Anton Nekrutenko

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.

Panagram reveals pangenome architectures underlying trait variation in plants and animals

Alignment-free pan-k-mer profiles track minimap2 similarity (whole-chromosome r^2 0.959-0.968), profile 605 vertebrate genomes in about a day on 40 cores, and nominate trait-linked loci across plants and animals.

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.

Evaluating open LLMs for agentic analysis orchestration in a typical biomedical lab

The paper evaluates open LLMs for agentic analysis in biomedical labs, finding that qwen3.6:27b matches frontier accuracy on variant calling tasks using a local setup.

The Common Fund Data Ecosystem (CFDE)

The paper describes the Common Fund Data Ecosystem (CFDE), which integrates NIH Common Fund data resources to enable discovery, analysis, and collaboration across heterogeneous datasets.

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.

BUSTED-PH: Isolating the genomic signatures of convergent phenotypes

BUSTED-PH identifies genes associated with convergent phenotypes by detecting episodic diversifying selection across mammalian species.

Standardizing RNA-seq Analysis of Fungal Pathogens Using BRC-Analytics and Agentic AI: A Candidozyma auris Case Study

The paper demonstrates a framework using BRC-Analytics and agentic AI to standardize RNA-seq analysis of fungal pathogens, achieving reproducible results across studies with differing annotations.

KegAlign: Optimizing pairwise alignments with diagonal partitioning

KegAlign improves pairwise genome alignment speed using GPU acceleration and diagonal partitioning, achieving 150x faster alignment than lastZ for human/mouse genomes.

From data to publication in a browser with BRC-Analytics: Evolutionary dynamics of coding overlaps in measles virus

The paper introduces BRC-Analytics, a browser-based platform for pathogen genomics, demonstrating its use in analyzing measles virus evolutionary dynamics and revealing asymmetric frame evolution under selective pressures.

Evaluation of sequencing reads at scale using rdeval

The paper introduces rdeval, a tool for efficiently evaluating and visualizing sequencing read metrics, showing improvements in read quality and genome assembly with PacBio data.

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.

Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

The paper presents a scalable pipeline for reference genome assembly and evaluation, demonstrating its effectiveness across 51 vertebrate species using Galaxy.

Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy

The paper presents a pipeline for predicting genome-wide protein-protein interactions and generating structural models, validated on human and yeast genomes and applied to SARS-CoV2 proteins.

Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses

Planemo is a command-line toolkit for developing, deploying, and executing Galaxy tools and workflows, promoting best practices in scientific data analysis.

RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis

RASCL rapidly assesses SARS-CoV-2 clades using molecular sequence analysis to detect selection pressures in emerging variants.

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)

The paper describes AnVIL, a cloud-based platform that enables genomic data analysis without data transfer, improving security, scalability, and collaboration.

Stepwise evolution and exceptional conservation of ORF1a/b overlap in coronaviruses

The paper analyzes the evolution of the ORF1a/b overlap in coronaviruses, showing it evolved as discrete nucleotide stretches with phylogenetic specificity and is highly conserved across sequences.

Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring

The paper presents a global, community-maintained platform for analyzing SARS-CoV-2 genomic data, demonstrating its utility in variant detection and reanalysis of existing datasets.

Increased yields of duplex sequencing data by a series of quality control tools

The paper develops quality control tools to improve duplex sequencing data yields by reducing data loss and enhancing variant calling accuracy.

A Single-cell RNA-seq Training and Analysis Suite using the Galaxy Framework

The paper introduces a Galaxy-based suite for scRNA-seq analysis, offering workflows, training resources, and tools for preprocessing, normalization, and clustering across 10x and alternative platforms.

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.

The landscape of SARS-CoV-2 RNA modifications

This study uses direct RNA sequencing to identify RNA modifications in SARS-CoV-2 isolated from human lung cells, revealing conserved modification patterns across isolates.

Family reunion via error correction: An efficient analysis of duplex sequencing data

The paper corrects errors in duplex sequencing data to reunite reads and improve the efficiency of variant detection.

A high resolution view of adaptive events

This study tracks mutations during coadaptation between E. coli and plasmid pBR322 using duplex sequencing, revealing clonal interference and chromosomal variant emergence as key adaptive events.

Understanding trivial challenges of microbial genomics: An assembly example

The paper highlights challenges in microbial genomics due to lack of standardized tools and computational expertise, using genome assembly as an example.

Practical computational reproducibility in the life sciences

The paper presents technologies that make computational reproducibility practical by integrating package management, containerization, and workflow systems.

Community-driven data analysis training for biology

The paper presents a community-driven framework for interactive data analytics training in life sciences, enabling researchers to learn through web-based computation without software installation.