Publications by authors named "Justin D Silverman"

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Wastewater surveillance of SARS-CoV-2 and influenza in a dynamic university community: understanding how wastewater measurements correspond to reported cases.
Matthew J Jones, Rukayya Ibrahim, Shirley Clark, Yolanda M Brooks, Heather E Preisendanz, Justin D Silverman

Sci Total Environ· October 2025

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Explicit Scale Simulation for analysis of RNA-sequencing count data with ALDEx2.
Gregory B Gloor, Michelle Pistner Nixon, Justin D Silverman

NAR Genom Bioinform· September 2025

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Uncertainty Modeling Outperforms Machine Learning for Microbiome Data Analysis.
Maxwell A Konnaris, Manan Saxena, Nicole Lazar, Justin D Silverman

bioRxiv· September 2025

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Replacing normalizations with interval assumptions enhances differential expression and differential abundance analyses.
Kyle C McGovern, Justin D Silverman

BMC Bioinformatics· July 2025

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PCR Bias Impacts Microbiome Ecological Analyses.
Dharmik Rathod, Justin D Silverman

bioRxiv· July 2025

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Infection risk of rituximab monotherapy versus combination therapy with rituximab and mycophenolic acid in systemic sclerosis: A retrospective cohort study.
Joyce B Kang, Katherine Nabel Smith, Emily M Meara, MiJin Cho, Justin D Silverman

J Am Acad Dermatol· May 2025

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Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization.
Michelle Pistner Nixon, Gregory B Gloor, Justin D Silverman

Genome Biol· May 2025

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From pre-test and post-test probabilities to medical decision making.
Michelle Pistner Nixon, Farhani Momotaz, Claire Smith, Jeffrey S Smith, Mark Sendak, Justin D Silverman

BMC Med Inform Decis Mak· July 2024

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Changes in the type 2 diabetes gut mycobiome associate with metformin treatment across populations.
Emily Van Syoc, Michelle Pistner Nixon, Justin D Silverman, Yuhong Luo, Frank J Gonzalez

mBio· June 2024

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Beyond Normalization: Incorporating Scale Uncertainty in Microbiome and Gene Expression Analysis.
Michelle Pistner Nixon, Gregory B Gloor, Justin D Silverman

bioRxiv· April 2024

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From Pre-test and Post-test Probabilities to Medical Decision Making.
Michelle Pistner Nixon, Farhani Momotaz, Claire Smith, Jeffrey S Smith, Mark Sendak, Justin D Silverman

medRxiv· February 2024

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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, Justin D Silverman

Nat Microbiol· December 2023

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Changes in the Type 2 diabetes gut mycobiome associate with metformin treatment across populations.
Emily Van Syoc, Michelle Pistner Nixon, Justin D Silverman, Yuhong Luo, Frank J Gonzalez

bioRxiv· November 2023

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Addressing erroneous scale assumptions in microbe and gene set enrichment analysis.
Kyle C McGovern, Michelle Pistner Nixon, Justin D Silverman

PLoS Comput Biol· November 2023

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Quantitative Geometric Modeling of Blood Cells from X-ray Histotomograms of Whole Zebrafish Larvae.
Maksim A Yakovlev, Ke Liang, Carolyn R Zaino, Daniel J Vanselow, Andrew L Sugarman, Justin D Silverman

bioRxiv· May 2023

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Phosphorylation barcodes direct biased chemokine signaling at CXCR3.
Dylan S Eiger, Jeffrey S Smith, Tujin Shi, Tomasz Maciej Stepniewski, Chia-Feng Tsai, Justin D Silverman

Cell Chem Biol· April 2023

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Phosphorylation barcodes direct biased chemokine signaling at CXCR3.
Dylan S Eiger, Jeffrey S Smith, Tujin Shi, Tomasz Maciej Stepniewski, Chia-Feng Tsai, Justin D Silverman

bioRxiv· March 2023

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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

PLoS One· February 2023

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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

Nat Commun· September 2022

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Metformin modulates the gut microbiome in broiler breeder hens.
Emily Van Syoc, Evelyn Weaver, Connie J Rogers, Justin D Silverman, Ramesh Ramachandran

Front Physiol· September 2022

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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, Justin D Silverman

Microbiome· July 2022

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Measuring and mitigating PCR bias in microbiota datasets.
Justin D Silverman, Rachael J Bloom, Sharon Jiang, Heather K Durand, Eric Dallow

PLoS Comput Biol· July 2021

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DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid.
Erika Ganda, Kristen L Beck, Niina Haiminen, Justin D Silverman, Ban Kawas

mSystems· June 2021

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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, Justin D Silverman

Science· April 2021

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Naught all zeros in sequence count data are the same.
Justin D Silverman, Kimberly Roche, Sayan Mukherjee, Lawrence A David

Comput Struct Biotechnol J· September 2020

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