformatics 25: 2897-2905.
  • Carabetta, V.J., B.K. Mohanty, S.R. Kushner and T.J. Silhavy. 2009. The response regulator SprE (RssB) modulates polyadenylation and mRNA stability in Escherichia coli. J. Bacteriology 191: 6812-6821.
  • Mohanty, B.K., H. Giladi, V. Maples and S.R. Kushner. 2008. Pp. 3-29. Analysis of RNA Decay, Processing, and Polyadenylation in Escherichia coli and Other Prokaryotes. In Methods in Enzymology, volume 447. L.E. Maquat and C.M. Arraiano (eds.). Academic Press, Burlington.
  • Mohanty, B.K. and S.R. Kushner. 2008. Rho-independent transcription terminators inhibit RNase P processing of the secG leuU and metT tRNA polycistronic transcripts in Escherichia coli. Nucleic Acids Research 36: 364-375.
  • Perwez, T., D. Hami, V. Maples, Z. Min, B.-C.Wang and S.R. Kushner. 2008. Intragenic suppressors of temperature-sensitive rne mutations lead to the dissociation of RNase E activity on mRNA and tRNA substrates in Escherichia coli. Nucleic Acids Research 36: 5306-5318.
  • Kushner, S.R. 2007. Chapter 4.6.4. Messenger RNA decay. In, Escherichia coli and Salmonella: cellular and molecular biology. A. Böck, R. Curtis III., Gross, C.A., J.B. Kaper, F.C. Neidhardt, T. Nyström, K.E, Rudd, and C. L. Squires (eds.). American Society for Microbiology Press, Washington, DC.
  • Mohanty, B.K. and S.R. Kushner. 2007. Ribonuclease P processes polycistronic tRNA transcripts in Escherichia coli independent of ribonuclease E. Nucleic Acids Research 35: 7614-25.
  • Mohanty, B.K. and S.R. Kushner. 2006. The majority of E. coli mRNAs undergo post-transcriptional modification in exponentially growing cells. Nucleic Acids Research 34: 5695-5704.
  • Suzuki, K., P. Babitske, S.R. Kushner, and T. Romeo. 2006. Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E. Genes and Development 20: 2605-2617.
  • Perwez, T.  and S.R. Kushner. 2006. RNase Z in Escherichia coli plays a significant role in mRNA decay. Molec. Microbiol. 60: 723-737.
  • Kushner, S.R. 2004. mRNA decay in prokaryotes and eukaryotes: different approaches to a similar problem. IUBMB Life 56: 585-594.
  • Mohanty, B.K., V.F. Maples and S.R. Kushner. 2004. The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli. Molec. Microbiol. 54: 645-658.

Jessica Kissinger

Distinguished Research Professor
Ph.D. (1995) Indiana University

Research Interests 

How do eukaryotic and organellar genome sequences evolve? Our lab is interested in parasite genomics and the biology of genome evolution. The nuclear and organellar genome sequences of parasitic eukaryotes are often highly-reduced, devoid of recognizable mobile elements and riddled with intracellular and lateral gene transfers. Our approach is to apply molecular, computational and phylogenetic tools to the analysis of complete parasite genome sequences. Projects include the development of tools for data integration, data mining, comparative genomics and the systems biology of host-pathogen interactions. Kissinger is a member of the NIH/NIAID Bioinformatic Resource Center, VEuPathDB.org leadership team. Research focuses on the apicomplexan protist pathogens, Toxoplasma gondii and several species of Cryptosporidium and Plasmodium. Researchers in our group work at the bench, the computer, or both.

Kissinger Lab Website
Podcasts

Honors & Awards

  • Lamar Dodd Creative Research Award, UGA, 2024
  • Fulbright US Scholar, Fulbright Scholar Program, 2022
  • Fellow, American Association for the Advancement of Science, 2021
  • Fellow, American Society for Tropical Medicine & Hygiene, 2020
  • Distinguished Research Professor, UGA, 2017
  • Richard F. Reiff Internationalization Award, UGA, 2016
  • SEC Academic Leadership Development Program Fellow, 2015-2016
  • Faculty Excellence in Diversity Award, UGA, 2013
  • Creative Research Medal, UGA, 2009
  • Kavli Fellow, Frontiers of Science 2005-2006, 2008

Select Professional Service

  • Deputy Director, African Centers of Excellence Global Council (ACE) (2021 – Present)
  • Global Council Member, NIAID ACE (2019 – 2021)
  • Director, Institute of Bioinformatics (IOB), (2010-2019)
  • Scientific Advisory Group, Institute Pasteur de Tunis, EU2020 PHINDaccess (2018 – 2022)
  • Editor, Microbial Genomics (2015 - 2020)
  • Member, Editorial Board of Academic Editors, PeerJ (2012 – 2020)
  • External Advisory Committee, Louisiana NIH INBRE (2011 – 2017)
Visit Kissinger's  ORCID
Education:
  • 1989     A.B. cum laude University of Chicago
  • 1995     PhD Molecular, Cellular & Developmental Biology, Indiana University, Mentor: Rudy Raff
  • 1995-1996 NSF/Sloan post-doctoral Fellow NIH/NIAID/LPD, Mentor: Tom McCutchan
  • 1996-1998 CNPq post-doctoral Fellow CPqRR-FIOCRUZ, Brazil
  • 1998-2002 Post-doctoral Fellow & Lecturer UPENN, Mentor: David Roos
Research Areas:
Molecular Genetics
Genomics and Bioinformatics
Evolutionary Genetics
Research Interests:

Systems biology of host-pathogen interactions, Nuclear and organellar genome evolution in eukaryotic parasites, Databases, Ontologies, Data mining and Data integration of 'omics (genome, transcriptome, proteome, metabolome, lipidome), clinical, immunological, epidemiological and experimental metadata.  

