Scholars@Duke

• Background
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  Education, Training, & Certifications

  • Ph.D., Johns Hopkins University 2006
• Research
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  Selected Grants

  • The Genetic Basis of Bone Disease in Mycobacterial Infection awarded by National Institutes of Health 2017 - 2021
  • Coordinated Regulation of Virulence Genes in C. neoformans awarded by National Institutes of Health 2016 - 2021
  • Genetics of Cryptococcus sexual reproduction awarded by National Institutes of Health 1997 - 2021
  • NRT: Integrative Bioinformatics for Investigating and Engineering Microbiomes (IBIEM) awarded by  National Science Foundation 2015 - 2020
  • Structure, function, and evolution of the Cryptococcus MAT locus awarded by National Institutes of Health 2002 - 2019
  • A hands-on, integrative next-generation sequencing course: design, experiment, and analysis awarded by National Institutes of Health 2016 - 2019
  • Forward and Reverse Genetics in Chlamydia awarded by National Institutes of Health 2012 - 2018
  • The Genetic Basis of Bone Disease in Mycobacterial Infection awarded by National Institutes of Health 2014 - 2017
• Publications & Artistic Works
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  Selected Publications

  • Journal Articles

    • Sun, S, Yadav, V, Billmyre, RB, Cuomo, CA, Nowrousian, M, Wang, L, Souciet, J-L, Boekhout, T, Porcel, B, Wincker, P, Granek, JA, Sanyal, K, and Heitman, J. "Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination." PLoS Biology 15, no. 8 (August 11, 2017): e2002527-.  Full Text
    • Chow, EWL, Clancey, SA, Billmyre, RB, Averette, AF, Granek, JA, Mieczkowski, P, Cardenas, ME, and Heitman, J. "Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans." PLoS Genetics 13, no. 4 (April 4, 2017): e1006667-.  Full Text
    • Esher, SK, Granek, JA, and Alspaugh, JA. "Rapid mapping of insertional mutations to probe cell wall regulation in Cryptococcus neoformans." Fungal genetics and biology : FG & B 82 (September 2015): 9-21.  Full Text
    • Kokes, M, Dunn, JD, Granek, JA, Nguyen, BD, Barker, JR, Valdivia, RH, and Bastidas, RJ. "Integrating chemical mutagenesis and whole-genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia." Cell Host and Microbe 17, no. 5 (May 13, 2015): 716-725.  Full Text
    • Kokes, M, Dunn, JD, Granek, JA, Nguyen, BD, Barker, JR, Valdivia, RH, and Bastidas, RJ. "Integrating chemical mutagenesis and whole-genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia." Cell host & microbe 17, no. 5 (May 2015): 716-725.  Full Text
    • Calo, S, Shertz-Wall, C, Lee, SC, Bastidas, RJ, Nicolás, FE, Granek, JA, Mieczkowski, P, Torres-Martínez, S, Ruiz-Vázquez, RM, Cardenas, ME, and Heitman, J. "Antifungal drug resistance evoked via RNAi-dependent epimutations." Nature 513, no. 7519 (September 2014): 555-558.  Full Text
    • Esher, SK, Granek, JA, and Alspaugh, JA. "AIM-HII: a new method to rapidly identify agrobacterium-mediated insertion sites in C. neoformans." MYCOSES 57 (May 2014): 79-80.  Link to Item
    • Granek, JA, Murray, D, Kayrkçi, Ö, and Magwene, PM. "The genetic architecture of biofilm formation in a clinical isolate of Saccharomyces cerevisiae." Genetics 193, no. 2 (February 2013): 587-600.  Full Text  Link to Item
    • Granek, JA, Kayıkçı, Ö, and Magwene, PM. "Pleiotropic signaling pathways orchestrate yeast development." Curr Opin Microbiol 14, no. 6 (December 2011): 676-681. (Review)  Full Text  Link to Item
    • Magwene, PM, Kayıkçı, Ö, Granek, JA, Reininga, JM, Scholl, Z, and Murray, D. "Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae." Proc Natl Acad Sci U S A 108, no. 5 (February 1, 2011): 1987-1992.  Full Text  Link to Item
    • Granek, JA, and Magwene, PM. "Environmental and genetic determinants of colony morphology in yeast. (Published online)" PLoS Genet 6, no. 1 (January 22, 2010): e1000823-.  Full Text  Open Access Copy  Link to Item
    • Liu, X, Lee, C-K, Granek, JA, Clarke, ND, and Lieb, JD. "Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection." Genome Research 16, no. 12 (2006): 1517-1528.  Full Text
    • Granek, JA, and Clarke, ND. "Explicit equilibrium modeling of transcription-factor binding and gene regulation." Genome biology 6, no. 10 (2005): R87-.  Full Text
    • Carroll, KL, Pradhan, DA, Granek, JA, Clarke, ND, and Corden, JL. "Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts." Molecular and Cellular Biology 24, no. 14 (2004): 6241-6252.  Full Text
    • Clarke, ND, and Granek, JA. "Rank order metrics for quantifying the association of sequence features with gene regulation." Bioinformatics 19, no. 2 (2003): 212-218.  Full Text
    • Senkevich, TG, White, CL, Weisberg, A, Granek, JA, Wolffe, EJ, Koonin, EV, and Moss, B. "Expression of the vaccinia virus A2.5L redox protein is required for virion morphogenesis." Virology 300, no. 2 (2002): 296-303.  Full Text
    • Noll, DM, Gogos, A, Granek, JA, and Clarke, ND. "The C-terminal domain of the adenine-DNA glycosylase MutY confers specificity for 8-oxoguanine · adenine mispairs and may have evolved from MutT, an 8-oxo-dGTPase." Biochemistry 38, no. 20 (1999): 6374-6379.  Full Text
• Teaching & Mentoring
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  Recent Courses

  • CEE 690: Advanced Topics in Civil and Environmental Engineering 2017

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