Justin Silverman
Assistant Professor of Information Sciences and Technology
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E375 Westgate
University Park, PA - jds6696@psu.edu
- 814-863-8304
Research Summary
Statistical methods for the analysis of biomedical data (or any other interesting data/questions)
Huck Graduate Students
Huck Affiliations
Links
Publication Tags
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Microbiota Dna Gastrointestinal Microbiome Milk Datasets Severe Acute Respiratory Syndrome Coronavirus Wastewater Microorganisms Phylogeny Pandemics Logistics Prebiotics Microbiome Pediatric Obesity England Nucleic Acids Fluid Fluids Food Volatile Fatty Acids Health Methodology Genes TherapeuticsMost Recent Publications
Microbiota responses to different prebiotics are conserved within individuals and associated with habitual fiber intake
Zachary C. Holmes, Max M. Villa, Heather K. Durand, Sharon Jiang, Eric P. Dallow, Brianna L. Petrone, Justin D. Silverman, Pao Hwa Lin, Lawrence A. David, 2022, Microbiome
Decoding the olfactory map through targeted transcriptomics links murine olfactory receptors to glomeruli
Kevin W. Zhu, Shawn D. Burton, Maira H. Nagai, Justin D. Silverman, Claire A. de March, Matt Wachowiak, Hiroaki Matsunami, 2022, Nature Communications
Multiomics implicate gut microbiota in altered lipid and energy metabolism in Parkinson’s disease
Pedro A.B. Pereira, Drupad K. Trivedi, Justin Silverman, Ilhan Cem Duru, Lars Paulin, Petri Auvinen, Filip Scheperjans, 2022, npj Parkinson's Disease
Metformin modulates the gut microbiome in broiler breeder hens
E Van Syoc, E Weaver, Connie Jo Rogers, J , Justin Silverman, Ramesh Ramachandran, Erika Ganda, 2022, Frontiers in Physiology on p. 1000144
Impacts of the COVID-19 pandemic on pharmaceuticals in wastewater treated for beneficial reuse: Two case studies in central Pennsylvania
Kathryn Hayden, Matthew Jones, Kyle Elkin, Michael Shreve, William Clees, Shirley Clark, Michael L. Mashtare, Tamie Veith, Hershel Elliott, J Watson, Justin Silverman, Thomas L. Richard, Andrew F. Read, Heather E. Preisendanz, 2022, Journal of Environmental Quality on p. 1066-1082
Bayesian Multinomial Logistic Normal Models through Marginally Latent Matrix-T Processes
Justin D. Silverman, Kimberly Roche, Zachary C. Holmes, Lawrence A. David, Sayan Mukherjee, 2022, Journal of Machine Learning Research
Measuring and mitigating PCR bias in microbiota datasets
Justin D. Silverman, Rachael J. Bloom, Sharon Jiang, Heather K. Durand, Eric Dallow, Sayan Mukherjee, Lawrence A. David, 2021, PLoS Computational Biology
DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid
Erika Ganda, Kristen Beck, Niina Haiminen, J Silverman, Ban Kawas, Brittany Cronk, Renee Anderson, Laura Goodman, Martin Wiedmann, 2021, mSystems
Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England
Nicholas G. Davies, Sam Abbott, Rosanna C. Barnard, Christopher I. Jarvis, Adam J. Kucharski, James D. Munday, Carl A.B. Pearson, Timothy W. Russell, Damien C. Tully, Alex D. Washburne, Tom Wenseleers, Amy Gimma, William Waites, Kerry L.M. Wong, Kevin van Zandvoort, Justin D. Silverman, Karla Diaz-Ordaz, Ruth Keogh, Rosalind M. Eggo, Sebastian Funk, Mark Jit, Katherine E. Atkins, W. John Edmunds, 2021, Science
The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights
Jessica R. McCann, Nathan A. Bihlmeyer, Kimberly Roche, Cameron Catherine, Jayanth Jawahar, Lydia Coulter Kwee, Noelle E. Younge, Justin Silverman, Olga Ilkayeva, Charles Sarria, Alexandra Zizzi, Janet Wootton, Lisa Poppe, Paul Anderson, Michelle Arlotto, Zhengzheng Wei, Joshua A. Granek, Raphael H. Valdivia, Lawrence A. David, Holly K. Dressman, Christopher B. Newgard, Svati H. Shah, Patrick C. Seed, John F. Rawls, Sarah C. Armstrong, 2021, Obesity on p. 569-578
Most-Cited Papers
Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England
