Genomics and Phylogenetic Studies

genomesizeR predicts genome sizes for Archaea, Bacteria, or Eukaryotes using statistical models and NCBI databases.

The paper presents a high-quality haplotype-resolved genome assembly and annotation of Malus baccata 'Jackii', revealing detailed gene content and structure.

The paper identifies foldback artifacts in long-read sequencing data and introduces Breakinator, a tool to detect these artifacts and chimeric reads across different sequencing platforms.

MoGAAAP automates genome assembly and annotation using HiFi and other long-read data, producing quality assessments for comparative genomics.

NGSTroubleFinder detects and quantifies contamination and kinship in human NGS data, providing detailed reports for data integrity.

Eukan is a genome annotation pipeline that improves accuracy for diverse eukaryotes by integrating RNA-Seq data and consensus modeling, outperforming existing tools in challenging genomes.

ANOMALY identifies NuMTs from long-read sequencing data with high accuracy, demonstrating the advantages of long-read over short-read data for resolving complex NuMTs.

The paper introduces a fast and accurate barcode calling method using k-mer filtering, achieving higher accuracy and speed than existing methods.

The paper evaluates challenges in creating consistent pangene sets across pangenomes, showing that annotation inconsistencies lead to misleading presence-absence variation interpretations.

The paper introduces DNAscope Hybrid, a pipeline combining short and long-read sequencing for improved variant calling accuracy and efficiency.

Panalyze constructs, analyzes, and annotates virus pangenome variation graphs, offering scalability and automation for viral genomic diversity studies.

The paper introduces CycSim, a context-aware simulator for long-read mapping that improves parameter optimization, achieving faster mapping and better accuracy across different sequencing platforms.

FEDRANN improves long-read overlap detection using dimensionality reduction and approximate nearest neighbors, outperforming existing methods on real data.

This study examines how data errors affect phylogenetic network inference and shows that many methods are vulnerable to these errors, leading to unreliable results.

This study identifies convergent substitutions in teleost fish genomes and shows they are associated with intermediate pleiotropy, enabling adaptive variation during ecological shifts.

This study proves that gene tree parsimony estimators using duplication, loss, and deep coalescence costs are statistically inconsistent under the multispecies coalescent process.

DipGNNome introduces a deep learning framework for diploid genome assembly using graph neural networks and beam-search, achieving results comparable to state-of-the-art methods.

XhetRel analyzes X heterozygosity and relatedness in sequencing data to improve quality control and identify sources of error in variant calling.

HVRLocator identifies hypervariable regions in 16S rRNA datasets to improve metadata quality and enable accurate large-scale microbiome analysis.

This study evaluates long single-end barcoded reads for structural variant detection, showing improved accuracy with longer read lengths compared to short-read and pangenome-based methods.

This study evaluates room temperature preservation methods for mosquitoes to generate high-quality reference genomes, finding that squished samples in ethanol or Allprotect work best for Hi-C data.

The paper introduces a web tool and R package for analyzing the evolutionary origins of maize proteins, providing interactive visualizations and gene data for 26 maize inbreds.

The paper presents a chromosome-level reference genome for Chrosomus eos and analyzes its syntenic relationship with the zebrafish genome.

The paper introduces a modified Levenshtein distance to improve genome comparison by accounting for mobile element insertions, showing improved discrimination between specific mobile elements in phage genomes.

The paper isolates and characterizes two Myxococcus faecalis strains from mangroves in Brazil, showing genomic similarity to strains from soil and human feces.

PopMAG automates population genetics analysis of MAGs, detecting antibiotic-driven selection in Pseudomonas aeruginosa from cystic fibrosis lung metagenomes.

The paper introduces DepStep, a one-step rRNA depletion method for non-model organisms, which efficiently removes rRNA and reduces costs compared to commercial kits.

This paper evaluates pseudo-likelihood-based Bayesian inference for species tree estimation under the multispecies coalescent, showing theoretical guarantees and empirical performance on synthetic and biological data.

The paper introduces a metric for comparing LGT networks based on edit operations and demonstrates its computational complexity and applicability through experiments.

The paper presents a chromosome-level, haplotype-resolved genome assembly for the barn owl, resolving microchromosomes and enabling structural variation studies.