Grants:

Grant Support 

  • NIH 75N93019R00028, “Center for Influenza Disease and Emergence Research (CIDER)” (2021-2028) Role: Co-I
  • NIH R01AI148667, “Capturing the genomic variation present in Cryptosporidium and cryptosporidiosis” (2020-2024) Role: Joint-PI with Travis Glenn
  • "Bioinformatics resources for kinetoplastid organisms and their hosts", Wellcome Trust (2020-2025), Role: Co-applicant with Andy Jones & David Roos 
  • “Integrated Informatics Resources for Eukaryotic Microbial Pathogens and Invertebrate Vectors of Disease” i.e. VEuPathDB.org, NIH/NIAID (2019-2024), Role: Co-I  
Selected Publications:
Recent Publications (*= Graduate student; # = Undergraduate student)

Jonathan Eggenschwiler

Associate Professor
Ph.D. (1998) Columbia University, New York
  • Undergraduate Affairs Committee (Genetics)
  • University Research Animal Resources, Faculty Advisory Committee
  • Developmental Biology Alliance Executive Committee
  • March of Dimes Basil O’Connor Starter Scholar Award
  • Faculty of 1000 member, Pattern Formation
  • Editorial advisory board member:  Cilia; Development
  • Current grant support: "Regulation of Hedgehog signaling transcriptional responses by the cell cycle" NIH/NICHD; “Control of TGF-beta signals by Rab23 and Megf8 in mammalian left-right patterning” NIH/NICHD;  EDGE: Establishment of genome-editing and transgenic tools in Anolis lizards. (Menke, Eggenschwiler, Lauderdale), NSF
  • Courses Taught at UGA:GENE4310: Genetic Approaches to Developmental Neuroscience; GRSC 7770; BCMB/CBIO/GENE 8112/8113/8212; GENE8880; GENE4950, GENE3200, GENE4230L.
  • Research Interests -
    • Our laboratory is interested in the mechanisms controlling tissue patterning during mammalian embryonic development. Using the mouse as a model, we exploit a combination of reverse and forward genetic approaches to investigate signaling pathways that function in cell fate specification in different contexts. Our work has primarily focused on identification of novel regulators of the Hedgehog signaling pathway acting within the developing central nervous system. In addition, we have recently begun to examine the regulation of Nodal signaling in the control of patterning along the left-right axis of the mouse embryo. Building upon our genetic analyses, we are working to elucidate the specific functions of these novel regulatory factors at the cellular and biochemical levels.
Education:
  • 1984-1988. B.A., Biology, University of California, Santa Cruz, CA
  • 1990-1998. Ph.D., M. Phil., Department of Genetics and Development, College of Physicians and Surgeons, Columbia University, New York, NY, Dr. Argiris Efstratiadis, advisor
  • 1998- 2003. Postdoctoral Research, Molecular Biology Program, Sloan-Kettering Institute, New York, NY, Dr. Kathryn Anderson, advisor
Research Areas:
Molecular Genetics
Developmental Biology
Research Interests:

Mammalian developmental genetics: mechanisms that control tissue patterns during mammalian embryonic development; signaling pathways that function in cell fate specification; identification of novel regulators of Hedgehog signaling pathways in central nervous system

Grants:

"Regulation of Hedgehog signaling transcriptional responses by the cell cycle" NIH/NICHD

“Control of TGF-beta signals by Rab23 and Megf8 in mammalian left-right patterning” NIH/NICHD

"EDGE: Establishment of genome-editing and transgenic tools in Anolis lizards." (Menke, Eggenschwiler, Lauderdale, Co-PIs). NSF

Selected Publications:

Lupu F, Burnett, J, and Eggenschwiler, J. (2018). Cell cycle-related kinase regulates mammalian eye development through positive and negative regulation of the Hedgehog pathway. Developmental Biology. 2018 Feb 1;434(1):24-35. doi: 10.1016/j.ydbio.2017.10.022. Epub 2017 Nov 21.PMID:29166577.

Burnett, J, Lupu, F, and Eggenschwiler, J.T. (2017). Proper ciliary assembly is critical for restricting Hedgehog signaling during early eye development in mice. Dev. Biol. Oct 1;430(1):32-40. doi: 10.1016/j.ydbio.2017.07.012. Epub 2017 Aug 1. PMID: 28778798

Snouffer, A., Brown, D., Lee, H., Walsh, J. D., Lupu, F. L., Norman, R., Lechtreck,, K., Ko, H.W., and Eggenschwiler, J. (2017). Cell Cycle-Related Kinase (CCRK) regulates ciliogenesis and Hedgehog signaling in mice. PLoS Genetics Aug 17;13(8):e1006912. doi: 10.1371/journal.pgen.1006912. eCollection 2017 Aug. PMID: 28817564

Sornborger, A. T., Li, J., Timmons, C., Lupu, F., Eggenschwiler, J., Takahama, Y., and Manley, N. R. (2017). MiCASA: A new method for quantifying tissue organization. Nat. Commun. May 30;8:15619. doi: 10.1038/ncomms15619.

Wingfield. J.L., Mengoni I., Bomberger, H., Jiang, Y., Walsh, J.D., Brown, J.M., Picariello, T., Cochran, D.A., Zhu, B., Pan, J., Eggenschwiler, J.T., Gaertig, J., Witman, G.B., Kner, P., and Lechtreck, K. (2017). IFT trains in different stages of assembly queue at the flagellar base for consecutive release into cilia. eLife. May 31;6. pii: e26609. doi: 10.7554/eLife.26609.

Moon, H., Song, J. Jeong-Oh Shin, J-O, Lee, H., Kim, H-K, Eggenschwiler, J., Bok, J. and Ko, H.W. (2014). The endocrine-cerebro-osteodysplasia (ECO) syndrome protein, intestinal cell kinase is a key regulator of ciliary length control and Hedgehog signaling. Proc. Natl. Acad. Sci. U.S.A, Jun 10;111(23):8541-6.

