Professional Interests

I have been interested in the emergence of viral pathogens since first studying viral evolution in the late 1990’s; a pivotal time in virology that saw the emergence of deadly viruses such as Sin Nombre hantavirus in the US, Nipah virus in Malaysia, and H5N1 avian influenza virus in Hong Kong. In the decades since then, sequencing technology has changed drastically and interpretation of the massive sets of data generated by next generation sequencing platforms requires close interaction between virologists and bioinformaticists to understand the patterns of evolution buried in the millions of sequencing reads. I have enjoyed being part of multidisciplinary teams studying the mechanisms used by different viral families during cross-species transmission. In particular I am interested in developing methods that provide deep insight into how viruses emerge and evolve, with the ultimate goal of combining biological research with computer modeling to enable predictive biology. I am also interested in developing new methods for biosurveillance and forensic studies.

Massey TL, Borucki MK, Paik SY, Fuhrer KW, Bora M, Kane SR, Haque R-uM, Baxamusa SH. 2021. Quantitative Fit Evaluation of N95 Filtering Facepiece Respirators and Coronavirus Inactivation Following Heat Treatment. Annals of Work Exposures and Health doi:10.1093/annweh/wxab020.

 Lau EY, Negrete OA, Bennett WFD, Bennion BJ, Borucki M, Bourguet F, Epstein A, Franco M, Harmon B, He S, Jones D, Kim H, Kirshner D, Lao V, Lo J, McLoughlin K, Mosesso R, Murugesh DK, Saada EA, Segelke B, Stefan MA, Stevenson GA, Torres MW, Weilhammer DR, Wong S, Yang Y, Zemla A, Zhang X, Zhu F, Allen JE, Lightstone FC. 2021. Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline. 2021 Jul 9;8:678701. doi: 10.3389/fmolb.2021.678701.

 Lemos D, Stuart JB, Louie W, Singapuri A, Ramírez AL, Watanabe J, Usachenko J, Keesler RI, Martin CS-S, Li T, Martyn C, Oliveira G, Saraf S, Grubaugh ND, Andersen KG, Thissen J, Allen J, Borucki M, Tsetsarkin KA, Pletnev AG, Chiu CY, Rompay KKAV, Coffey LL, Parrish CR. 2020. Two Sides of a Coin: a Zika Virus Mutation Selected in Pregnant Rhesus Macaques Promotes Fetal Infection in Mice but at a Cost of Reduced Fitness in Nonpregnant Macaques and Diminished Transmissibility by Vectors.  94:e01605-20.

 Juarez JG, Garcia-Luna SM, Medeiros MCI, Dickinson KL, Borucki MK, Frank M, Badillo-Vargas I, Chaves LF, Hamer GL. 2021. The Eco-Bio-Social Factors That Modulate Aedes aegypti Abundance in South Texas Border Communities.  12:183.

 Collette NM, Lao VHI, Weilhammer DR, Zingg B, Cohen SD, Hwang M, Coffey LL, Grady SL, Zemla AT, Borucki MK. 2020. Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo. Viruses 12:1295.

 Borucki MK, Collette NM, Coffey LL, Van Rompay KKA, Hwang MH, Thissen JB, Allen JE, Zemla AT. 2019. Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence. PLoS ONE 14:e0225699.

Peña, J., H. Chen-Harris, J. Allen, M. Hwang, M. Elsheikh, S. Mabery, H. Bielefeldt-Ohmann, A. Zemla, R. Bowen, and M. Borucki. 2016. Sendai virus intra-host population dynamics and host immunocompetence influence viral virulence during in vivo passage Viral Evol. 2 (1), vew008. 2016 Apr 09.

Borucki, M. K., V. Lao, M. Hwang, S. Gardner, D. Adney, V. Munster, R. Bowen, and J. E. Allen. 2016. Middle East Respiratory Syndrome Coronavirus Intra-Host Populations Are Characterized by Numerous High Frequency Variants. PLoS ONE 11:e0146251.

Gardner, S.N., Jaing, C.J., Elsheikh, M.M, Peña, J., Hysom, D.A., Borucki, M.K. “Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes,” 2014. Advances in Bioinformatics, Article ID 101894, doi:10.1155/2014/101894

Devault, A.M., McLoughlin, K., Jaing, C., Gardner, S., Porter, T.M., Enk, J.M., Thissen, J., Allen, J., Borucki, M., DeWitte, S.N., Dhody, A.N., Poinar, H.N., 2014. Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array. Scientific Reports 4, Article number: 4245. doi:10.1038/srep04245

Chen-Harris, H., Borucki, M.K., Torres, C., Slezak, T.R., Allen, J.E., 2013. Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs. BMC Genomics 14, 96.

Borucki, M.K., Allen, J.E., Chen-Harris, H., Zemla, A., Vanier, G., Mabery, S., Torres, C., Hullinger, P., Slezak, T., 2013a. The role of viral population diversity in adaptation of bovine coronavirus to new host environments. PLoS ONE 8, e52752.

