Genomics and Phylogenetic Studies

Divergent NUMT mimicking functional coding region of the mitochondrial genome

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

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.

Transcript quantification using context-aware MAPQ modeling

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

Twenty-five new microsporidian genomes: Insights into ploidy, reproduction, and the group's pangenome

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

DGM Is Dead; Long Live DGM-Star! A Quantization-Theoretic Approach to Gamma Rate Discretization

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

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.

Alignment-Free k-mer Analysis Reveals Age-Associated k-mer Signals in Canine Buccal DNA and Cell-Free DNA

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.

Assembly of minimally fragmented metagenomic pangenome graphs

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

Towards a complete diploid chicken genome

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: An Unbiased Gaussian Framework for High-Precision Transcript Quantification with a Programmable Self-Benchmark Model

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

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.

IG-28 enables identification and quantification of high-confidence isoforms from large bulk and single-cell full-length cDNA datasets

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: a mitochondrial report software

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: 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.

A haplotype-resolved, near telomere-to-telomere genome assembly of the desiccation-tolerant plant Vellozia tubiflora

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.

Manta and devil ray genome assemblies uncover signatures of pelagic adaptation

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

OTTER: Orchestrated Transcriptomic, Tumor-xenograft (PDX/CDX), and Epigenomic Reporting Workflow

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

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.

A New Information Theoretic Approach Shows that Mixture Models Outperform Partition Models for Phylogenetic Analyses of Amino Acid Data

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

ONT-LibQC: rapid quality control of chromatin assay libraries using shallow nanopore sequencing

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

Two opposite failure modes in alignment-based conservation scores, one inflating and one concealing constraint, are computable before the score is used

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

Clean Breaks: Attention Force Field Deconvolution of Recombination Across Sequence Manifolds

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

Estimating Gene Prevalence with Incomplete Genomes: Application to the Prochlorococcus Pangenome

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: a centralized database of proteins in arthropod cuticles

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

Described eukaryotic species in published species-level phylogenies: placement by molecular data, dates and date uncertainty

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

Panagram reveals pangenome architectures underlying trait variation in plants and animals

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: a GPU-accelerated BWA-aln algorithm for palaeogenomics

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

T2G: fast and accurate transcriptome to genome BAM liftover for short and long read RNA sequencing

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

Differential sensitivity of k-mer based identification tools using closely related database sequences affects relative abundance estimation

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.

Reference mapping and whole-genome alignment yield comparable phylogenomic inferences

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