Fuller, K.P., Tse, J., Mauti, O., and Eggenschwiler, J.T. (2014) Rab23 regulates Nodal signaling in left-right patterning of the mouse embryo. Dev. Biol. Jul 15;391(2)

Eggenschwiler, J.T. and Liu, A. (2014) Identifying essential genes in mouse development via an ENU-based forward genetic approach. Meth. Mol. Biol.;1092:95-118.

Eggenschwiler J.T. (2012). Hedgehog signaling and the cilium: in the zone. Dev Cell. 23: 677-8.

Ochbina P.J.R., J.T. Eggenschwiler, I. Moskowitz and K.V. Anderson (2011). Complex Interactions Between Genes Controlling Trafficking in Primary Cilia. Nat. Genet. 43: 547-53.

Qin, J., Y. Lin, H.W. Ko and J.T. Eggenschwiler (2011). IFT122 antagonizes Sonic Hedgehog signaling and controls ciliary localization of pathway components. Proc. Natl. Acad. Sci. 108: 1456-61.

Ko H.W., R.X. Norman, J. Tran, K.P. Fuller, M. Fukuda and J.T. Eggenschwiler (2010). Broad-minded links cell cycle-related kinase to cilia assembly and Hedgehog signal transduction. Dev. Cell 18: 237-247.

Walczak-Sztulpa J., J.T. Eggenschwiler, D. Osborn, D. Brown, F. Emma, C. Klingenberg, R.C. Hennekam, T. Giuliano, M. Garshasbi, A. Tzschach, M. Szczepanska, M. Krawczynski, J. Zachwieja, Zwolinska, P.L. Beales, H. Ropers, A. Latos-Bielenska and A. Kuss (2010). Cranioectodermal dysplasia (Sensenbrenner Syndrome) is a ciliopathy caused by mutations in the IFT122 gene. Am. J. Hum. Genet. 86: 949-56.

Norman R.X., H.W. Ko, V. Huang, C.M. Eun, L.L. Abler, Z. Zhang, X. Sun and J.T. Eggenschwiler (2009). Tubby-like protein 3 (TULP3) regulates patterning in the mouse embryo through inhibition of Hedgehog signaling. Hum. Mol. Genet. 18: 1740-54.

Ko H.W., A. Liu and J.T. Eggenschwiler (2009). Analysis of hedgehog signaling in mouse intraflagellar transport mutants. Meth. Cell Biol. Vol. 93. Eds: King, S.M. and Pazour, G.P. ISBN: 978-0-12-381377-0

Cho A., H.W. Ko and J.T. Eggenschwiler (2008). FKBP8 cell-autonomously controls neural tube patterning through a Gli2- and Kif3a-dependent mechanism. Dev. Biol. 321: 27-39.

Eggenschwiler J.T. and K.V. Anderson (2007). Cilia and Developmental Signaling. Ann. Rev. Cell Dev. Biol. 23: 345-73.

Eggenschwiler, J.T., J. Qin, O. Bulgakov, T. Li and K.V. Anderson. (2006). Mouse Rab23 regulates Hedgehog signaling from Smoothened to Gli proteins. Dev. Biol. 290: 1-12.

Garcia-Garcia, M.J., J.T. Eggenschwiler, T. Caspary, H.L. Alcorn, M.W. Wyler, D. Huangfu, A.S. Rakeman, J.D. Lee, E.H. Feinberg, J.R. Timmer and K.V. Anderson (2005). Analysis of mouse embryonic patterning and morphogenesis by forward genetics. Proc. Natl. Acad. Sci. 102: 5913-9.

Bulgakov, O.V. *, J.T. Eggenschwiler*, D. Hong, K.V. Anderson and T. Li. (2004). FKBP8 is a neural-specific negative regulator of Sonic hedgehog signaling. Development 131: 2149-59. * Equal contribution

Caspary, T., M.J. Garcia-Garcia, D. Huangfu, J.T. Eggenschwiler, M.W. Wyler, A.S. Rakeman, H.L. Alcorn and K.V. Anderson (2002). Mouse Dispatched homologue1 is required for long-range but not juxtacrine Hh signaling. Curr. Biol. 12: 1628-32.

Eggenschwiler, J.T., E. Espinoza and Anderson, K.V. (2001). Rab23 is an essential negative regulator of the mouse Sonic hedgehog signaling pathway. Nature 412: 194-8.

Eggenschwiler, J.T. and K. Anderson (2000). Dorsal and lateral fates in the mouse neural tube require the cell-autonomous activity of the open brain gene. Dev. Biol. 227: 648-660.

Eggenschwiler, J.T., T. Ludwig, P. Fisher, P. Leighton, S. Tilghman and A. Efstratiadis (1997). Mouse mutant embryos overexpressing IGF-II exhibit phenotypic features of the Beckwith-Wiedemann and Simpson-Golabi-Behmel syndromes. Genes Dev. 11: 3128-3142.

Ludwig, T., J. Eggenschwiler, P. Fisher, A.J. D'Ercole, M.L. Davenport and A. Efstratiadis (1996). Mouse mutants lacking the type 2 IGF receptor (IGF2R) are rescued from perinatal lethality in Igf2 and Igf1r null backgrounds. Dev. Biol. 177: 517-35.

Leighton, P.A., R.S. Ingram, J. Eggenschwiler, A. Efstratiadis and S.M. Tilghman (1995). Disruption of imprinting caused by deletion of the H19 gene region in mice. Nature 375: 34-9.

Kelly Dyer

Professor
Director, Integrated Life Sciences Program
Director, NIH T32 Genetics Training Grant
Ph.D. (2004) University of Rochester

Research Interests:   Evolutionary genetics in Drosophila

What shapes genetic and phenotypic diversity in natural populations? We are broadly interested in the interaction between evolution, genetics, and ecology. The first main topic of research in the lab is how organisms adapt to their environment. We study the genetic basis of ecologically important traits and how evolutionary forces such as selection and gene flow interact in the processes of adaptation and speciation. The second main topic of research is how the genetic environment affects gene evolution. For example, factors such as the pattern of inheritance, the level of recombination, and the presence of selection at nearby genes can have significant consequences for how a gene responds to selection. To address these questions we combine genomic techniques and classical Drosophila genetics with theoretical modeling, behavioral observations, and field studies. We use various species of Drosophila because they are tractable in both genetic and ecological studies.

