Amy D. Willis

Scalable fold-change estimation from microbial metagenomics

The paper introduces fastEmu, a scalable method for estimating differential abundance in microbial metagenomics data, achieving faster runtime with minimal impact on error rates.

happi: a Hierarchical Approach to Pangenomics Inference

happi tests gene enrichment hypotheses while accounting for genome quality in metagenome-assembled genomes.

Analyzing microbial evolution through gene and genome phylogenies

The paper introduces an interactive method for analyzing gene-level phylogenies in microbial evolution, enabling visualization and comparison of gene histories across bacterial strains.

Differences in gut metagenomes between dairy workers and community controls: a cross-sectional study

The paper compares gut metagenomes of dairy workers and community controls to assess antibiotic resistance and pathogen exposure risks.

Implications of taxonomic bias for microbial differential-abundance analysis

The paper examines how taxonomic bias affects differential-abundance analysis in microbiome studies and proposes methods to mitigate its effects.

Meta-analysis of metagenomes via machine learning and assembly graphs reveals strain switches in Crohn's disease

The paper identifies five bacterial strains associated with Crohn's disease using a novel method combining machine learning and assembly graphs for metagenomic analysis.

Segment number threshold determines juvenile onset of germline cluster proliferation in Platynereis dumerilii

The paper investigates how segment number thresholds influence germline cluster proliferation and gametogenesis in juvenile Platynereis dumerilii, finding a correlation between growth state and developmental stages.

A multi-view model for relative and absolute microbial abundances

The paper proposes a method to estimate absolute microbial abundances using both relative and absolute abundance data, improving accuracy by accounting for detection efficiencies.

Gene-level metagenomics identifies genome islands associated with immunotherapy response

The paper introduces a tool for gene-level metagenomic analysis to identify genomic islands linked to immunotherapy response in microbiome data.

Estimation of cell lineage trees by maximum-likelihood phylogenetics

This paper introduces a statistical model and method for estimating cell lineage trees using maximum-likelihood phylogenetics, showing improved accuracy over existing methods in simulations and zebrafish development.

DivNet: Estimating diversity in networked communities

DivNet estimates diversity in networked communities, improving alpha- and beta-diversity accuracy by incorporating ecological interactions, especially in high-diversity ecosystems.

Consistent and correctable bias in metagenomic sequencing measurements

The paper identifies and corrects systematic bias in metagenomic sequencing by modeling how bias distorts measurements and validating it across different protocols and datasets.

Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease

The paper introduces a computational method to cluster microbial genes by co-abundance, identifying reproducible gene groups linked to colorectal cancer and inflammatory bowel disease.