The main focus of the Burk laboratory is to utilize population-based longitudinal studies from large epidemiological cohorts including those with and without HIV to study the dynamics of host-microbe interactions. These include HPV and development of cancer, and the human microbiome and disease outcomes (cancer, infectious diseases, cardiovascular disease, diabetes, obesity, aging).

To understand complex ecological community of bacteria, fungi, viruses and other organisms and how that might interact for disease outcomes.  These studies are built on understanding the application of laboratory tests to population-based studies. They employ NGS and state of the art bioinformatics.

Other interests of the lab include the genetics of complex human disease (prostate cancer, excessive sweating) using large case-control clinical collections of genomic DNAs with candidate gene sequencing; and, the cell biology of VHL and its role in primary cilia formation and activity and its disruption in renal cancer.

The lab is dedicated to creating a warm environment based on collaborative science and teamwork.  Our mission is to facilitate each individual reaching his or her potential through learning, experimentation and sharing in the pursuit of knowledge to promote human health and development.

(out of 503 published papers; google h-index 126)

Gradissimo A, Clarke MA, Xue X, Castle PE, Raine-Bennett TR, Schiffman M, Wentzensen N, Strickler HD, Burk RD. A Novel HPV/Host DNA Methylation-Score and Detection of Cervical Adenocarcinoma. J Natl Cancer Inst. 2023. Epub 2023/07/19. doi: 10.1093/jnci/djad134. PMID: 37467068; PMC1069984.

Usyk M, Peters B, Karthikeyan S, McDonald D, Sollecito C, Vazquez-Baeza Y, Shaffer J, Gellman M, Talavera G, Daviglus M, Thyagarajan B, Knight R, Qi Q, Kaplan RC, and Burk, R.D. Comprehensive Evaluation of Shotgun Metagenomics, Amplicon Sequencing and Harmonization of These Platforms for Epidemiological Studies. Cell Report Methods 2023 Jan 23;3(1):100391. eCollection 2023 Jan 23. PMID: 36814836; PMC9939430

Schiffman M, Mirabello L, Egemen D, Befano B, Xiao Y, Wentzensen N, Raine-Bennett T, Nayar R, Cheung LC, Rositch A, Beaty T, Perkins RB, de Sanjose S, Lorey T, Castle PE, Burk RD. The combined finding of HPV 16, 18, or 45 and cytologic Atypical Glandular Cells (AGC) indicates a greatly elevated risk of in situ and invasive cervical adenocarcinoma. Gynecol Oncol. 2023;174:253-61. Epub 2023/05/27. doi: 10.1016/j.ygyno.2023.05.011. PMID: 37243996

Burk RD, Mirabello L, DeSalle R. Distinguishing Genetic Drift from Selection in Papillomavirus Evolution. Viruses. 2023;15(8). Epub 2023/08/26. doi: 10.3390/v15081631. PMID: 37631973; PMC10458755.

Usyk M, Schlecht NF, Pickering S, Williams L, Sollecito CC, Gradissimo A, Porras C, Safaeian M, Pinto L, Herrero R, Strickler HD, Viswanathan S, Nucci-Sack A, Diaz A, Burk RD.molBVreveals immune landscape of bacterial vaginosis and predicts human papillomavirus infection natural history. Nat Commun. 2022;13(1):233. Epub 2022/01/13. doi: 10.1038/s41467-021-27628-3. PMID: 35017496; PMC8752746.

Schlecht NF, Diaz A, Nucci-Sack A, Shyhalla K, Shankar V, Guillot M, Hollman D, Strickler HD, Burk RD. Incidence and Types of Human Papillomavirus Infections in Adolescent Girls and Young Women Immunized With the Human Papillomavirus Vaccine. JAMA Netw Open. 2021 Aug 2;4(8):e2121893. doi: 10.1001/jamanetworkopen.2021.21893. PMID: 34424304; PMC8383132.

Gressel GM, Usyk M, Frimer M, Kuo DYS, Burk RD. Characterization of the endometrial, cervicovaginal and anorectal microbiota in post-menopausal women with endometrioid and serous endometrial cancers. PLoS One. 2021 Nov 5;16(11):e0259188. doi: 10.1371/journal.pone.0259188. PMID: 34739493; PMC8570463.

Chen Z, Utro F, Platt D, DeSalle R, Parida L, Chan PKS, Burk RD. K-Mer Analyses Reveal Different Evolutionary Histories of Alpha, Beta, and Gamma Papillomaviruses. Int J Mol Sci. 2021 Sep 6;22(17):9657. doi: 10.3390/ijms22179657. PMID: 34502564; PMC8432194.

Kurilshikov,  A. . . . Burk, R.D. . . . Zhernakova, A. Large-scale association analyses identify host factors influencing human gut microbiome composition. Nat. Genet. 53: 156-165, 2021. doi: 10.1038/s41588-020-00763-1; PMID: 33462485; PMC8515199.

Kaplan, R.C., Wang, Z., Usyk, M., Sotres-Alvarez, D., Daviglus, M.L., Schneiderman, N., Talavera, G.A., Gellman, M.D., Thyagarajan, B., Moon, J-Y, Vasquez-Baeza, Y., McDonald, D., Williams-Nguyen, J.S., Wu, M.C., North, K.E. Shaffer, J., Sollecito, C.C., Qi, Q., Isasi, C.R., Wang, T., Knight, R. and Burk, R.D.  Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors and obesity. Genome Biol. 2019, 20(1):219. PMID:31672155; PMC6824043.

Chen, Z., DeSalle, R., Schiffman, M., Herrero, R., Wood, C.E., Ruiz, J.C., Clifford, G.M., Chan, P.K.S. and Burk, R.D.  Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans. PLoS Pathog. 2018, 14(11): e1007352. PMID: 30383862; PMC6211759.

Mirabello. L., Yeager, M., Yu, K., Clifford, G.M., Xiao, Y., Zhu, B., Cullen, M., Boland, J.F., Wentzensen, N., Nelson, C.W., Raine-Bennett, T., Chen, Z., Bass, S., Song, L., Yang, Q., Steinberg, M., Burdett, L., Dean, M., Roberson, D., Mitchell, J., Lorey, T., Franceschi, S., Castle, P.E., Walker, J., Zuna, R., Kreimer, A.R., Beachler, D.C., Hildesheim, A., Gonzalez, P., Porras, C., Burk, R.D.* (co-last author), Schiffman, M.*HPV16 E7 Genetic Conservation Is Critical to Carcinogenesis. Cell. 2017 Sep 7;170(6):1164-1174.PMID: 28886384; PMC5674785