Of Note:

  • Director, Integrated Life Sciences Program, 2023 - Current
  • Director, NIH T32 Genetics Training Grant, 2020 - Current
  • Graduate Coordinator, Department of Genetics, 2016 - 2023
  • UGA Teaching Academy, Class of 2019
  • Richard B. Russell Award for Excellence in Undergraduate Teaching, 2017
  • Senior Editor, PLoS Genetics, 2023 - Current
  • Associate Editor, GENETICS, 2021 - Current
  • Associate Editor, PLoS Genetics, 2017 - 2023
  • Secretary, American Genetics Association, 2017-2019
  • Council Member, Society for the Study of Evolution, 2014-2017
  • Council Member, European Society for Evolutionary Biology, 2013-2017
  • CAREER Award, National Science Foundation, 2012
  • Council Member, American Genetics Association, 2011-2013
  • Associate Editor, Evolution, 2010-2012
  • Lilly Teaching Fellow, 2009-2011
  • New Scholar in Aging, Ellison Medical Foundation, 2009
  • Reviewing Editor, Journal of Evolutionary Biology, 2009-2012

Grant Support:

  • "Dimensions: Collaborative research: Integrating phylogenetic, genetic, and functional approaches to dissect the role of toxin tolerance in shaping Drosophila biodiversity."  (NSF, with L. Reed, C. Scott Chialvo, and T. Werner)
Research Areas:
Evolutionary Genetics
Research Interests:

Population genetics and molecular evolution; genetic basis of adaptation and speciation; intragenomic conflict and selfish genetic elements; host-parasite interactions; insect ecology and evolution

Selected Publications:
  • Dyer, K. A. and D. W. Hall. 2019. Fitness consequences of a non-recombining sex-ratio drive chromosome can explain its prevalence in the wild. Proceedings of the Royal Society, Series B 286: 20192529.
  • Ginsberg, P. S., D. P. Humphreys, and K. A. Dyer. 2019. Ongoing hybridization obscures phylogenetic relationships in the Drosophila subquinaria species complex. Journal of Evolutionary Biology 32: 1093-1105.
  • Scott Chialvo, C.H., B. E. White, L. K. Reed, and K. A. Dyer. 2019. A phylogenetic examination of host use evolution in the quinaria and testacea groups of Drosophila. Molecular Phylogenetics and Evolution 130: 233-243. 
  • Pieper, K. E., R. L. Unckless, and K. A. Dyer. 2018. A fast-evolving X-linked duplicate of importin-a2 is overexpressed in sex-ratio drive in Drosophila neotestacea. Molecular Ecology 27: 5165-5179.
  • Dyer, K. A.*, E. R. Bewick*, B. E. White, M. J. Bray, and D. P. Humphreys. 2018. Fine scale geographic patterns and consequences of reinforcing selection in natural populations of Drosophila subquinaria and Drosophila recens. Molecular Ecology 27: 3655-3670. (* equal contribution)
  • Pieper, K. E. and K. A. Dyer. 2018. Meiotic Drive. Oxford Bibliographies in Evolutionary Biology.
  • Pieper, K. E. and K. A. Dyer. 2016. Occasional recombination may allow a selfish sex-ratio X-chromosome to persist at high frequencies in the wild. Journal of Evolutionary Biology 29: 2229-2241.  
  • Lindholm, A. K., K. A. Dyer, R. C. Firman, et al. 2016. The ecology and evolutionary dynamics of meiotic drive. Trends in Ecology & Evolution 31: 315-326.
  • Humphreys, D. P., H. D. Rundle, and K. A. Dyer. 2016. Patterns of reproductive isolation in the Drosophila subquinaria complex: Can reinforced premating isolation cascade to other species? Current Zoology 62: 183-191.  
  • Rundle, H. D. and K. A. Dyer. 2015. Reproductive character displacement of female mate preferences for male cuticular hydrocarbons in Drosophila subquinaria. Evolution 69: 2625-2637.
  • Conn, C. E., R. Bythell-Douglas, D. Neumann, S. Yoshida, B. Whittington, J. H. Westwood, K. Shirasu, C. S. Bond, K. A. Dyer, and D. C. Nelson. 2015. Convergent evolution enabled host detection in parasitic plants. Science 349: 540-543.
  • Arthur, N. J., and K. A. Dyer. 2015. Asymmetrical sexual isolation but no postmating isolation between the closely related species Drosophila suboccidentalis and D. occidentalis. BMC Evolutionary Biology 15:38.

