Geoffrey J. Barton

Slivka and Slivka-bio: a lightweight framework for presenting executables as web services and its application in bioinformatics.

Slivka and Slivka-bio provide a lightweight framework for deploying bioinformatics tools as web services, enabling easy execution of code via HTTP and demonstrating with 15+ protein and RNA analysis tools.

Mutations within the predicted fragment-binding region of FAM83G/SACK1G abolish its interaction with the Ser/Thr kinase CK1α

The paper identifies mutations in SACK1G that disrupt its interaction with CK1α, using computational modeling and experimental validation.

Disruption of the mRNA m6A writer complex triggers autoimmunity in Arabidopsis

This study shows that disrupting the mRNA m6A writer complex in Arabidopsis triggers autoimmunity, with temperature-dependent effects on gene expression and pathogen resistance.

Sequence clustering with PaSiMap in Jalview

The paper introduces a protocol for using PaSiMap within Jalview to analyze protein-sequence relationships and provides an R script for data visualization.

The evolution of splice site sequence preference is linked to the U6 snRNA m6A methyltransferase METTL16

The paper shows that variation in 5 splice site sequence preferences correlates with the presence of METTL16 and SNRNP27K, using inter-species association mapping in Saccharomycotina species.

m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site

The paper shows that m6A modification of U6 snRNA affects splicing accuracy and efficiency, revealing two major classes of 5' splice sites in eukaryotes.

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

This paper presents a chromosome-scale genome assembly and genetic map for greater yam, identifies quantitative trait loci for disease and quality traits, and reveals domestication-related genetic patterns.

Missense variants in human ACE2 modify binding to SARS-CoV-2 Spike

The paper investigates how ACE2 missense variants affect SARS-CoV-2 Spike binding, identifying variants that enhance or inhibit binding and their potential impact on infection risk.

Ankyrin repeats in context with human population variation

The paper analyzes human population variants in ankyrin repeats using structural and evolutionary data to identify functionally important sites.

Yanocomp: robust prediction of m6A modifications in individual nanopore direct RNA reads.

Yanocomp predicts m6A modifications in Nanopore direct RNA reads by modeling adjacent kmers and accounting for outliers, enabling stoichiometry measurement and correlation with RNA processing events.

Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA

The paper shows that the FPA protein causes premature termination of NLR gene transcripts in Arabidopsis thaliana, regulating their expression and immune function.

Two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

The paper improves intron detection in long-read RNA sequencing by filtering spurious splice junctions using machine learning and a two-pass alignment approach.

Missense variants in ACE2 are predicted to encourage and inhibit interaction with SARS-CoV-2 Spike and contribute to genetic risk in COVID-19

The paper predicts ACE2 missense variants that enhance or inhibit SARS-CoV-2 Spike binding, identifies protective and susceptibility variants, and suggests their implications for COVID-19 risk and therapeutic design.

Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome

This study uses nanopore direct RNA sequencing to map the m6A epitranscriptome in Arabidopsis, revealing its role in mRNA processing and circadian rhythms.

How well do RNA-Seq differential gene expression tools perform in a eukaryote with a complex transcriptome?

This study evaluates DGE tools' performance in Arabidopsis thaliana, finding that their false positive rates are not strongly affected by transcriptome complexity.

Detection and Mitigation of Spurious Antisense RNA-seq Reads with RoSA

RoSA detects and corrects spurious antisense RNA-seq reads in strand-specific datasets, improving accuracy in antisense transcription analysis.

Proteus: an R package for downstream analysis of MaxQuant output

Proteus is an open-source R package with Shiny interactive visualization that aggregates MaxQuant proteomics evidence data and uses limma to improve differential expression sensitivity over Perseus random imputation.

A study of the structural properties of sites modified by the O-linked 6-N-acetylglucosamine transferase

This study analyzes the structural properties of O-GlcNAc sites and finds no prevalent three-dimensional motif for OGT recognition, but suggests disordered regions may play a role.

Identifying differential isoform abundance with RATs: a universal tool and a warning

RATs identifies differential transcript usage from transcript abundance estimates, finds novel events, and highlights annotation dependency issues in RNA-seq data.

Human Missense Variation is Constrained by Domain Structure and Highlights Functional and Pathogenic Residues

The paper identifies functionally important protein residues by analyzing missense variant distribution across human protein domains and finds these residues are enriched in disease-associated variants.