Genomics and Phylogenetic Studies

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 introduces BioSIFTR, a tool that uses shallow shotgun sequencing and biome-specific databases to generate accurate taxonomic and functional profiles, validated against deep sequencing data.

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

Carbon-A annotates protein-coding genes across eukaryotic genomes using a large encoder model, achieving high accuracy and enabling the creation of a comprehensive annotation database.

The paper evaluates how strain heterogeneity affects the accuracy of genomic profiling in mixed-strain Escherichia coli metagenomes using simulated data and various bioinformatic tools.

An AI-assisted C++17 port of VarDictJava gives byte-identical calls on five exome samples while running 3.7-4.8 times faster on one core and needing 8-17 times less memory.

This paper demonstrates strain-level resolution and quantification of bacterial microbiomes using nanopore sequencing of the ribosomal RNA operon, showing accurate relative abundance quantification over multiple orders of magnitude.

The paper benchmarks microbiome methods to improve metagenomic sequencing of lower respiratory tract samples by optimizing DNA purification strategies.

The paper presents high-quality reference genomes for three sympatric Cyprinodon pupfish species to study speciation mechanisms and genomic architecture.

This paper introduces a parametrisation of phylogenetic tree space using unconstrained Euclidean coordinates, enabling new methods for Bayesian phylogenetic inference.

DCSMAP improves read alignment accuracy and efficiency by selectively applying pangenome graph alignment to reads with unreliable linear placements.

PeakLocus assigns RNA features to transcript intervals with high accuracy, outperforming existing tools in benchmark tests across multiple species.

HyARQ is a Snakemake workflow for allele-specific read counting and quality control across multiple assays in F1 hybrids, showing accurate recovery of parental proportions.

The paper generates a chromosome-level reference genome for Crassostrea virginica using PacBio HiFi, Illumina, and Hi-C data, achieving high completeness and reduced duplication.

DIMPLE infers phylogenetic networks from large-scale data using a divide-and-conquer approach, achieving accurate merging and improved reticulation recovery over existing methods.

Metalink integrates taxonomic and functional profiling across resolution scales in metagenomes and metatranscriptomes, improving accuracy and enabling mechanistic insights.

DeepD is a genome foundation model that enables accurate sequence-to-function prediction and controllable genome-scale sequence generation across domains of life.

The paper presents a telomere-to-telomere genome assembly of the naked mole-rat and compares it with a related species to identify gene losses and duplications associated with unique traits.

dFEL extends FEL to model lineage-specific GC/AT drift as per-branch mixtures of three shared regime matrices, correcting selection calls at 1%–4% of boundary codons.

The paper benchmarks preprocessing pipelines for Oxford Nanopore reads in bacterial genomics, finding that no single approach optimally balances variant calling and assembly performance across all metrics.

SLAFIT infers viral fitness and detects structural variants from third-generation sequencing data by analyzing linkage disequilibrium and haplotype frequencies.

This study improves the estimation of evolutionary distances and tree inference by accounting for substitution rate heterogeneity across prokaryotic genomes.

IsoMatch integrates transcript models across references, showing how reference choice affects estimates of transcript novelty.

DecoDiPhy deconvolves phylogenetic distance mixtures to improve interpretability and downstream analysis in metagenomics.

DIPLER identifies structurally complex loci using k-mer analysis and de novo assembly from low-coverage sequencing data.