R. Kelly Dawe

Distinguished Research Professor
Ph.D. (1989) University of California, Berkeley
  • Creative Research Medal, University of Georgia, 2000
  • Grant Support -
    • “Functional Genomics of Maize Centromeres,” NSF
    • “Functional Genomics of Maize Chromatin,” NSF
  • Research Interests -
    • How do chromosomes move? Remarkably little is known about this basic motility event in higher plants. Our approach has been to combine immunocytochemistry, high-resolution 3D light microscopy, and forward genetics to understand the movement of chromosomes in maize. The organelle primarily responsible for chromosome movement is the kinetochore, which binds to centromeric DNA. Much of our current work is directed towards fulfilling the goals of a recently-renewed genome project on maize centromeres. We have ongoing projects on the roles of Centromeric Histone H3 and Centromere Protein C (CENH3, CENPC) in centromere/kinetochore structure. In addition we are focusing the epigenetic control of centromeres as well as chromatin-level gene silencing in maize heterochromatin. The spectacular cytology of the maize meiocyte, combined with deconvolution-based 3D light microscopy provides us with unparalleled resolution in our analyses.
Research Areas:
Molecular Genetics
Selected Publications:
  • Phan B.H., W Jin., C.N. Topp, C.X. Zhong, J. Jiang, R.K. Dawe and W.A. Parrott. 2007. Insertion of >100 kb centromeric repeat arrays into the rice genome by biolistic DNA transfer. Transgenic Res. 16: 341-351.
  • Du, Y. and R.K. Dawe 2007. Maize NDC80 is a constitutive feature of the central kinetochore. Chromosome Res. 15: 767-775.
  • Leebens-Mack, J., R.K. Dawe and S.R. Wessler. 2007. Genomes and evolution. Curr. Opin, Gen. Dev. 17: 471-472.
  • Shi, J. and R.K. Dawe. 2006. Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27. Genetics 173: 1571-1583.
  • Mroczek, R.J., J.R. Melo, A.C. Luce, E.N. Hiatt and R.K. Dawe 2006. The maize Ab10 meiotic drive system maps to supernumerary sequences in a large complex haplotype. Genetics 174: 145-154.
  • Luce, A., A. Sharma, O.S.B. Mollere, T.K. Wolfgruber, K. Nagaki, J. Jiang, G.G. Presting, R.K. and Dawe. 2006. Precise centromere mapping using a combination of repeat Junction markers and ChIP-PCR. Genetics 174: 1057–1061.
  • Dawe, R.K. and S. Henikoff. 2006. Centromeres put epigenetics in the driver's seat. Trends Biochem. Sci. 31: 662-669.
  • Topp, C.N. and R.K. Dawe. 2006. Reinterpreting pericentromeric heterochromatin. Curr. Opin. Plant Biol. 9:647–653.
  • Dawe, R.K. 2005. Centromere renewal and replacement in the plant kingdom. Proc. Nat. Acad. Sci. USA 102: 11573-11574.
  • Jin, W., J.C. Lamb, J.M. Vega, R.K. Dawe, J.A. Birchler and J. Jiang. 2005. Molecular and functional dissection of the maize B chromosome centromere. Plant Cell 17: 1412-1423.
  • Dawe, R.K., E.A. Richardson and X. Zhang. 2005. The simple ultrastructure of the maize kinetochore fits a two-domain model. Cytogenet. Genome Res. 109: 128-133.
  • Zhang, X., X. Li, J.B. Marshall, C.X. Zhong and R.K. Dawe. 2005. Phosphoserines on maize CENTROMERIC HISTONE H3 and histone H3 demarcate the centromere and pericentromere duringchromosome segregation. Plant Cell 17: 572-583.
  • Dawe, R.K. 2004. RNA interference on chromosomes. Nat Genet. 36: 1141-1142.
  • Topp, C.N., C.X. Zhong and R.K. Dawe. 2004. Centromere-encoded RNAs are integral components of the maize kinetochore. Proc. Natl. Acad. Sci. USA. 101: 15986-15991.
  • Lawrence, C.J., R.K. Dawe, K.R. Christie, D.W. Cleveland, S.C. Dawson, S.A. Endow, L.S.B. Goldstein, H.V. Goodson, N. Hirokawa, J. Howard, R.L. Malmberg, J.R. McIntosh, H. Miki, T.J. Mitchison, Y. Okada, A.S.N. Reddy, W.M. Saxton, M. Schliwa, J.M. Scholey, R.D. Vale, C.E. Walczak, and L. Wordeman. 2004. A standardized kinesin nomenclature. J. Cell Biol. 167: 19-22.
