Joshua Aaron Granek
Assistant Professor in Biostatistics & Bioinformatics
We have broad interests in using microbial genomics to understand how microbes interact with each other and their hosts. This interest includes the roles played by both beneficial and harmful bacteria, fungi, and viruses and how they interact with the immune system. We study single microbes and microbial communities, primarily using high-throughput sequencing methods. We have a particular interest in developing new experimental and analytical methods that leverage the power of high-throughput sequencing. We are also interested in using deep learning in microbiology research.
Current Appointments & Affiliations
- Assistant Professor in Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2021
Contact Information
- 2424 Erwin Rd,, 10044 Hock Plaza, Durham, NC 27710
- Box 2721, Durham, NC 27710
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joshua.granek@duke.edu
(919) 684-0333
- Background
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Education, Training, & Certifications
- Ph.D., Johns Hopkins University 2006
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Previous Appointments & Affiliations
- Assistant Professor in Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2020
- Assistant Professor in Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2019 - 2020
- Assistant Professor in Biostatistics and Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2012 - 2019
- Research
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Selected Grants
- Training Program in Bioinformatics at the Intersection of Cancer Immunology and Microbiome awarded by National Institutes of Health 2020 - 2025
- Quantitative Methods for HIV/AIDS Research awarded by National Institutes of Health 2018 - 2023
- The Genetic Basis of Bone Disease in Mycobacterial Infection awarded by National Institutes of Health 2017 - 2022
- Coordinated Regulation of Virulence Genes in C. neoformans awarded by National Institutes of Health 2016 - 2022
- NRT: Integrative Bioinformatics for Investigating and Engineering Microbiomes (IBIEM) awarded by National Science Foundation 2015 - 2021
- A hands-on, integrative next-generation sequencing course: design, experiment, and analysis awarded by National Institutes of Health 2016 - 2020
- The Genetic Basis of Bone Disease in Mycobacterial Infection awarded by National Institutes of Health 2014 - 2017
- Forward and Reverse Genetics in Chlamydia awarded by National Institutes of Health 2012 - 2017
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External Relationships
- Adobe Systems
- Alphabet Inc
- Amazon.Com, Inc
- Facebook Coporation
- Home Depot Inc
- Microsoft Corporation
- Paypal Hldgs Inc Com
- Thermo Fisher Scientific, Inc.
- UnitedHealth Group
- Visa Inc Com CL A
- Zoetis Inc
- Publications & Artistic Works
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Selected Publications
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Academic Articles
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Telzrow CL, Zwack PJ, Esher Righi S, Dietrich FS, Chan C, Owzar K, et al. Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries. G3 (Bethesda). 2021 Oct 19;11(11).Full Text Link to Item
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Telzrow C, Zwack P, Righi SE, Dietrich F, Chan C, Owzar K, et al. Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries. 2021 Mar 2;Full Text
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McCann JR, Bihlmeyer NA, Roche K, Catherine C, Jawahar J, Kwee LC, et al. The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights. Obesity (Silver Spring). 2021 Mar;29(3):569–78.Full Text Open Access Copy Link to Item
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Johnson-Weaver BT, Choi HW, Yang H, Granek JA, Chan C, Abraham SN, et al. Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens. Front Immunol. 2021;12:730346.Full Text Link to Item
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McCann J, Bihlmeyer N, Roche K, Catherine C, Jawahar J, Kwee LC, et al. The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights. 2020 Jun 11;Full Text
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Bornbusch SL, Greene LK, McKenney EA, Volkoff SJ, Midani FS, Joseph G, et al. A comparative study of gut microbiomes in captive nocturnal strepsirrhines. Am J Primatol. 2019 Oct;81(10–11):e22986.Full Text Link to Item
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Finn SMB, Scheuermann U, Holzknecht ZE, Gao Q, Ibrahim MM, Parker W, et al. The effect of levofloxacin on the lung microbiota of laboratory rats. Exp Lung Res. 2019 Sep;45(7):200–8.Full Text Link to Item
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Lin J, Gresham J, Wang T, Kim SY, Alvarez J, Damrauer JS, et al. bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens. Bioinformatics. 2018 Oct 15;34(20):3581–3.Full Text Link to Item
