Genomics and Phylogenetic Studies

This study compares HGT inference methods, finding that gene presence-absence analysis outperforms gene tree-based approaches in detecting horizontal gene transfer.

This paper presents the first near chromosome-level genome of a sea spider, revealing a single Hox cluster without abdominal-A/Hox9, supporting shared evolutionary patterns in arthropods.

SegFinder identifies RNA virus genome segments by analyzing co-occurrence across samples, discovering novel segments and expanding known segmented virus families.

The paper benchmarks genomic interval querying tools using simulated datasets, evaluating performance, memory usage, and precision across different tools and data structures.

Oarfish improves long read transcriptome quantification by incorporating a novel coverage score into its probabilistic model, leading to more accurate quantification estimates.

DeepPolisher improves genome assembly accuracy by reducing errors using a transformer model and phasing method, achieving over 70% indel error reduction.

Verkko2 improves genome assembly by integrating proximity ligation data with long-read De Bruijn graphs, enabling complete telomere-to-telomere assemblies for diploid human genomes.

This paper introduces a seed-chain-extend alignment workflow using elastic founder graphs to improve sequence-to-graph alignment accuracy and efficiency in pangenomics.

grepq filters FASTQ files using regular expressions efficiently, offering performance, scalability, and tools for variant enumeration and SQLite output.

This paper introduces a convolutional neural network to detect interspecific positive selection, achieving higher accuracy and robustness to alignment errors compared to traditional statistical methods.

Kaptive v3 improves antigen typing accuracy and speed for KpSC genomes by addressing assembly fragmentation issues, enabling efficient in silico serotyping.

PubPlant catalogs over 1800 sequenced plant genomes, offering visualizations and phylogenetic insights, and highlights gaps in food crop genome sequencing.

The paper introduces Python libraries for computing average nucleotide identity, matching existing tools' results and integrating with BioPython for workflow use.

The paper improves somatic mutation detection in a highly heterozygous oak genome by using a read assignment strategy, increasing the mutation rate estimate by fivefold.

The paper introduces a new open-source tool for efficient genomic sequence digestion using minimizers, modimizers, or syncmers.

CLARC refines bacterial ortholog groups by integrating linkage and annotation data, reducing accessory gene estimates and improving evolutionary predictions in Streptococcus pneumoniae.

KPop provides a scalable method for comparing microbial genomes using sequence embeddings, accurately separating sequences at species and sub-species levels.

This paper evaluates small RNA alignment techniques using a multi-alignment framework, finding STAR and Bowtie2 to be more effective than BBMap, with STAR-Salmon being the most reliable approach.

Mumemto efficiently computes multi-MUMs across large pangenomes to visualize synteny and detect structural variations.

The paper improves rRNA depletion for mouse cecal metatranscriptome analysis by designing probes based on sequence abundance rather than taxonomy, increasing mRNA reads and reducing bias.

This study compares structure-based and sequence-based methods for phylogenetic reconstruction and finds that sequence-based methods still outperform structure-based ones in large-scale phylogenomics.

This paper introduces GeneLM, a genomic language model that improves bacterial gene prediction and translation initiation site identification, outperforming traditional methods.

This paper evaluates recent improvements in Oxford Nanopore sequencing for bacterial genomic surveillance, showing that new software tools significantly enhance accuracy and reproducibility.

The paper presents a high-quality chromosome-scale genome assembly and transcriptome of the Ural owl to support conservation efforts and genetic research.

This paper provides genome and transcriptomic sequences of three invasive insect species, offering resources for population genomics and pest management.

The paper identifies new divergent protein groups in ancient gene families from marine metagenomes, highlighting environmental diversity and potential biological novelty.

The paper develops an iterative lysis protocol to enrich cyanobacterial DNA from xenic cultures, improving genome assembly quality and reducing heterotrophic microbiome contamination.

The paper introduces LACA, a de novo clustering workflow for long-read amplicons that improves phylogenetic analysis and phenotype characterization in microbiome data.

This study evaluates protein-coding sequence detection tools, finding most are inaccurate and inefficient, with only three out of nine performing better than a naive scheme.

diverse-seq provides alignment-free methods to select and cluster biological sequences, improving computational efficiency for phylogenetic and other workflows.