  • Dawe, R.K. and E.N. Hiatt. 2004. Plant neocentromeres: fast, focused and driven. Chromosome Res. 12: 655-669.
  • Lawrence, C.J., C.M. Zmasek, R.K. Dawe and R.L. Malmberg. 2004. LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference. Bioinformatics 20: 1977-1979.
  • Jin. W., J.R. Melo, K. Nagaki, P.B. Talbert, S. Henikoff, R.K. Dawe and J. Jiang. 2004. Maize centromeres: fine structure and functional adaptation in the genetic background of oat. Plant Cell 16: 571-581.
  • Jiang, J., J.A. Birchler, W.A. Parrott and R.K. Dawe. 2003. A molecular view of plant centromeres. Trends Plant Sci. 8: 570-575.
  • Mroczek, R.J. and R.K. Dawe. 2003. Distribution of retroelements in centromeres and neocentromeres of maize. Genetics 165: 809-819.
  • Birchler, J.A., R.K. Dawe and J.F. Doebley. 2003. Marcus Rhoades: Preferential segregation and meiotic drive. Genetics 164: 835-841.
  • Hiatt, E.N. and R.K. Dawe. 2003. Four loci on Abnormal chromosome 10 contribute to meiotic drive in maize. Genetics 164: 699-709.
  • Nagaki, K., P.B. Talbert, C.X. Zhong, R.K. Dawe, S. Henikoff and J. Jiang. 2003. Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. Genetics 163: 1221-1225.
  • Nagaki, K., J. Song, R. Stupar, A.S. Parokonny, Q. Yuan, S. Ouyang, J. Liu, R.K. Dawe, C.R. Buell, and J. Jiang. 2003. Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 163: 759-770.
  • Hiatt, E.N. and R.K. Dawe. 2003. The meiotic drive system on maize abnormal chromosome 10 contains few essential genes. Genetica 117: 67-76.
  • Dawe, R.K. 2003. RNA interference, transposons, and the centromere. Plant Cell 15: 297-301.
  • Hiatt, E.N., E. Kentner and R.K. Dawe. 2002. Independently-regulated neocentromere activity of two classes of tandem repeat arrays. Plant Cell 14: 407-420.
  • Zhong C.X., J.B. Marshall, C. Topp, R.J. Mroczek, C.R.A Kato, K. Nagaki, J.A. Birchler, J. Jiang and R.K. Dawe. 2002. Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. Plant Cell 14: 2825-2836.
  • Lawrence, C.J., R.L. Malmberg, M.G. Muszynski and R.K. Dawe. 2002. Maximum likelihood methods reveal conservation of function among closely related kinesin families. J. Mol. Evol. 54: 42-53.
  • Lawrence, C.J, N.R. Morris, R.B. Meagher and R.K. Dawe. 2001. Dyneins have run their course in the plant lineage. Traffic 2: 362-363.
  • Yu, H.-G., E.N. Hiatt and R.K. Dawe. 2000. The plant kinetochore. Trends Plant Sci. 5: 543-547.
  • Yu, H.-G. and R.K. Dawe. 2000. Functional redundancy in the maize meiotic kinetochore. J. Cell Biol. 151: 131-141.
  • Dawe, R. K., L.M. Reed, H.-G. Yu, M.G. Muszynski and E.N. Hiatt. 1999. A maize homolog of mammalian CENP-C is a constitutive component of the inner kinetochore. Plant Cell 11: 1227-1238.
  • Yu, H.-G., M. G. Muszynski and R.K. Dawe. 1999. The maize homolog of the cell cycle checkpoint protein MAD2 reveals kinetochore substructure and contrasting mitotic and meiotic localization patterns. J. Cell Biol. 145: 425-435.
  • Buckler, E.S. IV, K. Phelps, C.S. Buckler, R.K. Dawe, J.F. Doebley and T.P. Holtsford. 1999. Meiotic drive of knobs reshaped the maize genome. Genetics 153: 415-426.
  • R. K. Dawe. 1998. Meiotic chromosome organization and segregation in plants. Ann. Rev. Plant Phys. Plant Mol. Biol. 49: 371-395.
  • Richards, E. J. and R.K. Dawe. 1998. Plant centromeres: structure, function and control. Curr. Opin. Plant Biol. 1: 130-135.
  • Yu, H-G., E. N. Hiatt, A. Chan, M. Sweeney and R.K. Dawe. 1997. Neocentromere-mediated chromosome movement in maize. J. Cell Biol. 139: 831-840.
  • Dawe, R.K. and W. Z. Cande. 1996. Induction of centromeric activity in maize by Suppressor of meiotic drive 1. Proc. Natl. Acad. Sci USA 93: 8512-8517.
  • Dawe, R.K., J.W. Sedat, D.A. Agard and W. Z. Cande. 1994. Chromosome synapsis in maize is associated with a novel chromatin organization. Cell 76: 901-912.

