Genomics and Phylogenetic Studies

AutoRNAseq provides an automated bulk RNA-seq analysis pipeline to ensure consistent and reproducible processing across experiments.

Metaxa is a transformer-based model for classifying long Nanopore reads, outperforming existing tools on out-of-sample data and across different sequencing chemistries.

CrossFilt improves cross-species genomic analysis by filtering reads that map reciprocally between species, leading to more accurate gene expression comparisons.

This study compares short and long read sequencing technologies for human genome profiling, finding they are equivalent for SNVs but long reads excel in structural variants and haplotype phasing.

The paper searches a petabase-scale dataset to discover new Papillomaviruses, identifying 383 novel types across 105 host species and highlighting biodiversity hotspots.

The paper validates the CvP-bias as a robust genomic marker for hyperthermostability across 1,963 microbial genomes, confirming its significance with high statistical confidence.

The paper introduces a web platform for exploring gene conservation in fission yeasts using orthogroup data from multiple species.

MutaPhy detects genotype-phenotype associations in pathogens by analyzing phylogenetic trees, revealing lineage-level associations while reducing false positives.

The paper improves the genome assembly of two peach doubled haploid varieties using third-generation sequencing and enhances gene and NLR annotations.

The paper evaluates differential expression methods for metatranscriptomes, identifies limitations, and proposes improvements using real datasets from gnotobiotic mice and clinical studies.

The paper introduces DBCO-modified PCR primers for enzyme-free click chemistry ligation in nanopore amplicon sequencing, achieving higher pore occupation and reads than commercial solutions.

This paper presents the first chromosome-level genome assembly of the sponge Halisarca dujardinii, along with mitochondrial genome and comprehensive annotation.

The paper develops embeRNA, a method to predict microbial functions from 16S rRNA sequences without reference databases, showing better performance in novel environments.

The paper introduces CATS, a tool for assessing transcriptome assembly quality using reference-free and reference-based approaches, showing improved accuracy and sensitivity over existing methods.

OpusTaxa provides an open-source workflow for streamlined shotgun metagenomic analysis, enabling taxonomic profiling, assembly, and functional analysis with minimal user configuration.

The paper introduces RICE, a method to quantify chimeric RNA expression, validates it with qPCR and siRNA, and applies it to prostate cancer data to identify differentially expressed chimeric RNAs.

LongHap improves genome-wide haplotype reconstruction by integrating methylation data, increasing phase block lengths and reducing switch errors across diverse datasets.

The paper benchmarks transcript classifiers to identify ambiguous mRNA-lncRNA classifications by analyzing uncertainty and feature contributions.

The paper identifies a sequencing artifact in Illumina NovaSeq 6000 two-color chemistry that causes T>G substitutions, affecting low-VAF somatic variant detection.

GANGE is a deep-learning system that generates accurate genomic sequences from low-coverage, error-prone reads, reducing sequencing costs and enabling regulomics research without genome data.

vcfilt is a high-performance VCF filter that achieves significant speedups over existing tools by using a zero-allocation byte-scan parser for common filtering criteria.

The paper presents the first genome assembly of Abrothrix olivacea and uses it to study gene expression and genetic divergence in kidney tissue across contrasting environments.

pylifemap maps biological data onto the NCBI Taxonomy tree, enabling interactive visualization of datasets like the IUCN Red List and metagenomics results.

This paper develops workflows for whole-genome sequencing to identify genetic variation in Synechocystis strains and highlights the importance of strain validation in knock-out studies.

BABAPPAlign improves multiple sequence alignment by using a learned residue-level scoring function, outperforming existing tools on standard benchmarks.

The paper introduces a pipeline for automated viral genome reconstruction and variant analysis from metagenomic data, validated on simulated and real datasets.

The paper presents a high-quality reference genome for the critically endangered Philippine Eagle, revealing its evolutionary relationships and population history.

ExTRaCT is a gene search pipeline that identifies APOBEC3 Z-domains in novel bat genomes with high accuracy and efficiency.

The paper uses high-resolution metagenomic sequencing to reveal contrasting population structures in a microbial community, showing distinct evolutionary strategies coexisting within a single sample.

FAMSA2 provides high-accuracy multiple sequence alignments for large-scale protein datasets with significantly improved speed.