Genomics and Phylogenetic Studies

VariantFlow efficiently processes large variant datasets by selectively decoding only necessary fields, improving speed and memory usage compared to existing tools.

The paper evaluates 54 tree shape indices on 45 million empirical trees, revealing rooting and size dependencies, and recommends selecting uncorrelated indices for reliable tree shape analysis.

The paper introduces Centrolign, a tool for aligning centromeric regions, revealing mutation dynamics and enabling variant calling in human centromeres.

The paper introduces a new pangenome viewer for maize that integrates graph and linear genome visualization to enhance structural variation analysis and locus characterization.

This paper introduces an alignment-last approach to transcriptomic analysis, enabling rapid biomarker discovery by using reads directly and revealing new transposable-element signatures and prognostic reads in cancer.

The paper shows that deep sequencing increases artificial diversity estimates in microbial studies and suggests using no-diversity amplicons to optimize sequencing parameters.

Rclade streamlines taxonomic collapsing and geological annotation of phylogenetic trees by integrating multiple functions into a single R package with improved rendering and format handling.

AmPair designs species-level discriminatory primers for metataxonomics by targeting housekeeping genes, outperforming standard 16S rRNA primers in specificity and resolution.

The paper introduces XpBrew, a Python workflow for RNA-seq processing, and PanXpresso, a gene expression dataset collection across multiple taxa.

The paper measures resource usage of 16S rRNA pipeline stages, finding denoising scales with sequencing depth while classification has a fixed cost.

The paper presents DogMAG, a canine gut metagenome resource with assembled bacterial genomes and viral candidates using long-read and hybrid sequencing.

TomatoPGFM is a graph-conditioned foundation model for tomato pangenomes that improves sequence representation using graph context, achieving higher classification performance than DNABERT-2.

Vipsania is an unsupervised deep learning model for gene finding in eukaryotic genomes, achieving higher accuracy than supervised methods across most clades.

The paper benchmarks metagenomic pipelines using age- and body site-specific synthetic communities, showing THMCv2 has higher recall and F1 scores while MetaPhlAn4 has higher precision.

This paper introduces a high-throughput sequencing method using Oxford Nanopore Technologies to sequence over 1,200 gut microbiome samples with near-full-length 16S rRNA gene amplicons, achieving high accuracy and scalability.

PyiTOL provides reproducible Python workflows for iTOL annotation and taxonomic monophyly assessment, with accurate results on benchmark datasets.

SALRR provides a scalable platform for long-read RNA-seq analysis, identifying novel splice variants in human brain tissue.

The paper evaluates a practical tissue sampling strategy for non-model reptiles, demonstrating that ethanol-preserved samples can yield high-quality genomic data and provide insights into the evolutionary history of a threatened species.

FigTreeKit provides a Python toolkit for programmatically styling and auditing phylogenetic trees, with scalability testing on large bacterial and archaeal datasets.

Anniemap improves viral short-read alignment by using vector similarity search, achieving higher sensitivity and throughput, especially for divergent genomes like HIV and HCV.

This paper introduces a framework for creating population-specific genome references using alternate-contig awareness, demonstrating improved variant calling in Vietnamese populations compared to GRCh38.

HLA-Resolve improves HLA typing and MHC variant detection using long-read sequencing and hybrid capture, achieving high accuracy across diverse samples.

ROADIES-XP enables efficient incremental species tree updates from raw genomic assemblies using GPU acceleration, achieving high speedups and maintaining topological accuracy.

This study resolves the debate on the origin of taxonomically restricted genes in yeast by showing most are de novo genes while others derive from diverged ancestors.

ppigFinder integrates genome annotation and AlphaFold 3 for PPI screening, identifying high-confidence interactions in Xanthomonas citri.

The paper reconstructs a genome-wide protein-interaction network for Varroa destructor and evaluates orthology-based host gene absence calls, finding over-calling of host absence in three tests.

TxNova identifies recurrent unannotated intergenic splice junctions from bulk RNA-seq alignments, providing candidate leads for experimental validation.

This study compares the effects of incomplete lineage sorting and gene tree estimation error on species tree inference using simulated and real datasets.

The paper presents a chromosome-level genome assembly of the northern white-throated dipper using ONT and Hi-C, resolving previously collapsed dot-chromosomes and showing advantages of ONT over HiFi for repeat-rich regions.

The paper presents haplotype-resolved chromosome-level genome assemblies for four European white oak species, providing resources for comparative genomics and pangenome studies.