Steven Weaver

Auditing Biomedical Literature with Blinded AI Peer Review: Where Peer Review Works, Where It Fails, and How to Strengthen It

This paper evaluates the effectiveness of a blinded AI peer review system (BARS) in auditing biomedical literature, finding it improves consistency and detects flaws while highlighting issues with megajournals and template studies.

Verifiable Agentic Science on Public Infrastructure

This paper demonstrates agentic science on public infrastructure to ensure reproducibility by making all agent actions and workflows publicly accessible.

Clean Breaks: Attention Force Field Deconvolution of Recombination Across Sequence Manifolds

RhizAeon deconvolves reticulate evolution by analyzing sequence mosaics and detecting recombination breakpoints with high accuracy and efficiency.

Beyond Invariable Sites: Using Evolutionary Stasis to Map Multi-Layered Constraints on the Evolution of Viral and Mammalian Genomes

This paper introduces B-STILL, a Bayesian framework to detect functional constraints in genomes by analyzing evolutionary stasis, identifying significant clusters of invariant sites in viral and mammalian genomes.

Characterizing Physicochemical Selection in Protein Evolution with Property-Informed Models (PRIME)

PRIME models physicochemical selection in protein evolution by incorporating biophysical properties, improving model fit and revealing adaptive tuning mechanisms in protein structures.

Minus the Error: Testing for Positive Selection in the Presence of Residual Alignment Errors

BUSTED-E detects positive selection while identifying residual alignment errors in genome-scale datasets, improving accuracy and biological interpretation.

AUTO-TUNE: SELECTING THE DISTANCE THRESHOLD FOR INFERRING HIV TRANSMISSION CLUSTERS

The paper introduces a heuristic method to adaptively select a genetic distance threshold for HIV transmission network inference, demonstrating its utility in identifying clusters with different risk factors.

TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity

TopHap infers phylogenetic structures from common haplotypes in large genome collections, improving accuracy and speed for SARS-CoV-2 variant phylogeny.

Extra base hits: widespread empirical support for instantaneous multiple-nucleotide changes

The paper finds widespread statistical support for multiple-nucleotide substitutions in codons using empirical data and provides a software tool for analysis.

Contrast-FEL: a test for differences in selective pressures at individual sites among clades and sets of branches.

Contrast-FEL identifies sites with different selective pressures across multiple branches in phylogenetic trees, showing high power and low false positives.

No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics

The paper highlights the importance of open data and analytics in responding to public health emergencies, using COVID-19 genomic data to demonstrate the effectiveness of community-driven software tools and infrastructure.

Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons

FLEA is a tool for analyzing long-read sequencing data of HIV-1 env, improving accuracy in reconstructing viral sequences and analyzing evolutionary dynamics.