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Finn SMB, Scheuermann U, Holzknecht ZE, Parker W, Granek JA, Lin SS, et al. Effect of gastric fluid aspiration on the lung microbiota of laboratory rats. Exp Lung Res. 2018 May;44(4–5):201–10.Full Text Link to Item
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Sun S, Yadav V, Billmyre RB, Cuomo CA, Nowrousian M, Wang L, et al. Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination. Plos Biol. 2017 Aug;15(8):e2002527.Full Text Link to Item
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Chow EWL, Clancey SA, Billmyre RB, Averette AF, Granek JA, Mieczkowski P, et al. Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans. Plos Genet. 2017 Apr;13(4):e1006667.Full Text Link to Item
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Esher SK, Granek JA, Alspaugh JA. Rapid mapping of insertional mutations to probe cell wall regulation in Cryptococcus neoformans. Fungal Genet Biol. 2015 Sep;82:9–21.Full Text Link to Item
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Kokes M, Dunn JD, Granek JA, Nguyen BD, Barker JR, Valdivia RH, et al. Integrating chemical mutagenesis and whole-genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia. Cell Host Microbe. 2015 May 13;17(5):716–25.Full Text Link to Item
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Calo S, Shertz-Wall C, Lee SC, Bastidas RJ, Nicolás FE, Granek JA, et al. Antifungal drug resistance evoked via RNAi-dependent epimutations. Nature. 2014 Sep 25;513(7519):555–8.Full Text Link to Item
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Esher SK, Granek JA, Alspaugh JA. AIM-HII: a new method to rapidly identify agrobacterium-mediated insertion sites in C. neoformans. Mycoses. 2014 May 1;57:79–80.Link to Item
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Granek JA, Murray D, Kayrkçi Ö, Magwene PM. The genetic architecture of biofilm formation in a clinical isolate of Saccharomyces cerevisiae. Genetics. 2013 Feb;193(2):587–600.Full Text Link to Item
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Granek JA, Kayıkçı Ö, Magwene PM. Pleiotropic signaling pathways orchestrate yeast development. Curr Opin Microbiol. 2011 Dec;14(6):676–81.Full Text Link to Item
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Magwene PM, Kayıkçı Ö, Granek JA, Reininga JM, Scholl Z, Murray D. Outcrossing, mitotic recombination, and life-history trade-offs shape genome evolution in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1987–92.Full Text Link to Item
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Granek JA, Magwene PM. Environmental and genetic determinants of colony morphology in yeast. Plos Genet. 2010 Jan 22;6(1):e1000823.Full Text Open Access Copy Link to Item
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Liu X, Lee C-K, Granek JA, Clarke ND, Lieb JD. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res. 2006 Dec;16(12):1517–28.Full Text Link to Item
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Granek JA, Clarke ND. Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol. 2005;6(10):R87.Full Text Link to Item
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Carroll KL, Pradhan DA, Granek JA, Clarke ND, Corden JL. Identification of cis elements directing termination of yeast nonpolyadenylated snoRNA transcripts. Mol Cell Biol. 2004 Jul;24(14):6241–52.Full Text Link to Item
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Clarke ND, Granek JA. Rank order metrics for quantifying the association of sequence features with gene regulation. Bioinformatics. 2003 Jan 22;19(2):212–8.Full Text Link to Item
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Senkevich TG, White CL, Weisberg A, Granek JA, Wolffe EJ, Koonin EV, et al. Expression of the vaccinia virus A2.5L redox protein is required for virion morphogenesis. Virology. 2002 Sep 1;300(2):296–303.Full Text Link to Item
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Noll DM, Gogos A, Granek JA, 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. 1999 May 18;38(20):6374–9.Full Text Link to Item
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Troy JD, Granek J, Samsa GP, Pomann G-M, Updike S, Grambow SC, et al. A Course in Biology and Communication Skills for Master of Biostatistics Students. Journal of Curriculum and Teaching. 11(4):120–120.Full Text
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- Teaching & Mentoring
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Recent Courses
- BIOSTAT 703: Introduction to the Practice of Biostatistics I 2022
- BIOSTAT 703L: Introduction to the Practice of Biostatics I Lab 2022
- BIOSTAT 703: Introduction to the Practice of Biostatistics I 2021
- BIOSTAT 703L: Introduction to the Practice of Biostatics I Lab 2021
- CEE 690: Advanced Topics in Civil and Environmental Engineering 2021
- BIOSTAT 703: Introduction to the Practice of Biostatistics I 2020
- BIOSTAT 703L: Introduction to the Practice of Biostatics I Lab 2020
- CEE 690: Advanced Topics in Civil and Environmental Engineering 2020
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