benchmarking

41% of Gram-negative bacteria encode a Type Six Secretion System

The paper quantifies T6SS prevalence in Gram-negative bacteria using genome analysis and finds it is present in 41% of well-sampled genera.

The biochemical composition of coronavirus Nucleocapsid proteins drives the bicistronic properties of their sub-genomic mRNAs

The paper identifies conserved overlapping accessory ORFs in coronavirus N genes and shows that nucleotide and codon biases drive their formation.

Learning Strand-Equivariant Tokenizations of DNA with MirrorDNA

This paper introduces MirrorDNA, a DNA language model with a strand-equivariant tokenizer that improves prediction consistency across DNA strands.

Theoretical prediction of assembly contiguity

The paper derives a formula (Z-value) to predict contig length from read length, coverage, and genome properties, showing high accuracy and practical applications for assembler choice and experimental design.

TIGRdisco: a tool for the discovery of TIGR arrays and TIGR-associated Tas proteins from nucleotide sequences

TIGRdisco identifies TIGR arrays and Tas proteins from nucleotide sequences, recovering most array units and uncovering unannotated loci across datasets.

GPBench: A benchmark framework for genomic prediction

GPBench provides a standardized benchmark framework for genomic prediction, evaluating 21 models across 16 species and offering tools for analysis and comparison.

An end-to-end in silico framework for truth-based validation and regression testing of clinical genome sequencing pipelines, from simulated reads to reportable findings

This paper introduces an end-to-end in silico framework to validate and test clinical genome sequencing pipelines from simulated reads to reportable findings using a fixed truth set.

Synthetic MPRA perturbation supervision improves variant-effect prediction in sequence-to-function models

This paper improves variant-effect prediction in sequence-to-function models using synthetic MPRA data generated from distilled model predictions.

Unsupervised prioritization of gene-regulatory variants with isolation forests

The paper introduces eQIF, an unsupervised machine-learning method that integrates Enformer predictions to prioritize gene-regulatory variants, showing strong performance in predicting eQTLs and GWAS variants.

Guide-tree bias of whole genome alignment can mislead phylogenomic analyses

The paper shows guide-tree bias in whole-genome alignment can mislead phylogenomic analyses and proposes a consensus alignment strategy to reduce this bias.

Cell-in-drop genotyping detects megabase-scale loss of heterozygosity as a quantitative marker for CRISPR-Cas9 on-target toxicity

The metabolic resistance blueprint: Genomic dissection of DDT resistance in historical kdr-free East African Anopheles gambiae

This paper identifies genomic loci and mutations associated with DDT metabolic resistance in Anopheles gambiae using bulk segregant analysis and confirms their selection in natural populations.

Reconstructing human gene regulatory evolution using deep learning

This study uses deep learning to predict cis-regulatory effects of human-specific mutations across 305 tissues, revealing their role in gene expression evolution.

Genomic forecasting links climate-associated variation to spring phenology in the European wild apple, a crop wild relative of the cultivated apple

The paper tests if climate-associated genomic variation predicts phenotypic adaptation in European wild apple, finding genomic offsets link to bud-break timing but not other traits.

Dynamic evolution of diaphorin biosynthetic genes against a background of genome conservation in Profftella

The paper compares Profftella genomes across Diaphorina species, finding conserved gene organization but lineage-specific variation in diaphorin biosynthetic genes, particularly in ACP domain amplification.

Fox: Predicting rates of host-symbiont co-evolution events with association-aware attention

Fox predicts host-symbiont co-evolution event rates directly from sequence alignments without tree reconstruction, achieving high accuracy and speed compared to existing methods.

Aneuploidy profiling among different types of brain metastases reveals a colon cancer-specific chromosomal signature

This study identifies a unique aneuploidy profile in colorectal cancer brain metastases compared to other cancer types and metastatic sites.

mock-fastq-generator: A synthetic FASTQ generator

mock-fastq-generator creates synthetic FASTQ files for testing bioinformatics pipelines without using biological data.

DeepPhage: leveraging the power of NGS phage display data, an in-depth analysis for the identification of Eu3+-binding peptides

DeepPhage identifies Eu3+-binding peptides from NGS phage display data by analyzing sequence biases and comparing multiple experimental conditions.

Influenza A virus H5Nx genotypes assigned by genetic similarity are incongruent with global phylogenies

This paper evaluates H5Nx influenza virus genotyping tools and finds they often group viruses with distinct evolutionary histories due to reassortment and reference bias.

BaitBench: a comprehensive tool for building, as-sessing, and predicting outcomes for hybrid capture enrichment probes

BaitBench is a tool for designing, assessing, and simulating hybrid capture probes, validated with high correlation to real data.

GBactPro: cross-species bacterial promoter prediction using element-resolved promoter definitions

GBactPro improves cross-species bacterial promoter prediction using element-resolved promoter definitions, achieving high AUROC across multiple species and outperforming existing predictors.

Efficient biological design via genomic in-context learning

This paper demonstrates that in-context learning in the genome language model Evo 2 enables efficient biological sequence design without additional training.

The B-value calculator: expected diversity with background selection

The paper introduces Bvalcalc, a tool to calculate B-values, which quantify the effect of background selection on genetic diversity, and validates it using simulations and public data.

Creator 1.0: Phylogeny-Guided Stagewise Pretraining for Plant Genome Foundation Models across 1,000 Species

Creator 1.0 is a plant genome foundation model pretrained on 1,000 species using phylogeny-guided stagewise pretraining, achieving strong performance on plant-related tasks.

Conserved genes, discordant structure: a pangenomic view of plant mitochondrial genome evolution

This study analyzes over 300 plant mitochondrial genomes to show that gene content is conserved but structural complexity varies, driven by repeat proliferation and recombination rather than intergenomic DNA transfer.

LDscnR: LD-aware complexity reduction for genome scans

LDscnR reduces genome scan tests by grouping correlated markers using LD decay, improving precision while maintaining recall, and showing structure can explain outlier regions.

Using SpliceAI to triage splice-altering variants in 7,220 individuals with rare conditions highlights limitations of the precomputed scores

The paper evaluates precomputed SpliceAI scores for splice-altering variant prioritization in NDD cohorts, finding inaccuracies and providing a tool to improve variant triage.

VenusGenome: Genome-Aware Masked Autoencoding for Microbial Genome Representation Learning

VenusGenome improves microbial genome representation learning by using a genome-aware masked autoencoder, achieving high performance in phenotype prediction and gene-level tasks.

Robustness of the inference of the distribution of fitness effects to selective sweeps

This study evaluates how selective sweeps affect DFE inference using fitdadi, finding that performance declines at low recombination rates and with unfolded SFS, but remains largely unbiased with a flexible demographic model.