Jeffrey Bennetzen

Norman and Doris Giles Professor
Georgia Research Alliance Eminent Scholar
Ph.D. (1980) University of Washington
  • Elected Member, US National Academy of Sciences, 2004
  • Elected Fellow, American Association for the Advancement of Science, 2005
  • Fulbright Awards, 2008 and 1990
  • Guggenheim Fellow, 2008
  • 1000 Talents Award, Chinese Academy of Sciences, 2012
  • Lamarr Dodd Creative Research Award, 2014
  • Distinguished Visiting Researcher Award, CSIRO, Australia, 2017
  • Elected Foreign Fellow of the Indian National Science Academy, 2020
  • Stebbins Medal (shared), 2021
  • Grant Support -
    • "Systems Analysis of the Beneficial Associations of Sorghum with Arbuscular Mycorrhizal Fungi Studied with Genetics, Genomics, Imaging and Microbiomics," DOE
    • "Consolidated Bioprocessing Initiative," DOE
  • Research Interests -
    • My lab is interested in plant genome structure and evolution, especially the nature of rearrangements and the contributions of transposable elements. We also study the relationship between genome structure, evolution and gene function. Our most active current research involves studies of microbe-microbe interactions in plant roots and surrounding soil.  We have long-standing interests in genetic diversity and its use in under-utilized crops of the developing world, and biomass improvement for production of biofuels.
Research Areas:
Biotechnology
Genomics and Bioinformatics
Molecular Genetics
Selected Publications:
  • Kabir, K. H., M. A. Rahman, M. M. Rahman, P. Brailey-Jones, K-W. Lee and J. L. Bennetzen (2022) Mechanistic assessment of tolerance to iron deficiency mediated by Trichoderma hazianum in soybean roots. J. Appl. Microbiol. DOI: 10.1111/jam.15651.
  • Khan, A. L., A. Al-Harrasi, J.-P. Wang, S. Asaf, J.-J. M. Riethoven, T. Shehzad, C.-S. Liew, X.-M. Song, D. P. Schachtman, C. Liu, J.-G. Yu, Z.-K. Zhang, F.-B. Meng, J.-Q. Yuan, C. Wei, H. Guo, X. Wang, A. Al-Rawahi, I.-J. Lee, J. L. Bennetzen and X.-Y. Wang (2022) Genome structure and evolutionary history of frankincense producing Boswellia sacra. iScience. DOI: 10.1016/j.isci.2022.104574.
  • Sudalaimuthuasari, N., R. Ali, M. Kottackal, M. Rafi, M. Al Nuaimi, B. Kundu, R. S. Al-Maskari, X. Wang, A. K. Mishra, J. Balan, S. R. Chaluvadi, F. Al Ansari, J. L. Bennetzen, M. D. Purugganan, K. M. Hazzouri and K. M. A. Amiri (2022) The genome of mimosoid legume Prosopis cineraria, a desert tree. Int. J. Mol. Sci. 23. DOI: 10.3390/ijms231585030.
  • Johnson, A. C., T. H. Pendergast IV, S. Chaluvadi, J. L. Bennetzen and K. M. Devos (2022) Identification of microRNAs responsive to arbuscular mycorrhizal fungi in Panicum virgatum (switchgrass). BMC Genomics. DOI: 10.1186/s12864-022-08797-x.
  • Garg, V. and 44 other authors, including J. L. Bennetzen (2022) Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement. J. Adv. Res. 42:315-329. DOI: 10.1016/j.jare.2021.10.009.
  • Chalopin, D., L. G. Clark, W. P. Wysocki, M. Park, M. R. Duvall and J. L. Bennetzen (2021) Integrated genomic analyses from low-depth sequencing help resolve phylogenetic incongruence in the bamboos (Poaceae: Bambusoideae). Frontiers Plant Sci. DOI: 10.3389/fpls.2021.725728.
  • Varshney, R. K., and 53 other authors, including J. L. Bennetzen (2021) A global reference for chickpea genetic variation based on the sequencing of 3,366 genomes. Nature. 599:622-627.
  • Wang, L. and 25 others, including H. Zhou and J. L. Bennetzen (2021) Aegilops tauschii genome assembly Aet v5.0 features greater sequence continuity and improved annotation. G3 (11, jkab325).
  • Tong, W., J. Yu, Q. Wu, L. Hu, D. Tabys, Y. Wang, C. Wei, T. Ling, M. A. Inayat and J. L. Bennetzen (2021) Black tea quality is highly affected during processing by its leaf surface microbiome. J. Agric. Food Chem. 69:7115-7126.
  • Bahulikar, R. A., S. R. Chaluvadi, I. Torres-Jerez, J. Mosali, J. L. Bennetzen and M. K. Udvardi (2021) Nitrogen fertilization reduces nitrogen fixation activity of diverse diazotrophs in switchgrass roots. Phytobiomes J. 5:80-87.
  • Park, M., P. Christin, J. L. Bennetzen. (2021) Sample sequence analysis of panicoid grass genomes uncovers episodic amplification and frequent horizontal transfer of LTR-retrotransposons. G3 Mol. Biol. Evol. May 8;msab133. DOI: 10.1093/molbev/msab133.
  • Govindarajulu, R., A. N. Hostetler, Y. Xiao, S. R. Chaluvadi, M. Mauro-Herrera, M. L. Siddoway, C. Whipple, J. L. Bennetzen, K. M. Devos, A. N. Doust, J. S. Hawkins. (2021) Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum. G3 Feb 9;11(2):jkab024. DOI: 10.1093/g3journal/jkab024.
  • Wang, X., S. Chen, X. Ma, A. E. J. Yssel, S. R. Chaluvadi, M. S. Johnson, P. Gangashetty, F. Hamidou, M. D. Sanogo, A. Zwaenepoel, J. Wallace, Y. V. Peer, J. L. Bennetzen, A. V. Deynze. (2021) Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis). GigaScience. Volume 10, Issue 3, March 2021, giab013. DOI: 10.1093/gigascience/giab013
  • Varshney, R. K., P. Sinha, V. K. Singh, A. Kumar, Q. Zhang and J. L. Bennetzen (2020) 5Gs for crop improvement. Curr. Opin. Plant Biol., 56, 190-196. DOI:10.1016/j.pbi.2019.12.004.
  • Dai, X., Y. Liu, J. Zhuang, S. Yao, L. Liu, X. Jiang, K. Zhou, D. Xie, J. L. Bennetzen, L. Gao and T. Xia (2020) Discovery and characterization of tannase genes in plants: Roles for hydrolysis of tannins. New Phytol.226(4), 1104-1116. DOI:10.1111/nph.16425.
  • Johnen, L., T. Boldieri de Souza, D. R. Rocha, L. M. Parteka, M. S. González-Elizondo, R. Trevisan, S. R. Chaluvadi, J. L. Bennetzen, and A. L. Laforga Vanzela (2020) Allopolyploidy and genomic differentiation in the holocentric species of Eleocharis montana complex (Cyperaceae). Plant Syst. Evol. 306:1-17. DOI:10.1007/s00606-020-01666-8.
  • Zhang, S., S. R. Chaluvadi, and J. L. Bennetzen (2020) Genome sequence analysis of Enterobacter sp. C6 found in the pitcher fluids of Sarracenia rosea. Microbiol. Resour. Announc., 9:e01214-19. DOI:10.1128/MRA.01214-19.
  • Zhang, S., S. R. Chaluvadi, and J. L. Bennetzen (2020) Draft genome sequence of a Serratia marcescens strain isolated from the pitcher fluids of a Sarracenia pitcher plant. Microbiol. Resour. Announc. 9:e01216-19.DOI:10.1128/MRA.01216-19.
