Genomics and Phylogenetic Studies

The paper identifies a divergent NUMT in a sawfly species that mimics mitochondrial coding regions and suggests it may result from recent mitochondrial introgression.

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

CALMeR improves transcript quantification by context-aware MAPQ modeling, recovering more spike-in transcripts and better matching known concentrations.

The paper presents 25 new microsporidian genomes, revealing extreme pangenome diversity and novel tetraploid structures in some species.

The paper introduces a new method to discretize Gamma rate distributions in phylogenetics, reducing branch length bias compared to the standard DGM.

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

This study identifies age-associated k-mer signals in canine buccal and cell-free DNA using alignment-free k-mer analysis and ridge regression models.

The paper introduces PANIMaSTA, a method to construct minimally fragmented metagenomic pangenome graphs for highly diverse viral genomes, improving graph topology for comparative analysis.

This paper presents a nearly complete haplotype-resolved chicken genome using trio-sequencing and long-read data, identifying gaps and structural variants in dot chromosomes.

GaussF improves isoform quantification by using a theoretical Gaussian model to correct sequencing biases without empirical data, outperforming existing tools.

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

IG-28 identifies and quantifies high-confidence isoforms from large bulk and single-cell full-length cDNA datasets more effectively than existing tools.

mito-overview integrates mitochondrial coverage, allele fractions, annotations, and read co-occurrence to identify and analyze candidate variants in mitochondrial genomic reports.

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.

This paper presents a near telomere-to-telomere, haplotype-resolved genome assembly of Vellozia tubiflora, a desiccation-tolerant plant, providing genomic resources for evolutionary and comparative studies.

The paper generates high-quality genome assemblies for two manta and devil ray species and identifies structural variations linked to pelagic adaptation.

OTTER improves bisulfite deconvolution in tumor xenograft sequencing by restoring recall to 52%-54% while preserving transcriptomic accuracy.

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

The paper compares mixture and partition models for phylogenetic analyses using the mAIC and finds mixture models consistently outperform partition models.

ONT-LibQC uses shallow nanopore sequencing to rapidly assess chromatin assay library quality before deep sequencing, showing consistent results with Illumina sequencing.

The paper identifies two opposite failure modes in alignment-based conservation scores and shows how to correct them to improve score accuracy.

RhizAeon deconvolves reticulate evolution by analyzing sequence mosaics and detecting recombination breakpoints with high accuracy and efficiency.

The paper develops a maximum-likelihood framework to estimate gene prevalence from incomplete genomes and applies it to Prochlorococcus, revealing a pangenome dominated by rare genes.

Cuticulome.org provides a curated database of arthropod cuticle proteins with standardized nomenclature and tools for sequence analysis and dataset customization.

The paper analyzes published eukaryotic phylogenies to assess molecular placement, dating, and uncertainty across species groups.

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.

G-ALN accelerates BWA-aln for ancient DNA analysis using GPU, achieving faster indexing and alignment speeds with identical output.

T2G converts transcriptome-aligned BAM files to genome coordinates, improving specificity and splice junction accuracy across RNA sequencing technologies.

This study evaluates how k-mer based tools affect abundance estimation in metagenomic data with closely related references, showing differential performance based on sample-reference distance and reference similarity.

The paper compares phylogenomic inferences from reference mapping and whole-genome alignment across Ursidae species, finding comparable results despite sequence loss.