Genomics and Phylogenetic Studies

This paper introduces a hierarchical clock-mixture model for Bayesian phylogenetic dating to better handle uncertainty in clock choice and improve timescale estimation.

The paper introduces LongPolyASE, a framework for allele-specific gene and isoform analysis in polyploids using long-read RNA-seq, demonstrating its application on rice and potato.

The paper presents the first HiFi long-read assembled genome of the dipluran species Occasjapyx japonicus, providing a high-quality reference for comparative and evolutionary studies.

Panomap maps raw nanopore signals to pangenome variation graphs, improving mapping accuracy and reducing reference bias compared to linear-reference methods.

Evo 2 7B assigns higher perplexity to plant gene alleles carrying randomly simulated single-nucleotide substitutions than to those observed in vivo, in Arabidopsis and rice; significant but small effect.

This paper introduces grapHiC, a contrastive learning framework for reference-free haplotype phasing in de novo genome assembly, achieving results comparable to state-of-the-art methods.

This study introduces CLOAK, an MSA cleaning algorithm that improves gene tree inference by removing alignment errors while preserving informative residues.

This paper reports the annotation of three tiger beetle genomes, providing draft reference genomes for evolutionary and conservation studies.

This paper develops a DNA extraction protocol for museum-grade insects, enabling long-read sequencing, phylogenetics, and methylation profiling from degraded samples.

This paper introduces a de novo method to identify transposable elements and inexact repeats from RNA-seq data without a reference genome, showing effectiveness in both model and non-model species.

The paper develops deep-learning-based scores to assess MSA quality, showing they outperform the SP score in identifying accurate alignments and improving phylogenetic reconstruction.

The paper describes the gene model for the ortholog of tgo in Drosophila persimilis using a specific gene annotation protocol.

The paper identifies non-B DNA structures as the cause of sequencing bias against simple satellite DNA in long-read sequencing and suggests solutions to mitigate this bias.

This paper introduces a de novo algorithm to reconstruct allele sequences from Oxford Nanopore amplicon reads, demonstrating its application to CYP2D6 and HLA with high accuracy.

The paper investigates genomic mechanisms underlying independent transitions to terrestrial life across species, finding lineage-specific gene changes that converge functionally.

The paper presents a haplotype-resolved genome assembly of the pomegranate cultivar 'Wonderful' using DNA from haploid pollen grains and long-read sequencing technologies.

The paper introduces BIRT, a method for RNA sequencing that integrates barcoding and 3'-end capture during reverse transcription, improving accuracy and efficiency for low-input samples.

The paper evaluates how different k-mer settings in MEGAHIT affect functional gene recovery in metagenomes, showing trade-offs between computational efficiency and gene discovery.

This paper introduces fMEM, a fungal microbial enrichment method that enables direct fungal metagenomic analysis from clinical samples, recovering MAGs with high completeness and resolving clinically relevant genes.

Standardized Snakemake pipelines on GitHub Actions fetch open sequence data, curate it, and publish daily or weekly updated phylogenies for 21 viruses and Mycobacterium tuberculosis.

The paper demonstrates that long-read sequencing detects more mitochondrial genome variants than short-read sequencing or microarrays in a Korean population.

DIPScan detects and corrects defective viral genomes in sequencing data to improve consensus genome accuracy for influenza virus.

The paper benchmarks 16S rRNA, FastANI, Mash, and FastAAI on 30,495 prokaryotic genomes to evaluate their taxonomic resolution across ranks, finding no single method is optimal across all levels.

The paper describes the gene model for the raptor ortholog in Drosophila eugracilis as part of a dataset studying IIS pathway evolution.

Phylogenize2 links microbial gene families to abundance phenotypes across diverse environments, identifying genes associated with specific ecological roles.

The paper describes the gene model for the DENR ortholog in D. grimshawi using a specific genome assembly and annotation protocol.

CAPHEINE automates evolutionary analysis of pathogen sequences, performing selection dynamics and positive selection studies.

This study compares nanopore direct RNA and PCR-cDNA sequencing protocols, showing distinct 5' and 3' coverage biases affecting transcript-level analysis but similar gene-level accuracy.

This study evaluates four taxonomic profilers using real metagenomic data to show how tool choice and parameters affect diversity analysis outcomes.

The paper develops a sequence-based classifier to identify phenotype-associated genes in plants, validated across maize, rice, and arabidopsis.