Genomics and Phylogenetic Studies

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

The paper presents the first high-quality long-read genome assemblies for three clownfish-hosting sea anemone species, enabling comparative genomic studies of their symbiotic relationship with clownfish.

The paper updates 16S rRNA gene identity thresholds for prokaryotic taxonomy using sequence data from nearly 18,000 type strains, showing overlapping boundaries across taxonomic ranks.

TIPP3 and TIPP3-fast improve metagenomic abundance profiling accuracy, especially for novel genomes and error-containing reads, with TIPP3-fast offering faster runtime while maintaining high accuracy.

The paper develops a lineage-specific gene prediction method for metagenomic data, improving protein prediction accuracy and enabling functional analysis of the human gut microbiome.

This study evaluates how realistic evolutionary heterogeneity affects ancestral sequence reconstruction and finds that ASR is robust to such heterogeneity, with phylogenetic signal being the primary determinant.

UnigeneFinder reduces transcriptome assembly redundancy and automates gene calling without a reference genome, improving accuracy for non-model organisms.

SeqTagger demultiplexes direct RNA nanopore sequencing datasets with high precision and recall, supporting multiple chemistries and library types.

This paper introduces GNNome, a geometric deep learning framework for de novo genome assembly that improves contiguity compared to existing tools across multiple species.

This paper introduces ska lo, a reference-free variant calling tool that uses a coloured De Bruijn graph to detect SNPs, insertions, deletions, and recombination events in pathogen genomes.

SQANTI-reads assesses long-read RNA-seq data quality using SQANTI3 metrics, identifying under-annotated genes and splicing site variation across samples.

MotifScope identifies and visualizes tandem repeats in population context using a de novo k-mer approach, outperforming existing tools in motif discovery and representation.

The paper develops a human genome standard E701 through whole-genome sequencing, identifying genomic variants and mitochondrial DNA coverage for quality metrics.

Realfreq provides real-time base modification analysis for nanopore sequencing, enabling live data analysis during sequencing.

The paper introduces a two-step metagenomic classification method that improves precision and scalability using sample-tailored minimizer libraries, achieving higher species-level read classification.

Uncalled4 improves nanopore signal alignment for DNA and RNA modification detection, identifying more modifications than existing tools in human cell lines.

This paper introduces an algorithm to reconstruct semi-directed phylogenetic level-1 networks from four-leaved networks or sequence alignments, demonstrating its performance on simulated and real data.

ProteoSeeker is a metagenomic analysis tool that identifies proteins and host taxonomy from whole-genome sequencing data, enabling accessible and comprehensive exploration.

The paper presents a chromosome-level genome assembly for brook trout using Hi-C and long-read sequencing, achieving high contiguity and annotation coverage.

The paper identifies genes under positive selection in desert tortoises linked to reproductive isolation mechanisms and environmental adaptation.

This study quantifies how errors in species tree estimation affect cophylogenetic reconstruction accuracy using simulations and genomic data from symbiotic systems.

This paper presents two new Kudoa genomes assembled from contaminated fish samples, revealing conserved gene order and rapid sequence evolution despite genomic simplification.

The paper develops new Centrifuge-compatible nt databases to improve metagenomic classification accuracy by addressing reference database inconsistencies and growth challenges.

This study presents the first nuclear genome assembly for Zenia insignis, a threatened plant species in the Fabaceae family, providing a resource for phylogenomic research.

This paper develops a scalable protocol for microbial isolate genotyping using colony PCR and a four-barcode indexing scheme, achieving 90% identification accuracy on 93 environmental samples.

This paper presents a high-quality chromosome-scale genome assembly for the Australian alpine skink Bassiana duperreyi using long-read technologies, achieving high completeness and providing a resource for sex determination and thermolabile sex reversal studies.

This study benchmarks Nanopore long read RNA sequencing in human cell lines, showing improved isoform resolution compared to short reads.

Phyloformer uses deep learning to quickly and accurately reconstruct phylogenetic trees from protein sequences, outperforming existing methods on simulated and real data.

The paper presents chromosomal-level genome assemblies for two clams using PacBio HiFi and Omni-C reads, providing genomic resources for conservation and ecological studies.