[J23] Jimenez-Lopez, O., Ray, T., Dean, C., Slizovskiy, I.B., Deere, J., Wolf, T., Moore, S., Primus, A., Høy-Petersen, J., Finstad, S., Mo, J., Sørum, H., Noyes, N. The gut microbiome and resistome of yellow perch (Perca flavescens) living in Minnesota lakes under varying anthropogenic pressure.  One Health. 2024.19:100933; https://doi.org/10.1016/j.onehlt.2024.100933

[J22] Bravo J., Slizovskiy, I.B., Bonin, N., Oliva, M., Noyes, N., Boucher, C. The TELCoMB protocol for high-sensitivity detection of ARG-MGE colocalizations in complex microbial communities.  Current Protocols. 2024.4:e70031; https://doi.org/10.1002/cpz1.70031

[J21] Slizovskiy, I.B., Bonin, N., Bravo, J.E., Ferm, P.M., Singer, J., Boucher, C., Noyes, N.R. Factors impacting target-enriched long-read sequencing of resistomes and mobilomes.  Genome Research. 2024.34:1-13; https://doi.org/10.1101/gr.279226.124

[J20] Gaire, T.N., Odland, C.A., Bingzhou, Z., Slizovskiy, I.B., Jorgenson, B., Wehri, T., Meneguzzi, M., Wass, B., Schuld, J., Hanson, D., Doster, E., Singer, J., Cannon, J., Asmus, A., Ray, T., Dee, S., Nerem, J., Davies, P., Noyes, N.R. Slaughtering process impact microbial communities and antimicrobial resistance genes of pig carcasses.  Science of the Total Environment. 2024.946:10; https://doi.org/10.1016/j.scitotenv.2024.174394

[J19] Makau, D.N.*, Slizovskiy, I.B.*, Obanda, V., Noyes, N.R., Johnson, J.R., Oakes, M., Travis, D., VanderWaal, K., Omondi, G.P. Factors influencing usage of antimicrobial drugs among pastoralists of Kenya. Tropical animal health and production. 2022.54:332; https://doi.org/10.1007/s11250-022-03326-0


[J18] Slizovskiy, I.B.*, Oliva, M.*, Settle, J.K., Zyskina, L.V., Boucher, C., Noyes, N.R. Targeted-enrichment and long-read sequencing (TELSeq) contextualizes antibiotic resistance genes in metagenomes. Microbiome. 2022;10:185; https://doi.org/10.1186/s40168-022-01368-y

[J17] Alanko J.N., Slizovskiy, I.B., Lokshtanov D., Gagie T., Noyes, N.R., Boucher, C. SYOTTI: Scalable bait design for DNA enrichment. Bioinformatics. 2022.38:i177-i184;  https://doi.org/10.1093/bioinformatics/btac226.  

[J16] Nayar G., Terrizzano, I., Seabolt, E., Agarwal, A., Boucher C., Ruiz J., Slizovskiy, I.B., Kaufman, J.H., Noyes, N.R. ggMOB: Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks. Front. Genet. 2022; (13);1024577; https://doi.org/10.3389/fgene.2022.1024577

[J15] Marini, S., Oliva, M., Slizovskiy, I.B., Das, R.A., Noyes, N.R., Kahveci, T., Boucher, C., Prosperi, M. AMR-meta: A k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data. GigaScience. 2022;11(giac029):1-11.; https://doi.org/10.1093/gigascience/giac029

[J14] Noyes, N.R., Slizovskiy, I.B., Singer, R.S. Beyond antimicrobial use: A framework for prioritizing antimicrobial resistance interventions. Annu. Rev. Anim. Biosci. 2021;9:313332.

[J13] Marini S., Slizovskiy, I.B., Noyes, N., Boucher C., Prosperi M. Learning antimicrobial resistance through secondary structure of protein variants. Front. Genet. 2021; (12); https://doi.org/10.3389/fgene.2021.564186

[J12] Dean, C., Slizovskiy, I.B., Crone, K.K., Pfennig, A.X., Heinz, B.J., Caixeta, L.S., Noyes, N.R. Sampling considerations for conducting large-scale microbial ecology studies of cow udder epithelium. J. Dairy Sci. 2021;104:644-661.

[J11] Kaufman, J.H., Terrizzano, I., Nayar, G., Seabolt, E., Agarwal, A., Slizovskiy, I.B., Noyes, N.R. Integrative and Conjugative Elements (ICE) and associated cargo genes within and across hundreds of bacterial genera. bioRxiv 2020.04.07.030320; https://doi.org/10.1101/2020.04.07.030320

[J10] Slizovskiy, I.B., Mukherjee, K., Dean, C.J., Boucher, C., Noyes, N. R. Mobilization of antibiotic resistance: Are current approaches for colocalizing resistomes and mobilomes useful? Front. Microbiol. 2020; (11) https://doi.org/10.3389/fmicb.2020.01376

[J9] Slizovskiy, I.B., Conti, L.A., Trufan S.J., Reif, J.S., Lamers, V.T., Stowe, M.H., Dziura, J., Rabinowitz P.M. Reported health conditions in animals residing near natural gas wells in southwestern Pennsylvania. J. Environ. Sci. Health, Part A, 2015;50(5): 473-481, Special Issue.

