Justin Silverman

Assistant Professor of Information Sciences and Technology

Justin Silverman

Research Summary

Statistical methods for the analysis of biomedical data (or any other interesting data/questions)

Huck Graduate Students

Huck Affiliations

Links

Publication Tags

These publication tags are generated from the output of this researcher. Click any tag below to view other Huck researchers working on the same topic.

Microbiota Gastrointestinal Microbiome Datasets Phylogeny Coronavirus Prebiotics Severe Acute Respiratory Syndrome Volatile Fatty Acids Gene Expression Chemical Analysis Artifacts Microorganisms Health Atopic Dermatitis Simulation Pandemics Time Human Influenza Decoding Linear Models Non Alcoholic Fatty Liver Disease Microbiome Odorant Receptors High Throughput Nucleotide Sequencing Energy Metabolism

Most Recent Publications

Analysis and visualization of epidemics on the timescale of burden: derivation and application of Epidemic Resistance Lines (ERLs) to COVID-19 outbreaks in the US

Alex Washburne, Justin Silverman, medRxiv

Investigating antibiotic free feed additives for growth promotion in poultry: effects on performance and microbiota

Ana Fonseca, Sophia Kenney, Emily Van Syoc, Stephanie Bierly, Francisco Dini-Andreote, Justin Silverman, J Boney, Erika Ganda, 2024, Poultry Science

Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain

Abigail S. Gancz, Andrew G. Farrer, Michelle P. Nixon, Sterling Wright, Luis Arriola, Christina Adler, Emily R. Davenport, Neville Gully, Alan Cooper, Kate Britton, Keith Dobney, Justin D. Silverman, Laura S. Weyrich, 2023, Nature Microbiology on p. 2315-2325

Addressing erroneous scale assumptions in microbe and gene set enrichment analysis

Kyle C. McGovern, Michelle Pistner Nixon, Justin D. Silverman, 2023, PLoS Computational Biology

Phosphorylation barcodes direct biased chemokine signaling at CXCR3

Dylan S. Eiger, Jeffrey S. Smith, Tujin Shi, Tomasz Maciej Stepniewski, Chia Feng Tsai, Christopher Honeycutt, Noelia Boldizsar, Julia Gardner, Carrie D. Nicora, Ahmed M. Moghieb, Kouki Kawakami, Issac Choi, Chloe Hicks, Kevin Zheng, Anmol Warman, Priya Alagesan, Nicole M. Knape, Ouwen Huang, Justin D. Silverman, Richard D. Smith, Asuka Inoue, Jana Selent, Jon M. Jacobs, Sudarshan Rajagopal, 2023, Cell Chemical Biology on p. 362-382.e8

Race, employment, and the pandemic: An exploration of covariate explanations of COVID-19 case fatality rate variance

Christopher Griffin, Ray Block, Justin D. Silverman, Jason Croad, Robert P. Lennon, 2023, PLoS One

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

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

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

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

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

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

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

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

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

News Articles Featuring Justin Silverman

Apr 12, 2024

Probiotic feed additive boosts growth, health in poultry in place of antibiotics

Antimicrobial resistance is an increasingly serious threat for public health, and the use of antimicrobials in livestock feed has been a major contributing factor in the emergence and spread of antimicrobial resistance to many drugs, according to the U.S. National Institutes of Health.

Full Article

Nov 29, 2023

Study of ancient British oral microbiomes reveals shift following Black Death

The Second Plague Pandemic may have led to oral microbiomes that contribute to modern-day chronic disease, according to new research

Full Article

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