[HTML][HTML] Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles

JT Morton, DM Jin, RH Mills, Y Shao, G Rahman… - Nature …, 2023 - nature.com
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by
heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut–brain …

[HTML][HTML] Insulin-regulated serine and lipid metabolism drive peripheral neuropathy

…, KE Frizzi, GH McGregor, C Martino, G Rahman… - Nature, 2023 - nature.com
Diabetes represents a spectrum of disease in which metabolic dysfunction damages multiple
organ systems including liver, kidneys and peripheral nerves 1 , 2 . Although the onset and …

Visualizing'omic feature rankings and log-ratios using Qurro

…, JT Morton, A González, G Rahman… - NAR genomics and …, 2020 - academic.oup.com
Many tools for dealing with compositional ‘ ’omics’ data produce feature-wise values that
can be ranked in order to describe features’ associations with some sort of variation. These …

Dietary weight loss-induced improvements in metabolic function are enhanced by exercise in people with obesity and prediabetes

…, K Kirbach, ML Kearney, J Yoshino, G Rahman… - Nature …, 2023 - nature.com
The additional therapeutic effects of regular exercise during a dietary weight loss program
in people with obesity and prediabetes are unclear. Here, we show that whole-body (primarily …

[HTML][HTML] SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

…, K Cantrell, L Jiang, C Martino, RE Diner, G Rahman… - Microbiome, 2021 - Springer
Background SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19)
pandemic. Viruses exist in complex microbial environments, and recent studies …

Uniform manifold approximation and projection (UMAP) reveals composite patterns and resolves visualization artifacts in microbiome data

G Armstrong, C Martino, G Rahman, A Gonzalez… - …, 2021 - Am Soc Microbiol
Microbiome data are sparse and high dimensional, so effective visualization of these data
requires dimensionality reduction. To date, the most commonly used method for …

[HTML][HTML] Applications and comparison of dimensionality reduction methods for microbiome data

G Armstrong, G Rahman, C Martino… - Frontiers in …, 2022 - frontiersin.org
Dimensionality reduction techniques are a key component of most microbiome studies,
providing both the ability to tractably visualize complex microbiome datasets and the starting …

[HTML][HTML] Quantifying tumor heterogeneity via MRI habitats to characterize microenvironmental alterations in HER2+ breast cancer

…, T Davis, MJ Bloom, S Mounho, G Rahman… - Cancers, 2022 - mdpi.com
Simple Summary Tumor heterogeneity influences tumor progression and response to
therapy, introducing a significant challenge in the treatment of breast cancer. We employed …

EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets

K Cantrell, MW Fedarko, G Rahman, D McDonald… - …, 2021 - Am Soc Microbiol
Standard workflows for analyzing microbiomes often include the creation and curation of
phylogenetic trees. Here we present EMPress, an interactive web tool for visualizing trees in the …

Effects of a ketogenic and low‐fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease

…, BJ Neth, KA West, J Zemlin, G Rahman… - Alzheimer's & …, 2023 - Wiley Online Library
INTRODUCTION The ketogenic diet (KD) is an intriguing therapeutic candidate for Alzheimer's
disease (AD) given its protective effects against metabolic dysregulation and seizures. …