Anthony A. Fodor

Winnow-tax: sensitive and precise taxonomic profiling of low-coverage organisms in shotgun metagenomes

Winnow-tax improves taxonomic profiling of low-coverage shotgun metagenomes by combining sensitive read-level classification with genome-level confirmation, achieving better precision-sensitivity balance than existing methods.

Circulating Microbial DNA as a Potential Cancer Biomarker: Technical Challenges and Controlled Evaluation

This paper evaluates circulating microbial DNA as a cancer biomarker, finding that observed patterns are largely artifacts of sequencing and analysis methods rather than biological signals.

Benchmarking Short-Read ITS2 and Full-Length ITS Sequencing Reveals Pipeline-Dependent Biases in Indoor Fungal Community Profiling

This paper compares short-read ITS2 and long-read full-length ITS sequencing for fungal community profiling, finding that full-length ITS improves taxonomic resolution and ecological inference.

From external-input sensitivity to resident persistence: community assembly in a sink p-trap model

The paper shows that microbial communities in retentive habitats shift from being sensitive to external input to being shaped by local history over time.

A Permutation-Based Framework for Evaluating Bias in Microbiome Differential Abundance Analysis

This study evaluates seven differential abundance methods across six datasets, finding that some produce biased p-values under null conditions, while classical tests perform reliably.

Integrated analysis reveals strong reproducible signals within and across studies of the built environment

The paper identifies reproducible microbiome patterns across different built environments using a unified ontology and multiple datasets.

Temporal stability and niche partitioning of bacterial communities in paired residential sink P-traps

This study examines bacterial community dynamics in paired residential sink P-traps over two months, showing that individual usage patterns significantly influence community structure and temporal stability.

Beta Diversity Meta-Analysis Shows Transformations Have Broadly Similar Performance in Machine Learning Applications Regardless of Compositional or Phylogenetic Awareness

This study compares beta diversity methods in machine learning, finding no substantial performance difference between phylogenetically aware and simpler methods.

Consumption of processed foods impairs memory function through dietary advanced glycation end-products

This study shows that an AGE-rich diet during adolescence impairs memory via hippocampal synaptic deficits and microbiome changes, which can be mitigated by AGE inhibitors.

Correction for spurious taxonomic assignments of k-mer classifiers in low microbial biomass samples using shuffled sequences

This study identifies issues with k-mer classifiers in low microbial biomass samples and proposes using shuffled sequences and controls to improve taxonomic accuracy.

The impact of transplant location on the gut microbiome and resistome in patients undergoing hematopoietic stem cell transplantation at home versus in the hospital

This study compares the gut microbiome and resistome of patients undergoing home versus hospital hematopoietic stem cell transplantation, finding no significant differences but noting confounding factors in secondary analyses.

Western diet consumption impairs memory function via dysregulated hippocampus acetylcholine signaling

This study shows that a western diet during development impairs memory by disrupting hippocampal acetylcholine signaling, which can be partially reversed with pharmacological intervention.

Systematic classification error profoundly impacts inference in high-depth Whole Genome Shotgun Sequencing datasets

This paper evaluates classification errors in WGS datasets using Kraken2 and Metaphlan2, finding that Kraken2's errors create 'phantom' taxa that affect statistical inference.

An integrative analysis of the biological clock hypothesis in human gut microbiome

The paper tests the biological clock hypothesis in the human gut microbiome by analyzing 11 datasets, finding that larger sample sizes are needed for consistent age-related microbial associations.

Lasting effects of low-calorie sweeteners on glucose regulation, sugar intake, and memory

This study shows that early-life low-calorie sweetener consumption in rodents leads to long-term metabolic, behavioral, and neural impairments without weight gain.

Early life Western diet-induced memory impairments and gut microbiome changes in female rats are long-lasting despite healthy dietary intervention

This study shows that adolescent Western diet consumption in female rats leads to long-lasting memory and gut microbiome issues that are not fully reversed by adult dietary changes.

Batch effects removal for microbiome data via conditional quantile regression (ConQuR)

This paper introduces ConQuR, a method to remove batch effects in microbiome data by using conditional quantile regression, demonstrating its effectiveness in preserving signals and improving analysis.

HashSeq: A Simple, Scalable, and Conservative De Novo Variant Caller for 16S rRNA Gene Datasets

HashSeq detects single-nucleotide variants in 16S rRNA gene datasets using a fast HashMap-based approach and background error estimation, producing conservative and well-supported variant calls.

Inference based PICRUSt accuracy varies across sample types and functional categories

The paper evaluates PICRUSt's accuracy across different sample types and functional categories, finding it performs well for human samples but poorly for non-human and environmental samples.