2023
Escalante V, Nayak RR, Noecker C, Babdor J, Spitzer M, Deutschbauer AM, Turnbaugh PJ (2023). Simvastatin induces human gut bacterial cell surface genes. Mol Microbiol. 2023;00:1–15. pdf.
Bustion AE, Nayak RR, Agrawal A, Turnbaugh PJ, Pollard KS (2023). "SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations." Elife 2023 Jun 12;12:e82401. pdf.
2022
Nayak, R. R. (2022). "Fanning the flames of autoimmunity: the microbiome in rheumatic disease." Arthritis & Rheumatology 74 (4), 549-552. pdf
Alexander, M., Q. Y. Ang, R. R. Nayak, A. E. Bustion, M. Sandy, B. Zhang, V. Upadhyay, K. S. Pollard, S. V. Lynch and P. J. Turnbaugh (2022). "Human gut bacterial metabolism drives Th17 activation and colitis." Cell Host & Microbe 30 (1) 17-30. pdf
2021
Lam, K. N., P. Spanogiannopoulos, P. Soto-Perez, M. Alexander, M. J. Nalley, J. E. Bisanz, R. R. Nayak, A. M. Weakley, F. B. Yu and P. J. Turnbaugh (2021). "Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome." Cell Rep 37(5): 109930. pdf
Nayak, R. R. (2021). "Western Diet and Psoriatic-Like Skin and Joint Diseases: A Potential Role for the Gut Microbiota." J Invest Dermatol 141(7): 1630-1632. pdf
Nayak, R. R., M. Alexander, I. Deshpande, K. Stapleton-Gray, B. Rimal, A. D. Patterson, C. Ubeda, J. U. Scher and P. J. Turnbaugh (2021). "Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation." Cell Host Microbe 29(3): 362-377 e311. pdf
2020
Scher, J. U., R. R. Nayak, C. Ubeda, P. J. Turnbaugh and S. B. Abramson (2020). "Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response." Nat Rev Rheumatol 16(5): 282-292.
Artacho, A.*, S. Isaac*, R. Nayak*, A. Flor-Duro, M. Alexander, I. Koo, J. Manasson, P. B. Smith, P. Rosenthal, Y. Homsi, P. Gulko, J. Pons, L. Puchades-Carrasco, P. Izmirly, A. Patterson, S. B. Abramson, A. Pineda-Lucena, P. J. Turnbaugh, C. Ubeda and J. U. Scher (2020). "The Pre-treatment Gut Microbiome is Associated with Lack of Response to Methotrexate in New Onset Rheumatoid Arthritis." Arthritis Rheumatol. *equal contribution. pdf.
2016
Nayak, R. R. and P. J. Turnbaugh (2016). "Mirror, mirror on the wall: which microbiomes will help heal them all?" BMC Med 14: 72.
Mok, A., O. Solomon, R. R. Nayak, P. Coit, H. L. Quach, J. Nititham, A. H. Sawalha, L. F. Barcellos, L. A. Criswell and S. A. Chung (2016). "Genome-wide profiling identifies associations between lupus nephritis and differential methylation of genes regulating tissue hypoxia and type 1 interferon responses." Lupus Sci Med 3(1): e000183.
2014
Nayak, R. R., W. E. Bernal, J. W. Lee, M. J. Kearns and V. G. Cheung (2014). "Stress-induced changes in gene interactions in human cells." Nucleic Acids Res 42(3): 1757-1771.
2010
Dombroski, B. A.*, R. R. Nayak*, K. G. Ewens, W. Ankener, V. G. Cheung and R. S. Spielman (2010). "Gene expression and genetic variation in response to endoplasmic reticulum stress in human cells." Am J Hum Genet 86(5): 719-729. *equal contribution
Cheung, V. G., R. R. Nayak, I. X. Wang, S. Elwyn, S. M. Cousins, M. Morley and R. S. Spielman (2010). "Polymorphic cis- and trans-regulation of human gene expression." PLoS Biol 8(9).
2009
Nayak, R. R., M. Kearns, R. S. Spielman and V. G. Cheung (2009). "Coexpression network based on natural variation in human gene expression reveals gene interactions and functions." Genome Res 19(11): 1953-1962.
2006
Wallenfang, M. R., R. Nayak and S. DiNardo (2006). "Dynamics of the male germline stem cell population during aging of Drosophila melanogaster." Aging Cell 5(4): 297-304.