Genomics and Phylogenetic Studies

This study benchmarks low-coverage sequencing workflows for eggplant genotyping, finding that 3X coverage with Freebayes achieves high genotypic concordance and sensitivity.

The paper develops a targeted reference database, AQUAeD-DB, to improve taxonomic accuracy of 16S rRNA sequencing data from seafloor sediments using Oxford Nanopore Technologies.

Autocycler improves bacterial genome assembly accuracy by combining multiple long-read assemblies without user input, outperforming existing tools in error reduction and structural accuracy.

This paper validates a probabilistic method for relative dating of evolutionary events using gene trees and shows it correlates strongly with fossil-calibrated molecular clocks.

The paper introduces a method using ultra-long sequencing and bioinformatics to resolve haplotypes in the human immunoglobulin heavy chain locus, uncovering novel alleles and structural variants.

The paper determines the optimal sequencing depth for accurately measuring barcode concentrations in combinatorial genetic experiments by analyzing NGS data and incorporating a mathematical model of PCR amplification.

MiFoDB is a metagenomics workflow that identifies microbes in fermented foods with high taxonomic resolution, enabling strain tracking and functional analysis.

The paper presents a pipeline to identify viral variants from functional genomics data, showing it can accurately recover introduced mutations in HSV-1 mutants.

The paper analyzes the pan-genome of nearly 20,000 Enterobacteriaceae genomes to identify core and accessory metabolic genes, revealing core genes for mixed acid fermentation and accessory genes for anaerobic respiration and carbohydrate utilization.

metagRoot provides a database of 71,091 enriched protein families from plant root microbiomes, annotated with structural and functional information to aid in microbiome research.

This paper introduces FANTASIA, a tool using protein language models to annotate functions for thousands of animal proteomes, uncovering previously unknown functions across species.

This study evaluates weighted quartet methods for species tree inference, finding that GTF-based approaches outperform ASTRAL and SVDquartets in accuracy.

The paper constructs a pangenome graph reference for Japanese and Saudi Arabian populations, showing improved variant detection compared to linear references and comparable performance to existing pangenome graphs.

This paper introduces DNA language models to predict enzymatic potential in metagenomic reads, identifying new enzymes and expanding functional annotations.

This paper introduces ConvexML, a fast and accurate method for estimating branch lengths in phylogenetic trees under irreversible mutation models, with applications to CRISPR/Cas9 lineage tracing data.

Oatk combines a sparse syncmer assembler, profile HMM gene databases and graph path search to assemble plastomes and mitogenomes from HiFi reads for 195 plant species.

Varigraph improves variant genotyping accuracy in pangenome graphs for diploid and polyploid genomes, outperforming existing methods in non-human genomes.

GenMPI provides a scalable variant calling workflow for short and long-read sequencing data using MPI, achieving linear scaling and improved performance over existing methods.

This study proposes using AIC to select optimal window sizes for whole genome alignments, finding shorter windows for butterflies and longer for great apes, with varying impacts on topology recovery.

This study evaluates ONT R10.4.1 long-read sequencing for accurate genotyping of three respiratory pathogens, showing error rates below 1% for cgMLST.

PHLAME improves strain-resolved metagenomic analysis by combining reference-based methods with novelty detection, revealing new intraspecies associations in human microbiomes.

The paper presents a new gap-free, telomere-to-telomere reference genome for C. elegans, CGC1, improving upon previous assemblies and providing a more complete genome.

The paper creates a long-read benchmark for genetic variants using a large pedigree, improving variant calling performance and introducing new truth sets for tandem repeats and structural variants.

OpDetect uses RNA-seq data and deep learning to detect operons across bacterial and eukaryotic species with improved accuracy compared to existing methods.

StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities using shotgun metagenomic sequencing and k-mer normalization.

This study compares genomic data from Ralstonia spp. to show reduced pathogenicity in aquatic environments compared to plant and human-associated strains.

The paper uses Hidden Markov Models to analyze prokaryotic genomes and reveals the widespread presence and evolutionary patterns of Complex I.

Pedigree Painter (PePa) visualizes and quantifies genomic inheritance patterns from VCF files, revealing non-uniform recombination and parental contributions in fission yeast.

Phylo-rs provides a fast, extensible Rust library for phylogenetic analysis with WebAssembly support and open-source availability.

The paper presents algorithms for reconstructing past deletions in ancestral sequences using a deletion-only parsimony approach, providing exact solutions and graph-based representations of optimal reconstructions.