[J8] Shen, H., Heuzey, E., Mori, D., Colangelo, C., Chung, L., Bruce, C., Slizovskiy, I.B., Booth, C.J., Kreisel, D., Goldstein, D.R. Haptoglobin enhances cardiac transplant rejection. Circulation research. 2015; 116: 1670-1679.

[J7] Rabinowitz, P.M., Slizovskiy, I.B., Lamers, V., Trufan, S.J., Holford, T.R., Dziura, J.D., Peduzzi, P.N., Kane M.J., Reif, J.S., Weiss, T.R., Stowe, M.H. Proximity to natural gas wells and reported health status: Results of a household survey in Washington County, Pennsylvania. Environmental Health Perspectives. 2015;123(1): 21-26.

[J6] Slizovskiy, I.B. Health survey of households near shale gas extraction sites. Thesis. Yale University. ProQuest Dissertation Publishing. 2013. Publication no. 1569241.

[J5] Slizovskiy, I.B., Hatzinger, P.B., Kelsey, J.W. Surfactant-facilitated remediation of metalcontaminated soils: Efficacy and toxicological consequences to earthworms. J. Environmental Toxicology and Chemistry. 2011; 30:112–125.

[J4] Kelsey, J.W., Slizovskiy, I.B., Petriello, M., Butler, K. Influence of plant-earthworm interactions on SOM chemistry and p,p’­DDE bioaccumulation. Chemosphere. 2011; 83:897–902.

[J3] Slizovskiy, I.B. White, J.C.; Kelsey, J.W. Technical Note: Evaluation of extraction methodologies for the determination of pesticide residues in vegetation. Int. J. Phytorem. 2010; 12:820–832.

[J2] Kelsey, J.W. Slizovskiy, I.B., Peters, R., Melnick, A. Gamma irradiation and autoclaving affects chemical and physical properties of soil organic matter and the bioaccumulation of spiked p,p'-DDE and anthracene to the earthworms Eisenia fetida and Lumbricus terrestris. J. Environmental Pollution. 2010; 158: 2251–2257.

[J1] Slizovskiy, I.B., Kelsey, J.W. Soil sterilization techniques affect aging-related sequestration and bioavailability of p,p’­DDE and anthracene to earthworms. J. Environmental Pollution. 2010; 158: 3285–3289.

[C22] Jimenez-Lopez, O., Ray, T., Dean, C., Slizovskiy, I., Deere, J., Wolf, T., Primus, A., Hoy-Petersen, J., Finstad, S., Mo, J., Sorum, H., Noyes, N. Paired metagenomic and metatranscriptomic sequencing reveals the gastrointestinal resistome and microbiome of yellow perch (Perca flavescencs) in Minnesota lakes. The 15th European Wildlife Disease Conference. European Wildlife Disease Association (EWDA). Stralsund, Germany, 2024.


[C21] Diaz Ortiz, G.R., Slizovskiy, I.B., Torremorell, M., Noyes, N.R. A metagenomic investigation of the work-related microbiome in U.S. swine workers.  Cold Spring Harbor Laboratory Conference: Genome informatics. Cold Spring Harbor, NY, 2023.
 

[C20] Slizovskiy, I.B., Gaire, T.N., Ferm, P., Odland, C., Dee, S., Nerem, J., Boucher, C., Noyes, N.R. Profiling the agricultural labor-OME: Showering disrupts work-related shifts in swine worker skin microbiomes, resistome, and mobilomes. SafePork 2023; The 14th International Symposium on the Epidemiology and Control of Biological, Chemical and Physical Hazards in Pigs and Pork, New Orleans, LA, 2023.


[C19] Diaz, G.R., Gaire, T.N., Danesh, M., Ferm, P., Slizovskiy, I.B., Goldsmith, T., Caixeta, L., Armstrong, J., Noyes, N.R. Rapid rumen microbiome change driven by weaning strategy of beef calves. Conference of Research Workers in Animal Diseases (CRWAD), Chicago, IL, 2023.


[C18] Gaire, T.N., Wehri, T., Brown, D., Snow, C., Hsu, J., Slizovskiy, I.B., Jimenez-Lopez, O., Ortiz, G.R.D., Meneguzzi, M., Young, J., De Abreu C., Canturi, A.,     Pena-Mosca, F., Medrano, M., Miller, L., Lie, S., Ruch, M., Schwartz, M., Singer, R., Pieters, M., Noyes, N.R. Effect of commingling and dietary fiber interventions on select performance metrics of suckling and weaned pigs. Conference of Research Workers in Animal Diseases (CRWAD),Chicago, IL, 2023.


[C17] Slizovskiy, I.B., Gaire, T.N., Ferm, P., Odland, C., Dee, S., Nerem, J., Boucher, C., Noyes, N.R. Showering as a biosecurity intervention to disrupt work-related shifts in swine worker skin microbiomes. Conference of Research Workers in Animal Diseases (CRWAD), Chicago, IL, 2023.