Nicholas G. Davies, Sam Abbott, Rosanna C. Barnard, Christopher I. Jarvis, Adam J. Kucharski, James D. Munday, Carl A.B. Pearson, Timothy W. Russell, Damien C. Tully, Alex D. Washburne, Tom Wenseleers, Amy Gimma, William Waites, Kerry L.M. Wong, Kevin van Zandvoort, Justin D. Silverman, Karla Diaz-Ordaz, Ruth Keogh, Rosalind M. Eggo, Sebastian Funk, Mark Jit, Katherine E. Atkins, W. John Edmunds, 2021, Science
Establishing microbial composition measurement standards with reference frames
James T. Morton, Clarisse Marotz, Alex Washburne, Justin Silverman, Livia S. Zaramela, Anna Edlund, Karsten Zengler, Rob Knight, 2019, Nature Communications
A phylogenetic transform enhances analysis of compositional microbiota data
Justin D. Silverman, Alex D. Washburne, Sayan Mukherjee, Lawrence A. David, 2017, eLife
Allogenic Fecal Microbiota Transplantation in Patients with Nonalcoholic Fatty Liver Disease Improves Abnormal Small Intestinal Permeability: A Randomized Control Trial
Laura Craven, Adam Rahman, Seema Nair Parvathy, Melanie Beaton, Justin Silverman, Karim Qumosani, Irene Hramiak, Rob Hegele, Tisha Joy, Jon Meddings, Brad Urquhart, Ruth Harvie, Charles McKenzie, Kelly Summers, Gregor Reid, Jeremy P. Burton, Michael Silverman, 2020, American Journal of Gastroenterology on p. 1055-1065
Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets
Alex D. Washburne, Justin D. Silverman, Jonathan W. Leff, Dominic J. Bennett, John L. Darcy, Sayan Mukherjee, Noah Fierer, Lawrence A. David, 2017, PeerJ
Using influenza surveillance networks to estimate state-specific prevalence of SARS-CoV-2 in the United States
Justin D. Silverman, Nathaniel Hupert, Alex D. Washburne, 2020, Science Translational Medicine
Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection
Firas S. Midani, Ana A. Weil, Fahima Chowdhury, Yasmin A. Begum, Ashraful I. Khan, Meti D. Debela, Heather K. Durand, Aspen T. Reese, Sai N. Nimmagadda, Justin D. Silverman, Crystal N. Ellis, Edward T. Ryan, Stephen B. Calderwood, Jason B. Harris, Firdausi Qadri, Lawrence A. David, Regina C. Larocque, 2018, Journal of Infectious Diseases on p. 645-653
Dynamic linear models guide design and analysis of microbiota studies within artificial human guts
Justin D. Silverman, Heather K. Durand, Rachael J. Bloom, Sayan Mukherjee, Lawrence A. David, 2018, Microbiome
Short-chain fatty acid production by gut microbiota from children with obesity differs according to prebiotic choice and bacterial community composition
Zachary C. Holmes, Justin D. Silverman, Holly K. Dressman, Zhengzheng Wei, Eric P. Dallow, Sarah C. Armstrong, Patrick C. Seed, John F. Rawls, Lawrence A. David, 2020, mBio on p. 1-15
Naught all zeros in sequence count data are the same
Justin D. Silverman, Kimberly Roche, Sayan Mukherjee, Lawrence A. David, 2020, Computational and Structural Biotechnology Journal on p. 2789-2798
News Articles Featuring Justin Silverman
Jul 19, 2022
Could the Flu Uncover the Next Pandemic?
As the COVID-19 pandemic has raced across the globe and killed millions worldwide, people continue to ask: Could this have gone differently? The early months of 2020 marked a turning point where public health efforts shifted from containing the virus’ spread to mitigating its damage once that was no longer possible. But what if we had known about future surges in infection rates earlier, or had a better sense of the peaks?
Full Article
Sep 20, 2020
Wastewater sampling may give advanced warning of potential COVID-19 outbreaks
Wastewater sampling for coronavirus on campus and in the surrounding community could alert University decision makers to a potential outbreak several days before individuals exhibit symptoms of an infection. The initiative — part of Penn State’s multilayered approach to test, monitor and mitigate for COVID-19 — could enable leaders to take swift actions to minimize the virus’s spread with the goal of helping to protect the health and safety of the community.
Full Article