Genomics and Phylogenetic Studies

The paper presents a chromosome-scale genome and transcriptomic atlas of taro corm development, identifying genes associated with carbohydrate metabolism and corm-specific expression.

The paper shows that horizontal gene transfers can reveal information about extinct and unsampled lineages in species trees through gene tree analysis.

The paper introduces the MSC-DL model to account for gene duplication, loss, and coalescence, showing it generates many more gene tree topologies than previous models.

KEDROS is a web platform that performs phylogenetic profiling across proteomes to identify lineage-specific genes and functional divergence, offering a user-defined workflow for comparative genomics.

The paper develops a multi-tissue transcriptome for Pinus edulis to improve probe design for targeted exon-capture, showing that multi-tissue sampling enhances coverage and functional gene representation.

The paper analyzes protein duplication across 1,829 archaeal genomes to assess how gene duplication scales with genome size and identifies lineage-specific patterns and functional enrichments.

THRESHER calculates data-driven SNP thresholds for bacterial genomes to improve strain classification compared to fixed cutoffs.

This study benchmarks two demultiplexing tools for direct RNA sequencing using IVT spike-ins and species identity, showing their performance differences and the need for calibration.

The paper analyzes intergenic regions in mitochondrial and plastid genomes to show that opposite-polarity gene pairs have longer intergenic DNA than same-polarity pairs.

Winnow-tax improves taxonomic profiling of low-coverage shotgun metagenomes by combining sensitive read-level classification with genome-level confirmation, achieving better precision-sensitivity balance than existing methods.

The paper presents a chromosome-level genome assembly for the chilli thrips Scirtothrips dorsalis, providing genomic resources for studying its biology and pest status.

The paper introduces fastEmu, a scalable method for estimating differential abundance in microbial metagenomics data, achieving faster runtime with minimal impact on error rates.

This paper presents a statistical framework for correcting SARS-CoV-2 genomic sequences using phylogenetic priors, improving call rate and accuracy in challenging regions.

Anvaya analyzes chromosome fusion and mixing events to infer phylogenetic trees and detect whole-genome duplications using synteny data.

The paper introduces resources for large-scale metagenome comparison in the SRA, revealing trends in microbial discovery and improving assembly quality.

The paper introduces methods to improve consensus tree resolution using fine-grained dissimilarity measures, showing better performance on datasets with low to moderate phylogenetic signal.

HapSolo2 improves haplotig removal in diploid assemblies by optimizing performance and accuracy using GPU acceleration and updated ortholog datasets.

REFinder improves enzyme discovery from metagenomes by combining alignment-free annotation with targeted assembly, identifying more novel enzymes at lower cost than traditional methods.

RASTRO improves unitig graph path selection by using sequence-based models to identify read-supported branching points in HIV-1 and SARS-CoV-2 assemblies.

alamem and alasight are tools for fast and memory-efficient local alignment and horizontal gene transfer detection in bacterial genomes.

KENT enables fast metagenomic pathogen screening on low-memory hardware using NVIDIA Jetson Nano clusters, achieving speedups while maintaining accuracy comparable to desktop-based methods.

CRAIC provides tools to inspect and curate multiple sequence alignment uncertainty using posterior probabilities from pair-HMM models.

The paper analyzes metaparalog diversity in an Arctic Pelagibacterales population, showing high diversity within a single population and highlighting the importance of pangenome studies for microbiology.

The paper expands plasmid diversity by analyzing long-read metagenomes, identifying novel plasmid lineages and providing tools for plasmid discovery.

The paper uses conserved synteny analysis to reveal a shared saccharolytic lifestyle across Kiritimatiellia genomes.

D-plus improves introgression detection by addressing rate heterogeneity and ghost lineages, re-analyzing Jaltomata data to challenge prior interpretations.

The paper uses shotgun metagenomic host reads to detect mitochondrial heteroplasmy at allele fractions ≥5% in human respiratory tract samples.

Meta2Data automates retrieval, standardization, and processing of microbiome sequencing data from public repositories for downstream analysis.

MetagenomicsBench evaluates AI agents' ability to analyze metagenomic data through 100 verifiable tasks, finding that performance varies across domains and that technical plausibility does not guarantee correct biological interpretation.

The paper shows sampling bias in prokaryotic genome collections distorts diversity estimates and proposes a method to detect and reduce this bias.