[C16] Slizovskiy, I.B., Oliva, M., Settle, J.K., Zyskina, L.V., Prosperi, M.C.F., Boucher, C., Noyes, N.R. Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance risk in metagenomes. International Society for Computational Biology (ISCB), Madison, WI: 549. 2022.


[C15] Slizovskiy, I.B, Boucher, C.A., Noyes, N.R. Metagenomic profiling of foodborne pathogens, antimicrobial resistance, virulence, and mobilization potential in public health surveillance. International Association of Food Protection (IAFP): National Conference. Pheonix, AZ. 2021.


[C14] Slizovskiy, I.B, Alanko, J. Lokshtanov, D., Gagie, T., Boucher, C.A., Noyes, N.R. Molecular enrichment of whole bacterial genomes for metagenomic profiling of foodborne pathogens. Conference of Research Workers in Animal Diseases (CRWAD): Section of food safety. Chicago, IL, 2021.


[C13] Gaire, T. Slizovskiy, I., Crooker, B., Noyes, N. Holstein cow genotype affects mammary skin microbiome during experimentally induced E. coli mastitis. Conference of Research Workers in Animal Diseases (CRWAD): Section of food safety. Chicago, IL, 2021.


[C12] Kaufman, J.H., Agarwal A., Beck, K.L., Mukherjee V., Nayar G., Seabolt, E., Terrizzano,    I., Slizovskiy, I.B., Noyes, N.R. Evidence for mobile proteins associated with AMR, virulence, and CRISPR in genomes with integrative conjugative elements. American Society of Microbiology: MICROBE Conference. Chicago, IL, 2020.


[C11] Marini S., Slizovskiy, I., Noyes, N., Boucher C., Prosperi M. Learning antimicrobial resistance through secondary structure of protein variants. International Society for Computational Biology: Intelligent Systems for Molecular Biology. Virtual conference (https://www.iscb.org/ismb2020). 2016.


[C10] Makau D.N., Slizovskiy, I.B, VanderWaal, K., Obanda, V., Noyes, N.R., Johnson, J.R., Oakes, M., Travis, D., Omondi, G. Drivers of antimicrobial use in pastoral  communities in Kenya. Conference of Research Workers in Animal Diseases (CRWAD): Section in antimicrobial stewardship in cattle. Virtual Conference. 2020.


[C9] Slizovskiy, I.B, Settle, J.K., Boucher C., Noyes, N.R. Targeted-enrichment and long read sequencing (TELS) uncovers mobility potential of antibiotic resistance in microbiomes. American Society for Microbiology: Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines. Virtual Conference. 2020.


[C8] Iglesias, I. Slizovskiy, I.B., Perez A., Martinez, M., DE LA Torre, A., HPAI Risk mapping based on environmental factors in Ramsar wetlands of Europe. Spatial Statistics, Sitges, Spain. 2019.


[C7] Slizovskiy I.B., Kaufman J.H., Terrizzano I.G., Nayar G., Seabolt E.E., Agarwal A., Roth M.A., Noyes N.R. Big data survey of Integrative Conjugative Elements and associated cargo genes across hundreds of thousands of bacterial genera. 100th Annual Conference of Research Workers in Animal Diseases (CRWAD). Chicago, IL, 2019.


[C6] Dean, C., Slizovskiy, I.B., Crone, K., Heinz, B., Caixeta, L., Noyes, N. Sampling considerations for conducting large-scale microbial ecology studies of cow udder epithelium. Proceedings of the 99th Annual Conference of Research Workers in Animals Disease, Chicago, IL, 2015.


[C5] Slizovskiy, I.B., Dean, C.J., Belk, K.E., Morley, P.S., Noyes, N. R. Characterizing Risks of Mobilizing Antibiotic Resistance in Beef Production: A Metagenomics-Network Approach. Proceedings of the 99th Annual Conference of Research Workers in Animal Disease, Chicago, IL, 2018.


[C4] Surfactant-facilitated Remediation of Metal-contaminated Soils: Efficacy and Toxicological Consequences. Presented at the 27th Annual International Conference on Soils, Sediments, Water, and Energy, University of Massachusetts, Amherst, MA, USA. (2010).


[C3] Sterilization Affects Soil Organic Matter Chemistry and Bioaccumulation of Spiked p,p’DDE and Anthracene by Earthworms. Presented at the Student Research Symposium, Muhlenberg College, Allentown, Pennsylvania, USA. (2008).


[C2] Sterilization Affects Soil Organic Matter Chemistry and Bioaccumulation of Spiked p,p’-DDE and Anthracene by Earthworms. Presented at the Pennsylvania Undergraduate Research at the Capitol Program, Pennsylvania State Capitol, Harrisburg, Pennsylvania, USA. (2008).


[C1] Effect of Heavy Metal co-contamination on the Phytoremediation of p,p’­DDE by Cucurbita pepo spp. pepo Zucchini Squash Plants. Presented at the Student Research Symposium, Muhlenberg College, Allentown, Pennsylvania, USA. (2006).