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Recent Publications
Investigating antibiotic free feed additives for growth promotion in poultry: effects on performance and microbiota
Fonseca, A., Kenney, S., Van Syoc, E., Bierly, S., Dini-Andreote, F., Silverman, J., Boney, J. & Ganda, E., May 2024, In: Poultry science. 103, 5, 103604.Research output: Contribution to journal › Article › peer-review
Phosphorylation barcodes direct biased chemokine signaling at CXCR3
Eiger, D. S., Smith, J. S., Shi, T., Stepniewski, T. M., Tsai, C. F., Honeycutt, C., Boldizsar, N., Gardner, J., Nicora, C. D., Moghieb, A. M., Kawakami, K., Choi, I., Hicks, C., Zheng, K., Warman, A., Alagesan, P., Knape, N. M., Huang, O., Silverman, J. D., Smith, R. D., & 4 others, Apr 20 2023, In: Cell Chemical Biology. 30, 4, p. 362-382.e8Research output: Contribution to journal › Article › peer-review
Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain
Gancz, A. S., Farrer, A. G., Nixon, M. P., Wright, S., Arriola, L., Adler, C., Davenport, E. R., Gully, N., Cooper, A., Britton, K., Dobney, K., Silverman, J. D. & Weyrich, L. S., Dec 2023, In: Nature Microbiology. 8, 12, p. 2315-2325 11 p.Research output: Contribution to journal › Article › peer-review
Race, employment, and the pandemic: An exploration of covariate explanations of COVID-19 case fatality rate variance
Griffin, C., Block, R., Silverman, J. D., Croad, J. & Lennon, R. P., Feb 2023, In: PloS one. 18, 2 February, e0274470.Research output: Contribution to journal › Article › peer-review
Addressing erroneous scale assumptions in microbe and gene set enrichment analysis
McGovern, K. C., Nixon, M. P. & Silverman, J. D., Nov 2023, In: PLoS computational biology. 19, 11, e1011659.Research output: Contribution to journal › Article › peer-review
Impacts of the COVID-19 pandemic on pharmaceuticals in wastewater treated for beneficial reuse: Two case studies in central Pennsylvania
Hayden, K. R., Jones, M., Elkin, K. R., Shreve, M. J., Clees, W. I., Clark, S., Mashtare, M. L., Veith, T. L., Elliott, H. A., Watson, J. E., Silverman, J., Richard, T. L., Read, A. F. & Preisendanz, H. E., Sep 1 2022, In: Journal of Environmental Quality. 51, 5, p. 1066-1082 17 p.Research output: Contribution to journal › Article › peer-review
Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake
Holmes, Z. C., Villa, M. M., Durand, H. K., Jiang, S., Dallow, E. P., Petrone, B. L., Silverman, J. D., Lin, P. H. & David, L. A., Dec 2022, In: Microbiome. 10, 1, 114.Research output: Contribution to journal › Article › peer-review
Multiomics implicate gut microbiota in altered lipid and energy metabolism in Parkinson’s disease
Pereira, P. A. B., Trivedi, D. K., Silverman, J., Duru, I. C., Paulin, L., Auvinen, P. & Scheperjans, F., Dec 2022, In: npj Parkinson's Disease. 8, 1, 39.Research output: Contribution to journal › Article › peer-review
Bayesian Multinomial Logistic Normal Models through Marginally Latent Matrix-T Processes
Silverman, J. D., Roche, K., Holmes, Z. C., David, L. A. & Mukherjee, S., 2022, In: Journal of Machine Learning Research. 23Research output: Contribution to journal › Article › peer-review
Metformin modulates the gut microbiome in broiler breeder hens
Van Syoc, E., Weaver, E., Rogers, C. J., Silverman, J. D., Ramachandran, R. & Ganda, E., Sep 14 2022, In: Frontiers in Physiology. 13, 1000144.Research output: Contribution to journal › Article › peer-review
Decoding the olfactory map through targeted transcriptomics links murine olfactory receptors to glomeruli
Zhu, K. W., Burton, S. D., Nagai, M. H., Silverman, J. D., de March, C. A., Wachowiak, M. & Matsunami, H., Dec 2022, In: Nature communications. 13, 1, 5137.Research output: Contribution to journal › Article › peer-review
DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid
Ganda, E., Beck, K. L., Haiminen, N., Silverman, J. D., Kawas, B., Cronk, B. D., Anderson, R. R., Goodman, L. B. & Wiedmann, M., Jun 2021, In: mSystems. 6, 3, e00619-21.Research output: Contribution to journal › Article › peer-review
The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights
McCann, J. R., Bihlmeyer, N. A., Roche, K., Catherine, C., Jawahar, J., Kwee, L. C., Younge, N. E., Silverman, J., Ilkayeva, O., Sarria, C., Zizzi, A., Wootton, J., Poppe, L., Anderson, P., Arlotto, M., Wei, Z., Granek, J. A., Valdivia, R. H., David, L. A., Dressman, H. K., & 5 others, Mar 2021, In: Obesity. 29, 3, p. 569-578 10 p.Research output: Contribution to journal › Article › peer-review
Measuring and mitigating PCR bias in microbiota datasets
Silverman, J. D., Bloom, R. J., Jiang, S., Durand, H. K., Dallow, E., Mukherjee, S. & David, L. A., Jul 2021, In: PLoS computational biology. 17, 7, e1009113.Research output: Contribution to journal › Article › peer-review
Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England
CMMID COVID-19 Working Group & COVID-19 Genomics UK (COG-UK) Consortium, Apr 9 2021, In: Science. 372, 6538, eabg3055.Research output: Contribution to journal › Article › peer-review