  • VanBuren, R., C. M. Wai, X. Wang, J. Pardo, A. E. Yocca, H. Wang, S. R. Chaluvadi, G. Han, D. Bryant, P. P. Edger, W. Zhang, J. Messing, M. E. Sorrells, T. C. Mockler, J. L. Bennetzen, and T. P. Michael (2020) Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia. Nature Comm. 11:1-11. DOI:10.1038/s41467-020-14724-z.
  • VanBuren, R. V., C. M. Wai, J. Pardo, A. El Yocca, X. Wang, H. Wang, S. R. Chaluvadi, D. Bryant, P. P. Edger, J. L. Bennetzen, T. C. Mockler and T. P. Michael (2019) Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia. Nature Comm 580720.
  • Li, Y., X. Wang, Q. Ban, X. Zhu, C. Jiang, C. Wei and J. L. Bennetzen (2019) Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis. BMC Genomics 20: article #624.
  • Chen, L.-Y. and 44 others, including H. Zhou, H. Wang and J. L. Bennetzen (2019) The bracteatus pineapple genome and domestication of clonally propagated crops. Nature Genetics 51:1549-1558.
  • Xia, E. and 44 others including T. Wei and J. L. Bennetzen (2019) The tea plant reference genome and improved gene annotation using long-read and paired-end sequencing data. Sequence Data 6: 122 pages.
  • Xu, C.-Q. and 19 others, including X. Wang and J. L. Bennetzen (2019) Genome sequence of Malania oleifera, a threatened tree with great value for nervonic acid production. GigaScience 8. DOI: 10.1093/gigascience/giy164.
  • Dunning, L. T., J. K. Olofsson, C. Parisod, R. Choudhury, J. J. Moreno-Villena, T. Handasyde, Y. Yang, J. Dionora, W. P. Quick, M. Park, J. L. Bennetzen, P. Nosil, C. P. Osborne and P.-A. Christin (2019) Lateral transfers of large DNA fragments spread functional genes among eukaryotes. Proc. Natl. Acad. Sci., USA 116:4416-4425.
  • Bennetzen, J. L. (2019) Better research for better tea. Nature 566:S5.
  • Chaluvadi, S. R., P. Young, K. Thompson, B. A. Barhi, B. Gajera, S. Narayanan, R. Krueger and J. L. Bennetzen (2019) Phoenix phylogeny, and analysis of genetic diversity in a diverse collection of date palm (Phoenix dactylifera) and its wild relatives. Plant Diversity DOI:10.1016/j.pld.2018.11.005. 
  • Frailey, D. C., S. R. Chaluvadi, J. N. Vaughn, C. G. Coatney, and J. L. Bennetzen (2018) Gene loss and genome rearrangement in the plastids of five hemiparasites in the family Orobanchaceae. BMC Plant Biol. 18:30. DOI: 10.1186/s12870-018-1249-x.
  • Wuyun, T. and 30 other authors, including X. Wang and J. L. Bennetzen (2018) The hardy rubber tree genome reveals the evolution of polyisoprene biosynthesis. Mol. Plant 5:429-442. DOI: 10.1016/jmolp.2017.11.014.
  • Hoffbert, S. L., N. J. Troendle, T. C. Glenn, O. Mahmud, D. Chalopin, J. L. Bennetzen and R. Mauricio (2018) A high-quality reference genome for the invasive mosquitofish Gambusia affinis using a Chicago library. G3 8:1855-1861.
  • Wei, C. and 42 others, including W. Tong and J. L. Bennetzen (2018) Draft genome sequence of Camellia sinensis var. sinensis provides insights into the evolution of the tea genome and tea quality. Proc. Natl. Acad. Sci. USA 115:E4151-E4158.
  • Bennetzen, J. L. and M. Park (2018) Distinguishing friends, foes and freeloaders in giant genomes. Curr. Opin. Gen. Dev. 49:49-55.
  • Bennetzen, J. L. and X. Wang (2018) Relationships between gene structure and genome instability in flowering plants. Mol. Plant DOI: 10.1016/jmolp.2018.02.003.
  • Arthur, R. A. and J. L. Bennetzen (2018) Discovery of lineage-specific genome change in rice through analysis of resequencing data. Genetics 209:617-626.
  • Souza, T. B., S. R. Chaluvadi, L. Johnen, A. Marques, M. S. Gonzalez-Elizondo, J. L. Bennetzen and A. L. L. Vanzela (2018) Analysis of retrotransposon abundance, diversity and distribution in holocentric Eleocharis (Cyperaceae) genomes. Annals Bot., 122:279-290.
  • Wang, X., S. Yang, Y. Chen, S. Zhang, Q. Zhao, M. Li, Y. Gao, L. Yang and J. L. Bennetzen (2018) Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana. BMC Genomics, 19:500.
  • Manski, C. and >310 other NAS Members, including J. Bennetzen (2018) Statement to restore science-based policy in government by concerned members of the U.S. National Academy of Sciences. Open letter, reproduced at several internet and press sites, including https://scientistsforsciencebasedpolicy.org/.
  • Dai, X., H. Wang, H. Zhou, J. Dvořák, J. L. Bennetzen and H.-G. Müller (2018) Birth and death of LTR-retrotransposons in Aegilops tauschii. Genetics, 210:1039-1051.
  • Chaluvadi, S. R. and J. L. Bennetzen (2018) Species-associated differences in the below-ground microbiomes of wild and domesticated Setaria. Frontiers Plant Sci., 9: 1183 DOI:10.3389/fpls.2018.01183.
  • Wei, T., J. Yu, Y. Hou, Q. Zhou, F. Li, X. Wang, C. Wei, and J. L. Bennetzen (2018) Circular RNA architecture and differentiation during leaf bud to young leaf development in tea (Camellia sinensis). Planta, 248:1417-1429.
  • Bennetzen, J., S. Flint-Garcia, C. Hirsch, and R. Tuberosa (eds.) (2018) The Maize Genome, Springer Nature, Switzerland.
  • Bennetzen, J. L. (2018) Maize transposable element dynamics. In: The Maize Genome (eds. J. Bennetzen, S. Flint-Garcia, C. Hirsch, and R. Tuberosa), Springer Nature, Switzerland, pp. 49-58.
  • Varshney, R. K. and 65 other authors, including H. Wang and J. L. Bennetzen (2017) Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Biotech. 35:969-976.
  • Chen, Y., J. Dong, J. L. Bennetzen, M. Zhong, J. Yang, J. Zhang, S. Li, X. Hao, Z. Zhang, and X. Wang (2017) Integrating transcriptome and microRNA analysis identifies genes and microRNAs for AHO-induced systemic acquired resistance in N. tabacum. Scientific Reports 7: DOI: 10.1038/s41598-017-12249-y.
  • Kim, S. and 40 other authors, including M. Park and J. L. Bennetzen (2017) New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol. 18:210 DOI: 10.1186/s13059-017-1341-9.
  • Luo, M.-C. and 45 other authors, including H. Wang and J. L. Bennetzen (2017) Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551:498-502.
  • Wolpe, P. R. and 81 other authors, including J. L. Bennetzen (2017) Ethical principles for the use of cellular biotechnologies. Nature Biotech. 35:1050-1058.
  • Nelson, R. S. and 29 other authors, including R. Percifield and J. L. Bennetzen (2017) Development and use of a switchgrass (Panicum virgatum L.) transformation pipeline by the BioEnergy Science Center to evaluate plants for reduced cell wall recalcitrance. Biotech. Biofuels 10:309 DOI: 10.1186/s13068-017-0991-x.
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