Borucki, M.K., Chen-Harris, H., Lao, V., Vanier, G., Wadford, D.A., Messenger, S., Allen, J.E., 2013b. Ultra-deep sequencing of intra-host rabies virus populations during cross-species transmission. PLoS Neglected Tropical Diseases 7, e2555.

Kim, S.H., Gorski, L., Reynolds, J., Orozco, E., Fielding, S., Park, Y.H., Borucki, M.K., 2006. Role of uvrA in the growth and survival of Listeria monocytogenes under UV radiation and acid and bile stress. Journal of Food Protection 69, 3031-3036.

Borucki, M.K., Gay, C.C., Reynolds, J., McElwain, K.L., Kim, S.H., Call, D.R., Knowles, D.P., 2005. Genetic diversity of Listeria monocytogenes strains from a high-prevalence dairy farm. Applied and Environmental Microbiology 71, 5893-5899.

Borucki, M.K., Reynolds, J., Call, D.R., Ward, T.J., Page, B., Kadushin, J., 2005. Suspension microarray with dendrimer signal amplification allows direct and high-throughput subtyping of Listeria monocytogenes from genomic DNA. Journal of Clinical Microbiology 43, 3255-3259.

Borucki, M.K., Kim, S.H., Call, D.R., Smole, S.C., Pagotto, F., 2004. Selective discrimination of Listeria monocytogenes epidemic strains by a mixed-genome DNA microarray compared to discrimination by pulsed-field gel electrophoresis, ribotyping, and multilocus sequence typing. Journal of Clinical Microbiology 42, 5270-5276.

Kim, S.H., Bakko, M.K., Knowles, D., Borucki, M.K., 2004. Oral inoculation of A/J mice for detection of invasiveness differences between Listeria monocytogenes epidemic and environmental strains. Infection and Immunity 72, 4318-4321.

Borucki, M.K., Reynolds, J., Gay, C.C., McElwain, K.L., Kim, S.H., Knowles, D.P., Hu, J., 2004. Dairy farm reservoir of Listeria monocytogenes sporadic and epidemic strains. Journal of Food Protection 67, 2496-2499.

Call, D.R., Borucki, M.K., Besser, T.E., 2003. Mixed-genome microarrays reveal multiple serotype and lineage-specific differences among strains of Listeria monocytogenes. Journal of Clinical Microbiology 41, 632-639.

Borucki, M.K., Call, D.R., 2003. Listeria monocytogenes serotype identification by PCR. Journal of Clinical Microbiology 41, 5537-5540.

Borucki, M.K., Peppin, J.D., White, D., Loge, F., Call, D.R., 2003. Variation in biofilm formation among strains of Listeria monocytogenes. Applied and Environmental Microbiology 69, 7336-7342.

Borucki, M.K., Krug, M.J., Muraoka, W.T., Call, D.R., 2003. Discrimination among Listeria monocytogenes isolates using a mixed genome DNA microarray. Veterinary Microbiology 92, 351-362.

Call, D.R., Borucki, M.K., Loge, F.J., 2003. Detection of bacterial pathogens in environmental samples using DNA microarrays. Journal of Microbiological Methods 53, 235-243.

Meissner, J.D., Rowe, J.E., Borucki, M.K., St Jeor, S.C., 2002. Complete nucleotide sequence of a Chilean hantavirus. Virus Research 89, 131-143.

Borucki, M.K., Kempf, B.J., Blitvich, B.J., Blair, C.D., Beaty, B.J., 2002. La Crosse virus: replication in vertebrate and invertebrate hosts. Microbes and Infection 4, 341-350.

Borucki, M.K., Kempf, B.J., Blair, C.D., Beaty, B.J., 2001. The effect of mosquito passage on the La Crosse virus genotype. The Journal of General Virology 82, 2919-2926.

Borucki, M.K., Boone, J.D., Rowe, J.E., Bohlman, M.C., Kuhn, E.A., DeBaca, R., St Jeor, S.C., 2000. Role of maternal antibody in natural infection of Peromyscus maniculatus with Sin Nombre virus. Journal of Virology 74, 2426-2429.

Borucki, M.K., Chandler, L.J., Parker, B.M., Blair, C.D., Beaty, B.J., 1999. Bunyavirus superinfection and segment reassortment in transovarially infected mosquitoes. The Journal of General Virology 80 ( Pt 12), 3173-3179.

Chandler, L.J., Borucki, M.K., Dobie, D.K., Wasieloski, L.P., Thompson, W.H., Gundersen, C.B., Case, K., Beaty, B.J., 1998. Characterization of La Crosse virus RNA in autopsied central nervous system tissues. Journal of Clinical Microbiology 36, 3332-3336.

Cano, R.J., Borucki, M.K., 1995. Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber. Science 268, 1060-1064.

Cano, R.J., Borucki, M.K., Higby-Schweitzer, M., Poinar, H.N., Poinar, G.O., Jr., Pollard, K.J., 1994. Bacillus DNA in fossil bees: an ancient symbiosis? Applied and Environmental Microbiology 60, 2164-2167.