Genomics and Phylogenetic Studies

The paper introduces ArchaeaHQ, a curated database of 21,644 archaeal genomes with quality control and metadata, to improve representation in computational biology tools.

This study evaluates and improves low-frequency somatic mutation detection across multiple sequencing platforms using a simulated benchmark and a machine learning-based caller.

This study analyzes PRPS enzyme evolution across domains of life, identifying new classes and regulatory mechanisms through phylogenetic and biochemical approaches.

The paper benchmarks variant calling tools in inbred mouse strains, finding tradeoffs between recall and precision and recommending ensemble approaches for optimal results.

The paper resolves a long-standing paradox in lysozyme evolution by showing that recombination and incomplete lineage sorting explain apparent molecular convergence without requiring fixation of deleterious intermediates.

GeneScanner links laboratory genetic mutations to natural population variation in bacteria, enabling genotype-phenotype association studies across large genome collections.

The paper quantifies and predicts multiple sequence alignment difficulty using AlDiScore, achieving high R2 scores on unseen datasets.

UltraRes-rrn uses Nanopore sequencing and hierarchical rRNA operon profiling to achieve genomovar-level taxonomy resolution and microdiversity detection in microbial communities.

AEGIS standardizes and validates genome annotation files, enabling reliable downstream analysis through error correction and comparative genomics tools.

Aardvark benchmarks genomic variant calling accuracy by comparing haplotype sequences with a basepair score, supporting multiple variant types and outperforming hap.py.

This paper introduces a rigorous framework for haplotype-aware long-read error correction, achieving accuracy comparable to existing methods in de novo contexts.

This paper presents a high-quality genome assembly and tissue expression atlas for the European lobster, along with divergence time estimates and gene duplication analyses related to immunity and longevity.

OrthoGuide provides pre-computed evolutionary rooting data for COGs across eight model species, enabling rapid access to orthology-based evolutionary analysis.

This study benchmarks seven variant callers for detecting low-frequency variants in M. tuberculosis using simulated short-read data, finding FreeBayes performs best and introducing an error model to filter false positives.

This study demonstrates that RNA from herbarium specimens can be used for transcriptomics, validating the functional use of archival mRNA from a 1956 plant specimen.

StrainCascade automates bacterial genome reconstruction and characterization using long-read sequencing, enabling high-resolution comparative genomics and functional analysis.

BacTaxID provides a universal framework for bacterial classification using whole-genome k-mer sketches, achieving concordance with species and sub-species systems and capturing strain-level diversity.

This paper introduces a polyhedral framework for ancestral reconstruction in phylogenetic trees, enabling efficient algorithms with additional constraints and improved performance on real datasets.

The paper introduces a new method to detect and characterize introgression in large species trees by analyzing discordant attachment frequencies of gene trees, demonstrating its application in cichlids and Drosophila.

The paper develops a framework to discover new protein paralogs by integrating sequence, structure, and embedding-based methods with family-specific models, identifying 7 new protease and 3 new kinase paralogs.

This paper introduces ECToBlob, an algorithm to estimate the tree of blobs from quartet concordance factors, providing a statistically consistent method for inferring phylogenetic networks.

The paper introduces a cohort-HMM marker recruitment pipeline to improve phylogenomic supermatrix construction by addressing biases in orthogroup recovery and paralog filtering across different taxonomic scales.

The paper improves viral protein clustering by combining diversified sequence profiles with structural information, revealing a more accurate picture of viral protein diversity.

HyDRA integrates long- and short-read RNAseq data to improve transcriptome assembly, identifying over 50,000 new long noncoding RNAs in ovarian and fallopian tube samples.

Savont improves ASV recovery from long-read amplicon sequencing with high accuracy and lower sequencing depth.

This paper evaluates a correctness-gated coding agent for improving the runtime of the Neighbour Joining algorithm in phylogenetics, showing significant speedup on benchmark datasets.

The paper introduces rammap, a Rust reimplementation of minimap2 with improved performance and memory safety, demonstrating compatibility and efficiency improvements.

SQANTI-browser converts SQANTI3 classifications into UCSC Genome Browser Track Hubs for visualizing and curating long-read transcriptomes with metadata and filtering capabilities.

LucaPhylo infers phylogenetic trees from unaligned protein sequences using hyperbolic geometry and protein language models, achieving accuracy comparable to alignment-based methods for divergent RNA viruses.

This paper evaluates complex indel detection methods, finding FreeBayes best represents simulated complex indels as single variant records and develops a parsing workflow to extract complex indels from VCF output.